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  • Public Library of Science
  • Blackwell Publishing Ltd
  • 2020-2024  (94)
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  • 1
    Publication Date: 2024-02-07
    Description: Sinking marine aggregates have been studied for a long time to understand their role in carbon sequestration. Traditionally, sinking speed and respiration rates have been treated as independent variables, but two recent papers suggest that there is a connection albeit in contrasting directions. Here we collected recently formed (〈2 days old) aggregates from sediment traps mounted underneath mesocosms during two different experiments. The mesocosms were moored off Gran Canaria, Spain (~ 27.9 N; 15.4 E) in a coastal, sub-tropical and oligotrophic ecosystem. We determined the respiration rates of organisms (mainly heterotrophic prokaryotes) attached to aggregates sinking at different velocities. The average respiration rate of fast sinking aggregates (〉100 m d-1) was 0.12 d-1 ± 0.08 d-1 (SD). Slower sinking aggregates (〈50 m d-1) had on average higher (p 〈0.001) and more variable respiration rates (average 0.31 d-1 ± 0.16 d-1, SD). There was evidence that slower sinking aggregates had higher porosity than fast sinking aggregates, and we hypothesize that higher porosity increase the settlement area for bacteria and the respiration rate. These findings provide insights into the efficiency of the biological carbon pump and help resolve the apparent discrepancy in the recent studies of the correlation between respiration and sinking speed. © 2023 Spilling et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
    Format: text
    Format: other
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  • 2
    Publication Date: 2024-02-07
    Description: Settlement crises in ancient cultures of Western Asia are commonly thought to be caused by climatic events such as severe droughts. However, the insufficient climate proxy situation in this region challenges the inference of clear relationships between climate and settlement dynamics. We investigate the Holocene climatic changes on the Varamin Plain in the context of the climatic history of Western Central Asia by using a transient comprehensive Earth System Model simulation (8 ka BP to pre-industrial), a high-resolution regional snapshot simulation and a synthesis of pollen-based climate reconstructions. In line with the reconstructions, the models reveal only slightly varying mean climatic conditions on the Varamin Plain but indicate substantial changes in seasonality during the Holocene. Increased precipitation during spring, combined with lower temperature and potentially stronger snow accumulation on the upstream Alborz mountains may have led to an increased water supply on the alluvial fan during the vegetation period and thus to more favourable conditions for agricultural production during the Mid-Holocene compared to modern times. According to the model, dry periods on the Central Iranian Plateau are related to particularly weak Westerly winds, fostering the subsidence in the mid-troposphere and hampering precipitation over the region. The model reveals that dry periods have spatially heterogenous manifestations, thus explaining why they do not appear in all proxy records in the wider study region. In fact, the climatic signal may depend on local environmental conditions. The interaction of the topography with the atmospheric circulation leads to additional spatial heterogeneity. Although our results provide several indications for a connection between climate and settlement dynamics, the small overall changes in moisture call into question whether climate is the main driver for settlement discontinuities on the Central Iranian Plateau. To shed further light on this issue, more high-resolution long-term proxy records are needed.
    Type: Article , PeerReviewed
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  • 3
    Publication Date: 2023-12-12
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Infrared spectroscopy in the visible to near‐infrared (vis–NIR) and mid‐infrared (MIR) regions is a well‐established approach for the prediction of soil properties. Different data fusion and training approaches exist, and the optimal procedures are yet undefined and may depend on the heterogeneity present in the set and on the considered scale. The objectives were to test the usefulness of partial least squares regressions (PLSRs) for soil organic carbon (SOC), total carbon (C〈sub〉t〈/sub〉), total nitrogen (N〈sub〉t〈/sub〉) and pH using vis–NIR and MIR spectroscopy for an independent validation after standard calibration (use of a general PLSR model) or using memory‐based learning (MBL) with and without spiking for a national spectral database. Data fusion approaches were simple concatenation of spectra, outer product analysis (OPA) and model averaging. In total, 481 soils from an Austrian forest soil archive were measured in the vis–NIR and MIR regions, and regressions were calculated. Fivefold calibration‐validation approaches were carried out with a region‐related split of spectra to implement independent validations with n ranging from 47 to 99 soils in different folds. MIR predictions were generally superior over vis–NIR predictions. For all properties, optimal predictions were obtained with data fusion, with OPA and spectra concatenation outperforming model averaging. The greatest robustness of performance was found for OPA and MBL with spiking with 〈italic toggle="no"〉R〈/italic〉〈sup〉2〈/sup〉 ≥ 0.77 (N), 0.85 (SOC), 0.86 (pH) and 0.88 (C〈sub〉t〈/sub〉) in the validations of all folds. Overall, the results indicate that the combination of OPA for vis–NIR and MIR spectra with MBL and spiking has a high potential to accurately estimate properties when using large‐scale soil spectral libraries as reference data. However, the reduction of cost‐effectiveness using two spectrometers needs to be weighed against the potential increase in accuracy compared to a single MIR spectroscopy approach.〈/p〉
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Keywords: ddc:631.4 ; data fusion ; independent validation ; infrared spectroscopy ; MBL ; nitrogen ; outer product analysis ; pH ; soil organic carbon ; spiking ; total carbon
    Language: English
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  • 4
    Publication Date: 2023-08-29
    Description: This study focuses on the changes in diet and mobility of people buried in the La Sassa cave (Latium, Central Italy) during the Copper and Bronze Ages to contribute to the understanding of the complex contemporary population dynamics in Central Italy. To that purpose, carbon and nitrogen stable isotope analyses, strontium isotope analyses, and FT-IR evaluations were performed on human and faunal remains from this cave. The stable isotope analyses evidence a slight shift in diet between Copper and Bronze Age individuals, which becomes prominent in an individual, dating from a late phase, when the cave was mainly used as a cultic shelter. This diachronic study documents an increased dietary variability due to the introduction of novel resources in these protohistoric societies, possibly related to the southward spread of northern human groups into Central Italy. This contact between different cultures is also testified by the pottery typology found in the cave. The latter shows an increase in cultural intermingling starting during the beginning of the middle Bronze Age. The local mobility during this phase likely involved multiple communities scattered throughout an area of a few kilometers around the cave, which used the latter as a burial site both in the Copper and Bronze ages.
    Description: Published
    Description: e0288637
    Description: 6A. Geochimica per l'ambiente e geologia medica
    Description: 6SR VULCANI – Servizi e ricerca per la società
    Description: 7SR AMBIENTE – Servizi e ricerca per la società
    Description: JCR Journal
    Keywords: La Sassa cave (Central Italy) ; population dynamics ; nitrogen isotope ; strontium isotope
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 5
    Publication Date: 2024-01-19
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉In recent years, many two‐dimensional (2D) hydrodynamic models have been extended to include the direct rainfall method (DRM). This allows their application as a hydrological‐hydrodynamic model for the determination of floodplains in one model system. In previous studies on DRM, the role of catchment hydrological processes (CaHyPro) and its interaction with the calibration process was not investigated in detail. In the present, case‐oriented study, the influence of the spatiotemporal distribution of the processes precipitation and runoff formation in combination with the 2D model HEC‐RAS is investigated. In a further step, a conceptual approach for event‐based interflow is integrated. The study is performed on the basis of a single storm event in a small rural catchment (low mountain range, 38 km〈sup〉2〈/sup〉) in Hesse (Germany). The model results are evaluated against six quality criteria and compared to a simplified baseline model. Finally, the calibrated improved model is contrasted with a calibrated baseline model. The results show the enhancement of the model results due to the integration of the CaHyPro and highlight its interplay with the calibrated model parameters.〈/p〉
    Keywords: ddc:551.48 ; 2D hydrodynamic modeling ; calibration ; direct rainfall modeling ; hydrological processes ; radar data ; runoff formation
    Language: English
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  • 6
    Publication Date: 2023-11-18
    Description: Spatiotemporal characterisation of the soil redox status within the capillary fringe (CF) is a challenging task. Air‐filled porosities (ε), oxygen concentration (O〈sub〉2〈/sub〉) and soil redox potential (EH) are interrelated soil variables within active biogeochemical domains such as the CF. We investigated the impact of water table (WT) rise and drainage in an undisturbed topsoil and subsoil sample taken from a Calcaric Gleysol for a period of 46 days. We merged 1D (EH and matric potential) and 2D (O〈sub〉2〈/sub〉) systems to monitor at high spatiotemporal resolution redox dynamics within self‐constructed redoxtron housings and complemented the data set by a 3D pore network characterization using X‐ray microtomography (X‐ray μCT). Depletion of O〈sub〉2〈/sub〉 was faster in the organic matter‐ and clay‐rich aggregated topsoil and the CF extended 〉10 cm above the artificial WT. The homogeneous and less‐aggregated subsoil extended only 4 cm above the WT as indicated by ε–O〈sub〉2〈/sub〉–EH data during saturation. After drainage, 2D O〈sub〉2〈/sub〉 imaging revealed a fast aeration towards the lower depths of the topsoil, which agrees with the connected ε derived by X‐ray μCT (ε〈sub〉CT_conn〈/sub〉) of 14.9% of the total porosity. However, small‐scaled anoxic domains with O〈sub〉2〈/sub〉 saturation 〈5% were apparent even after lowering the WT (down to 0.25 cm〈sup〉2〈/sup〉 in size) for 23 days. These domains remained a nucleus for reducing soil conditions (E〈sub〉H〈/sub〉 〈 −100 mV), which made it challenging to characterise the soil redox status in the CF. In contrast, the subsoil aeration reached O〈sub〉2〈/sub〉 saturation after 8 days for the complete soil volume. Values of ε〈sub〉CT_conn〈/sub〉 around zero in the subsoil highlighted that soil aeration was independent of this parameter suggesting that other variables such as microbial activity must be considered when predicting the soil redox status from ε alone. The use of redoxtrons in combination with localised redox‐measurements and image based pore space analysis resulted in a better 2D/3D characterisation of the pore system and related O〈sub〉2〈/sub〉 transport properties. This allowed us to analyse the distribution and activity of microbiological niches highly associated with the spatiotemporal variable redox dynamics in soil environments. Highlights: The time needed to turn from reducing to oxidising (period where all platinum electrodes feature E〈sub〉H〈/sub〉 〉 300 mV) condition differ for two samples with contrasting soil structure. The subsoil with presumably low O〈sub〉2〈/sub〉 consumption rates aerated considerably faster than the topsoil and exclusively by O〈sub〉2〈/sub〉 diffusion through medium‐ and fine‐sized pores. To derive the soil redox status based upon the triplet ε–O〈sub〉2〈/sub〉–E〈sub〉H〈/sub〉 is challenging at present in heterogeneous soil domains and larger soil volumes than 250 cm〈sup〉3〈/sup〉. Undisturbed soil sampling along with 2D/3D redox measurement systems (e.g., redoxtrons) improve our understanding of redox dynamics within the capillary fringe.
    Keywords: ddc:631.4 ; environmental monitoring ; incubation experiments ; redox processes ; soil reducing conditions ; undisturbed soil ; X‐ray microtomography
    Language: English
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  • 7
    Publication Date: 2023-11-17
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈sec xmlns:mml="http://www.w3.org/1998/Math/MathML" id="ejss13362-sec-1003" xml:lang="en"〉 〈p xml:lang="en"〉Long‐term experiments (LTEs) have provided data to modellers and agronomists to investigate changes and dynamics of soil organic carbon (SOC) under different cropping systems. As treatment changes have occurred due to agricultural advancements, so too have analytical soil methods. This may lead to method bias over time, which could affect the robust interpretation of data and conclusions drawn. This study aims to quantify differences in SOC due to changes in dry combustion methods over time, using soil samples of a LTE established in 1963 that focuses on mineral and organic fertilizer management in the temperate zone of Northeast Germany. For this purpose, 1059 soil samples, collected between 1976 and 2008, have been analysed twice, once with their historical laboratory method right after sampling, and a second time in 2016 when all samples were analysed using the same elementary analyser. In 9 of 11 soil sampling campaigns, a paired 〈italic toggle="no"〉t〈/italic〉‐test provided evidence for significant differences in the historical SOC values when compared with the re‐analysed concentrations of the same LTE sample. In the sampling years 1988 and 2004, the historical analysis obtained about 0.9 g kg〈sup〉−1〈/sup〉 lower SOC compared with the re‐analysed one. For 1990 and 1998, this difference was about 0.4 g kg〈sup〉−1〈/sup〉. Correction factors, an approach often used to correct for different analytical techniques, could only be applied for 5 of 11 sampling campaigns to account for constant and proportional systematic method error. For this particular LTE, the interpretation of SOC changes due to agronomic management (here fertilization) deviates depending on the analytical method used, which may weaken the explanatory power of the historical data. We demonstrate that analytical method changes over time present one of many challenges in the interpretation of time series data of SOC dynamics. Therefore, LTE site managers need to ensure providing all necessary protocols and data in order to retrace method changes and if necessary recalculate SOC.〈/p〉 〈/sec〉〈sec xmlns:mml="http://www.w3.org/1998/Math/MathML" id="ejss13362-sec-0003" xml:lang="en"〉 〈title〉Highlights〈/title〉 〈p xml:lang="en"〉〈list list-type="bullet" id="ejss13362-list-0001"〉 〈list-item id="ejss13362-li-0001"〉〈p〉A total of 1059 LTE soil samples taken between 1976 and 2008 were re‐analysed for SOC in 2016〈/p〉〈/list-item〉 〈list-item id="ejss13362-li-0002"〉〈p〉Several methodological changes for SOC determination led to significant different SOC concentration in the same sample〈/p〉〈/list-item〉 〈list-item id="ejss13362-li-0003"〉〈p〉Interpretation and time series of LTE soil data suffer from consideration of analytical method changes and poor documentation of the same〈/p〉〈/list-item〉 〈list-item id="ejss13362-li-0004"〉〈p〉Soil archive establishment, thorough method protocols and diligent proficiency testing after soil method changes ameliorate the dilemma〈/p〉〈/list-item〉 〈/list〉〈/p〉 〈/sec〉
    Description: Brandenburger Staatsministerium für Wissenschaft, Forschung und Kultur http://dx.doi.org/10.13039/501100004581
    Description: Bundesministerium für Bildung und Forschung http://dx.doi.org/10.13039/501100004937
    Description: https://doi.org/10.4228/zalf-acge-b683
    Keywords: ddc:631.4 ; Bland–Altman ; carbon stocks ; data trueness ; Deming regression ; method bias ; soil archive ; soil survey
    Language: English
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  • 8
    Publication Date: 2024-01-24
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Flood risk assessments require different disciplines to understand and model the underlying components hazard, exposure, and vulnerability. Many methods and data sets have been refined considerably to cover more details of spatial, temporal, or process information. We compile case studies indicating that refined methods and data have a considerable effect on the overall assessment of flood risk. But are these improvements worth the effort? The adequate level of detail is typically unknown and prioritization of improvements in a specific component is hampered by the lack of an overarching view on flood risk. Consequently, creating the dilemma of potentially being too greedy or too wasteful with the resources available for a risk assessment. A “sweet spot” between those two would use methods and data sets that cover all relevant known processes without using resources inefficiently. We provide three key questions as a qualitative guidance toward this “sweet spot.” For quantitative decision support, more overarching case studies in various contexts are needed to reveal the sensitivity of the overall flood risk to individual components. This could also support the anticipation of unforeseen events like the flood event in Germany and Belgium in 2021 and increase the reliability of flood risk assessments.〈/p〉
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Description: BMBF http://dx.doi.org/10.13039/501100002347
    Description: Federal Environment Agency http://dx.doi.org/10.13039/501100010809
    Description: http://howas21.gfz-potsdam.de/howas21/
    Description: https://www.umwelt.niedersachsen.de/startseite/themen/wasser/hochwasser_amp_kustenschutz/hochwasserrisikomanagement_richtlinie/hochwassergefahren_und_hochwasserrisikokarten/hochwasserkarten-121920.html
    Description: https://download.geofabrik.de/europe/germany.html
    Description: https://emergency.copernicus.eu/mapping/list-of-components/EMSN024
    Description: https://data.jrc.ec.europa.eu/collection/id-0054
    Description: https://oasishub.co/dataset/surface-water-flooding-footprinthurricane-harvey-august-2017-jba
    Description: https://www.wasser.sachsen.de/hochwassergefahrenkarte-11915.html
    Keywords: ddc:551.48 ; decision support ; extreme events ; integrated flood risk management ; risk assessment
    Language: English
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  • 9
    Publication Date: 2024-01-26
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉The increasing demand for biomass for food, animal feed, fibre and bioenergy requires optimization of soil productivity, while at the same time, protecting other soil functions such as nutrient cycling and buffering, carbon storage, habitat for biological activity and water filter and storage. Therefore, one of the main challenges for sustainable agriculture is to produce high yields while maintaining all the other soil functions. Mechanistic simulation models are an essential tool to fully understand and predict the complex interactions between physical, biological and chemical processes of soils that generate those functions. We developed a soil model to simulate the impact of various agricultural management options and climate change on soil functions by integrating the relevant processes mechanistically and in a systemic way. As a special feature, we include the dynamics of soil structure induced by tillage and biological activity, which is especially relevant in arable soils. The model operates on a 1D soil profile consisting of a number of discrete layers with dynamic thickness. We demonstrate the model performance by simulating crop growth, root growth, nutrient and water uptake, nitrogen cycling, soil organic matter turnover, microbial activity, water distribution and soil structure dynamics in a long‐term field experiment including different crops and different types and levels of fertilization. The model is able to capture essential features that are measured regularly including crop yield, soil organic carbon, and soil nitrogen. In this way, the plausibility of the implemented processes and their interactions is confirmed. Furthermore, we present the results of explorative simulations comparing scenarios with and without tillage events to analyse the effect of soil structure on soil functions. Since the model is process‐based, we are confident that the model can also be used to predict quantities that have not been measured or to estimate the effect of management measures and climate states not yet been observed. The model thus has the potential to predict the site‐specific impact of management decisions on soil functions, which is of great importance for the development of a sustainable agriculture that is currently also on the agenda of the ‘Green Deal’ at the European level.〈/p〉
    Description: Bundesministerium für Bildung und Forschung http://dx.doi.org/10.13039/501100002347
    Description: https://git.ufz.de/bodium/bodium_v1.0
    Keywords: ddc:631.4 ; agriculture ; computational model ; simulation ; soil microbiology ; soil structure ; sustainable soil
    Language: English
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  • 10
    Publication Date: 2024-03-18
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Temperature and soil moisture are known to control pesticide mineralization. Half‐life times (DT〈sub〉50〈/sub〉) derived from pesticide mineralization curves generally indicate longer residence times at low soil temperature and moisture but do not consider potential changes in the microbial allocation of pesticide‐derived carbon (C). We aimed to determine carbon use efficiency (CUE, formation of new biomass relative to total C uptake) to better understand microbial utilization of pesticide‐derived C under different environmental conditions and to support the conventional description of degradation dynamics based on mineralization. We performed a microcosm experiment at two MCPA (2‐methyl‐4‐chlorophenoxyacetic acid) concentrations (1 and 20 mg kg〈sup〉−1〈/sup〉) and defined 20°C/pF 1.8 as optimal and 10°C/pF 3.5 as limiting environmental conditions. After 4 weeks, 70% of the initially applied MCPA was mineralized under optimal conditions but MCPA mineralization reached less than 25% under limiting conditions. However, under limiting conditions, an increase in CUE was observed, indicating a shift towards anabolic utilization of MCPA‐derived C. In this case, increased C assimilation implied C storage or the formation of precursor compounds to support resistance mechanisms, rather than actual growth since we did not find an increase in the 〈italic toggle="no"〉tfdA〈/italic〉 gene relevant to MCPA degradation. We were able to confirm the assumption that under limiting conditions, C assimilation increases relative to mineralization and that C redistribution, may serve as an explanation for the difference between mineralization and MCPA dissipation‐derived degradation dynamics. In addition, by introducing CUE to the temperature‐ and moisture‐dependent degradation of pesticides, we can capture the underlying microbial constraints and adaptive mechanisms to changing environmental conditions.〈/p〉
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Changing environmental conditions alter the MCPA degradation dynamics and the allocation of pesticide‐derived carbon to anabolic or catabolic metabolism.〈boxed-text position="anchor" content-type="graphic" id="ejss13417-blkfxd-0001" xml:lang="en"〉 〈graphic position="anchor" id="jats-graphic-1" xlink:href="urn:x-wiley:13510754:media:ejss13417:ejss13417-toc-0001"〉 〈/graphic〉 〈/boxed-text〉〈/p〉
    Description: Collaborative Research Center 1253 CAMPOS (DFG)
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Description: DFG Priority Program 2322 “Soil System”
    Description: Ellrichshausen Foundation
    Description: Research Training Group “Integrated Hydrosystem modeling”
    Description: https://doi.org/10.5281/zenodo.5081655
    Keywords: ddc:631.4 ; anabolism ; carbon use efficiency ; catabolism ; effect of soil moisture and temperature ; gene‐centric process model ; MCPA biodegradation
    Language: English
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  • 11
    Publication Date: 2024-02-09
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Gas transport in soils is usually assumed to be purely diffusive, although several studies have shown that non‐diffusive processes can significantly enhance soil gas transport. These processes include barometric air pressure changes, wind‐induced pressure pumping and static air pressure fields generated by wind interacting with obstacles. The associated pressure gradients in the soil can cause advective gas fluxes that are much larger than diffusive fluxes. However, the contributions of the respective transport processes are difficult to separate. We developed a large chamber system to simulate pressure fields and investigate their influence on soil gas transport. The chamber consists of four subspaces in which pressure is regulated by fans that blow air in or out of the chamber. With this setup, we conducted experiments with oscillating and static pressure fields. CO〈sub〉2〈/sub〉 concentrations were measured along two soil profiles beneath the chamber. We found a significant relationship between static lateral pressure gradients and the change in the CO〈sub〉2〈/sub〉 profiles (R〈sup〉2〈/sup〉 = 0.53; 〈italic toggle="no"〉p〈/italic〉‐value 〈2e‐16). Even small pressure gradients between −1 and 1 Pa relative to ambient pressure resulted in an increase or decrease in CO〈sub〉2〈/sub〉 concentrations of 8% on average in the upper soil, indicating advective flow of air in the pore space. Positive pressure gradients resulted in decreasing, negative pressure gradients in increasing CO〈sub〉2〈/sub〉 concentrations. The concentration changes were probably caused by an advective flow field in the soil beneath the chamber generated by the pressure gradients. No effect of oscillating pressure fields was observed in this study. The results indicate that static lateral pressure gradients have a substantial impact on soil gas transport and therefore are an important driver of gas exchange between soil and atmosphere. Lateral pressure gradients in a comparable range can be induced under windy conditions when wind interacts with terrain features. They can also be caused by chambers used for flux measurements at high wind speed or by fans used for head‐space mixing within the chambers, which yields biased flux estimates.〈/p〉
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Keywords: ddc:631.4 ; advective flux ; chamber flux measurements ; static air pressure fields ; wind‐induced pressure pumping
    Language: English
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  • 12
    Publication Date: 2024-02-07
    Description: Coexistence of fish populations (= stocks) of the same species is a common phenomenon. In the Baltic Sea, two genetically divergent stocks of Atlantic cod (Gadus morhua), Western Baltic cod (WBC) and Eastern Baltic cod (EBC), coexist in the Arkona Sea. Although the relative proportions of WBC and EBC in this area are considered in the current stock assessments, the mixing dynamics and ecological mechanisms underlying coexistence are not well understood. In this study, a genetically validated otolith shape analysis was used to develop the most comprehensive time series of annual stock mixing data (1977–2019) for WBC and EBC. Spatio-temporal mixing analysis confirmed that the two stocks coexist in the Arkona Sea, albeit with fluctuating mixing proportions over the 43-year observation period. Depth-stratified analysis revealed a strong correlation between capture depth and stock mixing patterns, with high proportions of WBC in shallower waters (48–61% in 〈20m) and increasing proportions of EBC in deeper waters (50–86% in 40-70m). Consistent depth-specific mixing patterns indicate stable differences in depth distribution and habitat use of WBC and EBC that may thus underlie the long-term coexistence of the two stocks in the Arkona Sea. These differences were also reflected in significantly different proportions of WBC and EBC in fisheries applying passive gears in shallower waters (more WBC) and active gears in deeper waters (more EBC). This highlights the potential for fishing gear-specific exploitation of different stocks, and calls for stronger consideration of capture depth and gear type in stock assessments. This novel evidence provides the basis for improved approaches to research, monitoring and management of Baltic cod stocks.
    Type: Article , PeerReviewed
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  • 13
    Publication Date: 2024-02-07
    Description: Using transient climate forcing based on simulations from the Alfred Wegener Institute Earth System Model (AWI-ESM), we simulate the evolution of the Greenland Ice Sheet (GrIS) from the last interglacial (125 ka, kiloyear before present) to 2100 AD with the Parallel Ice Sheet Model (PISM). The impact of paleoclimate, especially Holocene climate, on the present and future evolution of the GrIS is explored. Our simulations of the past show close agreement with reconstructions with respect to the recent timing of the peaks in ice volume and the climate of Greenland. The maximum and minimum ice volume at around 18–17 ka and 6–5 ka lag the respective extremes in climate by several thousand years, implying that the ice volume response of the GrIS strongly lags climatic changes. Given that Greenland’s climate was getting colder from the Holocene Thermal Maximum (i.e., 8 ka) to the Pre-Industrial era, our simulation implies that the GrIS experienced growth from the mid-Holocene to the industrial era. Due to this background trend, the GrIS still gains mass until the second half of the 20th century, even though anthropogenic warming begins around 1850 AD. This is also in agreement with observational evidence showing mass loss of the GrIS does not begin earlier than the late 20th century. Our results highlight that the present evolution of the GrIS is not only controlled by the recent climate changes, but is also affected by paleoclimate, especially the relatively warm Holocene climate. We propose that the GrIS was not in equilibrium throughout the entire Holocene and that the slow response to Holocene climate needs to be represented in ice sheet simulations in order to predict ice mass loss, and therefore sea level rise, accurately.
    Type: Article , PeerReviewed
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  • 14
    Publication Date: 2023-01-21
    Description: Charcoal‐rich Technosols on century‐old relict charcoal hearths (RCHs) are the subject of ongoing research regarding potential legacy effects that result from historic charcoal production and subsequent charcoal amendments on forest soil properties and forest ecosystems today. RCHs consist mostly of Auh horizons that are substantially enriched in soil organic carbon (SOC), of which the largest part seems to be of pyrogenic origin (PyC). However, the reported range of SOC and PyC contents in RCH soil also suggests that they are enriched in nonpyrogenic SOC. RCH soils are discussed as potential benchmarks for the long‐term influence of biochar amendment and the post‐wildfire influences on soil properties. In this study, we utilised a large soil sample dataset (n = 1245) from 52 RCH sites in north‐western Connecticut, USA, to quantify SOC contents by total element analysis. The contents of condensed highly aromatic carbon as a proxy for black carbon (BC) were predicted by using a modified benzene polycarboxylated acid (BPCA) marker method in combination with diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy‐based partial least square regression (r2 = 0.89). A high vertical spatial sampling resolution allowed the identification of soil organic matter (SOM) enrichment and translocation processes. The results show an average 75% and 1862% increase in TOC and BPCA‐derived carbon, respectively, for technogenic Auh horizons compared to reference soils. In addition to an increase in aromatic properties, increased carboxylic properties of the RCH SOC suggest self‐humification effects of degrading charcoal and thereby the continuing formation of leachable aromatic carbon compounds, which could have effects on pedogenic processes in buried soils. Indeed, we show BPCA‐derived carbon concentrations in intermediate technogenic Cu horizons and buried top/subsoils that suggest vertical translocation of highly aromatic carbon originating in RCH Auh horizons. Topmost Auh horizons showed a gradual decrease in total organic carbon (TOC) contents with increasing depth, suggesting accumulation of recent, non‐pyrogenic SOM. Lower aliphatic absorptions in RCH soil spectra suggest different SOM turnover dynamics compared to reference soils. Furthermore, studied RCH soils featured additional TOC enrichment, which cannot be fully explained now. Highlights BC to TOC ratio and high resolution vertical SOC distribution in 52 RCH sites were studied. RCH soils non‐BC pool was potentially different to reference soils. RCH soils feature TOC accumulation in the topmost horizon. There is BC translocation into buried soils on RCH sites.
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Keywords: ddc:631.4 ; benzene polycarboxylated acid marker (BPCA) ; black carbon ; charcoal degradation ; charcoal kiln ; pyrogenic carbon ; relict charcoal hearth ; biochar
    Language: English
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  • 15
    Publication Date: 2023-01-26
    Description: Erosion is a severe threat to the sustainable use of agricultural soils. However, the structural resistance of soil against the disruptive forces steppe soils experience under field conditions has not been investigated. Therefore, 132 topsoils under grass‐ and cropland covering a large range of physico‐chemical soil properties (sand: 2–76%, silt: 18–80%, clay: 6–30%, organic carbon: 7.3–64.2 g kg−1, inorganic carbon: 0.0–8.5 g kg−1, pH: 4.8–9.5, electrical conductivity: 32–946 μS cm−1) from northern Kazakhstan were assessed for their potential erodibility using several tests. An adjusted drop‐shatter method (low energy input of 60 Joule on a 250‐cm3 soil block) was used to estimate the stability of dry soil against weak mechanical forces, such as saltating particles striking the surface causing wind erosion. Three wetting treatments with various conditions and energies (fast wetting, slow wetting, and wet shaking) were applied to simulate different disruptive effects of water. Results indicate that aggregate stability was higher for grassland than cropland soils and declined with decreasing soil organic carbon content. The results of the drop‐shatter test suggested that 29% of the soils under cropland were at risk of wind erosion, but only 6% were at high risk (i.e. erodible fraction 〉60%). In contrast, the fast wetting treatment revealed that 54% of the samples were prone to become “very unstable” and 44% “unstable” during heavy rain or snowmelt events. Even under conditions comparable to light rain events or raindrop impact, 53–59% of the samples were “unstable.” Overall, cropland soils under semi‐arid conditions seem much more susceptible to water than wind erosion. Considering future projections of increasing precipitation in Kazakhstan, we conclude that the risk of water erosion is potentially underestimated and needs to be taken into account when developing sustainable land use strategies. Highlights Organic matter is the important binding agent enhancing aggregation in steppe topsoils. Tillage always declines aggregate stability even without soil organic carbon changes. All croplands soil are prone to wind or water erosion independent of their soil properties. Despite the semi‐arid conditions, erosion risk by water seems higher than by wind.
    Description: Bundesministerium für Bildung und Forschung http://dx.doi.org/10.13039/501100002347
    Keywords: ddc:631.4 ; climate change ; land use ; soil organic carbon ; soil texture ; water erosion ; wind erosion
    Language: English
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  • 16
    Publication Date: 2023-01-20
    Description: Stable hydrogen isotope ratios (δ2H values) in structural hydroxyl groups of pedogenic clay minerals are inherited from the surrounding water at the time of their formation. Only non‐exchangeable H preserves the environmental forensic and paleoclimate information (δ2Hn value). To measure δ2Hn values in structural H of clay minerals and soil clay fractions, we adapted a steam equilibration method by accounting for high hygroscopicity. Our δ2Hn values for USGS57 biotite (−95.3 ± SD 0.9‰) and USGS58 muscovite (30.7 ± 1.4‰) differed slightly but significantly from the reported δ2H values (−91.5 ± 2.4‰ and −28.4 ± 1.6‰), because the minerals contained 1.1%–4.4% of exchangeable H. The low SD of replicate measurements (n = 3) confirmed a high precision. The clay separation method including destruction of Fe oxides, carbonates and soil organic matter, and dispersion did not significantly change the δ2Hn values of five different clay minerals. However, we were unable to remove all organic matter from the soil clay fractions resulting in an estimated bias of 1‰ in two samples and 15‰ in the carbon‐richest sample. Our results demonstrate that δ2Hn values of structural H of clay minerals and soil clay fractions can be reliably measured without interference from atmospheric water and the method used to separate the soil clay fraction. Highlights We tested steam equilibration to determine stable isotope ratios of structural H in clay. Gas‐tight capsule sealing in Ar atmosphere was necessary to avoid remoistening. Our steam equilibration method showed a high accuracy and precision. The clay separation method did not change stable isotope ratios of structural H in clay.
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Keywords: ddc:549 ; controlled isotope exchange technique ; deuterium ; montmorillonite ; soil clay separation ; soil organic matter removal ; steam equilibration ; structural H ; USGS57 biotite ; vermiculite ; δ2H
    Language: English
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  • 17
    Publication Date: 2024-03-22
    Description: Soil fauna drives crucial processes of energy and nutrient cycling in agricultural systems, and influences the quality of crops and pest incidence. Soil tillage is the most influential agricultural manipulation of soil structure, and has a profound influence on soil biology and its provision of ecosystem services. The objective of this study was to quantify through meta‐analyses the effects of reducing tillage intensity on density and diversity of soil micro‐ and mesofaunal communities, and how these effects vary among different pedoclimatic conditions and interact with concurrent management practices. We present the results of a global meta‐analysis of available literature data on the effects of different tillage intensities on taxonomic and functional groups of soil micro‐ and mesofauna. We collected paired observations (conventional vs. reduced forms of tillage/no‐tillage) from 133 studies across 33 countries. Our results show that reduced tillage intensity or no‐tillage increases the total density of springtails (+35%), mites (+23%), and enchytraeids (+37%) compared to more intense tillage methods. The meta‐analyses for different nematode feeding groups, life‐forms of springtails, and taxonomic mite groups showed higher densities under reduced forms of tillage compared to conventional tillage on omnivorous nematodes (+53%), epedaphic (+81%) and hemiedaphic (+84%) springtails, oribatid (+43%) and mesostigmatid (+57%) mites. Furthermore, the effects of reduced forms of tillage on soil micro‐ and mesofauna varied with depth, climate and soil texture, as well as with tillage method, tillage frequency, concurrent fertilisation, and herbicide application. Our findings suggest that reducing tillage intensity can have positive effects on the density of micro‐ and mesofaunal communities in areas subjected to long‐term intensive cultivation practices. Our results will be useful to support decision making on the management of soil faunal communities and will facilitate modelling efforts of soil biology in global agroecosystems. HIGHLIGHTS Global meta‐analysis to estimate the effect of reducing tillage intensity on micro‐ and mesofauna Reduced tillage or no‐tillage has positive effects on springtail, mite and enchytraeid density Effects vary among nematode feeding groups, springtail life forms and mite suborders Effects vary with texture, climate and depth and depend on the tillage method and frequency
    Description: Bundesministerium für Bildung und Forschung http://dx.doi.org/10.13039/501100002347
    Description: https://doi.org/10.20387/bonares-eh0f-hj28
    Keywords: ddc:631.4 ; agricultural land use ; conservation agriculture ; conventional agriculture ; soil biodiversity ; soil cultivation
    Language: English
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  • 18
    Publication Date: 2024-02-28
    Description: 〈title xmlns:mml="http://www.w3.org/1998/Math/MathML"〉Abstract〈/title〉〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Hydrogeological information about an aquifer is difficult and costly to obtain, yet essential for the efficient management of groundwater resources. Transferring information from sampled sites to a specific site of interest can provide information when site‐specific data is lacking. Central to this approach is the notion of site similarity, which is necessary for determining relevant sites to include in the data transfer process. In this paper, we present a data‐driven method for defining site similarity. We apply this method to selecting groups of similar sites from which to derive prior distributions for the Bayesian estimation of hydraulic conductivity measurements at sites of interest. We conclude that there is now a unique opportunity to combine hydrogeological expertise with data‐driven methods to improve the predictive ability of stochastic hydrogeological models.〈/p〉
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉〈italic〉Article impact statement〈/italic〉: This article introduces hierarchical clustering as a method for defining a notion of site similarity; the aim of this method is to improve the derivation of prior distributions in Bayesian methods in hydrogeology.〈/p〉
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Description: https://github.com/GeoStat-Bayesian/geostatDB
    Description: https://github.com/GeoStat-Bayesian/exPrior
    Description: https://github.com/GeoStat-Bayesian/siteSimilarity
    Keywords: ddc:551.49 ; hydrogeological sites ; hydrogeological modeling
    Language: English
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  • 19
    Publication Date: 2024-02-07
    Description: Sponges produce distinct fatty acids (FAs) that (potentially) can be used as chemotaxonomic and ecological biomarkers to study endosymbiont-host interactions and the functional ecology of sponges. Here, we present FA profiles of five common habitat-building deep-sea sponges (class Demospongiae, order Tetractinellida), which are classified as high microbial abundance (HMA) species. Geodia hentscheli, G. parva, G. atlantica, G. barretti, and Stelletta rhaphidiophora were collected from boreal and Arctic sponge grounds in the North-Atlantic Ocean. Bacterial FAs dominated in all five species and particularly isomeric mixtures of mid-chain branched FAs (MBFAs, 8- and 9-Me-C16:0 and 10- and 11-Me-C18:0) were found in high abundance (together ≥ 20% of total FAs) aside more common bacterial markers. In addition, the sponges produced long-chain linear, mid- and a(i)-branched unsaturated FAs (LCFAs) with a chain length of 24‒28 C atoms and had predominantly the typical Δ5,9 unsaturation, although the Δ9,19 and (yet undescribed) Δ11,21 unsaturations were also identified. G. parva and S. rhaphidiophora each produced distinct LCFAs, while G. atlantica, G. barretti, and G. hentscheli produced similar LCFAs, but in different ratios. The different bacterial precursors varied in carbon isotopic composition (δ13C), with MBFAs being more enriched compared to other bacterial (linear and a(i)-branched) FAs. We propose biosynthetic pathways for different LCFAs from their bacterial precursors, that are consistent with small isotopic differences found in LCFAs. Indeed, FA profiles of deep-sea sponges can serve as chemotaxonomic markers and support the concept that sponges acquire building blocks from their endosymbiotic bacteria.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
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  • 20
    Publication Date: 2024-03-21
    Description: Acesta excavata (Fabricius, 1779) is a slow growing bivalve from the Limidae family and is often found associated with cold-water coral reefs along the European continental margin. Here we present the compositional variability of frequently used proxy elemental ratios (Mg/Ca, Sr/Ca, Na/Ca) measured by laser-ablation mass spectrometry (LA-ICP-MS) and compare it to in-situ recorded instrumental seawater parameters such as temperature and salinity. Shell Mg/Ca measured in the fibrous calcitic shell section was overall not correlated with seawater temperature or salinity; however, some samples show significant correlations with temperature with a sensitivity that was found to be unusually high in comparison to other marine organisms. Mg/Ca and Sr/Ca measured in the fibrous calcitic shell section display significant negative correlations with the linear extension rate of the shell, which indicates strong vital effects in these bivalves. Multiple linear regression analysis indicates that up to 79% of elemental variability is explicable with temperature and salinity as independent predictor values. Yet, the overall results clearly show that the application of Element/Ca (E/Ca) ratios in these bivalves to reconstruct past changes in temperature and salinity is likely to be complicated due to strong vital effects and the effects of organic material embedded in the shell. Therefore, we suggest to apply additional techniques, such as clumped isotopes, in order to exactly determine and quantify the underlying vital effects and possibly account for these. We found differences in the chemical composition between the two calcitic shell layers that are possibly explainable through differences of the crystal morphology. Sr/Ca ratios also appear to be partly controlled by the amount of magnesium, because the small magnesium ions bend the crystal lattice which increases the space for strontium incorporation. Oxidative cleaning with H2O2 did not significantly change the Mg/Ca and Sr/Ca composition of the shell. Na/Ca ratios decreased after the oxidative cleaning, which is most likely a leaching effect and not caused by the removal of organic matter.
    Type: Article , PeerReviewed
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  • 21
    Publication Date: 2021-10-29
    Description: Purpose The purpose of this study was to characterize the nasopharyngeal microbiota of infants with possible and confirmed pertussis compared to healthy controls. Methods This prospective study included all infants
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 22
    Publication Date: 2021-10-29
    Description: ERBB family members and their ligands play an essential role in embryonic heart development and adult heart physiology. Among them, ERBB3 is a binding partner of ERBB2; the ERBB2/3 complex mediates downstream signaling for cell proliferation. ERBB3 has seven consensus binding sites to the p85 regulatory subunit of PI3K, which activates the downstream AKT pathway, leading to the proliferation of various cells. This study generated a human ERBB3 knock-in mouse expressing a mutant ERBB3 whose seven YXXM p85 binding sites were replaced with YXXA. Erbb3 knock-in embryos exhibited lethality between E12.5 to E13.5, and showed a decrease in mesenchymal cell numbers and density in AV cushions. We determined that the proliferation of mesenchymal cells in the atrioventricular (AV) cushion in Erbb3 knock-in mutant embryos was temporarily reduced due to the decrease of AKT and ERK1/2 phosphorylation. Overall, our results suggest that AKT/ERK activation by the ERBB3-dependent PI3K signaling is crucial for AV cushion morphogenesis during embryonic heart development.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 23
    Publication Date: 2021-10-29
    Description: Fungal infection and synthesis of mycotoxins in coffee leads to significant economic losses. This study aimed to investigate the prevalence of toxigenic fungi, their metabolites, and the effect of traditional roasting and brewing on ochratoxin A (OTA) and aflatoxins (AFs) contents of naturally contaminated coffee samples. In addition, in vivo biocontrol assays were performed to explore the antagonistic activities of Bacillus simplex 350–3 (BS350-3) on the growth and mycotoxins synthesis of Aspergillus ochraceus and A. flavus. The relative density of A. niger, A. flavus, Penicillium verrucosum and A. carbonarius on green coffee bean was 60.82%, 7.21%, 3.09% and 1.03%, respectively. OTA contents were lowest in green coffee beans (2.15 μg/kg), followed by roasted (2.76 μg/kg) and soluble coffee (8.95 μg/kg). Likewise, AFs levels were highest in soluble coffee (90.58 μg/kg) followed by roasted (33.61 μg/kg) and green coffee (9.07 μg/kg). Roasting naturally contaminated coffee beans at three traditional methods; low, medium and high, followed by brewing resulted in reduction of 58.74% (3.50 μg/kg), 60.88% (3.72 μg/kg) and 64.70% (4.11 μg/kg) in OTA and 40.18% (34.65 μg/kg), 47.86% (41.17 μg/kg) and 62.38% (53.73 μg/kg) AFs contents, respectively. Significant inhibitions of AFs and OTA synthesis by A. flavus and A. carbonarius, respectively, on infected coffee beans were observed in presence of Bacillus simplex BS350-3 volatiles. Gas chromatography mass spectrochemistry (GC-MS/MS) analysis of head-space BS350-3 volatiles showed quinoline, benzenemethanamine and 1-Octadecene as bioactive antifungal molecules. These findings suggest that marketed coffee samples are generally contaminated with OTA and AFs, with a significant level of roasted and soluble coffee contaminated above EU permissible limits for OTA. Further, along with coffee roasting and brewing; microbial volatiles can be optimized to minimize the dietary exposure to mycotoxins.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 24
    Publication Date: 2021-10-29
    Description: Background Non-small cell lung cancer (NSCLC) harms human health, but its pathogenesis remains unclear. We wish to provide more molecular therapeutic targets for NSCLC. Methods The NSCLC tissue and normal tissue samples were screened for genetic comparison in the TCGA database. The predicted lncRNA and mRNA in BEAS2B and A549 cells were detected. Results Volcano plot displayed differentially expressed lncRNAs and mRNAs in adjacent tissues and NSCLC tissues. The survival curve showed that the lncRNA and mRNA had a significant impact on the patient’s survival. The results of GO term enrichment analysis indicated that mRNA functions were enriched in cell cycle-related pathways. In the ceRNA interaction network, 13 lncRNAs and 20 miRNAs were found to have an interactive relationship. Finally, 3 significantly different lncRNAs (LINC00968, lnc-FAM92A-9 and lnc-PTGFR-1) and 6 mRNAs (CTCFL, KRT5, LY6D, TMEM, GBP6, and TMEM179) with potential therapeutic significance were screened out. And the cell experiment verified our results. Conclusion We screened out clinically significant 3 lncRNAs and 6 mRNAs involved in the ceRNA network, which were the key to our future research on the treatment of NSCLC.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 25
    Publication Date: 2021-10-29
    Description: Influenza viruses cause respiratory tract infections and substantial health concerns. Infection may result in mild to severe respiratory disease associated with morbidity and some mortality. Several anti-influenza drugs are available, but these agents target viral components and are susceptible to drug resistance. There is a need for new antiviral drug strategies that include repurposing of clinically approved drugs. Drugs that target cellular machinery necessary for influenza virus replication can provide a means for inhibiting influenza virus replication. We used RNA interference screening to identify key host cell genes required for influenza replication, and then FDA-approved drugs that could be repurposed for targeting host genes. We examined the effects of Clopidogrel and Triamterene to inhibit A/WSN/33 (EC50 5.84 uM and 31.48 uM, respectively), A/CA/04/09 (EC50 6.432 uM and 3.32 uM, respectively), and B/Yamagata/16/1988 (EC50 0.28 uM and 0.11 uM, respectively) replication. Clopidogrel and Triamterene provide a druggable approach to influenza treatment across multiple strains and subtypes.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 26
    Publication Date: 2021-10-29
    Description: Rhodopsins are light-detecting proteins coupled with retinal chromophores essential for visual function. Coincidentally, dysfunctional rhodopsin homeostasis underlies retinal degeneration in humans and model organisms. Drosophila ninaEG69D mutant is one such example, where the encoded Rh1 protein imposes endoplasmic reticulum (ER) stress and causes light-dependent retinal degeneration. The underlying reason for such light-dependency remains unknown. Here, we report that Drosophila fatty acid binding protein (fabp) is a gene induced in ninaEG69D/+ photoreceptors, and regulates light-dependent Rhodopsin-1 (Rh1) protein clearance and photoreceptor survival. Specifically, our photoreceptor-specific gene expression profiling study in ninaEG69D/+ flies revealed increased expression of fabp together with other genes that control light-dependent Rh1 protein degradation. fabp induction in ninaEG69D photoreceptors required vitamin A and its transporter genes. In flies reared under light, loss of fabp caused an accumulation of Rh1 proteins in cytoplasmic vesicles. The increase in Rh1 levels under these conditions was dependent on Arrestin2 that mediates feedback inhibition of light-activated Rh1. fabp mutants exhibited light-dependent retinal degeneration, a phenotype also found in other mutants that block light-induced Rh1 degradation. These observations reveal a previously unrecognized link between light-dependent Rh1 proteostasis and the ER-stress imposing ninaEG69D mutant that cause retinal degeneration.
    Print ISSN: 1553-7390
    Electronic ISSN: 1553-7404
    Topics: Biology
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  • 27
    Publication Date: 2021-10-29
    Description: Multidrug-resistant tuberculosis (MDR-TB) has become a major threat to the control of tuberculosis globally. Uganda is among the countries with a relatively high prevalence of tuberculosis despite significant control efforts. In this study, the drug resistance of Mycobacterium tuberculosis to rifampicin (RIF) and isoniazid (INH) was investigated among patients diagnosed with pulmonary tuberculosis in Southwestern Uganda. A total of 283 sputum samples (266 from newly diagnosed and 17 from previously treated patients), collected between May 2018 and April 2019 at four different TB diagnostic centres, were assessed for RIF and INH resistance using high-resolution melt curve analysis. The overall prevalence of monoresistance to INH and RIF was 8.5% and 11% respectively, while the prevalence of MDR-TB was 6.7%. Bivariate analysis showed that patients aged 25 to 44 years were at a higher risk of developing MDR-TB (cOR 0.253). Furthermore, among the newly diagnosed patients, the prevalence of monoresistance to INH, RIF and MDR-TB was 8.6%, 10.2% and 6.4% respectively; while among the previously treated cases, these prevalence rates were 5.9%, 23.5% and 11.8%. These rates are higher than those reported previously indicating a rise in MTB drug resistance and may call for measures used to prevent a further rise in drug resistance. There is also a need to conduct frequent drug resistance surveys, to monitor and curtail the development and spread of drug-resistant TB.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 28
    Publication Date: 2021-10-29
    Description: During the Paleolithic period, bone marrow extraction was an essential source of fat nutrients for hunter-gatherers especially throughout cold and dry seasons. This is attested by the recurrent findings of percussion marks in osteological material from anthropized archaeological levels. Among them some showed indicators that the marrow extraction process was part of a butchery cultural practice, meaning that the inflicted fracturing gestures and techniques were recurrent, standardized and counter-intuitive. In order to assess the weight of the counter-intuitive factor in the percussion mark pattern distribution, we carried out an experiment that by contrast focuses on the intuitive approach of fracturing bones to extract marrow, involving individual without experience in this activity. We wanted to evaluate the influence of bone morphology and the individuals’ behaviour on the distribution of percussion marks. Twelve experimenters broke 120 limb bones, a series of 10 bones per individual. During the experiment, information concerning the fracture of the bones as well as individual behaviour was collected and was subsequently compared to data from the laboratory study of the remains. Then, we applied an innovative GIS (Geographic Information System) method to analyze the distribution of percussion marks to highlight recurrent patterns. Results show that in spite of all the variables there is a high similarity in the distribution of percussion marks which we consider as intuitive patterns. The factor influenced the distribution for the humerus, radius-ulna and tibia series is the bone morphology, while for the femur series individual behaviour seems to have more weight in the distribution. To go further in the subject we need to compare the intuitive models with the distributions of percussion marks registered in fossil assemblages. Thus, it would be possible to propose new hypotheses on butchering practices based on the results presented in this work.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 29
    Publication Date: 2021-10-29
    Description: The spatial distribution of visual items allows us to infer the presence of latent causes in the world. For instance, a spatial cluster of ants allows us to infer the presence of a common food source. However, optimal inference requires the integration of a computationally intractable number of world states in real world situations. For example, optimal inference about whether a common cause exists based on N spatially distributed visual items requires marginalizing over both the location of the latent cause and 2N possible affiliation patterns (where each item may be affiliated or non-affiliated with the latent cause). How might the brain approximate this inference? We show that subject behaviour deviates qualitatively from Bayes-optimal, in particular showing an unexpected positive effect of N (the number of visual items) on the false-alarm rate. We propose several “point-estimating” observer models that fit subject behaviour better than the Bayesian model. They each avoid a costly computational marginalization over at least one of the variables of the generative model by “committing” to a point estimate of at least one of the two generative model variables. These findings suggest that the brain may implement partially committal variants of Bayesian models when detecting latent causes based on complex real world data.
    Print ISSN: 1553-734X
    Electronic ISSN: 1553-7358
    Topics: Biology , Computer Science
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  • 30
    Publication Date: 2021-10-29
    Description: The EPOCH Measure of Adolescent Well-being measures five positive indicators of the well-being of adolescents: engagement, perseverance, optimism, connectedness and happiness. This five-factor structure along with other indicators of validity and reliability were supported for the original English version and the Chinese version. In this study, we tested the psychometric properties of the Swedish version of the EPOCH with a sample (n = 846) of Swedish high school adolescents aged 16–21 years (Mage = 18, SD = .85). The participants answered a questionnaire containing the EPOCH, Coping Self-Efficacy Scale, and 21-item Depression, Anxiety, and Stress Scale (DASS-21). A confirmatory factor analysis supported a the five-factor, inter-correlated model. The internal consistency was good for all the EPOCH subscales (Cronbach’s α = .76–.88, McDonald’s ω = .77 –.88). The criterion validity was established by replicating correlations between the five EPOCH subscales and positive (coping self-efficacy) and negative (DASS-21) aspects of well-being. This study shows that the Swedish version of the EPOCH is suitable for assessing multiple dimensions of adolescent well-being.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 31
    Publication Date: 2021-10-29
    Description: This paper uses publicly available data and various statistical models to estimate the basic reproduction number (R0) and other disease parameters for Ghana’s early COVID-19 pandemic outbreak. We also test the effectiveness of government imposition of public health measures to reduce the risk of transmission and impact of the pandemic, especially in the early phase. R0 is estimated from the statistical model as 3.21 using a 0.147 estimated growth rate [95% C.I.: 0.137–0.157] and a 15-day time to recovery after COVID-19 infection. This estimate of the initial R0 is consistent with others reported in the literature from other parts of Africa, China and Europe. Our results also indicate that COVID-19 transmission reduced consistently in Ghana after the imposition of public health interventions—such as border restrictions, intra-city movement, quarantine and isolation—during the first phase of the pandemic from March to May 2020. However, the time-dependent reproduction number (Rt) beyond mid-May 2020 does not represent the true situation, given that there was not a consistent testing regime in place. This is also confirmed by our Jack-knife bootstrap estimates which show that the positivity rate over-estimates the true incidence rate from mid-May 2020. Given concerns about virus mutations, delays in vaccination and a possible new wave of the pandemic, there is a need for systematic testing of a representative sample of the population to monitor the reproduction number. There is also an urgent need to increase the availability of testing for the general population to enable early detection, isolation and treatment of infected individuals to reduce progression to severe disease and mortality.
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
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  • 32
    Publication Date: 2021-10-29
    Description: Serum Paraoxonase 2 (PON2) level is a potential biomarker owing to its association with a number of pathophysiological conditions such as atherosclerosis and cardiovascular disease. Since cholinergic deficiency is closely linked with Alzheimer’s disease (AD) progression, acetylcholinesterase inhibitors (AChEIs) are the treatment of choice for patients with AD. However, there is a heterogenous response to these drugs and mostly the subjects do not respond to the treatment. Gene polymorphism, the simultaneous occurrence of two or more discontinuous alleles in a population, could be one of the important factors for this. Hence, we hypothesized that PON2 and its polymorphic forms may be hydrolyzing the AChEIs differently, and thus, different patients respond differently. To investigate this, two AChEIs, donepezil hydrochloride (DHC) and pyridostigmine bromide (PB), were selected. Human PON2 wildtype gene and four mutants, two catalytic sites, and two polymorphic sites were cloned, recombinantly expressed, and purified for in vitro analysis. Enzyme activity and AChE activity were measured to quantitate the amount of DHC and PB hydrolyzed by the wildtype and the mutant proteins. Herein, PON2 esterase activity and AChE inhibitor efficiency were found to be inversely related. A significant difference in enzyme activity of the catalytic site mutants was observed as compared to the wildtype, and subsequent AChE activity showed that esterase activity of PON2 is responsible for the hydrolysis of DHC and PB. Interestingly, PON2 polymorphic site mutants showed increased esterase activity; therefore, this could be the reason for the ineffectiveness of the drugs. Thus, our data suggested that the esterase activity of PON2 was mainly responsible for the hydrolysis of AChEI, DHC, and PB, and that might be responsible for the variation in individual response to AChEI therapy.
    Electronic ISSN: 1932-6203
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  • 33
    Publication Date: 2021-10-29
    Description: Introduction Sex-based clinical outcome differences in sickle cell disease (SCD) remain largely unknown despite evidence that female sex is associated with an increased lifespan. To better characterize sex-based differences in SCD, we assessed pain, treatment characteristics, laboratory measures and complications among males and females currently enrolled in the Sickle Cell Disease Implementation Consortium (SCDIC) registry. Methods The SCDIC consists of eight comprehensive SCD centers and one data coordinating center that received funding from the National Heart Lung and Blood Institute to improve outcomes for individuals with SCD. Eligibility criteria included: 15 to 45 years of age and a confirmed diagnosis of SCD. Self-report surveys were completed and data were also abstracted from the participants’ medical records. Results A total of 2,124 participants were included (mean age: 27.8 years; 56% female). The majority had hemoglobin SS SCD genotype. Females had worse reports of pain severity (mean (SD) T-score 51.6 (9.6) vs 49.3 (10), p
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  • 34
    Publication Date: 2021-10-29
    Description: Introduction Pregnant and postpartum women face major psychological stressors that put them at higher risk of developing common mental disorders, such as depression and anxiety. Yet, their limited access to and uptake of traditional mental health care is inequitable, especially during the COVID-19 pandemic. Mobile interventions emerged as a potential solution to this discontinued healthcare access, but more knowledge is needed about their effectiveness and impact on health equity. This equity-focused systematic review examined the effectiveness and equity impact of mobile interventions targeting common mental disorders among pregnant and postpartum women. Methods and results We systematically searched MEDLINE, EMBASE, PsychINFO and 3 other databases, from date of database inception and until January 2021, for experimental studies on mobile interventions targeting pregnant and postpartum women. We used pooled and narrative synthesis methods to analyze effectiveness and equity data, critically appraised the methodological rigour of included studies using Cochrane tools, and assessed the certainty of evidence using the GRADE approach. Our search identified 6148 records, of which 18 randomized and non-randomized controlled trials were included. Mobile interventions had a clinically important impact on reducing the occurrence of depression (OR = 0.51 [95% CI 0.41 to 0.64]; absolute risk reduction RD: 7.14% [95% CI 4.92 to 9.36]; p
    Electronic ISSN: 1932-6203
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  • 35
    Publication Date: 2021-10-29
    Description: Background Migrants are not routinely screened for hepatitis B virus (HBV), hepatitis C virus (HCV) and human immunodeficiency virus (HIV) in the Netherlands. We estimated the prevalence and determined factors associated with HBV, HCV and/or HIV infections among undocumented migrants and uninsured legal residents. Methods In this cross-sectional study, undocumented migrants and uninsured legal residents were recruited at a non governmental organization (NGO), healthcare facility in the Netherlands and were invited to be tested for hepatitis B surface antigen (HBsAg), anti-hepatitis B core antibodies (anti-HBcAb), HCV-RNA, and anti-HIV antibodies or HIV antigen at a local laboratory. Results Of the 1376 patients invited, 784 (57%) participated. Participants originated from Africa (35%), Asia (30%) and North/South America (30%). 451/784 (58%) participants went to the laboratory for testing. Of participants 30% were HBV exposed (anti-HBcAb-positive), with 27% (n = 119/438, 95% CI 23.1% to 31.6%) having resolved HBV infection (HBsAg-negative) and 2.5% (n = 11/438, 95%CI 1.3% to 4.5%, 64% new infection) having chronic HBV infection (HBsAg-positive). Compared to HBV non-exposed, HBV exposed individuals were older (p = 0.034) and more often originated from Africa (p
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  • 36
    Publication Date: 2021-10-29
    Description: Background Worldwide, strict infection control measures including visitation regulations were implemented due to the COVID-19 pandemic at Neonatal Intensive Care Units (NICUs). These regulations gave restricted access for parents to their hospitalized infants. The consequence was limited ability to involve in the care of their infants. At Oslo University Hospital entry to NICU was denied to all except healthy mothers in March 2020. The absolute access ban for fathers lasted for 10 weeks. The aim of this study was to explore parental experiences with an infant hospitalized in the NICU during this absolute visitation ban period. Methods We invited post discharge all parents of surviving infants that had been hospitalized for at least 14 days to participate. They were interviewed during autumn 2020 using an explorative semi-structured interview approach. Data were analyzed via inductive thematic analysis. Results Nine mothers and four fathers participated. The COVID-19 regulations strongly impacted the parent’s experiences of their stay. The fathers’ limited access felt life-impacting. Parents struggled to become a family and raised their voices to be heard. Not being able to experience parenthood together led to emotional loneliness. The fathers struggled to learn how to care for their infant. The regulations might lead to a postponed attachment. On the other hand, of positive aspect the parents got some quietness. Being hospitalized during this first wave was experienced as exceptional and made parents seeking alliances by other parents. Social media was used to keep in contact with the outside world. Conclusions The regulations had strong negative impact on parental experiences during the NICU hospitalization. The restriction to fathers’ access to the NICU acted as a significant obstacle to early infant-father bonding and led to loneliness and isolation by the mothers. Thus, these COVID-19 measures might have had adverse consequences for families.
    Electronic ISSN: 1932-6203
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  • 37
    Publication Date: 2021-10-29
    Description: Background Tunga penetrans, also known as sand flea, causes Tungiasis in humans and animals. Despite its notoriety as an entomological problem, however, the ectoparasite receives little consideration from public health professionals. It is against this background that this article aims to assess the prevalence of and factors associated with Tunga penetrans infestation among 5-14-year-olds in rural Western Ethiopia. Methods From November to December 2020, 487 children aged 5 to 14 were selected from four primary schools in a cross-sectional study using systematic random sampling. Clinical exams, Interviews with parents/guardians and observations of the housing and classroom environments were used to collect data. Descriptive statistics and multivariable regression were used to characterize the data and identify factors associated with Tunga penetrans infestation. Result Tunga penetrans infestation (Tungiasis) was diagnosed in 138 of the 487 children examined, placing the prevalence at 28.3% (95% CI: 24.2%, 32.2%). Mud plastered walls [AOR: 5.83, % CI (3.44–9.88)], having cats in the house [AOR: 5.91, 95% CI (3.51–10.11)], not having separated sleeping quarters for animals [AOR: 4.60, 95% CI (2.69–7.86)], using self-supplied water [AOR: 6.30, 95% CI (3.33–11.93)], walking〉30 minutes to school [AOR: 2.37, 95% CI (1.48–3.80)] were associated with Tungiasis. Conclusion In one way or another, several of the identified factors were linked to poverty. Improved house wall materials, fumigation of mud-plastered houses, dusting or spraying insecticides on domestic animals (such as cats), improved access to water, community education about keeping animals separated from living spaces, and hygiene promotion are all needed, with a focus on locally available, low-cost technologies that the poorest families can afford.
    Electronic ISSN: 1932-6203
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  • 38
    Publication Date: 2021-10-19
    Description: Over the past 40 years, actigraphy has been used to study rest-activity patterns in circadian rhythm and sleep research. Furthermore, considering its simplicity of use, there is a growing interest in the analysis of large population-based samples, using actigraphy. Here, we introduce pyActigraphy, a comprehensive toolbox for data visualization and analysis including multiple sleep detection algorithms and rest-activity rhythm variables. This open-source python package implements methods to read multiple data formats, quantify various properties of rest-activity rhythms, visualize sleep agendas, automatically detect rest periods and perform more advanced signal processing analyses. The development of this package aims to pave the way towards the establishment of a comprehensive open-source software suite, supported by a community of both developers and researchers, that would provide all the necessary tools for in-depth and large scale actigraphy data analyses.
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  • 39
    Publication Date: 2021-10-19
    Description: Faithful inheritance of mitochondrial DNA (mtDNA) is crucial for cellular respiration/oxidative phosphorylation and mitochondrial membrane potential. However, how mtDNA is transmitted to progeny is not fully understood. We utilized hypersuppressive mtDNA, a class of respiratory deficient Saccharomyces cerevisiae mtDNA that is preferentially inherited over wild-type mtDNA (rho+), to uncover the factors governing mtDNA inheritance. We found that some regions of rho+ mtDNA persisted while others were lost after a specific hypersuppressive takeover indicating that hypersuppressive preferential inheritance may partially be due to active destruction of rho+ mtDNA. From a multicopy suppression screen, we found that overexpression of putative mitochondrial RNA exonuclease PET127 reduced biased inheritance of a subset of hypersuppressive genomes. This suppression required PET127 binding to the mitochondrial RNA polymerase RPO41 but not PET127 exonuclease activity. A temperature-sensitive allele of RPO41 improved rho+ mtDNA inheritance over a specific hypersuppressive mtDNA at semi-permissive temperatures revealing a previously unknown role for rho+ transcription in promoting hypersuppressive mtDNA inheritance.
    Print ISSN: 1553-7390
    Electronic ISSN: 1553-7404
    Topics: Biology
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  • 40
    Publication Date: 2021-10-19
    Description: Translation of messenger RNAs (mRNAs) with premature termination codons produces truncated proteins with potentially deleterious effects. This is prevented by nonsense-mediated mRNA decay (NMD) of these mRNAs. NMD is triggered by ribosomes terminating upstream of a splice site marked by an exon-junction complex (EJC), but also acts on many mRNAs lacking a splice junction after their termination codon. We developed a genome-wide CRISPR flow cytometry screen to identify regulators of mRNAs with premature termination codons in K562 cells. This screen recovered essentially all core NMD factors and suggested a role for EJC factors in degradation of PTCs without downstream splicing. Among the strongest hits were the translational repressors GIGYF2 and EIF4E2. GIGYF2 and EIF4E2 mediate translational repression but not mRNA decay of a subset of NMD targets and interact with NMD factors genetically and physically. Our results suggest a model wherein recognition of a stop codon as premature can lead to its translational repression through GIGYF2 and EIF4E2.
    Print ISSN: 1553-7390
    Electronic ISSN: 1553-7404
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  • 41
    Publication Date: 2021-10-29
    Description: Reverse translation of polypeptide sequences to expressible mRNA constructs is a NP-hard combinatorial optimization problem. Each amino acid in the protein sequence can be represented by as many as six codons, and the process of selecting the combination that maximizes probability of expression is termed codon optimization. This work investigates the potential impact of leveraging quantum computing technology for codon optimization. A Quantum Annealer (QA) is compared to a standard genetic algorithm (GA) programmed with the same objective function. The QA is found to be competitive in identifying optimal solutions. The utility of gate-based systems is also evaluated using a simulator resulting in the finding that while current generations of devices lack the hardware requirements, in terms of both qubit count and connectivity, to solve realistic problems, future generation devices may be highly efficient.
    Electronic ISSN: 1932-6203
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  • 42
    Publication Date: 2021-10-29
    Description: Surveillance of the SARS-CoV-2 variants including the quickly spreading mutants by rapid and near real-time sequencing of the viral genome provides an important tool for effective health policy decision making in the ongoing COVID-19 pandemic. Here we evaluated PCR-tiling of short (~400-bp) and long (~2 and ~2.5-kb) amplicons combined with nanopore sequencing on a MinION device for analysis of the SARS-CoV-2 genome sequences. Analysis of several sequencing runs demonstrated that using the long amplicon schemes outperforms the original protocol based on the 400-bp amplicons. It also illustrated common artefacts and problems associated with PCR-tiling approach, such as uneven genome coverage, variable fraction of discarded sequencing reads, including human and bacterial contamination, as well as the presence of reads derived from the viral sub-genomic RNAs.
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  • 43
    Publication Date: 2021-10-29
    Description: Background Measurement of health-related quality of life (HRQOL) of people with chronic illnesses has become extremely important as the mortality rates associated with such illnesses have decreased and survival rates have increased. Thereby, such measurements not only provide insights into physical, mental and social dimensions of patient’s health, but also allow monitoring of the results of interventions, complementing the traditional methods based on morbidity and mortality. Objective The present study was conducted to describe the HRQOL of patients suffering from Rheumatic Fever (RF) and Rheumatic Heart Disease (RHD), and to identify socio-demographic and clinical factors as predictors of HRQOL. Methodology A cross-sectional study was conducted to assess the HRQOL among 702 RF and RHD patients using EuroQol 5-dimensions 5-levels instrument (EQ-5D-5L), EuroQol Visual Analogue Scale and Time Trade off method. Mean EQ-5D-5L quality of life scores were calculated using EQ5D index value calculator across different stages of RF and RHD. Proportions of patients reporting problems in different attributes of EQ-5D-5L were calculated. The impact of socio-economic determinants on HRQOL was assessed. Results The mean EQ-5D-5L utility scores among RF, RHD and RHD with Congestive heart failure patients (CHF) were estimated as 0.952 [95% Confidence Interval (CI): 0.929–0.975], 0.820 [95% CI: 0.799–0.842] and 0.800 [95% CI: 0.772–0.829] respectively. The most frequently reported problem among RF/RHD patients was pain/discomfort (33.8%) followed by difficulty in performing usual activities (23.9%) patients, mobility (22.7%) and anxiety/depression (22%). Patients with an annual income of less than 50,000 Indian National Rupees (INR) reported the highest EQ-5D-5L score of 0.872, followed by those in the income group of more than INR 200,000 (0.835), INR 50,000–100,000 (0.832) and INR 100,000–200,000 (0.828). Better HRQOL was reported by RHD patients (including RHD with CHF) who underwent balloon valvotomy (0.806) as compared to valve replacement surgery (0.645). Conclusion RF and RHD significantly impact the HRQOL of patients. Interventions aiming to improve HRQOL of RF/RHD patients should focus upon ameliorating pain and implementation of secondary prevention strategies for reducing the progression from ARF to RHD and prevention of RHD-related complications.
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  • 44
    Publication Date: 2021-10-29
    Description: Despite the often emphasized importance of water awareness, and notwithstanding the fact that calls for increasing public awareness are becoming commonplace, most studies do not define the concept, let alone operationalise it into measurable units. This is, however, essential to measure and evaluate efforts related to water awareness such as public campaigns, customer communication and behavioural interventions. To address this gap, we conceptualise, operationalise and assess tap water awareness, hereby differentiating between cognitive awareness (head), affectional awareness (heart), and behavioural awareness (hands). In parallel, we also differentiate between tap water quality, quantity and system. By building on a variety of contemporary conceptual insights in literature and a series of expert interviews, an assessment framework is developed. A cohesive set of nine awareness components are identified and operationalised into a set of tangible questions which are put to the test in a large-scale online survey (n = 1003) in the Netherlands, applying both a traditional and modern segmentation approach based on four types of perspectives (‘quality & health concerned’, ‘aware & committed’, ‘egalitarian & solidary’, and ‘down to earth & confident’). Based on the analysis of the results of the first empirical application of our tap water awareness assessment framework, we conclude that—with a score 53.5 points out of 100—tap water awareness in the Netherlands shows ample room for improvement. Interestingly, most significant variations in awareness are generally not related to sociodemographic factors but rather apply to the four customer perspectives on drinking water that are based on people’s subjective views and preferences.
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  • 45
    Publication Date: 2021-10-29
    Description: Background The objective of this study was to compare the prognostic impact of sarcopenia in patients with head and neck cancer (HNC) treated with surgery or radiation. Methods We systematically searched electronic databases to identify articles reporting the impact of sarcopenia on the prognosis of patients with HNC. Hazard ratios (HRs) and 95% confidence intervals (CIs) for overall survival (OS), disease-free survival (DFS), and disease-specific survival (DSS) were extracted and pooled. HR according to treatment modality were estimated using random-effects models. Statistical analyses were carried out using the Comprehensive Meta-Analysis software. Results In total, 18 studies enrolling 3,233 patients were included. Sarcopenia was associated with poor OS in both surgery and radiotherapy groups (hazard ratio [HR] 2.50, 95% confidence interval [CI] 1.95–3.21; HR 1.63, 95% CI 1.40–1.90, respectively). The HR was significantly higher in the surgery group than in the radiotherapy group (p = 0.004), with similar results obtained for DFS (HR 2.59, 95% CI 1.56–4.31; HR 1.56, 95% CI 1.24–1.97 for the surgery and radiotherapy groups, respectively) and DSS (HR 2.96, 95% CI 0.73–11.95; HR 2.67, 95% CI 1.51–4.73 for the surgery and RT groups, respectively). Conclusions Sarcopenia was a poor prognostic factor for HNC, regardless of the treatment modality. However, the adverse effects of sarcopenia on survival were more prominent in the surgery group than in the radiotherapy group. Sarcopenia assessment is required for appropriate treatment decision-making.
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  • 46
    Publication Date: 2021-10-29
    Description: The annual assessment of Family Planning (FP) indicators, such as the modern contraceptive prevalence rate (mCPR), is a key component of monitoring and evaluating goals of global FP programs and initiatives. To that end, the Family Planning Estimation Model (FPEM) was developed with the aim of producing survey-informed estimates and projections of mCPR and other key FP indictors over time. With large-scale surveys being carried out on average every 3–5 years, data gaps since the most recent survey often exceed one year. As a result, survey-based estimates for the current year from FPEM are often based on projections that carry a larger uncertainty than data informed estimates. In order to bridge recent data gaps we consider the use of a measure, termed Estimated Modern Use (EMU), which has been derived from routinely collected family planning service statistics. However, EMU data come with known limitations, namely measurement errors which result in biases and additional variation with respect to survey-based estimates of mCPR. Here we present a data model for the incorporation of EMU data into FPEM, which accounts for these limitations. Based on known biases, we assume that only changes in EMU can inform FPEM estimates, while also taking inherent variation into account. The addition of this EMU data model to FPEM allows us to provide a secondary data source for informing and reducing uncertainty in current estimates of mCPR. We present model validations using a survey-only model as a baseline comparison and we illustrate the impact of including the EMU data model in FPEM. Results show that the inclusion of EMU data can change point-estimates of mCPR by up to 6.7 percentage points compared to using surveys only. Observed reductions in uncertainty were modest, with the width of uncertainty intervals being reduced by up to 2.7 percentage points.
    Electronic ISSN: 1932-6203
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  • 47
    Publication Date: 2021-10-29
    Description: Aim Combined antiretroviral treatment (cART) traditionally consists of three antiretroviral medications, while two-drug regimens (2DR), historically used infrequently, recently been suggested to be non-inferior to three-drug regimens, is emerging as a potential treatment option and is currently a recommended option for treatment initiation in many guidelines. Purpose Characterize the indications and clinical efficacy of 2DR use at a real-life setting in a nation-wide survey. Methods A cross-sectional survey of Israeli patients treated by 2DR until July 2019, included demographic, immunologic, virologic, genotypic and biochemical/metabolic parameters at diagnosis, ART initiation, 2DR initiation and following 24, 48, 96 and 144 weeks of 2DR treatment. Results 176 patients were included in the study. In contrast to historical data implicating ART resistance and adverse effects as the major reasons leading to 2DR switching, treatment simplification was the main reason leading to 2DR treatment in 2019. 2DR that included INSTI and PI were more commonly used in cases of drug resistance, while a combination of INSTI and NNRTI was used in all other 2DR indications. A switch to 2DR induced a mean CD4 T cell increase from 599 cells/μl at treatment initiation to 680 cells/μl at 96 weeks of treatment p
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  • 48
    Publication Date: 2021-10-29
    Description: We evaluated phytochemical composition, antibacterial, antifungal, anti-oxidant and cytotoxic properties of aqueous (water) and organic extracts (methanol, ethyl acetate and n-hexane) of Chenopodium glaucum. Highest phenolic content 45 mg gallic acid equivalents (GAE)/g d.w was found in aqueous extract followed by ethyl acetate (41mg GAE/g d.w) and methanol extract (34.46 mg GAE/g d.w). Antibacterial potential of aqueous and organic extracts of C. glaucum was examined against Acinetobacter baumannii, Klebsiella pneumoniae, Escherichia coli and Staphylococcus epidermidis. The aqueous, methanolic, ethyl acetate, and n-hexane extract showed antibacterial activity against A. baumannii, K. pneumoniae, E. coli and S. epidermidis. However, against A. baumannii significantly higher inhibition zone (19 mm and 18.96 mm respectively) was shown by ethyl acetate and methanol extracts. Aqueous extract possessed highest growth inhibition (11 mm) against E. coli. Aqueous, ethyl acetate and methanol extracts showed 9 mm, 10 mm, and 10.33 mm zone of inhibition against the K. pneumoniae. For antifungal activity, the extracts were less effective against Aspergillus niger but showed strong antifungal activity against Aspergillus flavus (A. flavus). The antioxidant activity was measured as DPPH (2, 2-diphenyl-1-picrylhydrazyl), H2O2 and ABTS (2, 2’-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) scavenging activity of free radicals. All the organic extracts of C. glaucum possessed ABTS, DPPH and H2O2 scavenging properties. The highest cytotoxic activity measured as half maximal inhibitory concentration (IC50) against human lungs carcinoma cells was recorded for methanolic (IC50 = 16 μg/mL) and n-hexane (IC50 = 25 μg/mL) extracts, respectively. The Gas chromatography–mass spectrometry (GC-MS) analysis showed 4 major and 26 minor compounds in n-hexane extract and 4 major and 7 minor compounds in methanol extract of the C. glaucum. It is concluded that aqueous and organic extracts of C. glaucum would be potential therapeutic agents and could be exploited on a pilot scale to treat human pathogenic diseases.
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  • 49
    Publication Date: 2021-10-29
    Description: We have developed the program TwinCons, to detect noisy signals of deep ancestry of proteins or nucleic acids. As input, the program uses a composite alignment containing pre-defined groups, and mathematically determines a ‘cost’ of transforming one group to the other at each position of the alignment. The output distinguishes conserved, variable and signature positions. A signature is conserved within groups but differs between groups. The method automatically detects continuous characteristic stretches (segments) within alignments. TwinCons provides a convenient representation of conserved, variable and signature positions as a single score, enabling the structural mapping and visualization of these characteristics. Structure is more conserved than sequence. TwinCons highlights alternative sequences of conserved structures. Using TwinCons, we detected highly similar segments between proteins from the translation and transcription systems. TwinCons detects conserved residues within regions of high functional importance for the ribosomal RNA (rRNA) and demonstrates that signatures are not confined to specific regions but are distributed across the rRNA structure. The ability to evaluate both nucleic acid and protein alignments allows TwinCons to be used in combined sequence and structural analysis of signatures and conservation in rRNA and in ribosomal proteins (rProteins). TwinCons detects a strong sequence conservation signal between bacterial and archaeal rProteins related by circular permutation. This conserved sequence is structurally colocalized with conserved rRNA, indicated by TwinCons scores of rRNA alignments of bacterial and archaeal groups. This combined analysis revealed deep co-evolution of rRNA and rProtein buried within the deepest branching points in the tree of life.
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  • 50
    Publication Date: 2021-10-29
    Description: Background Virtual reality (VR) has proven effective in the treatment of specific phobias and trauma particularly when in-vivo exposure therapy might be costly (e.g. fear of flying, combat scenes). Similarly, VR has been associated with improvement of chronic pain and of acute pain during medical procedures. Despite its effectiveness as a healthcare tool, VR technology is not well-integrated into common practice. This qualitative study aims to explore the provider perception of the value of VR and identify barriers to VR implementation among healthcare providers. Methods A 66-item self-report survey was created to examine application of VR to clinical practice, perceived value of this treatment, ease of learning the technology, billing considerations, and other obstacles. 128 providers (MDs and PhDs) who were located in the United States and had used VR as a therapeutic tool in the past year were identified through research papers, as well as user lists and news articles from VR application websites. Of the 128 providers contacted, 17% (22) completed our online self-report measure. Of these, 13% of respondents (N = 17) completed greater than 75% of the questionnaire and were considered completers. Provider responses were collected over a one-month period and qualitatively analyzed. Results The majority of providers were from an academic institution (n = 12, 70.6%), and all providers practiced in the outpatient setting. Providers most commonly reported using VR for the treatment of acute pain and/or anxiety related to medical procedures (n = 11, 64.7%), followed by specific phobia (n = 6, 35.3%) and social phobia (n = 6, 35.3%). All providers agreed VR is a valuable tool they would recommend to colleagues. The majority (n = 15, 93.8%) believed VR helped their patients progress in treatment, compared with other methods. Providers cited the ability to individualize treatment (n = 14, 87.5%) and increase patient engagement (n = 15, 93.8%) as main benefits of VR. A minority reported negative feedback from patients about content (n = 4, 25%) or about the technology in general (n = 6, 37.5%), whereas all reported some form of positive feedback. The slight majority (n = 10, 58.8%) of providers did not find transitioning to VR difficult. Of those who did, cost was the most commonly cited barrier (n = 6). Regarding reimbursement, only 17.6% (n = 3) of providers reported the ability to bill for VR sessions. Most providers (n = 15, 88.2%) received training on their VR platform which they found beneficial. Comparing the trained and untrained groups found no significant difference in VR comfort level (p = 0.5058), the value of VR in practice (p = 0.551) or whether providers would recommend VR to others (p = 0.551), though sample sizes were small. Conclusions In corroboration with previous research, this study demonstrates that VR is well-received by patients and providers, allowing increased patient engagement and treatment individualization. However, associated costs, including an inability to bill for this service, can present a barrier to further implementation. These findings will guide further development of virtual reality as a standardized tool in psychiatry and pain management.
    Electronic ISSN: 1932-6203
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  • 51
    Publication Date: 2021-10-29
    Description: Urbanisation alters landscapes, introduces wildlife to novel stressors, and fragments habitats into remnant ‘islands’. Within these islands, isolated wildlife populations can experience genetic drift and subsequently suffer from inbreeding depression and reduced adaptive potential. The Western tiger snake (Notechis scutatus occidentalis) is a predator of wetlands in the Swan Coastal Plain, a unique bioregion that has suffered substantial degradation through the development of the city of Perth, Western Australia. Within the urban matrix, tiger snakes now only persist in a handful of wetlands where they are known to bioaccumulate a suite of contaminants, and have recently been suggested as a relevant bioindicator of ecosystem health. Here, we used genome-wide single nucleotide polymorphism (SNP) data to explore the contemporary population genomics of seven tiger snake populations across the urban matrix. Specifically, we used population genomic structure and diversity, effective population sizes (Ne), and heterozygosity-fitness correlations to assess fitness of each population with respect to urbanisation. We found that population genomic structure was strongest across the northern and southern sides of a major river system, with the northern cluster of populations exhibiting lower heterozygosities than the southern cluster, likely due to a lack of historical gene flow. We also observed an increasing signal of inbreeding and genetic drift with increasing geographic isolation due to urbanisation. Effective population sizes (Ne) at most sites were small (〈 100), with Ne appearing to reflect the area of available habitat rather than the degree of adjacent urbanisation. This suggests that ecosystem management and restoration may be the best method to buffer the further loss of genetic diversity in urban wetlands. If tiger snake populations continue to decline in urban areas, our results provide a baseline measure of genomic diversity, as well as highlighting which ‘islands’ of habitat are most in need of management and protection.
    Electronic ISSN: 1932-6203
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  • 52
    Publication Date: 2021-10-29
    Description: Ocean-going ships were key to rising maritime economies of the Early Modern period, and understanding how they were built is critical to grasp the challenges faced by shipwrights and merchant seafarers. Shipwreck timbers hold material evidence of the dynamic interplay of wood supplies, craftmanship, and evolving ship designs that helped shape the Early Modern world. Here we present the results of dendroarchaeological research carried out on Batavia’s wreck timbers, currently on display at the Western Australian Shipwrecks Museum in Fremantle. Built in Amsterdam in 1628 CE and wrecked on its maiden voyage in June 1629 CE in Western Australian waters, Batavia epitomises Dutch East India Company (Verenigde Oostindische Compagnie, or VOC) shipbuilding. In the 17th century, the VOC grew to become the first multinational trading enterprise, prompting the rise of the stock market and modern capitalism. Oak (Quercus sp.) was the preferred material for shipbuilding in northern and western Europe, and maritime nations struggled to ensure sufficient supplies to meet their needs and sustain their ever-growing mercantile fleets and networks. Our research illustrates the compatibility of dendrochronological studies with musealisation of shipwreck assemblages, and the results demonstrate that the VOC successfully coped with timber shortages in the early 17th century through diversification of timber sources (mainly Baltic region, Lübeck hinterland in northern Germany, and Lower Saxony in northwest Germany), allocation of sourcing regions to specific timber products (hull planks from the Baltic and Lübeck, framing elements from Lower Saxony), and skillful woodworking craftmanship (sapwood was removed from all timber elements). These strategies, combined with an innovative hull design and the use of wind-powered sawmills, allowed the Dutch to produce unprecedented numbers of ocean-going ships for long-distance voyaging and interregional trade in Asia, proving key to their success in 17th-century world trade.
    Electronic ISSN: 1932-6203
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  • 53
    Publication Date: 2021-10-29
    Description: In self-reports, socially desirable responding threatens the validity of prevalence estimates for sensitive personal attitudes and behaviors. Indirect questioning techniques such as the crosswise model attempt to control for the influence of social desirability bias. The crosswise model has repeatedly been found to provide more valid prevalence estimates than direct questions. We investigated whether crosswise model estimates are also less susceptible to deliberate faking than direct questions. To this end, we investigated the effect of “fake good” instructions on responses to direct and crosswise model questions. In a sample of 1,946 university students, 12-month prevalence estimates for a sensitive road traffic behavior were higher and thus presumably more valid in the crosswise model than in a direct question. Moreover, “fake good” instructions severely impaired the validity of the direct questioning estimates, whereas the crosswise model estimates were unaffected by deliberate faking. Participants also reported higher levels of perceived confidentiality and a lower perceived ease of faking in the crosswise model compared to direct questions. Our results corroborate previous studies finding the crosswise model to be an effective tool for counteracting the detrimental effects of positive self-presentation in surveys on sensitive issues.
    Electronic ISSN: 1932-6203
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  • 54
    Publication Date: 2021-10-29
    Description: Population-based genomic screening is at the forefront of a new approach to disease prevention. Yet the lack of diversity in genome wide association studies and ongoing debates about the appropriate use of racial and ethnic categories in genomics raise key questions about the translation of genomic knowledge into clinical practice. This article reports on an ethnographic study of a large pragmatic clinical trial of breast cancer screening called WISDOM (Women Informed to Screen Depending On Measures of Risk). Our ethnography illuminates the challenges of using race or ethnicity as a risk factor in the implementation of precision breast cancer risk assessment. Our analysis provides critical insights into how categories of race, ethnicity and ancestry are being deployed in the production of genomic knowledge and medical practice, and key challenges in the development and implementation of novel Polygenic Risk Scores in the research and clinical applications of this emerging science. Specifically, we show how the conflation of social and biological categories of difference can influence risk prediction for individuals who exist at the boundaries of these categories, affecting the perceptions and practices of scientists, clinicians, and research participants themselves. Our research highlights the potential harms of practicing genomic medicine using under-theorized and ambiguous categories of race, ethnicity, and ancestry, particularly in an adaptive, pragmatic trial where research findings are applied in the clinic as they emerge. We contribute to the expanding literature on categories of difference in post-genomic science by closely examining the implementation of a large breast cancer screening study that aims to personalize breast cancer risk using both common and rare genomic markers.
    Electronic ISSN: 1932-6203
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  • 55
    Publication Date: 2021-10-29
    Description: Studies examining age effects in autobiographical memory have produced inconsistent results. This study examined whether a set of typical autobiographical memory measures produced equivalent results in a single participant sample. Five memory tests (everyday memory, autobiographical memory from the past year, autobiographical memory from age 11–17, word-cued autobiographical memory, and word-list recall) were administered in a single sample of young and older adults. There was significant variance in the tests’ sensitivity to age: word-cued autobiographical memory produced the largest deficit in older adults, similar in magnitude to word-list recall. In contrast, older adults performed comparatively well on the other measures. The pattern of findings was broadly consistent with the results of previous investigations, suggesting that (1) the results of the different AM tasks are reliable, and (2) variable age effects in the autobiographical memory literature are at least partly due to the use of different tasks, which cannot be considered interchangeable measures of autobiographical memory ability. The results are also consistent with recent work dissociating measures of specificity and detail in autobiographical memory, and suggest that specificity is particularly sensitive to ageing. In contrast, detail is less sensitive to ageing, but is influenced by retention interval and event type. The extent to which retention interval and event type interact with age remains unclear; further research using specially designed autobiographical memory tasks could resolve this issue.
    Electronic ISSN: 1932-6203
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  • 56
    Publication Date: 2021-10-29
    Description: In a previous study, we developed a Multi-Locus VNTRs Analysis (MLVA) typing system, called MLVA-5, for the discrimination of Chlamydia trachomatis genovar E strain. The results suggested the clonal spread of a MLVA-5 type 21 strain among men who have sex with men (MSM). We applied the MLVA-5 typing method on 157 French anorectal genovar E specimens and 19 Swedish specimens collected between 2010 and 2015. A total of 29 MLVA-5 types was obtained, with three predominant types among French samples: 78 specimens belonged to MLVA-5 type 21, two other types, 11 and 13, included 9 and 14 specimens, respectively. In 15 cases, one unique MLVA-5 type was observed for a single patient, 7 of which were new types not previously described. The distribution of MLVA-5 types according to sexual orientation showed that the 7 anorectal specimens from heterosexual patients belonged to 6 genotypes, and the 12 anorectal specimens from bisexual patients comprised eight types. The 95 anorectal specimens from MSM were distributed into 22 types, but 55 (57.9%) of them belonged to MLVA-5 type 21. Among the Swedish specimens from MSM, eight were from MLVA-type 21 (4 urines and 4 anorectal specimens). The results support the hypothesis of the spread of clonal genovar E strain among MSM.
    Electronic ISSN: 1932-6203
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  • 57
    Publication Date: 2021-10-29
    Description: Background Women not only have worse diabetes complications, but also have menstrual cycle, pregnancy, and menopause which can make managing diabetes more difficult. The aim of this study was to investigate if radial pressure wave analysis may non-invasively screen for women’s risk of type 2 diabetes. Methods Spectrum analysis of the radial pressure wave was performed to evaluate the first five harmonic components, C1 to C5. The study consisted of a total of 808 non-pregnant female subjects aged 20–95 over the period of 4 years, and 404 of them were diagnosed with Type 2 diabetes as the case group. Result The first five harmonic components are significantly different in a comparison of the case group and the control group. In the logistic regression analysis, T2DM was found to be associated with C1 (OR = 1.055, CI = 1.037–1.074, p 〈 0.001), C2 (OR = 1.051, CI = 1.019–1.085, p = 0.002), and C3 (OR = 0.972, CI = 0.950–0.994, p = 0.013). In the Receiver Operating Characteristic curve analysis, the Area Under Curve of using C3 only (70%, p
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  • 58
    Publication Date: 2021-10-29
    Description: The Carpathian Basin represents the cradle of human agricultural development during the Neolithic period, when large parts were transformed into ‘cultural landscapes’ by first farmers from the Balkans. It is assumed that an Early Neolithic subsistence economy established along the hydrologic systems and on Chernozem soil patches, which developed from loess deposits. However, recent results from soil chemistry and geoarchaeological analyses raised the hypothesis that extensive Chernozem coverage developed from increased land-use activity and that Early Neolithic ‘cultural’ groups were not restricted to loess-covered surfaces but rather preferred hydromorphic soils that formed in the floodplains. This article performs multivariable statistics from large datasets of Neolithic sites in Hungary and allows tracing Early to Late Neolithic site preferences from digital environmental data. Quantitative analyses reveal a strong preference for hydromorphic soils, a significant avoidance of loess-covered areas, and no preference for Chernozem soils throughout the Early Neolithic followed by a strong transformation of site preferences during the Late Neolithic period. These results align with socio-cultural developments, large-scale mobility patterns, and land-use and surface transformation, which shaped the Carpathian Basin and paved the way for the agricultural revolution across Europe.
    Electronic ISSN: 1932-6203
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  • 59
    Publication Date: 2021-10-29
    Description: Background Since the beginning of the COVID-19 outbreak, many pharmaceutical companies have been racing to develop a safe and effective COVID-19 vaccine. Simultaneously, rumors and misinformation about COVID-19 are still widely spreading. Therefore, this study aimed to investigate the prevalence of COVID-19 misinformation among the Yemeni population and its association with vaccine acceptance and perceptions. Methods A cross-sectional online survey was conducted in four major cities in Yemen. The constructed questionnaire consisted of four main sections (sociodemographic data, misinformation, perceptions (perceived susceptibility, severity, and worry), and vaccination acceptance evaluation). Subject recruitment and data collection were conducted online utilizing social websites and using the snowball sampling technique. Descriptive and inferential analyses were performed using SPSS version 27. Results The total number of respondents was 484. Over 60% of them were males and had a university education. More than half had less than 100$ monthly income and were khat chewers, while only 18% were smokers. Misinformation prevalence ranged from 8.9% to 38.9%, depending on the statement being asked. Men, university education, higher income, employment, and living in urban areas were associated with a lower misinformation level (p
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  • 60
    Publication Date: 2021-10-29
    Description: Background The bidirectional relationship between health behavior and subjective well-being has previously been studied sparsely, and mainly for individual health behaviors and regression models. In the present study, we deepen this knowledge focusing on the four principal health behaviors and using structural equation modeling with selected covariates. Methods The follow-up data (n = 11,804) was derived from a population-based random sample of working-age Finns from two waves (2003 and 2012) of the Health and Social Support (HeSSup) postal survey. Structural equation modeling was used to study the cross-sectional, cross-lagged, and longitudinal relationships between the four principal health behaviors and subjective well-being at baseline and after the nine-year follow-up adjusted for age, gender, education, and self-reported diseases. The included health behaviors were physical activity, dietary habits, alcohol consumption, and smoking status. Subjective well-being was measured through four items comprising happiness, interest, and ease in life, and perceived loneliness. Results Bidirectionally, only health behavior in 2003 predicted subjective well-being in 2012, whereas subjective well-being in 2003 did not predict health behavior in 2012. In addition, the cross-sectional interactions in 2003 and in 2012 between health behavior and subjective well-being were statistically significant. The baseline levels predicted their respective follow-up levels, the effect being stronger in health behavior than in subjective well-being. Conclusion The four principal health behaviors together predict subsequent subjective well-being after an extensive follow-up. Although not particularly strong, the results could still be used for motivation for health behavior change, because of the beneficial effects of health behavior on subjective well-being.
    Electronic ISSN: 1932-6203
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  • 61
    Publication Date: 2021-10-29
    Description: We investigated the characteristics of extracellular matrix (ECM) in the soft tissue of two frozen baby woolly mammoths (Mammuthus primigenius) that died and were buried in Siberian permafrost approximately 40,000 years ago. Morphological and biochemical analyses of mammoth lung and liver demonstrated that those soft tissues were preserved at the gross anatomical and histological levels. The ultrastructure of ECM components, namely a fibrillar structure with a collagen-characteristic pattern of cross-striation, was clearly visible with transmission and scanning electron microscopy. Type I and type IV collagens were detected by immunohistochemical observation. Quantitative amino acid analysis of liver and lung tissues of the baby mammoths indicated that collagenous protein is selectively preserved in these tissues as a main protein. Type I and type III collagens were detected as major components by means of liquid chromatography–mass spectrometry analysis after digestion with trypsin. These results indicate that the triple helical collagen molecule, which is resistant to proteinase digestion, has been preserved in the soft tissues of these frozen mammoths for 40,000 years.
    Electronic ISSN: 1932-6203
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  • 62
    Publication Date: 2021-10-29
    Description: Kohlschütter-Tönz syndrome (KTS) manifests as neurological dysfunctions, including early-onset seizures. Mutations in the citrate transporter SLC13A5 are associated with KTS, yet their underlying mechanisms remain elusive. Here, we report that a Drosophila SLC13A5 homolog, I’m not dead yet (Indy), constitutes a neurometabolic pathway that suppresses seizure. Loss of Indy function in glutamatergic neurons caused “bang-induced” seizure-like behaviors. In fact, glutamate biosynthesis from the citric acid cycle was limiting in Indy mutants for seizure-suppressing glutamate transmission. Oral administration of the rate-limiting α-ketoglutarate in the metabolic pathway rescued low glutamate levels in Indy mutants and ameliorated their seizure-like behaviors. This metabolic control of the seizure susceptibility was mapped to a pair of glutamatergic neurons, reversible by optogenetic controls of their activity, and further relayed onto fan-shaped body neurons via the ionotropic glutamate receptors. Accordingly, our findings reveal a micro-circuit that links neural metabolism to seizure, providing important clues to KTS-associated neurodevelopmental deficits.
    Print ISSN: 1553-7390
    Electronic ISSN: 1553-7404
    Topics: Biology
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  • 63
    Publication Date: 2021-10-29
    Description: Maps of bottom type are essential to the management of marine resources and biodiversity because of their foundational role in characterizing species’ habitats. They are also urgently needed as countries work to define marine protected areas. Current approaches are time consuming, focus largely on grain size, and tend to overlook shallow waters. Our random forest classification of almost 200,000 observations of bottom type is a timely alternative, providing maps of coastal substrate at a combination of resolution and extents not previously achieved. We correlated the observations with depth, depth-derivatives, and estimates of energy to predict marine substrate at 100 m resolution for Canada’s Pacific shelf, a study area of over 135,000 km2. We built five regional models with the same data at 20 m resolution. In addition to standard tests of model fit, we used three independent data sets to test model predictions. We also tested for regional, depth, and resolution effects. We guided our analysis by asking: 1) does weighting for prevalence improve model predictions? 2) does model resolution influence model performance? And 3) is model performance influenced by depth? All our models fit the build data well with true skill statistic (TSS) scores ranging from 0.56 to 0.64. Weighting models with class prevalence improved fit and the correspondence with known spatial features. Class-based metrics showed differences across both resolutions and spatial regions, indicating non-stationarity across these spatial categories. Predictive power was lower (TSS from 0.10 to 0.36) based on independent data evaluation. Model performance was also a function of depth and resolution, illustrating the challenge of accurately representing heterogeneity. Our work shows the value of regional analyses to assessing model stationarity and how independent data evaluation and the use of error metrics can improve understanding of model performance and sampling bias.
    Electronic ISSN: 1932-6203
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  • 64
    Publication Date: 2021-10-29
    Description: Background High prevalence of tobacco smoking among young students remains a serious health concern given the positive association between smoking and NCDs. More recently, some studies also noted young smokers were more likely to get infected with COVID-19 compared to non-smokers. This study aims to assess the factors that influence smoking uptake among young students in Samoa. Findings from this study will provide valuable insight to policymakers and health authorities on policies and strategies to combat smoking among youth in Samoa and the Pacific Island Countries (PICs). Methods The 2017 Global Youth Tobacco Survey data of Samoa, available from the World Health Organization is used in the analysis. We use the multinominal logistic model to investigate the effects of socio-economic and demographics factors on young students’ uptake of smoking in Samoa. Result The main findings of this study indicate that sex, age, friendship, parental smoking, family discussion, outside influence, pocket money, and mother’s education are important determinants of tobacco smoking initiation among youths in Samoa. Conclusion Our findings contribute towards the evidence of the imperative health impact of friends, parents, and public smoking on students in Samoa. This warrants strategies that are effective in discouraging parents from smoking and implement measures that prevent smoking in public places. Moreover, educational efforts, particularly those that encourage more discussion at home settings on the harmful effects of smoking are strongly recommended. Parents are strongly encouraged to regularly monitor children’s spending behaviour.
    Electronic ISSN: 1932-6203
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    Publication Date: 2021-10-29
    Description: Purpose To investigate the postoperative course of patients who explanted a diffractive bifocal intraocular lens (IOL) due to waxy vision and implanted with an extended depth of focus IOL. Methods This study evaluated 29 eyes of 25 patients who underwent diffractive bifocal IOL explantation followed by TECNIS Symfony® implantation because of dissatisfaction due to waxy vision at the Takabatake West Eye Clinic between January 2018 and November 2019. The indication criteria for this surgery were patients with uncorrected distance visual acuity of 0.05 logMAR or better, without eye diseases that may affect visual function, and no dissatisfactions about photic phenomena. We investigated patient demographics, uncorrected and corrected visual acuity, manifest refraction, contrast sensitivity, subjective symptoms, time to IOL explantation, explanted IOL type, and spectacle independence. Results The time to the IOL exchange after the initial IOL implantation was 55.3 ± 50.4 days (range: 14–196 days). The logMAR corrected distance visual acuity before and after IOL exchange were −0.13 ± 0.06 and −0.14 ± 0.06, respectively (p = 0.273). After IOL exchange surgery, the area under log contrast sensitivity function increased significantly from 1.07 ± 0.12 to 1.21 ± 0.12 (p 〈 0.001), and the waxy vision symptoms improved. The spectacle independence rate at the last visit was 88.0%. Conclusion For patients who complain of waxy vision despite good visual acuity after diffractive bifocal IOL implantation, exchange to extended depth of focus IOL was considered one of the useful surgical options.
    Electronic ISSN: 1932-6203
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  • 67
    Publication Date: 2021-10-29
    Description: Metabolic syndrome (MetS) is highly prevalent worldwide. In the United States, estimates show that more than 30% of the adult population has MetS. MetS consists of multiple phenotypes, including obesity, dyslipidemia, and impaired glucose tolerance. Therefore, identifying the molecular mechanisms to explain this complex disease is critical for diagnosing and treating MetS. We previously showed 70 increased genes and 20 decreased genes in whole blood in MetS participants. The present study aimed to identify blood-based DNA methylation biomarkers in non-MetS versus MetS participants. The present study analyzed whole blood DNA samples from 184 adult participants of Latino descent from the Arizona Insulin Resistance (AIR) registry. We used the National Cholesterol Education Program Adult Treatment Panel III (NCEP: ATP III) criteria to identify non-MetS (n = 110) and MetS (n = 74) participants. We performed whole blood methylation analysis on select genes: ATP Synthase, H+ Transporting mitochondrial F1 Complex, Epsilon Subunit (ATP5E), Cytochrome C Oxidase Subunit VIc (COX6C), and Ribosomal Protein L9 (RPL9). The pyrosequencing analysis was a targeted approach focusing on the promoter region of each gene that specifically captured CpG methylation sites. In MetS participants, we showed decreased methylation in two CpG sites in COX6C and three CpG sites in RPL9, all p 〈 0.05 using the Mann-Whitney U test. There were no ATP5E CpG sites differently methylated in the MetS participants. Furthermore, while adjusting for age, gender, and smoking status, logistic regression analysis reaffirmed the associations between MetS and mean methylation within COX6C and RPL9 (both p 〈 0.05). In addition, Spearman’s correlation revealed a significant inverse relationship between the previously published gene expression data and methylation data for RPL9 (p 〈 0.05). In summary, these results highlight potential blood DNA methylation biomarkers for the MetS phenotype. However, future validation studies are warranted to strengthen our findings.
    Electronic ISSN: 1932-6203
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  • 68
    Publication Date: 2021-10-29
    Description: Background One of the factors contributing to a high maternal mortality rate is the utilization of non-healthcare facilities as a birthplace for women. This study analyzed determinants affecting birthplace in middle-to lower-class women in Indonesia. Methods This study analyzed the 2017 Indonesian Demographic and Health Survey (IDHS) data. The total national sample size was 49,627 eligible women. Our sample included 11,104 women, aged 15–49, who had delivered babies and were of low-to-middle economic status. The type of survey dataset was individual record dataset. Data were analyzed with chi-square and multivariate logistic regression tests using Stata 16 software. Results About 64.99% middle to lower class women in Indonesia delivered in healthcare facilities. Women aged 45–49 (OR = 2.103; 95% CI = 1.13–3.93), who graduated from higher schools (OR = 2.885; 95% CI = 1.76–4.73), whose husbands had higher education (OR = 2.826; 95% CI = 1.69–4.74) and were employed (OR = 2.523; 95% CI = 1.23–5.17), who considered access to healthcare facilities was not a problem (OR = 1.528; 95% CI = 1.28–1.82), who had a single child (OR = 2.349; 95% CI = 1.97–2.80), and who lived in urban areas (OR = 2.930; 95% CI = 2.40–3.57) were determinants that significantly correlated with women giving birth in healthcare facilities. Conclusion This study provides insights for policymakers and healthcare centers in the community to strengthen access to healthcare services and devise health promotion strategies for pregnant mothers. Policy interventions designed for middle- to lower-class women should be implemented to support vulnerable groups.
    Electronic ISSN: 1932-6203
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  • 69
    Publication Date: 2021-10-29
    Description: Environmental DNA (eDNA) is nuclear or mitochondrial DNA shed into the environment, and amplifying this DNA can serve as a reliable, noninvasive way to monitor aquatic systems for the presence of an invasive species. Assays based on the collection of eDNA are becoming increasingly popular, and, when optimized, can aid in effectively and efficiently tracking invasion fronts. We set out to update an eDNA assay to detect the invasive rusty crayfish, Faxonius rusticus. We tested for species specificity compared to other stream crayfish and field tested the assay at sites with known presence (N = 3) and absence (N = 4) in the Juniata River watershed in central Pennsylvania, USA. To maximize sensitivity, we field tested different storage buffers (Longmire’s buffer and ethanol), DNA extraction methods (Qiagen’s DNEasy and PowerWater kits), and quantitative polymerase chain reaction (qPCR) chemistries (TaqMan and SYBR green). Our assay confirmed the presence data and performed optimally when filter samples were stored in Longmire’s buffer, DNA was extracted with DNeasy Blood and Tissue Kit, and TaqMan qPCR chemistry was utilized. With proper sample processing, our assay allows for accurate, noninvasive detection of F. rusticus in streams.
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  • 70
    Publication Date: 2021-10-29
    Description: Background Housemaids are the most vulnerable group to sexual violence due to their working condition, isolation and school arrangements. Despite the ubiquity of sexual violence among the domestic work sector, particularly among housemaids, this area of research continues to be neglected. This study was aimed at examining the prevalence and factors pertaining to sexual violence among housemaids attending night school program in urban setups of Gedeo zone, Southern Ethiopia. Method A school based quantitative cross sectional study was conducted among 394 housemaids attending night schools in the urban setups of Gedeo Zone from April to May 2019. After stratifying of students using class grade, SRS technique was used to choose study subjects from each stratum. Quantitative data was collected using face to face interview and qualitative was collected using focus group discussion, in-depth interview and key informant interview. The data was entered and analyzed by SPSS version 20. Binary logistic regression was fitted to determine the association of each independent variable with the dependent variable. Result Based on the finding, the prevalence of sexual violence was 60.2%. The odds of experiencing sexual violence through working life-time as housemaid was higher for those who had migrated from rural to urban for work [AOR = 1.97: 95% CI, (1.07,3.63)], had less than 5 years of experience as housemaid [AOR = 3.10: 95% CI, (1.60, 6.00)], were in the age group of 15–19 [AOR = 3.75:95% CI (1.88, 7.46), ever used alcohol [AOR = 6.77: 95% CI, (2.65,17.33)] and whose fathers lacked formal education [AOR = 2.75:95%CI (1.24,6.08)]. On the other hand, unmarried /housemaids having no regular sexual partner were less likely to face sexual violence [AOR. = 0.28: 95% CI, (0.13, 0.57)]. Conclusion The level of sexual violence was found to be high among housemaids attending night schools in in this study. Housemaids from rural area, those newly starting the work, younger housemaids, and those who were married were more likely to be victims of sexual violence.
    Electronic ISSN: 1932-6203
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  • 71
    Publication Date: 2021-10-29
    Description: Sign Language (SL) is a continuous and complex stream of multiple body movement features. That raises the challenging issue of providing efficient computational models for the description and analysis of these movements. In the present paper, we used Principal Component Analysis (PCA) to decompose SL motion into elementary movements called principal movements (PMs). PCA was applied to the upper-body motion capture data of six different signers freely producing discourses in French Sign Language. Common PMs were extracted from the whole dataset containing all signers, while individual PMs were extracted separately from the data of individual signers. This study provides three main findings: (1) although the data were not synchronized in time across signers and discourses, the first eight common PMs contained 94.6% of the variance of the movements; (2) the number of PMs that represented 94.6% of the variance was nearly the same for individual as for common PMs; (3) the PM subspaces were highly similar across signers. These results suggest that upper-body motion in unconstrained continuous SL discourses can be described through the dynamic combination of a reduced number of elementary movements. This opens up promising perspectives toward providing efficient automatic SL processing tools based on heavy mocap datasets, in particular for automatic recognition and generation.
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    Publication Date: 2021-10-29
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  • 73
    Publication Date: 2021-10-29
    Description: Background Adequate tumor tissue is required to make the best treatment choice for non-small cell lung cancer (NSCLC). Transbronchial biopsy (TBB) by endobronchial ultrasonography with a guide sheath (EBUS-GS) is useful to diagnose peripheral lung lesions. The data of tumor cell numbers obtained by two different sizes of GSs is limited. We conducted this study to investigate the utility of a large GS kit to obtain many tumor cells in patients with NSCLC. Methods Patients with a peripheral lung lesion and suspected of NSCLC were prospectively enrolled. They underwent TBB with a 5.9-mm diameter bronchoscope with a large GS. When the lesion was invisible in EBUS, we changed to a thinner bronchoscope and TBB was performed with a small GS. We compared the tumor cell number prospectively obtained with a large GS (prospective large GS group) and those previously obtained with a small GS (small GS cohort). The primary endpoint was the tumor cell number per sample, and we assessed characteristics of lesions that could be obtained by TBB with large GS. Results Biopsy with large GS was performed in 55 of 87 patients (63.2%), and 37 were diagnosed with NSCLC based on histological samples. The number of tumor cells per sample was not different between two groups (658±553 vs. 532±526, estimated difference between two groups with 95% confidence interval (CI); 125 (-125–376), p = 0.32). The sample size of the large GS group was significantly larger than that of the small GS cohort (1.75 mm2 vs. 0.83 mm2, estimated difference with 95% CI; 0.92 (0.60–1.23) mm2, p = 0.00000019). The lesion involving a third or less bronchus generation was predictive factors using large GS. Conclusions The sample size obtained with large GS was significantly larger compared to that obtained with small GS, but there was no significant difference in tumor cell number. The 5.9-mm diameter bronchoscope with large GS can be used for lesions involving a third or less bronchus generation.
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    Publication Date: 2021-10-29
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  • 75
    Publication Date: 2021-10-29
    Description: Intensity modulated radiation therapy (IMRT) introduced marked changes to cancer treatment in animals by reducing dose to organs at risk (OAR). As the next technological step, volumetric modulated arc therapy (VMAT) has advantages (increased degrees-of-freedom, faster delivery) compared to fixed-field IMRT. Our objective was to investigate a possible advantage of VMAT over IMRT in terms of lower OAR doses in advanced-disease sinonasal tumors in dogs treated with simultaneously-integrated boost radiotherapy. A retrospective, analytical, observational study design was applied using 10 pre-existing computed tomography datasets on dogs with stage 4 sinonasal tumors. Each dataset was planned with both, 5-field IMRT and 2 arc VMAT with 10x4.83 Gy to the gross tumor volume and 10x4.2 Gy to the planning target volume. Adequate target dose coverage and normal tissue complication probability of brain ≤5% was required. Dose constraints aspired to were D60
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  • 76
    Publication Date: 2021-10-29
    Description: Cultivated cotton, such as Gossypium hirsutum L., produces extrafloral (EF) nectar on leaves (foliar) and reproductive structures (bracteal) as an indirect anti-herbivore defense. In exchange for this carbohydrate-rich substance, predatory insects such as ants protect the plant against herbivorous insects. Some EF nectar-bearing plants respond to herbivory by increasing EF nectar production. For instance, herbivore-free G. hirsutum produces more bracteal than foliar EF nectar, but increases its foliar EF nectar production in response to herbivory. This study is the first to test for systemically induced changes to the carbohydrate composition of bracteal EF nectar in response to foliar herbivory on G. hirsutum. We found that foliar herbivory significantly increased the sucrose content of bracteal EF nectar while glucose and fructose remained unchanged. Sucrose content is known to influence ant foraging behavior and previous studies of an herbivore-induced increase to EF nectar caloric content found that it led to increased ant activity on the plant. As a follow-up to our finding, ant recruitment to mock EF nectar solutions that varied in sucrose content was tested in the field. The ants did not exhibit any preference for either solution, potentially because sucrose is a minor carbohydrate component in G. hirsutum EF nectar: total sugar content was not significantly affected by the increase in sucrose. Nonetheless, our findings raise new questions about cotton’s inducible EF nectar responses to herbivory. Further research is needed to determine whether an herbivore-induced increase in sucrose content is typical of Gossypium spp., and whether it constitutes a corollary of systemic sucrose induction, or a potentially adaptive mechanism which enhances ant attraction to the plant
    Electronic ISSN: 1932-6203
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  • 77
    Publication Date: 2021-10-29
    Description: Porcine epidemic diarrhoea (PED) is a highly contagious enteric viral disease of pigs with a high morbidity and mortality rate, which ultimately results in huge economic losses in the pig production sector. The etiological agent of this disease is the porcine epidemic diarrhoea virus (PEDV) which is an enveloped, positive single-stranded RNA virus. The aim of this study was to perform molecular characterization of PEDV to identify the strains circulating in Poland. In this study, 662 faecal samples from 2015 to 2021 were tested with reverse transcription quantitative real-time PCR (RT-qPCR) and the results showed that 3.8% of the tested samples revealed a positive result for PEDV. A phylogenetic analysis of the complete genome and complete S gene sequences showed that Polish PEDV strains belonged to the G1b (S-INDEL) subgroup and were closely related to the European PEDV strains isolated from 2014 to 2019. Furthermore, RDP4 analysis revealed that the Polish PEDV strains harboured a recombinant fragment of ~400 nt in the 5’ end of S gene with PEDV and swine enteric coronavirus (SeCoV) being the major and minor parents, respectively. Antigenic analysis showed that the aa sequences of neutralizing epitopes were conserved among the Polish PEDV strains. Only one strain, #0100/5P, had a unique substitution in the COE epitope. However, Polish PEDV strains showed several substitutions, especially in the COE antigen, as compared to the classical strain CV777. To the best of our knowledge, this is the first report concerning the molecular characterization of porcine epidemic diarrhoea virus strains, as well as the first phylogenetic analysis for PEDV in Poland.
    Electronic ISSN: 1932-6203
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  • 78
    Publication Date: 2021-10-29
    Description: Tendinopathy is a complex multifaceted tendinopathy often associated with overuse and with its high prevalence resulting in significant health care costs. At present, the pathogenesis and effective treatment of tendinopathy are still not sufficiently elucidated. The purpose of this research is to intensely explore the genes, functional pathways, and immune infiltration characteristics of the occurrence and development of tendinopathy. The gene expression profile of GSE106292, GSE26051 and GSE167226 are downloaded from GEO (NCBI comprehensive gene expression database) and analyzed by WGCNA software bag using R software, GSE26051, GSE167226 data set is combined to screen the differential gene analysis. We subsequently performed gene enrichment analysis of Gene Ontology (GO) and "Kyoto Encyclopedia of Genes and Genomes" (KEGG), and immune cell infiltration analysis. By constructing the LASSO regression model, Support vector machine (SVM-REF) and Gaussian mixture model (GMMs) algorithms are used to screen, to identify early diagnostic genes. We have obtained a total of 171 DEGs through WGCNA analysis and differentially expressed genes (DEGs) screening. By GO and KEGG enrichment analysis, it is found that these dysregulated genes were related to mTOR, HIF-1, MAPK, NF-κB and VEGF signaling pathways. Immune infiltration analysis showed that M1 macrophages, activated mast cells and activated NK cells had infiltration significance. After analysis of THE LASSO SVM-REF and GMMs algorithms, we found that the gene MACROD1 may be a gene for early diagnosis. We identified the potential of tendon disease early diagnosis way and immune gene regulation MACROD1 key infiltration characteristics based on comprehensive bioinformatics analysis. These hub genes and functional pathways may as early biomarkers of tendon injuries and molecular therapy level target is used to guide drug and basic research.
    Electronic ISSN: 1932-6203
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  • 79
    Publication Date: 2021-10-29
    Description: Leishmaniasis is endemic and a mandatory reporting disease in Spain since 1982. However, between 1996 and 2014, surveillance on public health was decentralized and only some autonomous regions monitored the disease. The aim of this study is to estimate the incidence of leishmaniasis and to evaluate the extent of underreporting in Spain. A capture-recapture (CRC) study was conducted to calculate the incidence of human leishmaniasis using reports from the National Surveillance Network (RENAVE) and the Hospital Discharge Records of the National Health System (CMBD) for 2016 and 2017. During the study period, 802 cases were reported to RENAVE and there were 1,149 incident hospitalizations related to leishmaniasis. The estimated incidence rates through the CRC study were 0.79 per 100,000 inhabitants for visceral leishmaniasis (VL), 0.88 (cutaneous leishmaniasis (CL)) and 0.12 (mucocutaneous leishmaniasis (MCL)) in 2016 and 0.86 (VL), 1.04 (CL) and 0.12 (MCL) in 2017. An underreporting of 14.7–20.2% for VL and 50.4–55.1% for CL was found. The CRC method has helped us to assess the sensitivity and representativeness of leishmaniasis surveillance in Spain, being a useful tool to assess whether the generalization of leishmaniasis surveillance throughout the Spanish territory achieves a reduction in underreporting.
    Electronic ISSN: 1932-6203
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  • 80
    Publication Date: 2021-10-29
    Description: Background Burnout is a syndrome of emotional exhaustion, low personal accomplishment and depersonalization experienced by a health professional and it is more common in nurses due to high workload and job stress that is mostly caused by working proximity to patients and taking care of them. Burnout compromises the provision of quality health care. Despite this, there is no information in Ethiopia on burnout among nurses in study area. Objectives To determine the magnitude of burnout and associated factors among nurses working in public hospitals of Harari regional state and Dire Dawa administration, eastern Ethiopia, February 1–29, 2020. Methods Institutional based quantitative cross-sectional study was employed from February 1–29 among 412 randomly selected nurses who have been working in hospitals for the last 6 months. Simple random sampling method was employed and data was collected by self-administered, standardized, reliable and valid, questionnaire (Maslachs Burnout Inventory- Human Services Survey). Data was entered into EpiData Version 3.1 and exported to statistical package for social science version 20 for analysis. All covariate with P-value less than 0.25 in bivariable analysis were candidate for multivariable analysis. Level of statistical significance was declared at p-value 〈 0.05. Results Among 412 nurses taking part in this study, 183(44.4%) of nurses with 95% CI, had experienced burnout. Married marital status [AOR:2.3,95%CI:(1.2–4.3)], poor current health status [AOR:4.8, 95% CI:(1.1–21.4)] and fair current health status [AOR:12, 95% CI:(4.5–32)], working greater than eight hour per-day[AOR:0.52, 95%CI:(0.29–0.92)], intention to leave a job [AOR:0.48,95%CI:(0.2–0.88), being working in emergency room [AOR:0.3,95%CI:(0.1–0.98)] and using a different medication related to work related health problems were factors associated with nurses’ burnout. Conclusion The nurses’ burnout in this study is high and it is attributed by marriage, perceiving health status as poor and fair, whereas, having the intention to leave job, being working in emergency room and using a medication in relation to work related health problems reduced risk of developing burnout. So, the concerned bodies should provide trainings which focus on stress copying mechanisms and assertiveness program.
    Electronic ISSN: 1932-6203
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  • 81
    Publication Date: 2021-10-29
    Description: This exploration primarily aims to jointly apply the local FCN (fully convolution neural network) and YOLO-v5 (You Only Look Once-v5) to the detection of small targets in remote sensing images. Firstly, the application effects of R-CNN (Region-Convolutional Neural Network), FRCN (Fast Region-Convolutional Neural Network), and R-FCN (Region-Based-Fully Convolutional Network) in image feature extraction are analyzed after introducing the relevant region proposal network. Secondly, YOLO-v5 algorithm is established on the basis of YOLO algorithm. Besides, the multi-scale anchor mechanism of Faster R-CNN is utilized to improve the detection ability of YOLO-v5 algorithm for small targets in the image in the process of image detection, and realize the high adaptability of YOLO-v5 algorithm to different sizes of images. Finally, the proposed detection method YOLO-v5 algorithm + R-FCN is compared with other algorithms in NWPU VHR-10 data set and Vaihingen data set. The experimental results show that the YOLO-v5 + R-FCN detection method has the optimal detection ability among many algorithms, especially for small targets in remote sensing images such as tennis courts, vehicles, and storage tanks. Moreover, the YOLO-v5 + R-FCN detection method can achieve high recall rates for different types of small targets. Furthermore, due to the deeper network architecture, the YOL v5 + R-FCN detection method has a stronger ability to extract the characteristics of image targets in the detection of remote sensing images. Meanwhile, it can achieve more accurate feature recognition and detection performance for the densely arranged target images in remote sensing images. This research can provide reference for the application of remote sensing technology in China, and promote the application of satellites for target detection tasks in related fields.
    Electronic ISSN: 1932-6203
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  • 82
    Publication Date: 2021-10-29
    Description: Introduction Take-Home Naloxone programs have been introduced across North America in response to rising opioid overdose deaths. There is currently limited real-world data on bystander naloxone administration, overdose outcomes, and evidence related to adverse events following bystander naloxone administration. Methods The research team used descriptive statistics from Take-Home Naloxone administration forms. We explored reported demographic variables and adverse events among people who received by-stander administered naloxone in a suspected opioid overdose event between August 31, 2012 and December 31, 2018 in British Columbia. We examined and contextualized differences across years given policy, program and drug toxicity changes. We used multivariate logistic regression to examine whether an association exists between number of ampoules of naloxone administered and the odds that the recipient will experience withdrawal symptoms. Results A large majority (98.1%) of individuals who were administered naloxone survived their overdose and 69.2% had no or only mild withdrawal symptoms. Receiving three (Adjusted Odds Ratio (AOR) 1.64 (95% Confidence Interval (CI): 1.08–2.48)) or four or more (AOR 2.19 (95% CI: 1.32–3.62)) ampoules of naloxone was significantly associated with odds of moderate or severe withdrawal compared to receiving one ampoule of naloxone. Conclusions This study provides evidence from thousands of bystander reversed opioid overdoses using Take-Home Naloxone kits in British Columbia, and suggests bystander-administered naloxone is safe and effective for opioid overdose reversal. Data suggests an emphasis on titration during bystander naloxone training in situations where the person experiencing overdose can be adequately ventilated may help avoid severe withdrawal symptoms. We identified a decreasing trend in the likelihood of moderate or severe withdrawal over the study period.
    Electronic ISSN: 1932-6203
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  • 83
    Publication Date: 2021-10-29
    Description: When pharmaceutical interventions are unavailable to deal with an epidemic outbreak, adequate management of communication strategies can be key to reduce the contagion risks. On the one hand, accessibility to trustworthy and timely information, whilst on the other, the adoption of preventive behaviors may be both crucial. However, despite the abundance of communication strategies, their effectiveness has been scarcely evaluated or merely circumscribed to the scrutiny of public affairs. To study the influence of communication strategies on the spreading dynamics of an infectious disease, we implemented a susceptible-exposed-infected-removed-dead (SEIRD) epidemiological model, using an agent-based approach. Agents in our systems can obtain information modulating their behavior from two sources: (i) through the local interaction with other neighboring agents and, (ii) from a central entity delivering information with a certain periodicity. In doing so, we highlight how global information delivered from a central entity can reduce the impact of an infectious disease and how informing even a small fraction of the population has a remarkable impact, when compared to not informing the population at all. Moreover, having a scheme of delivering daily messages makes a stark difference on the reduction of cases, compared to the other evaluated strategies, denoting that daily delivery of information produces the largest decrease in the number of cases. Furthermore, when the information spreading relies only on local interactions between agents, and no central entity takes actions along the dynamics, then the epidemic spreading is virtually independent of the initial amount of informed agents. On top of that, we found that local communication plays an important role in an intermediate regime where information coming from a central entity is scarce. As a whole, our results highlight the importance of proper communication strategies, both accurate and daily, to tackle epidemic outbreaks.
    Electronic ISSN: 1932-6203
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  • 84
    Publication Date: 2021-10-29
    Description: Background Drug coated balloons (DCB) with paclitaxel (Ptx) dose of 2–3.5 μg/mm2 balloon surface inhibit restenosis with different effectiveness and duration of success. A clinical dose finding study is not known for any of the currently marketed products. The aim of the present preclinical trial was to investigate a novel DCB coated with 6 μg Ptx/mm2 in a porcine model. Methods and results The current study investigated a DCB with a novel, modified iopromide based matrix with 6 μg Ptx/mm2. Drug transfer to the vessel wall of peripheral arteries was compared with a dose of 3 μg Ptx/mm2 and two fully overlapping DCB with 3 μg Ptx/mm2, each. Ptx concentration in the vessel wall after drug transfer was about twice as high for balloons with 6 μg/mm2 (1957±1472 μg/g) and two overlapping DCB with 3 μg Ptx/mm2, each (1287±619 μg/g) compared to a single balloon with 3 μg Ptx/mm2, (787±738 μg/g), with statistical significant differences for 1x6 μg/mm2 vs. 1x3 μg/mm2 (p = 0.017) but not for 2x3 μg/mm2 vs. 1x3 μg/mm2 (p = 0.184) and 1x6 μg/mm2 vs. 2x3 μg/mm2 (p = 0.178). The proportion of residual Ptx on balloon after treatment was similar for all groups between 6±1% and 10±3% of dose on balloon. Conclusion The dose of 6 μg Ptx/mm2 was successfully as well as reproducibly coated on conventional balloon catheters. Increased Ptx on balloons resulted in increased drug concentration in the vessel wall. A single balloon with 6 μg Ptx/mm2 seems to provide double dose compared to 3 μg Ptx/mm2, facilitates the procedure, and may reduce medico-economic cost compared to the use of two standard DCB.
    Electronic ISSN: 1932-6203
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  • 85
    Publication Date: 2021-10-29
    Description: Background Nigeria has a high burden of hepatitis B virus (HBV) infection, commonly acquired through vertical transmission. However, there is a lack of an efficient surveillance system for monitoring and understanding the epidemiology of HBV among pregnant women. Building on a previous review on the prevalence of HBV in Nigeria (2000–2013), we conducted a systematic review and meta-analysis of HBV prevalence among pregnant women in Nigeria. Methods Four electronic databases PubMed, Embase, Global Health, and Scopus were systematically searched from January 2014 to February 2021. We also searched the African Journal Online and manually scanned the reference lists of the identified studies for potentially eligible articles. Observational studies that reported the prevalence of HBsAg and/or HBeAg among pregnant women in peer-reviewed journals were included in the study. We performed a meta-analysis using a random-effects model. We defined HBV infection as a positive test to HBsAg. Results From the 158 studies identified, 20 studies with a total sample size of 26, 548 were included in the meta-analysis. The pooled prevalence of HBV infection among pregnant women across the studies was 6.49% (95% confidence interval [CI] = 4.75–8.46%; I2 = 96.7%, p = 0.001; n = 20). The prevalence of HBV was significantly lower among pregnant women with at least secondary education compared with those with no education or primary education (prevalence ratio = 0.7, 95% CI = 0.58–0.87; n = 10). However, the prevalence of HBV was not significantly different by age, religion, marital status, or tribe. The prevalence of HBV was not significantly different among pregnant women with previous surgery, blood transfusion, multiple lifetime sex partners, tribal marks, tattoos, scarification, or sexually transmitted infections, compared with those without these risk factors. From a total sample size of 128 (n = 7), the pooled prevalence of HBeAg among HBV-infected pregnant women was 14.59% (95% CI = 4.58–27.99%; I2 = 65.5%, p = 0.01). Subgroup analyses of HBV infection by study region and screening method, and meta-regression analysis of the study year, sample size, and quality rating were not statistically significant. Conclusions There is an intermediate endemicity of HBV infection among pregnant women in Nigeria. Interventions, such as routine antenatal HBV screening, antiviral prophylaxis for eligible pregnant women, and infant HBV vaccination should be scaled up for the prevention of perinatal transmission of HBV infection in Nigeria.
    Electronic ISSN: 1932-6203
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  • 86
    Publication Date: 2021-10-29
    Description: Electrical impedance myography (EIM) using surface techniques has shown promise as a means of diagnosing and tracking disorders affecting muscle and assessing treatment efficacy. However, the relationship between such surface-obtained impedance values and pure muscle impedance values has not been established. Here we studied three groups of diseased and wild-type (WT) animals, including a Duchenne muscular dystrophy model (the D2-mdx mouse), an amyotrophic lateral sclerosis (ALS) model (the SOD1 G93A mouse), and a model of fat-related atrophy (the db/db diabetic obese mouse), performing hind limb measurements using a standard surface array and ex vivo measurements on freshly excised gastrocnemius muscle. A total of 101 animals (23 D2-mdx, 43 ALS mice, 12 db/db mice, and corresponding 30 WT mice) were studied with EIM across a frequency range of 8 kHz to 1 MHz. For both D2-mdx and ALS models, moderate strength correlations (Spearman rho values generally ranging from 0.3–0.7, depending on the impedance parameter (i.e., resistance, reactance and phase) were obtained. In these groups of animals, there was an offset in frequency with impedance values obtained at higher surface frequencies correlating more strongly to impedance values obtained at lower ex vivo frequencies. For the db/db model, correlations were comparatively weaker and strongest at very high and very low frequencies. When combining impedance data from all three disease models together, moderate correlations persisted (with maximal Spearman rho values of 0.45). These data support that surface EIM data reflect ex vivo muscle tissue EIM values to a moderate degree across several different diseases, with the highest correlations occurring in the 10–200 kHz frequency range. Understanding these relationships will prove useful for future applications of the technique of EIM in the assessment of neuromuscular disorders.
    Electronic ISSN: 1932-6203
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  • 87
    Publication Date: 2021-10-29
    Description: This paper analyses the effect of mortality rates (under-five and adult mortality) and population growth on the population ageing in a pooled sample of nine lower and upper middle European countries. Therefore, the main goal of this research is to investigate the ageing process of the population in the context of mortality mechanisms (under five and adult mortality) and of population growth in nine European LUMIs. The analysis is implemented in terms of Pooled least squares with cross-section fixed effects methodology. The novelty used within this research is White two-way cluster standard errors & covariance. This study is based on a database from the World Bank and UN covering the period 1995–2019. The expected results are making available quantitative analysis and insights in the context of mechanisms between the ageing process of population, mortality and population growth across these European LUMIs. Results are consistent with the notion that the increasing ageing process within these countries may be a consequence of the negative impact of population growth and from the influence of adult mortality for both sexes. The research results confirm the presence of solid ties of the mechanism between mortality, population growth and population ageing. Therefore, a clear point was provided that mortality acceleration will depend primarily on the level of population growth.
    Electronic ISSN: 1932-6203
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  • 88
    Publication Date: 2021-10-29
    Description: Historically, the database search algorithms have been the de facto standard for inferring peptides from mass spectrometry (MS) data. Database search algorithms deduce peptides by transforming theoretical peptides into theoretical spectra and matching them to the experimental spectra. Heuristic similarity-scoring functions are used to match an experimental spectrum to a theoretical spectrum. However, the heuristic nature of the scoring functions and the simple transformation of the peptides into theoretical spectra, along with noisy mass spectra for the less abundant peptides, can introduce a cascade of inaccuracies. In this paper, we design and implement a Deep Cross-Modal Similarity Network called SpeCollate, which overcomes these inaccuracies by learning the similarity function between experimental spectra and peptides directly from the labeled MS data. SpeCollate transforms spectra and peptides into a shared Euclidean subspace by learning fixed size embeddings for both. Our proposed deep-learning network trains on sextuplets of positive and negative examples coupled with our custom-designed SNAP-loss function. Online hardest negative mining is used to select the appropriate negative examples for optimal training performance. We use 4.8 million sextuplets obtained from the NIST and MassIVE peptide libraries to train the network and demonstrate that for closed search, SpeCollate is able to perform better than Crux and MSFragger in terms of the number of peptide-spectrum matches (PSMs) and unique peptides identified under 1% FDR for real-world data. SpeCollate also identifies a large number of peptides not reported by either Crux or MSFragger. To the best of our knowledge, our proposed SpeCollate is the first deep-learning network that can determine the cross-modal similarity between peptides and mass-spectra for MS-based proteomics. We believe SpeCollate is significant progress towards developing machine-learning solutions for MS-based omics data analysis. SpeCollate is available at https://deepspecs.github.io/.
    Electronic ISSN: 1932-6203
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  • 89
    Publication Date: 2021-10-29
    Description: Patterns of local adaptation can emerge in response to the selective pressures diseases exert on host populations as reflected in increased frequencies of respective, advantageous genotypes. Elucidating patterns of local adaptation enhance our understanding of mechanisms of disease spread and the capacity for species to adapt in context of rapidly changing environments such as the Arctic. Arctic rabies is a lethal disease that largely persists in northern climates and overlaps with the distribution of its natural host, arctic fox. Arctic fox populations display little neutral genetic structure across their North American range, whereas phylogenetically unique arctic rabies variants are restricted in their geographic distributions. It remains unknown if arctic rabies variants impose differential selection upon host populations, nor what role different rabies variants play in the maintenance and spread of this disease. Using a targeted, genotyping-by-sequencing assay, we assessed correlations of arctic fox immunogenetic variation with arctic rabies variants to gain further insight into the epidemiology of this disease. Corroborating past research, we found no neutral genetic structure between sampled regions, but did find moderate immunogenetic structuring between foxes predominated by different arctic rabies variants. FST outliers associated with host immunogenetic structure included SNPs within interleukin and Toll-like receptor coding regions (IL12B, IL5, TLR3 and NFKB1); genes known to mediate host responses to rabies. While these data do not necessarily reflect causation, nor a direct link to arctic rabies, the contrasting genetic structure of immunologically associated candidate genes with neutral loci is suggestive of differential selection and patterns of local adaptation in this system. These data are somewhat unexpected given the long-lived nature and dispersal capacities of arctic fox; traits expected to undermine local adaptation. Overall, these data contribute to our understanding of the co-evolutionary relationships between arctic rabies and their primary host and provide data relevant to the management of this disease.
    Electronic ISSN: 1932-6203
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  • 90
    Publication Date: 2021-10-29
    Description: Background Care institutions are recognised to be a high-risk setting for the emergence and spread of infections and antimicrobial-resistant organisms, which stresses the importance of infection prevention and control (IPC). Accurate implementation is crucial for optimal IPC practice. Despite the wide promotion of IPC and research thereof in the hospital and nursing home setting, similar efforts are lacking in disability care settings. Therefore, this study aimed to assess perceived barriers and facilitators to IPC among professionals working at residential care facilities (RCFs) for people with intellectual and developmental disabilities (IDD), as well as to identify professional-reported recommendations to improve IPC. Methods This qualitative study involved semi-structured interviews (before COVID-19) with twelve professionals from five Dutch RCFs for people with IDD. An integrated theoretical approach was used to inform data collection and analysis. Thematic analysis using inductive and deductive approaches was conducted. This study followed the COnsolidated criteria for REporting Qualitative research (COREQ) guidelines. Results Our findings revealed barriers and facilitators at the guideline, client, professional, professional interaction, professional client interaction, client interaction, organisational, community, and societal level. Six main themes covering multiple barriers and facilitators were identified: (1) guidelines’ applicability to (work)setting; (2) professionals’ cognitions and attitude towards IPC (related to educational background); (3) organisational support and priority; (4) educational system; (5) time availability and staff capacity; and (6) task division and change coaches. The main professional-reported recommendations were the introduction of tailored and practical IPC guidelines, structural IPC education and training among all professionals, and client participation. Conclusions To promote IPC, multifaceted and multilevel strategies should be implemented, with a preliminary need for improvements on the guideline, professional, and organisational level. Given the heterogeneous character, i.e., different professionals, clients and care needs, there is a need for a tailored approach to implement IPC and sustain it successfully in disability care. Our findings can inform future IPC practice improvements.
    Electronic ISSN: 1932-6203
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  • 91
    Publication Date: 2021-10-29
    Description: Participation and activity post stroke can be limited due to adverse weather conditions. This study aimed to: Quantify and compare summer and winter participation and activity, and explore how community dwelling people with stroke describe their feelings about their level of participation and activity by season. This embedded mixed-methods observational study took place in a city with weather extremes. Community dwelling individuals at least one year post-stroke, able to walk ≥50 metres +/- a walking aide were included. Evaluations and interviews occurred at participants’ homes in two seasons: Reintegration to Normal living Index (RNL), Activities-specific Balance Confidence (ABC) and descriptive outcomes. Participants wore activity monitors for one week each season. Analysis included descriptive statistics, non-parametric tests and an inductive approach to content analysis. Thirteen individuals participated in quantitative evaluation with eight interviewed. Mean age 61.5 years, 62% female and mean 6.2 years post-stroke. No differences between winter-summer values of RNL, ABC, or activity monitor outcomes. However, participants felt they could do more and were more independent in summer. The winter conditions such as ice, snow, cold and wind restricted participation and limited activities. Nonetheless, many participants were active and participated despite the winter challenges by finding other ways to be active, and relying on social supports and personal motivation. The qualitative findings explained unexpected quantitative results. Participants described many challenges with winter weather, but also ways they had discovered to participate and be active despite these challenges. Changes to future studies into seasonal differences are suggested.
    Electronic ISSN: 1932-6203
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  • 92
    Publication Date: 2021-10-19
    Description: Mutational processes shape the genomes of cancer patients and their understanding has important applications in diagnosis and treatment. Current modeling of mutational processes by identifying their characteristic signatures views each base substitution in a limited context of a single flanking base on each side. This context definition gives rise to 96 categories of mutations that have become the standard in the field, even though wider contexts have been shown to be informative in specific cases. Here we propose a data-driven approach for constructing a mutation categorization for mutational signature analysis. Our approach is based on the assumption that tumor cells that are exposed to similar mutational processes, show similar expression levels of DNA damage repair genes that are involved in these processes. We attempt to find a categorization that maximizes the agreement between mutation and gene expression data, and show that it outperforms the standard categorization over multiple quality measures. Moreover, we show that the categorization we identify generalizes to unseen data from different cancer types, suggesting that mutation context patterns extend beyond the immediate flanking bases.
    Print ISSN: 1553-734X
    Electronic ISSN: 1553-7358
    Topics: Biology , Computer Science
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  • 93
    Publication Date: 2023-02-08
    Description: Parental care elevates reproductive success by allocating resources into the upbringing of the offspring. However, it also imposes strong costs for the care-giving parent and can foster sexual dimorphism. Trade-offs between the reproductive system and the immune system may result in differential immunological capacities between the care-providing and the non-care-providing parent. Usually, providing care is restricted to the female sex making it impossible to study a sex-independent influence of parental investment on sexual immune dimorphism. The decoupling of sex-dependent parental investment and their influences on the parental immunological capacity, however, is possible in syngnathids, which evolved the unique male pregnancy on a gradient ranging from a simple carrying of eggs on the trunk (Nerophinae, low paternal investment) to full internal pregnancy (Syngnathus, high paternal investment). In this study, we compared candidate gene expression between females and males of different gravity stages in three species of syngnathids (Syngnathus typhle, Syngnathus rostellatus and Nerophis ophidion) with different male pregnancy intensities to determine how parental investment influences sexual immune dimorphism. While our data failed to detect sexual immune dimorphism in the subset of candidate genes assessed, we show a parental care specific resource-allocation trade-off between investment into pregnancy and immune defense when parental care is provided.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
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  • 94
    Publication Date: 2023-02-08
    Description: Litter and plastic pollution in the marine environment is of major concern when considering the health of ocean ecosystems, and have become an important focus of ocean research during recent years. There is still significant uncertainty surrounding the distribution and impact of marine plastic litter on ocean ecosystems, and in particular on the nano- and microplastic fractions that are difficult to observe and may be harmful to marine organisms. Current estimates of ocean plastic concentrations only account for a small fraction of the approximated 8 million tons of plastic litter entering the oceans on an annual basis. Here, we present the distribution of 100–500 μm microplastic particles within the ocean mixed layer, covering a significant fraction of the ocean, in a near-synoptic survey. During The Ocean Race 2017/2018 edition (formerly known as Volvo Ocean Race), two yachts served as ships of opportunity that regularly took samples of microplastics on a regular schedule during their circumnavigation. This effort resulted in information on microplastic distribution along the race track in the ocean’s upper, well-mixed, layer. We found concentrations ranging from 0–349 particles per cubic meter, but with large spatial variability. There was a tendency toward higher concentrations off south-western Europe and in the southwest Pacific, and indications of long-range transport of microplastic with major ocean currents.
    Type: Article , PeerReviewed
    Format: text
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