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  • 1
    Publication Date: 2020-07-10
    Description: Background Ischemia–reperfusion (IR) injury is the main cause of delayed graft function in solid organ transplantation. Hypoxia-inducible factors (HIFs) control the expression of genes related to preconditioning against IR injury. During normoxia, HIF-α subunits are marked for degradation by the egg-laying defective nine homolog (EGLN) family of prolyl-4-hydroxylases. The inhibition of EGLN stabilizes HIFs and protects against IR injury. The aim of this study was to determine whether the EGLN inhibitors sodium (S)-2-hydroxyglutarate [(S)-2HG] and succinic acid (SA) have a nephroprotective effect against renal IR injury in Wistar rats. Methods (S)-2HG was synthesized in a 22.96% yield from commercially available L-glutamic acid in a two-step methodology (diazotization/alkaline hydrolysis), and its structure was confirmed by nuclear magnetic resonance and polarimetry. SA was acquired commercially. (S)-2HG and SA were independently evaluated in male and female Wistar rats respectively after renal IR injury. Rats were divided into the following groups: sham (SH), nontoxicity [(S)-2HG: 12.5 or 25 mg/kg; SA: 12.5, 25, or 50 mg/kg], IR, and compound+IR [(S)-2HG: 12.5 or 25 mg/kg; SA: 12.5, 25, or 50 mg/kg]; independent SH and IR groups were used for each assessed compound. Markers of kidney injury (BUN, creatinine, glucose, and uric acid) and liver function (ALT, AST, ALP, LDH, serum proteins, and albumin), proinflammatory cytokines (IL-1β, IL-6, and TNF-α), oxidative stress biomarkers (malondialdehyde and superoxide dismutase), and histological parameters (tubular necrosis, acidophilic casts, and vascular congestion) were assessed. Tissue HIF-1α was measured by ELISA and Western blot, and the expression of Hmox1 was assessed by RT-qPCR. Results (S)-2HG had a dose-dependent nephroprotective effect, as evidenced by a significant reduction in the changes in the BUN, creatinine, ALP, AST, and LDH levels compared with the IR group. Tissue HIF-1α was only increased in the IR group compared to SH; however, (S)-2HG caused a significant increase in the expression of Hmox1, suggesting an early accumulation of HIF-1α in the (S)-2HG-treated groups. There were no significant effects on the other biomarkers. SA did not show a nephroprotective effect; the only changes were a decrease in creatinine level at 12.5 mg/kg and increased IR injury at 50 mg/kg. There were no effects on the other biochemical, proinflammatory, or oxidative stress biomarkers. Conclusion None of the compounds were hepatotoxic at the tested doses. (S)-2HG showed a dose-dependent nephroprotective effect at the evaluated doses, which involved an increase in the expression of Hmox1, suggesting stabilization of HIF-1α. SA did not show a nephroprotective effect but tended to increase IR injury when given at high doses.
    Electronic ISSN: 2167-8359
    Topics: Biology , Medicine
    Published by PeerJ
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  • 2
    Publication Date: 2020-10-30
    Description: Background A few papers studying healthy, first-degree relatives of people with borderline personality disorder (BPD) have found that this group presents attention and memory problems. However, current research has not analyzed their social cognition. Materials and Methods We designed an age-, gender- and education-level matched case-control study involving 57 people with BPD, 32 of their first-degree relatives, and 57 healthy controls in Spain in 2018–2019. All were assessed for social cognition and functioning using the Movie for Assessment of Social Cognition and the Social Functioning Scale; other potential confounders were also collected (marital status, occupation and household variables). Results There were differences in the social cognition domain of overmentalizing errors, with the BPD group scoring significantly higher than controls; however, there was no significant difference with relatives; in the social functioning domain of family relationships, with the controls showing the highest scores. Social engagement/withdrawal, interpersonal behavior, independence-competence, prosocial activities, full scale and categorization domains showed the same pattern: the BPD group had lower scores than their relatives and the controls. Relatives were significantly different from BPD patients in family relationships, social engagement/withdrawal and interpersonal behavior, as well as on the full Social Functioning Scale (both as a linear and categorical variable). However, only controls showed differences with relatives in family relationships. Conclusions All in all, relatives show similar levels of social cognition and functioning compared with controls, and people with BPD show some alterations in different domains of both social cognition and functioning.
    Electronic ISSN: 2167-8359
    Topics: Biology , Medicine
    Published by PeerJ
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  • 3
    Publication Date: 2021-04-08
    Description: Background The fish Totoaba macdonaldi is endemic to the Upper Gulf of California. Its migratory movements involve sites with high levels of trace elements in the environment that can accumulate in tissues. In this study, lead (Pb), copper (Cu), cadmium (Cd), zinc (Zn) and iron (Fe) concentrations in male and female totoaba liver and muscle were quantified at various sexual maturity stages along the species’ geographic distribution. Methods Generalized linear models were used to explore associations between trace element concentrations and season of the year, sex/maturity stage, and total fish length. Results No detectable Pb concentrations were recorded in liver or muscle; Cu, Cd, Zn and Fe contents in totoaba liver and muscle were typical of fish inhabiting areas with no contamination issues and are within international maximum permissible levels for human consumption. Variations in the content of Cd, Cu, Zn and Fe in liver of totoaba seem to be more related to the feeding and reproductive physiology of this species than as result of environmental exposure. Results suggest that consumption of totoaba muscle does not pose a public health risk. Furthermore, depending on the sex/maturity stage of totoaba, this fish’s muscle may provide approximately 70% Cu, 60% Zn and 100% Fe of the recommended dietary reference intake.
    Electronic ISSN: 2167-8359
    Topics: Biology , Medicine
    Published by PeerJ
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  • 4
    Publication Date: 2021-01-07
    Description: La Palma is one of the youngest of the Canary Islands, and historically the most active. The recent activity and unrest in the archipelago, the moderate seismicity observed in 2017 and 2018 and the possibility of catastrophic landslides related to the Cumbre Vieja volcano have made it strongly advisable to ensure a realistic knowledge of the background surface deformation on the island. This will then allow any anomalous deformation related to potential volcanic unrest on the island to be detected by monitoring the surface deformation. We describe here the observation results obtained during the 2006–2010 period using geodetic techniques such as Global Navigation Satellite System (GNSS), Advanced Differential Synthetic Aperture Radar Interferometry (A-DInSAR) and microgravimetry. These results show that, although there are no significant associated variations in gravity, there is a clear surface deformation that is spatially and temporally variable. Our results are discussed from the point of view of the unrest and its implications for the definition of an operational geodetic monitoring system for the island
    Description: This research was mainly funded by the Spanish Ministerio de Ciencia, Innovación y Universidades research project DEEP-MAPS, grant agreement number RTI2018-093874-B-I00. It was also partially supported by the CSIC project 201530E019 and the project GEOSIR, grant agreement AYA2010-17448 from the Spanish Ministerio de Ciencia e Innovación.
    Description: Published
    Description: 2566
    Description: 2V. Struttura e sistema di alimentazione dei vulcani
    Description: JCR Journal
    Keywords: A-DInSAR ; GNSS ; gravimetry ; La Palma ; Canary Islands ; volcanic unrest ; 04. Solid Earth ; 04.03. Geodesy ; 04.02. Exploration geophysics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 5
    Publication Date: 2021-03-19
    Description: Bacterial diversity was explored among field samples and cultured isolates from coral reefs within the Veracruz Reef System. Bacterioplankton and bacteriobenthos were characterized by pyrosequencing 16S rRNA genes. Identified sequences belonged to the kingdom Bacteria and classified into 33 phyla. Proteobacteria (likely SAR11 clade) dominated in collective field samples, whereas Firmicutes were the most abundant taxa among cultured isolates. Bioinformatic sorting of sequences to family level revealed 223 bacterial families. Pseudomonadaceae, Exiguobacteraceae and Bacillaceae were dominant among cultured isolates. Vibrionaceae, Alteromonadaceae, and Flavobacteriaceae dominated in reef-associated sediments, whereas Rickettsiaceae and Synechoccaceae were more highly represented in the water column. Bacterial communities from sediments were more diverse than from the water column. This study reveals cryptic bacterial diversity among microenvironmental components of marine microbial reef communities subject to differential influence of anthropogenic stressors. Such investigations are critical for constructing scenarios of environmentally induced shifts in bacterial biodiversity and species composition.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Format: application/pdf
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  • 6
    Publication Date: 2020
    Description: Digital territories focus on community transformation through sustainable development, saving resources in local governments, bridging the digital gap, and using technology to build smart infrastructure. This article presents the design and implementation of a smart system, called the Waste Treatment System (WTS), for controlling parameters of waste decomposition in the trash bins installed in Riobamba city (Ecuador). The prototype allows monitoring in real time both the amount of waste and the level of rottenness of garbage by means of the measurement of different parameters that indicate the characteristics of the leachates generated inside. The motivation of this work was to yield an efficient solution to urban waste treatment that optimizes resources in the collection process by providing real-time information to improve collection frequency vehicles and also reduce emissions by the decomposition of organic waste. The tests allowed assessing technical aspects such as the maximum coverage of wireless communication, the transmission channel capacity for each prototype, the data-processing requirements, and other more particular parameters such as the production of leachates due to the frequency of collection and the environmental conditions, which will be useful in future work on environmental impact.
    Electronic ISSN: 2078-2489
    Topics: Computer Science
    Published by MDPI
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  • 7
    Publication Date: 2020-04-13
    Description: Cancer classification is a topic of major interest in medicine since it allows accurate and efficient diagnosis and facilitates a successful outcome in medical treatments. Previous studies have classified human tumors using a large-scale RNA profiling and supervised Machine Learning (ML) algorithms to construct a molecular-based classification of carcinoma cells from breast, bladder, adenocarcinoma, colorectal, gastro esophagus, kidney, liver, lung, ovarian, pancreas, and prostate tumors. These datasets are collectively known as the 11_tumor database, although this database has been used in several works in the ML field, no comparative studies of different algorithms can be found in the literature. On the other hand, advances in both hardware and software technologies have fostered considerable improvements in the precision of solutions that use ML, such as Deep Learning (DL). In this study, we compare the most widely used algorithms in classical ML and DL to classify the tumors described in the 11_tumor database. We obtained tumor identification accuracies between 90.6% (Logistic Regression) and 94.43% (Convolutional Neural Networks) using k-fold cross-validation. Also, we show how a tuning process may or may not significantly improve algorithms’ accuracies. Our results demonstrate an efficient and accurate classification method based on gene expression (microarray data) and ML/DL algorithms, which facilitates tumor type prediction in a multi-cancer-type scenario.
    Electronic ISSN: 2376-5992
    Topics: Computer Science
    Published by PeerJ
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  • 8
    Publication Date: 2020-01-06
    Description: Background Stenotrophomonas are ubiquitous gram-negative bacteria, which can survive in a wide range of environments. They can use many substances for their growth and are known to be intrinsically resistant to many antimicrobial agents. They have been tested for biotechnological applications, bioremediation, and production of antimicrobial agents. Method Stenotrophomonas sp. Pemsol was isolated from a crude oil contaminated soil. The capability of this isolate to tolerate and degrade polycyclic aromatic hydrocarbons (PAH) such as anthraquinone, biphenyl, naphthalene, phenanthrene, phenanthridine, and xylene was evaluated in Bushnell Hass medium containing PAHs as the sole carbon sources. The metabolites formed after 30-day degradation of naphthalene by Pemsol were analyzed using Fourier Transform Infra-red Spectroscopic (FTIR), Ultra-Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS) and Gas Chromatography-Mass Spectrometry (GC-MS). The genome of Pemsol was also sequenced and analyzed. Results Anthraquinone, biphenyl, naphthalene, phenanthrene, and phenanthridine except xylene can be used as sole carbon sources for Pemsol’s growth in Bushnell Hass medium. The degradation of naphthalene at a concentration of 1 mg/mL within 30 days was tested. A newly formed catechol peak and the disappearance of naphthalene peak detected on the UPLC-MS, and GC-MS analyses spectra respectively confirmed the complete degradation of naphthalene. Pemsol does not produce biosurfactant and neither bio-emulsify PAHs. The whole genome was sequenced and assembled into one scaffold with a length of 4,373,402 bp. A total of 145 genes involved in the degradation of PAHs were found in its genome, some of which are Pemsol-specific as compared with other 11 Stenotrophomonas genomes. Most specific genes are located on the genomic islands. Stenotrophomonas sp. Pemsol’s possession of few genes that are associated with bio-emulsification gives the genetic basis for its inability to bio-emulsify PAH. A possible degradation pathway for naphthalene in Pemsol was proposed following the analysis of Pemsol’s genome. ANI and GGDH analysis indicated that Pemsol is likely a new species of Stenotrophomonas. It is the first report on a complete genome sequence analysis of a PAH-degrading Stenotrophomonas. Stenotrophomonas sp. Pemsol possesses features that make it a good bacterium for genetic engineering and will be an excellent tool for the remediation of crude oil or PAH-contaminated soil.
    Electronic ISSN: 2167-8359
    Topics: Biology , Medicine
    Published by PeerJ
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  • 9
    Publication Date: 2020-01-06
    Description: Background The traditional allometric analysis relies on log- transformation to contemplate linear regression in geometrical space then retransforming to get Huxley’s model of simple allometry. Views assert this induces bias endorsing multi-parameter complex allometry forms and nonlinear regression in arithmetical scales. Defenders of traditional approach deem it necessary since generally organismal growth is essentially multiplicative. Then keeping allometry as originally envisioned by Huxley requires a paradigm of polyphasic loglinear allometry. A Takagi-Sugeno-Kang fuzzy model assembles a mixture of weighted sub models. This allows direct identification of break points for transition between phases. Then, this paradigm is seamlessly appropriate for efficient allometric examination of polyphasic loglinear allometry patterns. Here, we explore its suitability. Methods Present fuzzy model embraces firing strength weights from Gaussian membership functions and linear consequents. Weights are identified by subtractive clustering and consequents through recursive least squares or maximum likelihood. Intersection of firing strength factors set criterion to estimate breakpoints. A multi-parameter complex allometry model follows by adapting firing strengths by composite membership functions and linear consequents in arithmetical space. Results Takagi-Sugeno-Kang surrogates adapted complexity depending on analyzed data set. Retransformation results conveyed reproducibility strength of similar proxies identified in arithmetical space. Breakpoints were straightforwardly identified. Retransformed form implies complex allometry as a generalization of Huxley’s power model involving covariate depending parameters. Huxley reported a breakpoint in the log–log plot of chela mass vs. body mass of fiddler crabs (Uca pugnax), attributed to a sudden change in relative growth of the chela approximately when crabs reach sexual maturity. G.C. Packard implied this breakpoint as putative. However, according to present fuzzy methods existence of a break point in Huxley’s data could be validated. Conclusions Offered scheme bears reliable analysis of zero intercept allometries based on geometrical space protocols. Endorsed affine structure accommodates either polyphasic or simple allometry if whatever turns required. Interpretation of break points characterizing heterogeneity is intuitive. Analysis can be achieved in an interactive way. This could not have been obtained by relying on customary approaches. Besides, identification of break points in arithmetical scale is straightforward. Present Takagi-Sugeno-Kang arrangement offers a way to overcome the controversy between a school considering a log-transformation necessary and their critics claiming that consistent results can be only obtained through complex allometry models fitted by direct nonlinear regression in the original scales.
    Electronic ISSN: 2167-8359
    Topics: Biology , Medicine
    Published by PeerJ
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  • 10
    Publication Date: 2020-05-14
    Description: Animals often show high consistency in their social organisation despite facing changing environmental conditions. Especially in shoaling fish, fission–fusion dynamics that describe for which periods individuals are solitary or social have been found to remain unaltered even when density changed. This compensatory ability is assumed to be an adaptation towards constant predation pressure, but the mechanism through which individuals can actively compensate for density changes is yet unknown. The aim of the current study is to identify behavioural patterns that enable this active compensation. We compared the fission–fusion dynamics of two populations of the live-bearing Atlantic molly (Poecilia mexicana) that live in adjacent habitats with very different predator regimes: cave mollies that inhabit a low-predation environment inside a sulfidic cave with a low density of predatory water bugs (Belostoma sp.), and mollies that live directly outside the cave (henceforth called “surface” mollies) in a high-predation environment. We analysed their fission–fusion dynamics under two different fish densities of 12 and 6 fish per 0.36 m2. As expected, surface mollies spent more time being social than cave mollies, and this difference in social time was a result of surface mollies being less likely to discontinue social contact (once they had a social partner) and being more likely to resume social contact (once alone) than cave mollies. Interestingly, surface mollies were also less likely to switch among social partners than cave mollies. A random walk simulation predicted each population to show reduced social encounters in the low density treatment. While cave mollies largely followed this prediction, surface mollies maintained their interaction probabilities even at low density. Surface mollies achieved this by a reduction in the size of a convex polygon formed by the group as density decreased. This may allow them to largely maintain their fission–fusion dynamics while still being able to visit large parts of the available area as a group. A slight reduction (21%) in the area visited at low densities was also observed but insufficient to explain how the fish maintained their fission–fusion dynamics. Finally, we discuss potential movement rules that could account for the reduction of polygon size and test their performance.
    Electronic ISSN: 2167-8359
    Topics: Biology , Medicine
    Published by PeerJ
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