ALBERT

Description: The cryosphere stands for environments where water appears in a frozen form. It includes permafrost, glaciers, ice sheets, and sea ice and is currently more affected by Global Change than most other regions of the Earth. In the cryosphere, limited water availability and subzero temperatures cause extreme conditions for all kind of life which microorganisms can cope with extremely well. The cryosphere’s microbiota displays an unexpectedly large genetic potential, and taxonomic as well as functional diversity which, however, we still only begin to map. Also, microbial communities influence reaction patterns of the cryosphere towards Global Change. Altered patterns of seasonal temperature fluctuations and precipitation are expected in the Arctic and will affect the microbial turnover of soil organic matter (SOM). Activation of nutrients by thawing and increased active layer thickness as well as erosion renders nutrient stocks accessible to microbial activities. Also, glacier melt and retreat stimulate microbial life in turn influencing albedo and surface temperatures. In this context, the functional resilience of microbial communities in the cryosphere is of major interest. Particularly important is the ability of microorganisms and microbial communities to respond to changes in their surroundings by intracellular regulation and population shifts within functional niches, respectively. Research on microbial life exposed to permanent freeze or seasonal freeze-thaw cycles has led to astonishing findings about microbial versatility, adaptation, and diversity. Microorganisms thrive in cold habitats and new sequencing techniques have produced large amounts of genomic, metagenomic, and metatranscriptomic data that allow insights into the fascinating microbial ecology and physiology at low and subzero temperatures. Moreover, some of the frozen ecosystems such as permafrost constitute major global carbon and nitrogen storages, but can also act as sources of the greenhouse gases methane and nitrous oxide. In this book we summarize state of the art knowledge on whether environmental changes are met by a flexible microbial community retaining its function, or if the altered conditions also render the community in a state of altered properties that affect the Earth’s element cycles and climate. This book brings together research on the cryosphere’s microbiota including permafrost, glaciers, and sea ice in Arctic and Antarctic regions. Different spatial scales and levels of complexity are considered, spanning from ecosystem level to pure culture studies of model microbes in the laboratory. It aims to attract a wide range of parties with interest in the effect of climate change and/or low temperatures on microbial nutrient cycling and physiology.

Description: Amino acid ̶ (acyl carrier protein) ligases (AALs) are a relatively new family of bacterial amino acid adenylating enzymes with unknown function(s). Here, genomic enzymology tools that employ sequence similarity networks and genome context analyses were used to hypothesize the metabolic function(s) of AALs. In over 50% of species, aal and its cognate acyl carrier protein (acp) genes, along with three more genes, formed a highly conserved AAL cassette. AAL cassettes were strongly associated with surface polysaccharide gene clusters in Proteobacteria and Actinobacteria, yet were prevalent among soil and rhizosphere-associated α- and β-Proteobacteria, including symbiotic α- and β-rhizobia and some Mycolata. Based on these associations, AAL cassettes were proposed to encode a noncanonical Acp-dependent polysaccharide modification route. Genomic-inferred predictions were substantiated by published experimental evidence, revealing a role for AAL cassettes in biosynthesis of biofilm-forming exopolysaccharide in pathogenic Burkholderia and expression of aal and acp genes in nitrogen-fixing Rhizobium bacteroids. Aal and acp genes were associated with dltBD-like homologs that modify cell wall teichoic acids with D-alanine, including in Paenibacillus and certain other bacteria. Characterization of pathways that involve AAL and Acp may lead to developing new plant and human disease-controlling agents as well as strains with improved nitrogen fixation capacity.

Description: Background The results of a previous study verified that umbilical cord mesenchymal stem cells (UCMSCs) have good therapeutic effects for the treatment of HBV-related acute-on-chronic liver failure (ACLF) and liver cirrhosis (LC). Nevertheless, it is still unknown whether the effects of UCMSCs are affected by recipient age. Methods Patients treated with UCMSCs who met the criteria of HBV-related ACLF and liver cirrhosis were identified in this retrospective observational study. Patients were divided into subgroups according to the World Health Organization (WHO) age criteria (

Description: Aims Unmanned aerial vehicles (UAVs), i.e., drones, have recently emerged as cost-effective and flexible tools for acquiring remote sensing data with fine spatial and temporal resolution. It provides a new method and opportunity for plant ecologists to study issues from individual to regional scales. However, as a new method, UAVs remote sensing applications in plant ecology are still challenged. The needs of plant ecology research and the application development of UAVs remote sensing should be better integrated. This report provides a comprehensive review of UAV-based remote sensing applications in plant ecology to synthesize prospects of applying drones to advance plant ecology research. Important Findings Of the 400 references, 59% were published in remote sensing journals rather than in plant ecology journals, reflecting a substantial gap between the interests of remote sensing experts and plant ecologists. Most of the studies focused on UAV remote sensing's technical aspects, such as data processing and remote sensing inversion, with little attention on answering ecological questions. There were 61% of studies involved community-scale research. RGB and multispectral cameras were the most used sensors (75%). More ecologically meaningful parameters can be extracted from UAV data to better understand the canopy surface irregularity and community heterogeneity, identify geometrical characteristics of canopy gaps, and construct canopy chemical assemblies from living vegetation volumes. More cooperation between plant ecologists and remote sensing experts is needed to promote UAV remote sensing in advancing plant ecology research.

Description: Objectives To investigate the safety for clinic use and therapeutic effects of basic fibroblast growth factor (bFGF)-overexpressing human umbilical cord-derived mesenchymal stem cells (HUCMSCs) in mice with completely transected spinal cord injury (SCI). Methods Stable bFGF-overexpressing HUCMSCs clones were established by electrotransfection and then subjected to systematic safety evaluations. Then, bFGF-overexpressing and control HUCMSCs were used to treat mice with completely transected SCI by tail intravenous injection. Therapeutic outcomes were then investigated, including functional recovery of locomotion, histological structures, nerve regeneration, and recovery mechanisms. Results Stable bFGF-overexpressing HUCMSCs met the standards and safety of MSCs for clinic use. In the mouse SCI model, stable bFGF-overexpressing HUCMSCs markedly improved therapeutic outcomes such as reducing glial scar formation, improving nerve regeneration and proliferation of endogenous neural stem cells (NSCs), and increasing locomotion functional recovery of posterior limbs compared with the control HUCMSCs group. Furthermore, bFGF-overexpressing HUCMSCs promoted the proliferation and neuronal differentiation of NSCs in vitro through the PI3K-Akt-GSK-3β pathway. Conclusion bFGF-overexpressing HUCMSCs meet the requirements of clinical MSCs and improve evident therapeutic outcomes of mouse SCI treatment, which firmly supports the safety and efficacy of gene-modified MSCs for clinical application.

Description: Background Coronary artery disease (CAD) is considered as a multi-faceted chronic inflammatory disease involving reduced blood supply to the myocardium as a result of accumulating lipids in the atrial walls. Visceral adiposity with disrupted release of adipokines play a key role in its pathogenesis. Asprosin is a newly identified fasting-induced glucogenic adipokine that has been related with metabolic disorders such as type II diabetes mellitus and polycystic ovary syndrome. The preset study sought to assess circulating asprosin in context of CAD. Methods In this study, serum levels of asprosin were determined in 88 CAD patients and 88 non-CAD healthy controls. Serum IL-6, TNF-α, asprosin and adiponectin were assessed using ELISA kits. Results: Serum asprosin was found to be higher in CAD patients when compared to non-CAD subjects (7.84 ± 2.08 versus 5.02 ± 1.29 μg/mL, p 

Description: Pre-main sequence (PMS) stars evolve into main sequence (MS) phase over a period of time. Interestingly, we found a scarcity of studies in existing literature that examines and attempts to better understand the stars in PMS to MS transition phase. The purpose of the present study is to detect such rare stars, which we named as ‘Transition Phase’ (TP) candidates – stars evolving from the PMS to the MS phase. We identified 98 TP candidates using photometric analysis of a sample of 2167 classical Be (CBe) and 225 Herbig Ae/Be (HAeBe) stars. This identification is done by analyzing the near- and mid-infrared excess and their location in the optical colour-magnitude diagram. The age and mass of 58 of these TP candidates are determined to be between 0.1–5 Myr and 2–10.5 M⊙, respectively. The TP candidates are found to possess rotational velocity and colour excess values in between CBe and HAeBe stars, which is reconfirmed by generating a set of synthetic samples using the machine learning approach.

Description: Seismic facies analysis can generate a map to describe the spatial distribution characteristics of reservoirs, and therefore plays a critical role in seismic interpretation. To analyse the characteristics of the horizon of interest, it is usually necessary to extract seismic waveforms along the target horizon using a selected time window. The inaccuracy of horizon interpretation often produces some inconsistent phases and leads to inaccurate classification. Therefore, the developed adaptive phase K-means algorithm proposed a sliding time window to extract seismic waveforms. However, setting the maximum offset of the sliding window is difficult in a real data application. A value that is too large may cause the cross-layer problem, whereas a value that is too small reduces the flexibility of the algorithm. To address this disadvantage, this paper proposes a robust K-means (R-K-means) algorithm with a Gaussian-weighted sliding window for seismic waveform classification. The used weights punish those windows distant from the interpretation horizon in the objective function, consequently producing a smaller range of horizon adjustments even when using relatively large maximum offsets and benefitting the generation of stable and reliable seismic facies maps. The application of real seismic data from the F3 block proves the effectiveness of the proposed algorithm.

Description: Background Metabolic stress, as negative energy balance on one hand or obesity on the other hand can lead to increased levels of free fatty acids in the plasma and follicular fluid of animals and humans. In an earlier study, we showed that increased oleic acid (OA) concentrations affected the function of cultured bovine granulosa cells (GCs). Here, we focus on genome wide effects of increased OA concentrations. Results Our data showed that 413 genes were affected, of which 197 were down- and 216 up-regulated. Specifically, the expression of FSH-regulated functional key genes, CCND2, LHCGR, INHA and CYP19A1 and 17-β-estradiol (E2) production were reduced by OA treatment, whereas the expression of the fatty acid transporter CD36 was increased and the morphology of the cells was changed due to lipid droplet accumulation. Bioinformatic analysis revealed that associated pathways of the putative upstream regulators “FSH” and “Cg (choriogonadotropin)” were inhibited and activated, respectively. Down-regulated genes are over-represented in GO terms “reproductive structure/system development”, “ovulation cycle process”, and “(positive) regulation of gonadotropin secretion”, whereas up-regulated genes are involved in “circulatory system development”, “vasculature development”, “angiogenesis” or “extracellular matrix/structure organization”. Conclusions From these data we conclude that besides inhibiting GC functionality, increased OA levels seemingly promote angiogenesis and tissue remodelling, thus suggestively initiating a premature fulliculo-luteal transition. In vivo this may lead to impeded folliculogenesis and ovulation, and cause sub-fertility.

Description: Background Left-right (LR) asymmetry is an essential feature of bilateral animals. Studies in vertebrates show that LR asymmetry formation comprises three major steps: symmetry breaking, asymmetric gene expression, and LR morphogenesis. Although much progress has been made in the first two events, mechanisms underlying asymmetric morphogenesis remain largely unknown due to the complex developmental processes deployed by vertebrate organs. Results We here addressed this question by studying Pitx gene function in the basal chordate amphioxus whose asymmetric organogenesis, unlike that in vertebrates, occurs essentially in situ and does not rely on cell migration. Pitx null mutation in amphioxus causes loss of all left-sided organs and incomplete ectopic formation of all right-sided organs on the left side, whereas Pitx partial loss-of-function leads to milder phenotypes with only some LR organs lost or ectopically formed. At the N1 to N3 stages, Pitx expression is gradually expanded from the dorsal anterior domain to surrounding regions. This leads to activation of genes like Lhx3 and/or Prop1 and Pit, which are essential for left-side organs, and downregulation of genes like Hex and/or Nkx2.1 and FoxE4, which are required for right-side organs to form ectopically on the left side. In Pitx mutants, the left-side expressed genes are not activated, while the right-side genes fail to decrease expression on the left side. In contrast, in embryos overexpressing Pitx genes, the left-side genes are induced ectopically on the right side, and the right-side genes are inhibited. Several Pitx binding sites are identified in the upstream sequences of the left-side and right-side genes which are essential for activation of the former and repression of the latter by Pitx. Conclusions Our results demonstrate that (1) Pitx is a major (although not the only) determinant of asymmetric morphogenesis in amphioxus, (2) the development of different LR organs have distinct requirements for Pitx activity, and (3) Pitx controls amphioxus LR morphogenesis probably through inducing left-side organs and inhibiting right-side organs directly. These findings show much more dependence of LR organogenesis on Pitx in amphioxus than in vertebrates. They also provide insight into the molecular developmental mechanism of some vertebrate LR organs like the lungs and atria, since they show a right-isomerism phenotype in Pitx2 knockout mice like right-sided organs in Pitx mutant amphioxus. Our results also explain why some organs like the adenohypophysis are asymmetrically located in amphioxus but symmetrically positioned in vertebrates.

Description: Background After repairing double-strand breaks (DSBs) caused by CRISPR-Cas9 cleavage, genomic damage, such as large deletions, may have pathogenic consequences. Results We show that large deletions are ubiquitous but are dependent on editing sites and cell types. Human primary T cells display more significant deletions than hematopoietic stem and progenitor cells (HSPCs), whereas we observe low levels in induced pluripotent stem cells (iPSCs). We find that the homology-directed repair (HDR) with single-stranded oligodeoxynucleotides (ssODNs) carrying short homology reduces the deletion damage by almost half, while adeno-associated virus (AAV) donors with long homology reduce large deletions by approximately 80%. In the absence of HDR, the insertion of a short double-stranded ODN by NHEJ reduces deletion indexes by about 60%. Conclusions Timely bridging of broken ends by HDR and NHEJ vastly decreases the unintended consequences of dsDNA cleavage. These strategies can be harnessed in gene editing applications to attenuate unintended outcomes.

Description: Background C. sinensis is an important economic crop with fluoride over-accumulation in its leaves, which poses a serious threat to human health due to its leaf consumption as tea. Recently, our study has indicated that cell wall proteins (CWPs) probably play a vital role in fluoride accumulation/detoxification in C. sinensis. However, there has been a lack in CWP identification and characterization up to now. This study is aimed to characterize cell wall proteome of C. sinensis leaves and to develop more CWPs related to stress response. A strategy of combined cell wall proteomics and N-glycoproteomics was employed to investigate CWPs. CWPs were extracted by sequential salt buffers, while N-glycoproteins were enriched by hydrophilic interaction chromatography method using C. sinensis leaves as a material. Afterwards all the proteins were subjected to UPLC-MS/MS analysis. Results A total of 501 CWPs and 195 CWPs were identified respectively by cell wall proteomics and N-glycoproteomics profiling with 118 CWPs in common. Notably, N-glycoproteomics is a feasible method for CWP identification, and it can enhance CWP coverage. Among identified CWPs, proteins acting on cell wall polysaccharides constitute the largest functional class, most of which might be involved in cell wall structure remodeling. The second largest functional class mainly encompass various proteases related to CWP turnover and maturation. Oxidoreductases represent the third largest functional class, most of which (especially Class III peroxidases) participate in defense response. As expected, identified CWPs are mainly related to plant cell wall formation and defense response. Conclusion This was the first large-scale investigation of CWPs in C. sinensis through cell wall proteomics and N-glycoproteomics. Our results not only provide a database for further research on CWPs, but also an insight into cell wall formation and defense response in C. sinensis.

Description: Background Finding meaningful gene-gene interaction and the main Transcription Factors (TFs) in co-expression networks is one of the most important challenges in gene expression data mining. Results Here, we developed the R package “CeTF” that integrates the Partial Correlation with Information Theory (PCIT) and Regulatory Impact Factors (RIF) algorithms applied to gene expression data from microarray, RNA-seq, or single-cell RNA-seq platforms. This approach allows identifying the transcription factors most likely to regulate a given network in different biological systems — for example, regulation of gene pathways in tumor stromal cells and tumor cells of the same tumor. This pipeline can be easily integrated into the high-throughput analysis. To demonstrate the CeTF package application, we analyzed gastric cancer RNA-seq data obtained from TCGA (The Cancer Genome Atlas) and found the HOXB3 gene as the second most relevant TFs with a high regulatory impact (TFs-HRi) regulating gene pathways in the cell cycle. Conclusion This preliminary finding shows the potential of CeTF to list master regulators of gene networks. CeTF was designed as a user-friendly tool that provides many highly automated functions without requiring the user to perform many complicated processes. It is available on Bioconductor (http://bioconductor.org/packages/CeTF) and GitHub (http://github.com/cbiagii/CeTF).

Description: Blueberry (Vaccinium ssp.) is a perennial shrub belonging to the family Ericaceae, which is highly tolerant of acid soils and heavy metal pollution. In the present study, blueberry was subjected to cadmium (Cd) stress in simulated pot culture. The transcriptomics and rhizosphere fungal diversity of blueberry were analyzed, and the iron (Fe), manganese (Mn), copper (Cu), zinc (Zn) and cadmium (Cd) content of blueberry tissues, soil and DGT was determined. A correlation analysis was also performed. A total of 84 374 annotated genes were identified in the root, stem, leaf and fruit tissue of blueberry, of which 3370 were DEGs, and in stem tissue, of which 2521 were DEGs. The annotation data showed that these DEGs were mainly concentrated in a series of metabolic pathways related to signal transduction, defense and the plant–pathogen response. Blueberry transferred excess Cd from the root to the stem for storage, and the highest levels of Cd were found in stem tissue, consistent with the results of transcriptome analysis, while the lowest Cd concentration occurred in the fruit, Cd also inhibited the absorption of other metal elements by blueberry. A series of genes related to Cd regulation were screened by analyzing the correlation between heavy metal content and transcriptome results. The roots of blueberry rely on mycorrhiza to absorb nutrients from the soil. The presence of Cd has a significant effect on the microbial community composition of the blueberry rhizosphere. The fungal family Coniochaetaceae, which is extremely extremelytolerant, has gradually become the dominant population. The results of this study increase our understanding of the plant regulation mechanism for heavy metals, and suggest potential methods of soil remediation using blueberry.

Description: Several bioinformatic tools have been developed for genome-wide identification of orthologous and paralogous genes. However, no corresponding tool allows the detection of exon homology relationships. Here, we present ExOrthist, a fully reproducible Nextflow-based software enabling inference of exon homologs and orthogroups, visualization of evolution of exon-intron structures, and assessment of conservation of alternative splicing patterns. ExOrthist evaluates exon sequence conservation and considers the surrounding exon-intron context to derive genome-wide multi-species exon homologies at any evolutionary distance. We demonstrate its use in different evolutionary scenarios: whole genome duplication in frogs and convergence of Nova-regulated splicing networks (https://github.com/biocorecrg/ExOrthist).

Description: Objective To compare an objective with a subjective numeracy assessment for association with self-reported health status, where numeracy refers to “the degree to which individuals have the capacity to access, process, interpret, communicate, and act on numerical, quantitative, graphical, biostatistical, and probabilistic health information needed to make effective health decisions” Results We completed a secondary analysis of two population-based surveys, the Empire State Poll (n = 763) and the Program for the International Assessment of Adult Competencies (PIAAC; n = 2609). The first survey assessed numeracy with a 3-item subjective instrument. The second assessed numeracy with more than 20 math problems. Both used the same measure for self-reported health status. Lower numeracy, whether subjectively or objectively assessed, was associated with worse self-reported health, even after controlling for education and other sociodemographic confounders. The odds ratios for the association were very similar (0.91 and 0.90 respectively). A lengthy objective numeracy assessment and a brief self-report assessment had similar associations with health status. A brief self-report measure of numeracy has similar properties to a lengthy objective assessment and is likely to be more feasible to use to screen patients in practice.

Description: Background Sorghum yields in sub-Saharan Africa (SSA) are greatly reduced by parasitic plants of the genus Striga (witchweed). Vast global sorghum genetic diversity collections, as well as the availability of modern sequencing technologies, can be potentially harnessed to effectively manage the parasite. Results We used laboratory assays – rhizotrons to screen a global sorghum diversity panel to identify new sources of resistance to Striga; determine mechanisms of resistance, and elucidate genetic loci underlying the resistance using genome-wide association studies (GWAS). New Striga resistant sorghum determined by the number, size and biomass of parasite attachments were identified. Resistance was by; i) mechanical barriers that blocked parasite entry, ii) elicitation of a hypersensitive reaction that interfered with parasite development, and iii) the inability of the parasite to develop vascular connections with hosts. Resistance genes underpinning the resistance corresponded with the resistance mechanisms and included pleiotropic drug resistance proteins that transport resistance molecules; xylanase inhibitors involved in cell wall fortification and hormonal regulators of resistance response, Ethylene Response Factors. Conclusions Our findings are of fundamental importance to developing durable and broad-spectrum resistance against Striga and have far-reaching applications in many SSA countries where Striga threatens the livelihoods of millions of smallholder farmers that rely on sorghum as a food staple.

Description: Background Forest carbon models are recognized as suitable tools for the reporting and verification of forest carbon stock and stock change, as well as for evaluating the forest management options to enhance the carbon sink provided by sustainable forestry. However, given their increased complexity and data availability, different models may simulate different estimates. Here, we compare carbon estimates for Romanian forests as simulated by two models (CBM and EFISCEN) that are often used for evaluating the mitigation options given the forest-management choices. Results The models, calibrated and parameterized with identical or harmonized data, derived from two successive national forest inventories, produced similar estimates of carbon accumulation in tree biomass. According to CBM simulations of carbon stocks in Romanian forests, by 2060, the merchantable standing stock volume will reach an average of 377 m3 ha−1, while the carbon stock in tree biomass will reach 76.5 tC ha−1. The EFISCEN simulations produced estimates that are about 5% and 10%, respectively, lower. In addition, 10% stronger biomass sink was simulated by CBM, whereby the difference reduced over time, amounting to only 3% toward 2060. Conclusions This model comparison provided valuable insights on both the conceptual and modelling algorithms, as well as how the quality of the input data may affect calibration and projections of the stock and stock change in the living biomass pool. In our judgement, both models performed well, providing internally consistent results. Therefore, we underline the importance of the input data quality and the need for further data sampling and model improvements, while the preference for one model or the other should be based on the availability and suitability of the required data, on preferred output variables and ease of use.

Description: Background Significant investments have been made towards the implementation of mHealth applications and eRecord systems globally. However, fragmentation of these technologies remains a big challenge, often unresolved in developing countries. In particular, evidence shows little consideration for linking mHealth applications and eRecord systems. Botswana is a typical developing country in sub-Saharan Africa that has explored mHealth applications, but the solutions are not interoperable with existing eRecord systems. This paper describes Botswana’s eRecord systems interoperability landscape and provides guidance for linking mHealth applications to eRecord systems, both for Botswana and for developing countries using Botswana as an exemplar. Methods A survey and interviews of health ICT workers and a review of the Botswana National eHealth Strategy were completed. Perceived interoperability benefits, opportunities and challenges were charted and analysed, and future guidance derived. Results Survey and interview responses showed the need for interoperable mHealth applications and eRecord systems within the health sector of Botswana and within the context of the National eHealth Strategy. However, the current Strategy does not address linking mHealth applications to eRecord systems. Across Botswana’s health sectors, global interoperability standards and Application Programming Interfaces are widely used, with some level of interoperability within, but not between, public and private facilities. Further, a mix of open source and commercial eRecord systems utilising relational database systems and similar data formats are supported. Challenges for linking mHealth applications and eRecord systems in Botswana were identified and categorised into themes which led to development of guidance to enhance the National eHealth Strategy. Conclusion Interoperability between mHealth applications and eRecord systems is needed and is feasible. Opportunities and challenges for linking mHealth applications to eRecord systems were identified, and future guidance stemming from this insight presented. Findings will aid Botswana, and other developing countries, in resolving the pervasive disconnect between mHealth applications and eRecord systems.

Description: Objective The use of mice as animal models in biomedical research allows the standardization of genetic background and environmental conditions, which both affect phenotypic variability. As the use of both sexes in experiments is strongly recommended, sex-specific phenotypic variability is discussed with regard to putative consequences on the group size which is necessary for achieving valid and reproducible results. In this study, the sex-specific variability of 25 clinical chemical and hematological parameters which represent a comprehensive blood screen of laboratory mice, was analyzed in data sets which have been submitted to the Mouse Phenome Database. Results The overall analysis comprising all 25 clinical chemical and hematological parameters showed no evidence for substantial and robust general sex-specific variability. A large range of the ratio of the female and male coefficient of variation (CV) was found for every parameter among the respective strain data sets. This clearly demonstrated the appearance of unpredictable major interactions between genotype and environment regarding the sex-specific variability of the blood parameters analyzed.

Description: Objective Reported rainfall data from multiple rain gauges and its corresponding estimate from Dual-Polarization (Dual-Pol) radar is presented here. The ordered set of data pairs were collected from multiple peer reviewed publications spanning across the last decade. Data description Taken from multiple sources, the data set represents several radar sites and rain gauge sites combined for 12,734 data points. The data is relevant in various applications of hydrometeorology and engineering as well as weather forecasting. Further, the importance of accuracy in radar precipitation estimates continues to increase, necessitating the incorporation of as much data as possible.

Description: In the canonical random on-the-job search model with continuous firm heterogeneity, I show that a mean-preserving spread of the firm-productivity distribution raises the returns to mobility, i.e., the inter-firm mobility of workers as measured by the number of outside contacts per employment spell. Both sorting and rent-share mechanisms play a role. In a further contribution, I distinguish frictional and structural impediments to mobility in order to establish a link between mobility and skills via the concept of versatility. Versatility enhances a person’s mobility since a mismatch between job requirements and the person’s skill set is less likely to occur. I provide some statistics in support of the discussed mechanisms. The findings are particularly intriguing in light of the concurrent rise in the productivity dispersion across firms and in the skill premium in many countries.

Description: Recent searches for the hosts of z ∼ 4 damped Lyα absorbers (DLAs) have detected bright galaxies at distances of tens of kpc from the DLA. Using the FIRE-2 cosmological zoom simulations, we argue that these relatively large distances are due to a predominantly cool and neutral inner circumgalactic medium (CGM) surrounding high-redshift galaxies. The inner CGM is cool because of the short cooling time of hot gas in ≲ 1012 M⊙ haloes, which implies that accretion and feedback energy are radiated quickly, while it is neutral due to high volume densities and column densities at high redshift which shield cool gas from photoionization. Our analysis predicts large DLA covering factors ($gtrsim 50{{ m per cent}}$) out to impact parameters ∼0.3((1 + z)/5)3/2Rvir from the central galaxies at z ≳ 1, equivalent to a proper distance of $sim 21, M_{12}^{1/3} left(left(1+z ight)/5 ight)^{1/2}, { m kpc}$ (Rvir and M12 are the halo virial radius and mass in units of 1012 M⊙, respectively). This implies that DLA covering factors at z ∼ 4 may be comparable to unity out to a distance ∼10 times larger than stellar half-mass radii. A predominantly neutral inner CGM in the early universe suggests that its mass and metallicity can be directly constrained by absorption surveys, without resorting to the large ionization corrections as required for ionized CGM.

Description: Motivation Accurate automatic annotation of protein function relies on both innovative models and robust data sets. Due to their importance in biological processes, the identification of DNA-binding proteins directly from protein sequence has been the focus of many studies. However, the data sets used to train and evaluate these methods have suffered from substantial flaws. We describe some of the weaknesses of the data sets used in previous DNA-binding protein literature and provide several new data sets addressing these problems. We suggest new evaluative benchmark tasks that more realistically assess real-world performance for protein annotation models. We propose a simple new model for the prediction of DNA-binding proteins and compare its performance on the improved data sets to two previously published models. Additionally, we provide extensive tests showing how the best models predict across taxonomies. Results Our new gradient boosting model, which uses features derived from a published protein language model, outperforms the earlier models. Perhaps surprisingly, so does a baseline nearest neighbor model using BLAST percent identity. We evaluate the sensitivity of these models to perturbations of DNA-binding regions and control regions of protein sequences. The successful data-driven models learn to focus on DNA-binding regions. When predicting across taxonomies, the best models are highly accurate across species in the same kingdom and can provide some information when predicting across kingdoms. Code and Data Availability The data and results for this paper can be found at https://doi.org/10.5281/zenodo.5153906. The code for this paper can be found at https://doi.org/10.5281/zenodo.5153683. The code, data and results can also be found at https://github.com/AZaitzeff/tools_for_dna_binding_proteins.

Description: Background The abiotic stress such as soil salinization and heavy metal toxicity has posed a major threat to sustainable crop production worldwide. Previous studies revealed that halophytes were supposed to tolerate other stress including heavy metal toxicity. Though HMAD (heavy-metal-associated domain) was reported to play various important functions in Arabidopsis, little is known in Gossypium. Results A total of 169 G. hirsutum genes were identified belonging to the HMAD gene family with the number of amino acids ranged from 56 to 1011. Additionally, 84, 76 and 159 HMAD genes were identified in each G. arboreum, G. raimondii and G. barbadense, respectively. The phylogenetic tree analysis showed that the HMAD gene family were divided into five classes, and 87 orthologs of HMAD genes were identified in four Gossypium species, such as genes Gh_D08G1950 and Gh_A08G2387 of G. hirsutum are orthologs of the Gorai.004G210800.1 and Cotton_A_25987 gene in G. raimondii and G. arboreum, respectively. In addition, 15 genes were lost during evolution. Furthermore, conserved sequence analysis found the conserved catalytic center containing an anion binding (CXXC) box. The HMAD gene family showed a differential expression levels among different tissues and developmental stages in G. hirsutum with the different cis-elements for abiotic stress. Conclusions Current study provided important information about HMAD family genes under salt-stress in Gossypium genome, which would be useful to understand its putative functions in different species of cotton.

Description: Background Soybean is a globally important legume crop that provides a primary source of high-quality vegetable protein and oil. Seed protein content (SPC) is a valuable quality trait controlled by multiple genes in soybean. Results In this study, we performed quantitative trait loci (QTL) mapping, QTL-seq, and RNA sequencing (RNA-seq) to reveal the genes controlling protein content in the soybean by using the high protein content variety Nanxiadou 25. A total of 50 QTL for SPC distributed on 14 chromosomes except chromosomes 4, 12, 14, 17, 18, and 19 were identified by QTL mapping using 178 recombinant inbred lines (RILs). Among these QTL, the major QTL qSPC_20–1 and qSPC_20–2 on chromosome 20 were repeatedly detected across six tested environments, corresponding to the location of the major QTL detected using whole-genome sequencing-based QTL-seq. 329 candidate DEGs were obtained within the QTL region of qSPC_20–1 and qSPC_20–2 via gene expression profile analysis. Nine of which were associated with SPC, potentially representing candidate genes. Clone sequencing results showed that different single nucleotide polymorphisms (SNPs) and indels between high and low protein genotypes in Glyma.20G088000 and Glyma.16G066600 may be the cause of changes in this trait. Conclusions These results provide the basis for research on candidate genes and marker-assisted selection (MAS) in soybean breeding for seed protein content.

Description: Functional genomics experiments, like ChIP-Seq or ATAC-Seq, produce results that are summarized as a region set. There is no way to objectively evaluate the effectiveness of region set similarity metrics. We present Bedshift, a tool for perturbing BED files by randomly shifting, adding, and dropping regions from a reference file. The perturbed files can be used to benchmark similarity metrics, as well as for other applications. We highlight differences in behavior between metrics, such as that the Jaccard score is most sensitive to added or dropped regions, while coverage score is most sensitive to shifted regions.

Description: Background Hypertrophy is a critical process for chondrocyte differentiation and maturation during endochondral ossification, which is responsible for the formation of long bone and postnatal longitudinal growth. Increasing evidence suggests that melatonin, an indole hormone, plays a pivotal role in chondrogenesis. However, little is known about the effects of melatonin on the terminal differentiation of chondrocytes. Methods Mesenchymal stem cell (MSC)-derived chondrocytes generated by a high-density micromass culture system were induced to undergo hypertrophic differentiation. Melatonin-mediated hypertrophic differentiation was examined by reverse transcription polymerase chain reaction analysis (RT-PCR) analysis, histological staining and immunohistochemistry. Activation of the Wnt signaling pathway was evaluated by PCR array, RT-PCR, western blotting and immunofluorescence. XAV-939, a Wnt signaling pathway antagonist, was further used to determine whether the effect of melatonin on chondrocyte hypertrophic differentiation was mediated occurred by activation of Wnt signaling pathway. Results Histological staining showed melatonin increased chondrocyte cell volume and the expression of type X collagen but decreased the expression of type II collagen compared with the control group. RT-PCR showed that melatonin significantly up-regulated the gene expressions of biomarkers of hypertrophic chondrocytes, including type X collagen, alkaline phosphatase, runt-related transcription factor 2, Indian hedgehog and parathyroid hormone-related protein receptor, and melatonin down-regulated the mRNA expression of hallmarks of chondrocytes, including parathyroid hormone-related protein. PCR array showed that the effect of melatonin on chondrocyte hypertrophic differentiation was accompanied by the up-regulation of multiple target genes of the canonical Wnt signaling pathway, and this effect was blocked by XAV-939. Conclusions The current findings demonstrate that melatonin enhances the hypertrophic differentiation of MSC-derived chondrocytes through the Wnt signaling pathway. Our findings add evidence to the role of melatonin in promoting bone development and highlight the positive effects of melatonin on terminal differentiation of chondrocytes.

Description: Deciduous seasonal forests (DSFs) have a peculiar floristic composition, with species capable of surviving periods of high water deficit in a year. Our goal was to demonstrate that abiotic filters lead to the assembly of two DSF communities that have high floristic dissimilarity. For this, we characterized the environment of the areas and used the community-weighted mean (CWM), functional richness (FRic) and functional dispersion (FDis) indices for regional recognition of functional patterns. The local assessment of assembly rules was carried out using null models. We found differences in the FRic and FDis between the areas, which was attributed to the different floristic influences exercised on the communities. However, in both, the typical attributes of dry formations were dominant (CWM), indicating that, on the regional scale of study, the dry season acts as a filter in the composition of species in the communities. On a local scale, stochastic dispersion was identified as the most influential mechanism in the assembly of communities. We conclude that deterministic and stochastic processes act in the assembly of the studied communities, and the proportion of each of these depends on the scale, with abiotic filtration predominating on a regional scale and stochastic dispersion events on a local scale. Study Implications With the expansion of agriculture and climate change, tropical dry biomes, such as deciduous seasonal forests, are rapidly changing. In this study, we contribute to the recognition of functional standards and community assembly of this vegetation type to assist in management planning, restoration, and conservation. Understanding the different processes involved in building a community is crucial for anticipating how communities will behave under future environmental scenarios.

Description: Novel coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus-2. The virus causes an exaggerated immune response, resulting in a cytokine storm and acute respiratory distress syndrome, the leading cause of COVID-19-related mortality and morbidity. So far, no therapies have succeeded in circumventing the exacerbated immune response or cytokine storm associated with COVID-19. Mesenchymal stem cells (MSCs), through their immunomodulatory and regenerative activities, mostly mediated by their paracrine effect and extracellular vesicle production, have therapeutic potential in many autoimmune, inflammatory, and degenerative diseases. In this paper, we review clinical studies on the use of MSCs for COVID-19 treatment, including the salutary effects of MSCs on the pathophysiology of COVID-19 and the immunomodulation of the cytokine storm. Ongoing clinical trial designs, cell sources, dose and administration, and populations are summarized, and the paracrine mode of benefit is discussed. We also offer suggestions for optimizing MSC-based therapies, including genetic engineering, strategies for cell surface modification, nanotechnology applications, and combination therapies.

Description: Quantification of soil organic carbon (SOC) stocks in different land uses holds vital significance because of its implications regarding carbon sequestration as the largest terrestrial carbon pool. The current study was conducted to quantify and compare SOC stocks in forest land, agricultural land, and barren land-use categories in the subtropical ecosystems of the Himalayan foothills in Kashmir. Results showed the highest SOC value in the forest soil (75 ± 11.1 Mg C ha−1) followed by agricultural soil (58 ± 7.0 Mg C ha−1) and barren land (44 ± 6.5 Mg C ha−1). SOC stocks in different land uses showed broad variations with values as high as 106 ± 11.3 Mg C ha−1 (forest soils) and as low as 14.1 ± 7.1 Mg C ha−1 (barren land). The forest SOC values responded significantly to species composition with the highest values in Pinus roxburghii Sarg. pure stands as compared with broad leaved forests. Multivariate ordination analyses revealed that the variations in SOC stocks were significantly correlated with vegetation type, altitude, and soil bulk density. The study has identified anthropogenic disturbances as a major factor deteriorating local SOC stocks and recommends immediate soil restoration efforts to enhance the ecological significance of soils as vital regional carbon sinks. Study Implications The current study was designed to investigate the soil organic carbon (SOC) levels in different land uses of the Kashmir Himalayas, Pakistan. Results revealed forest soils as the major carbon sinks of the region, attributed to diverse species composition having a significant quantity of organic residues, followed by agricultural soils. Barren land-use class exhibited the lowest SOC values due to minimum vegetation cover, erosion, and degradation. Significant correlations of SOC stocks with geographical and edaphic variables were identified by multivariate ordination analysis in the investigated land-use classes. Results validate the significance of forests in enhancing SOC stocks, demanding forest restoration in the area by controlling the forest losses as well as afforestation. This article provides vital information required for better understanding of SOC stocks in different land-use classes in the subtropical ecosystems of the Kashmir region.

Description: Aims Acid grasslands are threatened both by agricultural intensification with nutrient addition and increased livestock densities as well as by land abandonment. In order to understand and quantify the effect of selected environmental and land-use factors on the observed variation and changes in the vegetation of acid grasslands, large-scale spatial and temporal pin-point plant cover monitoring data are fitted in a structural equation model. Methods The important sources of measurement and sampling uncertainties have been included using a hierarchical model structure. Furthermore, uncertainties associated with the measurement and sampling are separated from the process uncertainty, which is important when generating ecological predictions that may feed into local conservation management decisions. Important Findings Generally, increasing atmospheric nitrogen deposition led to more grass-dominated acid grassland habitats at the expense of the cover of forbs. Sandy soils were relatively more acidic, and the effects of soil type on the vegetation include both direct effects of soil type and indirect effects mediated by the effect of soil type on soil pH. Both soil type and soil pH affected the vegetation of acid grasslands. Even though only a relatively small proportion of the temporal variation in cover was explained by the model, it would still be useful to quantify the uncertainties when using the model for generating local ecological predictions and adaptive management plans.

Description: Acute myeloid leukemia (AML) is a serious, life-threatening, and hardly curable hematological malignancy that affects the myeloid cell progenies and challenges patients of all ages but mostly occurs in adults. Although several therapies are available including chemotherapy, allogeneic hematopoietic stem cell transplantation (alloHSCT), and receptor-antagonist drugs, the 5-year survival of patients is quietly disappointing, less than 30%. alloHSCT is the major curative approach for AML with promising results but the treatment has severe adverse effects such as graft-versus-host disease (GVHD). Therefore, as an alternative, more efficient and less harmful immunotherapy-based approaches such as the adoptive transferring T cell therapy are in development for the treatment of AML. As such, chimeric antigen receptor (CAR) T cells are engineered T cells which have been developed in recent years as a breakthrough in cancer therapy. Interestingly, CAR T cells are effective against both solid tumors and hematological cancers such as AML. Gradually, CAR T cell therapy found its way into cancer therapy and was widely used for the treatment of hematologic malignancies with successful results particularly with somewhat better results in hematological cancer in comparison to solid tumors. The AML is generally fatal, therapy-resistant, and sometimes refractory disease with a disappointing low survival rate and weak prognosis. The 5-year survival rate for AML is only about 30%. However, the survival rate seems to be age-dependent. Novel CAR T cell therapy is a light at the end of the tunnel. The CD19 is an important target antigen in AML and lymphoma and the CAR T cells are engineered to target the CD19. In addition, a lot of research goes on the discovery of novel target antigens with therapeutic efficacy and utilizable for generating CAR T cells against various types of cancers. In recent years, many pieces of research on screening and identification of novel AML antigen targets with the goal of generation of effective anti-cancer CAR T cells have led to new therapies with strong cytotoxicity against cancerous cells and impressive clinical outcomes. Also, more recently, an improved version of CAR T cells which were called modified or smartly reprogrammed CAR T cells has been designed with less unwelcome effects, less toxicity against normal cells, more safety, more specificity, longer persistence, and proliferation capability. The purpose of this review is to discuss and explain the most recent advances in CAR T cell-based therapies targeting AML antigens and review the results of preclinical and clinical trials. Moreover, we will criticize the clinical challenges, side effects, and the different strategies for CAR T cell therapy.

Description: Background One of the major trends in angiosperm evolution was the shift from woody to herbaceous habit. However, reversals known as derived woodiness have also been reported in numerous, distantly related clades. Among theories evoked to explain the factors promoting the evolution of derived woodiness are moderate climate theory and cavitation theory. The first assumes that woody habit evolves in response to mild climate allowing for prolonged life span, which in turn leads to bigger and woodier bodies. The second sees woodiness as a result of natural selection for higher cavitation resistance in seasonally dry environments. Here, we compare climatic niches of woody and herbaceous, mostly southern African, umbellifers from the Lefebvrea clade to assess whether woody taxa in fact occur in markedly drier habitats. We also calibrate their phylogeny to estimate when derived woodiness evolved. Finally, we describe the wood anatomy of selected woody and herbaceous taxa to see if life forms are linked to any particular wood traits. Results The evolution of derived woodiness in chamaephytes and phanerophytes as well as the shifts to short-lived annual therophytes in the Lefebvrea clade took place at roughly the same time: in the Late Miocene during a trend of global climate aridification. Climatic niches of woody and herbaceous genera from the Cape Floristic Region overlap. There are only two genera with distinctly different climatic preferences: they are herbaceous and occur outside of the Cape Floristic Region. Therefore, studied herbs have an overall climatic niche wider than their woody cousins. Woody and herbaceous species do not differ in qualitative wood anatomy, which is more affected by stem architecture and, probably, reproductive strategy than by habit. Conclusions Palaeodrought was likely a stimulus for the evolution of derived woodiness in the Lefebvrea clade, supporting the cavitation theory. The concurrent evolution of short-lived annuals withering before summer exemplifies an alternative solution to the same problem of drought-induced cavitation. Changes of the life form were most likely neither spurred nor precluded by any qualitative wood traits, which in turn are more affected by internode length and probably also reproductive strategy.

Description: Research in the past decade has demonstrated that a single reference genome is not representative of a species’ diversity. MaizeGDB introduces a pan-genomic approach to hosting genomic data, leveraging the large number of diverse maize genomes and their associated datasets to quickly and efficiently connect genomes, gene models, expression, epigenome, sequence variation, structural variation, transposable elements, and diversity data across genomes so that researchers can easily track the structural and functional differences of a locus and its orthologs across maize. We believe our framework is unique and provides a template for any genomic database poised to host large-scale pan-genomic data.

Description: SAR92 is one of the few examples of a widely distributed, abundant oligotroph that can be cultivated to study pathways of carbon oxidation in ocean systems. Genomic evidence for SAR92 suggests that this gammaproteobacterium might be a primary consumer of polysaccharides in the epipelagic zone, its main habitat. Here, we investigated cell growth, polysaccharide utilization gene expression, and carbohydrate-active enzyme abundance of a culturable SAR92 strain, HTCC2207, grown with different polysaccharides. Xylan and laminarin, two polysaccharides mainly produced by phytoplankton, supported the growth of HTCC2207 better than other polysaccharides. HTCC2207 possessed polysaccharide utilization loci (PULs) consisting of TonB-dependent receptor (TBDR) and glycoside hydrolase (GH) family genes. GH genes such as GH17 and GH3 presented no substrate-specificity and were induced by different sugar substrates, while expressions of GH16, GH10 and GH30 were enhanced in the glucose-treatment but suppressed in the polysaccharide-treatment, indicating complex polysaccharide utilization by HTCC2207. Metabolic pathways for laminarin and xylan were re-constructed in HTCC2207 based on the PULs genes and other predicted carbohydrate-active enzymes. This study reveals features of the epipelagic niche of SAR92 and provide insight into the biogeochemical cycling of labile, high-molecular carbohydrate compounds in the surface ocean.

Description: Background In most flowering plants, the plastid genome exhibits a quadripartite genome structure, comprising a large and a small single copy as well as two inverted repeat regions. Thousands of plastid genomes have been sequenced and submitted to public sequence repositories in recent years. The quality of sequence annotations in many of these submissions is known to be problematic, especially regarding annotations that specify the length and location of the inverted repeats: such annotations are either missing or portray the length or location of the repeats incorrectly. However, many biological investigations employ publicly available plastid genomes at face value and implicitly assume the correctness of their sequence annotations. Results We introduce , a Python package that automatically assesses the frequency of incomplete or incorrect annotations of the inverted repeats among publicly available plastid genomes. Specifically, the tool automatically retrieves plastid genomes from NCBI Nucleotide under variable search parameters, surveys them for length and location specifications of inverted repeats, and confirms any inverted repeat annotations through self-comparisons of the genome sequences. The package also includes functionality for automatic identification and removal of duplicate genome records and accounts for taxa that genuinely lack inverted repeats. A survey of the presence of inverted repeat annotations among all plastid genomes of flowering plants submitted to NCBI Nucleotide until the end of 2020 using , followed by a statistical analysis of potential associations with record metadata, highlights that release year and publication status of the genome records have a significant effect on the frequency of complete and equal-length inverted repeat annotations. Conclusion The number of plastid genomes on NCBI Nucleotide has increased dramatically in recent years, and many more genomes will likely be submitted over the next decade. enables researchers to automatically access and evaluate the inverted repeats of these plastid genomes as well as their sequence annotations and, thus, contributes to increasing the reliability of publicly available plastid genomes. The software is freely available via the Python package index at http://pypi.python.org/pypi/airpg.

Description: Objectives Peer support is rapidly being introduced into mental health services internationally, yet peer support interventions are often poorly described, limiting the usefulness of research in informing policy and practice. This paper reports the development of a peer support intervention that aims to improve outcomes of discharge from inpatient to community mental health care. People with experiential knowledge of using mental health services—peer workers and service user researchers—were involved in all stages of developing the intervention: generating intervention components; producing the intervention handbook; piloting the intervention. Results Systematic review and expert panels, including our Lived Experience Advisory Panel, identified 66 candidate intervention components in five domains: Recruitment and Role Description of Peer Workers; Training for Peer Workers; Delivery of Peer Support; Supervision and Support for Peer Workers; Organisation and Team. A series of Local Advisory Groups were used to prioritise components and explore implementation issues using consensus methods, refining an intervention blueprint. A peer support handbook and peer worker training programme were produced by the study team and piloted in two study sites. Feedback workshops were held with peer workers and their supervisors to produce a final handbook and training programme. The ENRICH trial is registered with the ISRCTN clinical trial register, number ISRCTN 10043328, and was overseen by an independent steering committee and a data monitoring committee.

Description: Background As effects of global climate change intensify, the interaction of biotic and abiotic stresses increasingly threatens current agricultural practices. The secondary cell wall is a vanguard of resistance to these stresses. Fusarium thapsinum (Fusarium stalk rot) and Macrophomina phaseolina (charcoal rot) cause internal damage to the stalks of the drought tolerant C4 grass, sorghum (Sorghum bicolor (L.) Moench), resulting in reduced transpiration, reduced photosynthesis, and increased lodging, severely reducing yields. Drought can magnify these losses. Two null alleles in monolignol biosynthesis of sorghum (brown midrib 6-ref, bmr6-ref; cinnamyl alcohol dehydrogenase, CAD; and bmr12-ref; caffeic acid O-methyltransferase, COMT) were used to investigate the interaction of water limitation with F. thapsinum or M. phaseolina infection. Results The bmr12 plants inoculated with either of these pathogens had increased levels of salicylic acid (SA) and jasmonic acid (JA) across both watering conditions and significantly reduced lesion sizes under water limitation compared to adequate watering, which suggested that drought may prime induction of pathogen resistance. RNA-Seq analysis revealed coexpressed genes associated with pathogen infection. The defense response included phytohormone signal transduction pathways, primary and secondary cell wall biosynthetic genes, and genes encoding components of the spliceosome and proteasome. Conclusion Alterations in the composition of the secondary cell wall affect immunity by influencing phenolic composition and phytohormone signaling, leading to the action of defense pathways. Some of these pathways appear to be activated or enhanced by drought. Secondary metabolite biosynthesis and modification in SA and JA signal transduction may be involved in priming a stronger defense response in water-limited bmr12 plants.

Description: Background Retinol binding protein 4 (RBP4) has been proposed to play a role in the pathophysiology of coronary artery disease (CAD), but previous findings on the association of RBP4 levels with CAD are inconsistent. Methods A meta-analysis based on observational studies was conducted to evaluate the association between circulating RBP4 levels and CAD. Databases including PubMed, Web of Science, Embase, Google Scholar and ClinicalTrials.gov database were searched for eligible studies published up to 12 July 2021. Standard mean differences (SMDs) with 95% confidence intervals (CIs) were calculated using the inverse variance heterogeneity (IVhet) and random-effects model for data with moderate and high heterogeneity (I2 〉 30%) and data with low heterogeneity were analysed using a fixed-effects model (I2 ≤ 30%). Moreover, a bias-adjusted quality-effects model was generated, and the prediction interval was also calculated under the random-effects model. Results Two nested case-control studies, one cohort study and twelve case–control studies with a total of 7111 participants were included. Circulating RBP4 levels in patients with CAD were comparable to those in the controls under the IVhet model (SMD: 0.25, 95% CI: − 0.29-0.79, I2: 96.00%). The quality-effects model produced consistent results. However, the association turned to be significant under the random-effect model (SMD: 0.46, 95% CI: 0.17–0.75, I2: 96.00%), whereas the 95% predictive interval (PI) included null values (95% PI: − 0.82-1.74). Subgroup analyses illustrated a positive relationship between CAD and RBP4 levels in patients with complications (SMD: 1.34, 95% CI: 0.38–2.29, I2: 96.00%). The meta-regression analysis revealed that the mean BMI of patients (P = 0.03) and complication status (P = 0.01) influenced the variation in SMD. Conclusions There was low-quality evidence that patients with CAD exhibited similar circulating RBP4 levels compared with controls, and high inter-study heterogeneity was also observed. Thus, RBP4 might not be a potential risk factor for CAD. Comparisons among different subtypes of RBP4 with larger sample size are needed in the future.

Description: Background To understand the mechanism of glucosinolates (GSs) accumulation in the specific organs, combined analysis of physiological change and transcriptome sequencing were applied in the current study. Taking Chinese kale as material, seeds and silique walls were divided into different stages based on the development of the embryo in seeds and then subjected to GS analysis and transcriptome sequencing. Results The main GS in seeds of Chinese kale were glucoiberin and gluconapin and their content changed with the development of the seed. During the transition of the embryo from torpedo- to the early cotyledonary-embryo stage, the accumulation of GS in the seed was accompanied by the salient decline of GS in the corresponding silique wall. Thus, the seed and corresponding silique wall at these two stages were subjected to transcriptomic sequencing analysis. 135 genes related to GS metabolism were identified, of which 24 genes were transcription factors, 81 genes were related to biosynthetic pathway, 25 genes encoded catabolic enzymes, and 5 genes matched with transporters. The expression of GS biosynthetic genes was detected both in seeds and silique walls. The high expression of FMOGS-OX and AOP2, which is related to the production of gluconapin by side modification, was noted in seeds at both stages. Interestingly, the expression of GS biosynthetic genes was higher in the silique wall compared with that in the seed albeit lower content of GS existed in the silique wall than in the seed. Combined with the higher expression of transporter genes GTRs in silique walls than in seeds, it was proposed that the transportation of GS from the silique wall to the seed is an important source for seed GS accumulation. In addition, genes related to GS degradation expressed abundantly in the seed at the early cotyledonary-embryo stage indicating its potential role in balancing seed GS content. Conclusions Two stages including the torpedo-embryo and the early cotyledonary-embryo stage were identified as crucial in GS accumulation during seed development. Moreover, we confirmed the transportation of GS from the silique wall to the seed and proposed possible sidechain modification of GS biosynthesis may exist during seed formation.

Description: Background Drug–drug interactions (DDIs) refer to processes triggered by the administration of two or more drugs leading to side effects beyond those observed when drugs are administered by themselves. Due to the massive number of possible drug pairs, it is nearly impossible to experimentally test all combinations and discover previously unobserved side effects. Therefore, machine learning based methods are being used to address this issue. Methods We propose a Siamese self-attention multi-modal neural network for DDI prediction that integrates multiple drug similarity measures that have been derived from a comparison of drug characteristics including drug targets, pathways and gene expression profiles. Results Our proposed DDI prediction model provides multiple advantages: (1) It is trained end-to-end, overcoming limitations of models composed of multiple separate steps, (2) it offers model explainability via an Attention mechanism for identifying salient input features and (3) it achieves similar or better prediction performance (AUPR scores ranging from 0.77 to 0.92) compared to state-of-the-art DDI models when tested on various benchmark datasets. Novel DDI predictions are further validated using independent data resources. Conclusions We find that a Siamese multi-modal neural network is able to accurately predict DDIs and that an Attention mechanism, typically used in the Natural Language Processing domain, can be beneficially applied to aid in DDI model explainability.

Description: Background Modulating the microbiota is a leading-edge strategy for the restoration and maintenance of a healthy, balanced environment. The use of health-promoting bacteria has demonstrated some potential benefits as an alternative for skin microbiota intervention. Here, we investigate the manipulation of mice skin microbiota using B. subtilis incorporated into a supportive Pluronic F-127 hydrogel formulation. The formula plays an important role in delivering the bacteria to the desired action site. Results The B. subtilis challenge induced a shift in the composition and abundance of the skin microbiota. Containment of B. subtilis in the Pluronic F-127 hydrogel accelerated bacterial modulation compared with free B. subtilis. The abundance of both Staphylococcus and Corynebacterium spp. was altered as a result of the live bacterial intervention: the abundance of Corynebacterium increased while that of Staphylococcus decreased. Four days after last application of the B. subtilis formulation, B. subtilis counts returned to its initial level. Conclusions B. subtilis intervention can induce a shift in the skin microbiota, influencing the abundance of commensal, beneficial, and pathogenic bacteria. Containment of B. subtilis in Pluronic hydrogel accelerates the microbial alteration, probably by facilitating bacterial attachment and supporting continuous growth. Our results reveal the ability of B. subtilis in Pluronic to modulate the skin microbiota composition, suggesting that the formulation holds therapeutic potential for skin disease treatment.

Description: Background Mycotoxins are among the environmental stressors whose oxidative action is currently widely studied. The aim of this paper was to investigate the response of seedling leaves to zearalenone (ZEA) applied to the leaves (directly) and to the grains (indirectly) in tolerant and sensitive wheat cultivars. Results Biochemical analyses of antioxidant activity were performed for chloroplasts and showed a similar decrease in this activity irrespective of plant sensitivity and the way of ZEA application. On the other hand, higher amounts of superoxide radical (microscopic observations) were generated in the leaves of plants grown from the grains incubated in ZEA solution and in the sensitive cultivar. Electron paramagnetic resonance (EPR) studies showed that upon ZEA treatment greater numbers of Mn - aqua complexes were formed in the leaves of the tolerant wheat cultivar than in those of the sensitive one, whereas the degradation of Fe-protein complexes occurred independently of the cultivar sensitivity. Conclusion The changes in the quantity of stable, organic radicals formed by stabilizing reactive oxygen species on biochemical macromolecules, indicated greater potential for their generation in leaf tissues subjected to foliar ZEA treatment. This suggested an important role of these radical species in protective mechanisms mainly against direct toxin action. The way the defense mechanisms were activated depended on the method of the toxin application.

Description: Background Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS. Results In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA. Conclusions Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.

Description: Background Panicle is a harvesting organ of rice, and its morphology and development are closely associated with grain yield. The current study was carried on a mutant screened through an EMS (ethyl-methane sulphonate) mutagenized population of a Japonica cultivar Kitaake (WT). Results A mutant, named as asp-lsl (aberrant spikelet-long sterile lemma), showed a significant decrease in plant height, number of tillers, thousand-grains weight, seed setting rate, spikelet length, kernel length and effective number of grains per panicle as compared to WT. Asp-lsl showed a pleiotropic phenotype coupled with the obvious presence of a long sterile lemma. Cross-sections of lemma showed an increase in the cell volume rather than the number of cells. Genetic segregation analysis revealed its phenotypic trait is controlled by a single recessive nuclear gene. Primary and fine mapping indicated that candidate gene controlling the phenotype of asp-lsl was located in an interval of 212 kb on the short arm of chromosome 8 between RM22445 and RM22453. Further sequencing and indels markers analysis revealed LOC_Os08g06480 harbors a single base substitution (G→A), resulting in a change of 521st amino acid(Gly→Glu. The homology comparison and phylogenetic tree analysis revealed mutation was occurred in a highly conserved domain and had a high degree of similarity in Arabidopsis, corn, and sorghum. The CRISPR/Cas9 mutant line of ASP-LSL produced a similar phenotype as that of asp-lsl. Subcellular localization of ASP-LSL revealed that its protein is localized in the nucleus. Relative expression analysis revealed ASP-LSL was preferentially expressed in panicle, stem, and leaves. The endogenous contents of GA, CTK, and IAA were found significantly decreased in asp-lsl as compared to WT. Conclusions Current study presents the novel phenotype of asp-lsl and also validate the previously reported function of OsREL2 (ROMOSA ENHANCER LOCI2), / ASP1(ABERRANT SPIKELET AND PANICLE 1).

Description: Background Recent advances in sequencing technologies have driven studies identifying the microbiome as a key regulator of overall health and disease in the host. Both 16S amplicon and whole genome shotgun sequencing technologies are currently being used to investigate this relationship, however, the choice of sequencing technology often depends on the nature and experimental design of the study. In principle, the outputs rendered by analysis pipelines are heavily influenced by the data used as input; it is then important to consider that the genomic features produced by different sequencing technologies may emphasize different results. Results In this work, we use public 16S amplicon and whole genome shotgun sequencing (WGS) data from the same dogs to investigate the relationship between sequencing technology and the captured gut metagenomic landscape in dogs. In our analyses, we compare the taxonomic resolution at the species and phyla levels and benchmark 12 classification algorithms in their ability to accurately identify host phenotype using only taxonomic relative abundance information from 16S and WGS datasets with identical study designs. Our best performing model, a random forest trained by the WGS dataset, identified a species (Bacteroides coprocola) that predominantly contributes to the abundance of leuB, a gene involved in branched chain amino acid biosynthesis; a risk factor for glucose intolerance, insulin resistance, and type 2 diabetes. This trend was not conserved when we trained the model using 16S sequencing profiles from the same dogs. Conclusions Our results indicate that WGS sequencing of dog microbiomes detects a greater taxonomic diversity than 16S sequencing of the same dogs at the species level and with respect to four gut-enriched phyla levels. This difference in detection does not significantly impact the performance metrics of machine learning algorithms after down-sampling. Although the important features extracted from our best performing model are not conserved between the two technologies, the important features extracted from either instance indicate the utility of machine learning algorithms in identifying biologically meaningful relationships between the host and microbiome community members. In conclusion, this work provides the first systematic machine learning comparison of dog 16S and WGS microbiomes derived from identical study designs.

Description: Background Aberrant expression of Aldo-Keto reductase family 1 member B10 (AKR1B10) was associated with tumor size and metastasis of breast cancer in our published preliminary studies. However, little is known about the detailed function and underlying molecular mechanism of AKR1B10 in the pathological process of breast cancer. Methods The relationship between elevated AKR1B10 expression and the overall survival and disease-free survival of breast cancer patients was analyzed by Kaplan–Meier Plotter database. Breast cancer cell lines overexpressing AKR1B10 (MCF-7/AKR1B10) and breast cancer cell lines with knockdown of AKR1B10 (BT-20/shAKR1B10) were constructed to analyze the impact of AKR1B10 expression on cell proliferation and migration of breast cancer. The expression levels of AKR1B10 were detected and compared in the breast cancer cell lines and tissues by RT-qPCR, western blot and immunohistochemistry. The proliferation of breast cancer cells was monitored by CCK8 cell proliferation assay, and the migration and invasion of breast cancer cells was observed by cell scratch test and transwell assay. The proliferation- and EMT-related proteins including cyclinD1, c-myc, Survivin, Twist, SNAI1, SLUG, ZEB1, E-cadherin, PI3K, p-PI3K, AKT, p-AKT, IKBα, p-IKBα, NF-κB p65, p-NF-κB p65 were detected by western blot in breast cancer cells. MCF-7/AKR1B10 cells were treated with LY294002, a PI3K inhibitor, to consider the impact of AKR1B10 overexpression on the PI3K/AKT/NF-κB signal cascade and the presence of NF-κB p65 in nuclear. In vivo tumor xenograft experiments were used to observe the role of AKR1B10 in breast cancer growth in mice. Results AKR1B10 expression was significantly greater in breast cancer tissue compared to paired non-cancerous tissue. The expression of AKR1B10 positively correlated with lymph node metastasis, tumor size, Ki67 expression, and p53 expression, but inversely correlated with overall and disease-free survival rates. Gene Ontology analysis showed that AKR1B10 activity contributes to cell proliferation. Overexpression of AKR1B10 facilitated the proliferation of MCF-7 cells, and induced the migration and invasion of MCF-7 cells in vitro in association with induction of epithelial-mesenchymal transition (EMT). Conversely, knockdown of AKR1B10 inhibited these effects in BT-20 cells. Mechanistically, AKR1B10 activated PI3K, AKT, and NF-κB p65, and induced nuclear translocation of NF-κB p65, and expression of proliferation-related proteins including c-myc, cyclinD1, Survivin, and EMT-related proteins including ZEB1, SLUG, Twist, but downregulated E-cadherin expression in MCF-7 cells. AKR1B10 silencing reduced the phosphorylation of PI3K, AKT, and NF-κB p65, the nuclear translocation of NF-κB p65, and the expression of proliferation- and migration-related proteins in BT-20 cells. LY294002, a PI3K inhibitor, attenuated the phosphorylation of PI3K, AKT, and NF-κB p65, and the nuclear translocation of NF-κB p65. In vivo tumor xenograft experiments confirmed that AKR1B10 promoted breast cancer growth in mice. Conclusions AKR1B10 promotes the proliferation, migration and invasion of breast cancer cells via the PI3K/AKT/NF-κB signaling pathway and represents a novel prognostic indicator as well as a potential therapeutic target in breast cancer.

Description: Background To enhance teleconsultation management, demands can be classified into different patterns, and the service of each pattern demand can be improved. Methods For the effective teleconsultation classification, a novel ensemble hierarchical clustering method is proposed in this study. In the proposed method, individual clustering results are first obtained by different hierarchical clustering methods, and then ensembled by one-hot encoding, the calculation and division of cosine similarity, and network graph representation. In the built network graph about the high cosine similarity, the connected demand series can be categorized into one pattern. For verification, 43 teleconsultation demand series are used as sample data, and the efficiency and quality of teleconsultation services are respectively analyzed before and after the demand classification. Results The teleconsultation demands are classified into three categories, erratic, lumpy, and slow. Under the fixed strategies, the service analysis after demand classification reveals the deficiencies of teleconsultation services, but analysis before demand classification can’t. Conclusion The proposed ensemble hierarchical clustering method can effectively category teleconsultation demands, and the effective demand categorization can enhance teleconsultation management.

Description: Aims Moso bamboo expansions into Japanese cedar forests are common. The expansion effects on soil nitrous oxide (N2O) emissions have not been thoroughly understood, and the underlying microbial mechanisms remain unclear. Methods We studied bacterial and fungal contribution to soil N2O emissions under moso bamboo or Japanese cedar by applying bacterial or fungal inhibitors using streptomycin and iprodione, respectively. Soil N2O emissions were measured and the relative contribution of bacteria and fungi to soil N2O emissions was calculated. Important Findings N2O emission from soil with moso bamboo was significantly higher than under Japanese cedar. Compared with control, bacterial or fungal inhibitor or their combination decreased N2O emissions, indicating substantial contribution of microbial activities to N2O emissions. However, the relative contribution of bacteria and fungi to N2O emissions was not affected by plants. Soil organic carbon, total and ammonium nitrogen were lower in soil under moso bamboo than Japanese cedar, suggesting faster microbial decomposition under moso bamboo. Fungal inhibitor and plants interactively affected soil pH, total phosphorus, and ammonium nitrogen, while bacterial inhibitor and plants interactively affected total nitrogen, indicating substantial dependence of effects by microbial communities on plant species. Moso bamboo and Japanese cedar differed in their effects on soil N2O emissions with higher emissions under moso bamboo. Stimulation of N2O emission under moso bamboo might occur due to higher nitrogen mineralization and subsequent denitrification induced by high root exudation. These results highlight the need to consider the effect of species shifts on N2O emissions in forests.

Description: N6-methyladenosine (m6A) is the most abundant form of mRNA modification and controls many aspects of RNA metabolism including gene expression. However, the mechanisms by which m6A regulates cell- and condition-specific gene expression are still poorly understood, partly due to a lack of tools capable of identifying m6A sites that regulate gene expression under different conditions. Here we develop m6A-express, the first algorithm for predicting condition-specific m6A regulation of gene expression (m6A-reg-exp) from limited methylated RNA immunoprecipitation sequencing (MeRIP-seq) data. Comprehensive evaluations of m6A-express using simulated and real data demonstrated its high prediction specificity and sensitivity. When only a few MeRIP-seq samples may be available for the cellular or treatment conditions, m6A-express is particularly more robust than the log-linear model. Using m6A-express, we reported that m6A writers, METTL3 and METTL14, competitively regulate the transcriptional processes by mediating m6A-reg-exp of different genes in Hela cells. In contrast, METTL3 induces different m6A-reg-exp of a distinct group of genes in HepG2 cells to regulate protein functions and stress-related processes. We further uncovered unique m6A-reg-exp patterns in human brain and intestine tissues, which are enriched in organ-specific processes. This study demonstrates the effectiveness of m6A-express in predicting condition-specific m6A-reg-exp and highlights the complex, condition-specific nature of m6A-regulation of gene expression.

Description: The Internal Linear Combination (ILC) method has been extensively used to extract the cosmic microwave background (CMB) anisotropy map from foreground contaminated multi-frequency maps. However, the performance of simple ILC is limited and can be significantly improved by heavily constraint equations, dubbed constrained ILC (cILC). The standard ILC and cILC works on spin-0 fields. Recently, a generalised version of ILC has been developed, named Polarization ILC (PILC), in which Q ± iU at multiple frequencies are combined using complex coefficients to estimate Stokes Q and U maps. A statistical moment expansion method has recently been developed for high precision modelling of the Galactic foregrounds. This paper develops a semi-blind component separation method combining the moment approach of foreground modelling with a generalised version of the PILC method for heavily constraint equations. The algorithm is developed in pixel space over a spin-2 field. We demonstrate the performance of the method on three sets of absolutely calibrated simulated maps at WMAP and Planck frequencies with varying foreground models. We apply this component separation technique in simultaneous estimation of Stokes Q and U maps of the thermal dust at 353 GHz and synchrotron at 30 GHz. We also recover both dust and synchrotron maps at 100 and 143 GHz, where separating two components is challenging.

Description: As the robustness for the wave equation-based inversion methods, wave equation migration velocity analysis (WEMVA) is stable for overcoming the multipathing problem and has become popular in recent years. As a rapidly developed method, differential semblance optimisation (DSO) is convenient to implement and can automatically detect the moveout existing in common image gathers (CIGs). However, by implementing in the image domain with the target of minimising moveouts and improving coherence of the CIGs, the DSO method often suffers from imaging artefacts caused by uneven illumination and irregular observation geometry, which may produce poor velocity updates with artefact contamination. To deal with this issue, in this paper, by introducing Wiener-like filters, we modify the conventional image matching-based objective function to a new one by introducing the quadratic Wasserstein metric technique. The new misfit function measures the distance of two distributions obtained by the convolutional filters and target functions. With the new misfit function, the adjoint sources and the corresponding gradients are improved. We apply the new method to two numerical examples and one field dataset. The corresponding results indicate that the new method is robust to compensate low frequency components of velocity models.

Description: Background The plant body in duckweed species has undergone reduction and simplification from the ancient Spirodela species towards more derived Wolffia species. Among the five duckweed genera, Wolffia members are rootless and represent the smallest and most reduced species. A better understanding of Wolffia frond architecture is necessary to fully explore duckweed evolution. Results We conducted a comprehensive study of the morphology and anatomy of Wolffia globosa, the only Wolffia species in China. We first used X-ray microtomography imaging to reveal the three-dimensional and internal structure of the W. globosa frond. This showed that new fronds rapidly budded from the hollow reproductive pocket of the mother fronds and that several generations at various developmental stages could coexist in a single W. globosa frond. Using light microscopy, we observed that the meristem area of the W. globosa frond was located at the base of the reproductive pocket and composed of undifferentiated cells that continued to produce new buds. A single epidermal layer surrounded the W. globosa frond, and the mesophyll cells varied from small and dense palisade-like parenchyma cells to large, vacuolated cells from the ventral to the dorsal part. Furthermore, W. globosa fronds contained all the same organelles as other angiosperms; the most prominent organelles were chloroplasts with abundant starch grains. Conclusions Our study revealed that the reproductive strategy of W. globosa plants enables the rapid accumulation of biomass and the wide distribution of this species in various habitats. The reduced body plan and size of Wolffia are consistent with our observation that relatively few cell types are present in these plants. We also propose that W. globosa plants are not only suitable for the study of structural reduction in higher plants, but also an ideal system to explore fundamental developmental processes of higher plants that cannot be addressed using other model plants.

Description: Background Structural variants (SVs) significantly drive genome diversity and environmental adaptation for diverse species. Unlike the prevalent small SVs (〈 kilobase-scale) in higher eukaryotes, large-size SVs rarely exist in the genome, but they function as one of the key evolutionary forces for speciation and adaptation. Results In this study, we discover and characterize several megabase-scale presence-absence variations (PAVs) in the maize genome. Surprisingly, we identify a 3.2 Mb PAV fragment that shows high integrity and is present as complete presence or absence in the natural diversity panel. This PAV is embedded within the nucleolus organizer region (NOR), where the suppressed recombination is found to maintain the PAV against the evolutionary variation. Interestingly, by analyzing the sequence of this PAV, we not only reveal the domestication trace from teosinte to modern maize, but also the footprints of its origin from Tripsacum, shedding light on a previously unknown contribution from Tripsacum to the speciation of Zea species. The functional consequence of the Tripsacum segment migration is also investigated, and environmental fitness conferred by the PAV may explain the whole segment as a selection target during maize domestication and improvement. Conclusions These findings provide a novel perspective that Tripsacum contributes to Zea speciation, and also instantiate a strategy for evolutionary and functional analysis of the “fossil” structure variations during genome evolution and speciation.

Description: Luminous active galactic nuclei and X-ray binaries often contain geometrically thin, radiatively cooled accretion discs. According to theory, these are – in many cases – initially highly misaligned with the black hole equator. In this work, we present the first general relativistic magnetohydrodynamic simulations of very thin (h/r ∼ 0.015–0.05) accretion discs around rapidly spinning (a ∼ 0.9) black holes and tilted by 45°–65°. We show that the inner regions of the discs with h/r ≲ 0.03 align with the black hole equator, though out to smaller radii than predicted by analytic work. The inner aligned and outer misaligned disc regions are separated by a sharp break in tilt angle accompanied by a sharp drop in density. We find that frame dragging by the spinning black hole overpowers the disc viscosity, which is self-consistently produced by magnetized turbulence, tearing the disc apart and forming a rapidly precessing inner sub-disc surrounded by a slowly precessing outer sub-disc. We find that the system produces a pair of relativistic jets for all initial tilt values. At small distances, the black hole launched jets precess rapidly together with the inner sub-disc, whereas at large distances they partially align with the outer sub-disc and precess more slowly. If the tearing radius can be modeled accurately in future work, emission model independent measurements of black hole spin based on precession-driven quasi-periodic oscillations may become possible.

Description: Atlantic salmon (Salmo salar) populations throughout the North Atlantic have declined in recent decades largely due to reduced marine survival, yet our understanding of marine distribution patterns and migratory routes remains limited. Here, we assigned archived individual samples (n = 3891) collected over a half century (1968–2018) throughout the North Atlantic to region of origin using range-wide genetic assignment. In the Northwest Atlantic, the distribution of assignments reinforced the importance of the Labrador Sea as an aggregation area, with 73% of all reporting groups detected. Moreover, individuals from six European reporting groups were identified in the Northwest Atlantic, and detections decreased with decreasing latitude spanning an area from Greenland to southern Newfoundland. In the Northeast Atlantic, six North American reporting groups were detected in samples from around the Faroe Islands. Based on the distribution of samples, estimates of trans-Atlantic migration distance averaged 3861 and 2889 km for North American and European salmon respectively. Our analysis highlights the widespread importance of the Labrador Sea and Faroe Islands to the species marine distribution patterns, and the prevalence of long-distance trans-Atlantic migration. Ultimately, the results suggest that environmental conditions experienced by many Atlantic salmon populations span much of the North Atlantic Ocean.

Description: Application of machine and deep learning methods in drug discovery and cancer research has gained a considerable amount of attention in the past years. As the field grows, it becomes crucial to systematically evaluate the performance of novel computational solutions in relation to established techniques. To this end, we compare rule-based and data-driven molecular representations in prediction of drug combination sensitivity and drug synergy scores using standardized results of 14 high-throughput screening studies, comprising 64 200 unique combinations of 4153 molecules tested in 112 cancer cell lines. We evaluate the clustering performance of molecular representations and quantify their similarity by adapting the Centered Kernel Alignment metric. Our work demonstrates that to identify an optimal molecular representation type, it is necessary to supplement quantitative benchmark results with qualitative considerations, such as model interpretability and robustness, which may vary between and throughout preclinical drug development projects.

Description: Motivation The investigation of quantitative trait loci (QTL) is an essential component in our understanding of how organisms vary phenotypically. However, many important crop species are polyploid (carrying more than two copies of each chromosome), requiring specialized tools for such analyses. Moreover, deciphering meiotic processes at higher ploidy levels is not straightforward, but is necessary to understand the reproductive dynamics of these species, or uncover potential barriers to their genetic improvement. Results Here, we present polyqtlR, a novel software tool to facilitate such analyses in (auto)polyploid crops. It performs QTL interval mapping in F1 populations of outcrossing polyploids of any ploidy level using identity-by-descent probabilities. The allelic composition of discovered QTL can be explored, enabling favourable alleles to be identified and tracked in the population. Visualization tools within the package facilitate this process, and options to include genetic co-factors and experimental factors are included. Detailed information on polyploid meiosis including prediction of multivalent pairing structures, detection of preferential chromosomal pairing and location of double reduction events can be performed. Availabilityand implementation polyqtlR is freely available from the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/package=polyqtlR. Supplementary information Supplementary data are available at Bioinformatics online.

Description: Circular RNAs (circRNAs) are widely expressed in highly diverged eukaryotes. Although circRNAs have been known for many years, their function remains unclear. Interaction with RNA-binding protein (RBP) to influence post-transcriptional regulation is considered to be an important pathway for circRNA function, such as acting as an oncogenic RBP sponge to inhibit cancer. In this study, we design a deep learning framework, CRPBsites, to predict the binding sites of RBPs on circRNAs. In this model, the sequences of variable-length binding sites are transformed into embedding vectors by word2vec model. Bidirectional LSTM is used to encode the embedding vectors of binding sites, and then they are fed into another LSTM decoder for decoding and classification tasks. To train and test the model, we construct four datasets that contain sequences of variable-length binding sites on circRNAs, and each set corresponds to an RBP, which is overexpressed in bladder cancer tissues. Experimental results on four datasets and comparison with other existing models show that CRPBsites has superior performance. Afterwards, we found that there were highly similar binding motifs in the four binding site datasets. Finally, we applied well-trained CRPBsites to identify the binding sites of IGF2BP1 on circCDYL, and the results proved the effectiveness of this method. In conclusion, CRPBsites is an effective prediction model for circRNA-RBP interaction site identification. We hope that CRPBsites can provide valuable guidance for experimental studies on the influence of circRNA on post-transcriptional regulation.

Description: Intratumoral heterogeneity is a well-documented feature of human cancers and is associated with outcome and treatment resistance. However, a heterogeneous tumor transcriptome contributes an unknown level of variability to analyses of differentially expressed genes (DEGs) that may contribute to phenotypes of interest, including treatment response. Although current clinical practice and the vast majority of research studies use a single sample from each patient, decreasing costs of sequencing technologies and computing power have made repeated-measures analyses increasingly economical. Repeatedly sampling the same tumor increases the statistical power of DEG analysis, which is indispensable toward downstream analysis and also increases one’s understanding of within-tumor variance, which may affect conclusions. Here, we compared five different methods for analyzing gene expression profiles derived from repeated sampling of human prostate tumors in two separate cohorts of patients. We also benchmarked the sensitivity of generalized linear models to linear mixed models for identifying DEGs contributing to relevant prostate cancer pathways based on a ground-truth model.

Description: Single-molecule (particle) tracking is a powerful method to study dynamic processes in cells at highest possible spatial and temporal resolution. We have developed SMTracker, a graphical user interface for automatic quantifying, visualizing and managing of data. Version 2.0 determines distributions of positional displacements in x- and y-direction using multi-state diffusion models, discriminates between Brownian, sub- or superdiffusive behaviour, and locates slow or fast diffusing populations in a standardized cell. Using SMTracker, we show that the Bacillus subtilis RNA degradosome consists of a highly dynamic complex of RNase Y and binding partners. We found similar changes in molecule dynamics for RNase Y, CshA, PNPase and enolase, but not for phosphofructokinase, RNase J1 and J2, to inhibition of transcription. However, the absence of PfkA or of RNase J2 affected molecule dynamics of RNase Y-mVenus, indicating that these two proteins are indeed part of the degradosome. Molecule counting suggests that RNase Y is present as a dimer in cells, at an average copy number of about 500, of which 46% are present in a slow-diffusive state and thus likely engaged within degradosomes. Thus, RNase Y, CshA, PNPase and enolase likely play central roles, and RNase J1, J2 and PfkA more peripheral roles, in degradosome architecture.

Description: Academic human capital (AHC) is a key element in the explanation of scientific productivity. However, few studies have analysed this topic in the academic context, and their conclusions about composition and measurement remain ambiguous. This study proposes a measurement scale to assess AHC, following a systemic procedure composed of two steps: qualitative and quantitative phases. First, the Delphi technique was applied to reach a consensus on the AHC factors, resulting in a scale of 22 items. Second, exploratory and confirmatory factor analyses were conducted to determine the underlying factorial structure of the scale, using a sample of 2,223 researchers in Spanish universities. The results provided a five-dimensional structure of AHC, measuring the knowledge and abilities required to perform research activities, as well as skills related to the organisation of scientific processes, alertness to research opportunities, and the openness to provide and receive criticism. This study poses interesting challenges for knowledge management in universities.

Description: Efforts to elucidate protein–DNA interactions at the molecular level rely in part on accurate predictions of DNA-binding residues in protein sequences. While there are over a dozen computational predictors of the DNA-binding residues, they are DNA-type agnostic and significantly cross-predict residues that interact with other ligands as DNA binding. We leverage a custom-designed machine learning architecture to introduce DNAgenie, first-of-its-kind predictor of residues that interact with A-DNA, B-DNA and single-stranded DNA. DNAgenie uses a comprehensive physiochemical profile extracted from an input protein sequence and implements a two-step refinement process to provide accurate predictions and to minimize the cross-predictions. Comparative tests on an independent test dataset demonstrate that DNAgenie outperforms the current methods that we adapt to predict residue-level interactions with the three DNA types. Further analysis finds that the use of the second (refinement) step leads to a substantial reduction in the cross predictions. Empirical tests show that DNAgenie’s outputs that are converted to coarse-grained protein-level predictions compare favorably against recent tools that predict which DNA-binding proteins interact with double-stranded versus single-stranded DNAs. Moreover, predictions from the sequences of the whole human proteome reveal that the results produced by DNAgenie substantially overlap with the known DNA-binding proteins while also including promising leads for several hundred previously unknown putative DNA binders. These results suggest that DNAgenie is a valuable tool for the sequence-based characterization of protein functions. The DNAgenie’s webserver is available at http://biomine.cs.vcu.edu/servers/DNAgenie/.

Description: Accurate prediction of immunogenic peptide recognized by T cell receptor (TCR) can greatly benefit vaccine development and cancer immunotherapy. However, identifying immunogenic peptides accurately is still a huge challenge. Most of the antigen peptides predicted in silico fail to elicit immune responses in vivo without considering TCR as a key factor. This inevitably causes costly and time-consuming experimental validation test for predicted antigens. Therefore, it is necessary to develop novel computational methods for precisely and effectively predicting immunogenic peptide recognized by TCR. Here, we described DLpTCR, a multimodal ensemble deep learning framework for predicting the likelihood of interaction between single/paired chain(s) of TCR and peptide presented by major histocompatibility complex molecules. To investigate the generality and robustness of the proposed model, COVID-19 data and IEDB data were constructed for independent evaluation. The DLpTCR model exhibited high predictive power with area under the curve up to 0.91 on COVID-19 data while predicting the interaction between peptide and single TCR chain. Additionally, the DLpTCR model achieved the overall accuracy of 81.03% on IEDB data while predicting the interaction between peptide and paired TCR chains. The results demonstrate that DLpTCR has the ability to learn general interaction rules and generalize to antigen peptide recognition by TCR. A user-friendly webserver is available at http://jianglab.org.cn/DLpTCR/. Additionally, a stand-alone software package that can be downloaded from https://github.com/jiangBiolab/DLpTCR.

Description: Unlike other developed countries, the Fourth Industrial Revolution (4IR) discourse has become the central element within technology governance in Korea. This paper examines the reasons for the discourse’s success and its political and social implications. Based on the analysis of policy documents and the media coverage, I argue that political and economic elites have actively introduced the 4IR discourse to create novel momentum for promoting Information and Communications Technology (ICT) and to justify deregulatory measures while re-enacting the developmentalist imaginary. I also highlight that the 4IR discourse’s promoters have drawn upon the dialectics between the desirable future and the nation’s shared fear to urge the Korean society to accept the measures privileging the industry as the means of making the nation a developed country and avoiding being colonized again.

Description: We present the second part of results of the ongoing project aimed at searching for and studying eXtremely Metal-Poor (XMP) – adopted as those with Zgas ≲ Z⊙/30, or with 12+log (O/H) ≲ 7.21 dex − very gas-rich blue dwarfs in voids. They were first identified in the course of the ‘unbiased’ study of the galaxy population in the nearby Lynx–Cancer void. These very rare and unusual galaxies seem to be the best proxies of so-called Very Young Galaxies (VYGs) defined recently in model simulations by Tweed et al. To date, for 16 pre-selected void XMP candidates, using the Big Telescope Alt-azimuth (BTA), the SAO 6-m telescope, we have obtained spectra suitable for the determination of O/H. For majority of the observed galaxies, the principal line [O iii] λ4363 , used for the direct classical Te method of O/H determination, is undetected. Therefore, to estimate O/H, we use a new ‘strong-lines’ method by Izotov et al. This appears to be the most accurate empirical O/H estimator for the range of 12+log (O/H) ≲ 7.4–7.5. For objects with higher O/H, we use the semi-empirical method by Izotov & Thuan with our modification accounting for variance of the excitation parameter O32. Six of those 16 candidates are found, with confidence, to be XMP dwarfs. In addition, eight studied galaxies are less metal-poor, with 12+log (O/H) = 7.24–7.33, and these can also fall into the category of VYG candidates. Taking into account our recently published work and the previously known (nine prototype galaxies) XMP gas-rich void objects, the new findings increase the number of this type of galaxy known to date to a total of 19.

Description: Glioblastoma (GB) is the most aggressive and common form of primary brain tumor characterized by fast proliferation, high invasion and resistance to current standard treatment. The average survival rate post-diagnosis is 14.6 months, despite the aggressive standard post-surgery radiotherapy concomitant with chemotherapy with temozolomide (TMZ). Currently, efforts are being endowed to develop new and more efficient therapeutic approaches capable to overcome chemoresistance, inhibit tumor progression and improve overall patient survival rate. Abnormal microRNA (miRNA) expression has been correlated with chemoresistance, proliferation and resistance to apoptosis, which result from their master regulatory role of gene expression. Altered cell metabolism, favoring glycolysis, was identified as an emerging cancer hallmark and has been described in GB, thus offering a new target for innovative GB therapies. In this work, we hypothesized that a gene therapy-based strategy consisting of the overexpression of a miRNA downregulated in GB and predicted to target crucial metabolic enzymes might promote a shift of GB cell metabolism, decreasing the glycolytic dependence of tumor cells and contributing to their sensitization to chemotherapy with TMZ. The increase of miR-200c levels in DBTRG cells resulted in downregulation of messenger RNA of enzymes involved in bioenergetics pathways and impaired cell metabolism and mobility. In addition, miR-200c overexpression prior to DBTRG cell exposure to TMZ resulted in cell cycle arrest. Overall, our results show that miR-200c overexpression could offer a way to overcome chemoresistance developed by GB cells in response to current standard chemotherapy, providing an improvement to current GB standard treatment, with benefit for patient outcome.

Description: The availability of nitrogen (N) in ocean surface waters affects rates of photosynthesis and marine ecosystem structure. In spite of low dissolved inorganic N concentrations, export production in oligotrophic waters is comparable to more nutrient replete regions. Prior observations raise the possibility that di-nitrogen (N2) fixation supplies a significant fraction of N supporting export production in the Gulf of Mexico. In this study, geochemical tools were used to quantify the relative and absolute importance of both subsurface nitrate and N2 fixation as sources of new N fueling export production in the oligotrophic Gulf of Mexico in May 2017 and May 2018. Comparing the isotopic composition (“δ15N”) of nitrate with the δ15N of sinking particulate N collected during five sediment trap deployments each lasting two to four days indicates that N2 fixation is typically not detected and that the majority (≥80%) of export production is supported by subsurface nitrate. Moreover, no gradients in upper ocean dissolved organic N and suspended particulate N concentration and/or δ15N were found that would indicate significant N2 fixation fluxes accumulated in these pools, consistent with low Trichodesmium spp. abundance. Finally, comparing the δ15N of sinking particulate N captured within vs. below the euphotic zone indicates that during late spring regenerated N is low in δ15N compared to sinking N.

Description: Heterotrophic protists are essential components of the marine ecosystem, yet they are often excluded from monitoring programmes. With limited resources, monitoring strategies need to be optimised considering both scientific knowledge and available resources. In doing so, it is crucial to understand how sampling frequency affects the value of the data. We analysed 11 years of weekly heterotrophic protist time-series data from Station L4 in the Western English Channel to explore how different sampling intervals impact data quality. In the L4 dataset, comprising 55 protist taxa, the reduction of sampling frequency from weekly to four times a year at specific seasons decreased the number of taxa encountered by 38% for ciliates and 29% for heterotrophic dinoflagellates while the mean annual biomass or its mean variation were not affected. Furthermore, when samples were taken only four times a year, biomass peaks of the ten most important taxa were often missed. The primary motivator for this study was furthering the development of the heterotrophic protist monitoring in temperate and subarctic marine areas, e.g. the Baltic Sea. Based on our findings, we give recommendations on sampling frequency to optimise the value of heterotrophic protist monitoring.

Description: The Lafaye orbicular body was emplaced in the Villatange tonalite-granodiorite unit of the Guéret magmatic complex (Massif Central, France). It consists of plagioclasic orbicules (4–35 cm diameter) embedded in homogeneous cordierite granodiorite. Orbicule cores consist mostly of residual metasedimentary xenoliths or autolithic plagioclasic cumulates. Rims (0.7–8 cm thickness) are single- or multi-layered; layers, mostly comb-textured, comprise alternating sheets dominated by cordierite (XFe = 0.32–0.37) or plagioclase (mostly An25–30). Additional mineral phases are minor biotite (XFe = 0.52; AlVI = 0.58–0.92 atoms per formula unit) and interstitial quartz. Plagioclase and cordierite morphologies (needle-like, skeletal, branching or fan-shaped) indicate growth under high initial supersaturation. However, the final polyhedral shapes and primary zoning of many individual plagioclase crystals, as well as evidence of partial recrystallization, imply significant textural maturation. Whole-rock major and trace element data (A/CNK = 1.12–1.46) and Sr and Nd isotopic compositions (εNd(355 Ma)  = −8.6 to −7.4; 87Sr/86Sr(355 Ma) = 0.7110–0.7147) suggest that the parental magma of the orbicules resulted from bulk assimilation of aluminous metasediments by a Villatange-type granodioritic magma. Heterogeneous nucleation and growth of plagioclase and cordierite around xenoliths/autoliths are interpreted in terms of (1) adiabatic decompression of magma pulses ascending in dykes leading to superheating and resorption of early solids, and (2) volatile exsolution, inducing undercooling, supersaturation, and rim crystallization. The variability of layers (number, thickness, mineral distribution, and texture) is considered to result from oscillatory crystallization combined with variable plagioclase growth rates linked to changes in the degree of supersaturation as a function of the extent of melt degassing, itself linked to magma transfer dynamics.

Description: La Réunion Island includes two major volcanic systems. About 0·5 Myr ago, Piton des Neiges volcano declined, while Piton de la Fournaise volcano grew on its flank. Since then the Piton de la Fournaise shield volcano has produced homogeneous lavas with chemical compositions transitional between alkali and tholeiitic basalts. In April 2007, the volcano emitted a very small volume of trachytic pumice during its largest historical eruption. We conducted a comprehensive petrological and geochemical study of the pumice to understand the occurrence of such silicic melt in the feeding system of this highly active basaltic volcano. Isotopes of Sr, Nd, Pb and O, together with trace elements, indicate that the trachyte is genetically related to the La Réunion mantle plume and derives from crystallization of a typical basalt. The trachyte chemistry records a long and complex history of differentiation and outgassing. The extensive depletion of moderately volatile elements (F, Cl, B, Cs, Cu, Li) and less volatile uranium is consistent with exsolution of dense fluids at depths of several kilometres. Lithium isotopes point to closed-system degassing during the very late stages of crystallization. U-series isotopes and radiogenic 208Pb*/206Pb* constrain the age of U loss to between 0·4 and 2·1 Ma. This age is as old as or older than the Piton de la Fournaise shield edifice. The 2007 trachyte could thus be a liquid remnant of an extinct volcano, such as Piton des Neiges or Les Alizés (Piton de la Fournaise proto-volcano). It could also result from partial melting of an old syenite intrusion or remobilization of interstitial melts not fully solidified. Thermal modelling indicates that the sustained heat flux from hot basaltic magmas rising from the mantle can maintain temperatures above 800 °C in the central feeding system, and prevent total solidification of magmas trapped in this hot core.

Description: Motivation The investigation of the structure of biological systems at the molecular level gives insights about their functions and dynamics. Shape and surface of biomolecules are fundamental to molecular recognition events. Characterizing their geometry can lead to more adequate predictions of their interactions. In the present work, we assess the performance of reference shape retrieval methods from the computer vision community on protein shapes. Results Shape retrieval methods are efficient in identifying orthologous proteins and tracking large conformational changes. This work illustrates the interest for the protein surface shape as a higher-level representation of the protein structure that (i) abstracts the underlying protein sequence, structure or fold, (ii) allows the use of shape retrieval methods to screen large databases of protein structures to identify surficial homologs and possible interacting partners and (iii) opens an extension of the protein structure–function paradigm toward a protein structure-surface(s)-function paradigm. Availabilityand implementation All data are available online at http://datasetmachat.drugdesign.fr. Supplementary information Supplementary data are available at Bioinformatics online.

Description: Fisheries management is usually supported by technical and financial measurements (i.e. logbooks and market data), which are helpful for ecological or economic assessments. Yet this information is not able to address social heterogeneity and fisher motivations, which are key to understanding fisher behaviour. This case study of the demersal segment in the Netherlands shows that combining quantitative analysis of logbooks with qualitative data collected by engaging with fishers can capture both fishing activity and its motivations, generating a more social understanding of fisher behaviour. A métier analysis of logbook data describes five dominant fishing practices among the selected segment. Twenty-five in-depth interviews with fishers along with focus groups including other experts identify three social factors that influence fisher behaviour in the Dutch demersal fleet: business structure, working rhythm, and polyvalence. The results show that motivations for fisher behaviour are more complex than complying with regulations or seeking profit: social factors also influence fishing activity. Furthermore, these social factors have real implications for the impacts of management measures on both the fishing communities and the environment, especially in times of change. These results are useful for management strategy development or evaluation because they are feasibly observable through existing data collection protocols.

Description: Harbour seals are surveyed aerially when they haul-out to moult in August. The proportion of the population hauled out throughout the year is related to temporal, environmental, and meteorological variables. Thus, monitoring is conducted under predefined ranges of conditions. Effects of variation within these ranges are rarely reviewed. We used linear models to assess effects of time, date and weather on the difference between counts predicted by a population growth model and observed counts, based on a 30-year time-series. Our top-ranked model explained 34.4% of the variance. Survey date and its interaction with survey year were the most important variables, with higher counts earlier in August, particularly early in the time series, where surveys may not have been timed optimally to capture the peak in the moult. Cloud cover, wind speed, temperature, and interactions between these were of lesser importance; there were fewer seals on land during cloudy, windy days and on clear, warm days. These effects of weather are likely related to temperature regulation. Power analyses suggested that correction for survey conditions would allow detection of a one percentage point annual change in population growth rate with 80% power 4 years sooner than without taking survey conditions into account.

Description: Sargassum forests play an important role in coastal waters as habitats for marine organisms, including commercial species. However, human activities have negatively affected their distribution causing a worldwide decline of Sargassum forests. Mapping and monitoring the distribution and biomass of these habitats using acoustic remote sensing techniques is key for their conservation. Nonetheless, most researches based on acoustic remote sensing methods focus on estimations of macrophyte area and its canopy height, and less researches reporting 3D visualization of these habitats. This study demonstrates the use of high-resolution multibeam echosounder (MBES) bathymetric data to visualize the 3D structure of Sargassum forests. Comparing acoustic data and underwater camera photos collected in field surveys, we identified Sargassum individuals as vertical clusters of contiguous sounding points with a base close to the sea bottom in the sounding data of the MBES. Using this criterion, we could distinguish Sargassum echoes, visualize the 3D structure of Sargassum forests and estimate the number of Sargassum individuals in the survey area. Using the relation between thallus length and dry weight of sampled Sargassum plants, standing stock and biomass could be estimated assuming the thallus length was the height of Sargassum plants identified with the MBES.

Description: This paper reviews application of the Daily Egg Production Method (DEPM) to sardine (Sardinops sagax) off southern Australia between 1995 and 2019. Coefficients of variation (CVs) of estimates of spawning biomass (SB) were reduced from 23–59% to 8–12% by: (i) estimating mean daily egg production (P0), spawning fraction (S), and sex ratio (R) from all historical data rather than annually; and (ii) combining batch fecundity (F) and female weight (W) into a single parameter, relative fecundity (F′ = F^/W). Total daily egg production was estimated most precisely from annual estimates of spawning area (A) and estimates of P0 obtained from historical data. Both S and R were estimated most precisely from historical data. Estimating W and F from historical data did not increase precision. F′ had lower CVs than both W and F, and was stable across years and a wide range of W. Findings demonstrate that A can be converted into a precise estimates of SB using estimates of P0, S, R, and F′ obtained from historical data. However, the possibility that DEPM parameters may change in the future cannot be discounted. Future monitoring should include annual estimation of P0 and periodic (e.g. 3–5 years) re-estimation of adult parameters.

Description: In his 1953 paper, Harald Sverdrup argued that the development of a spring bloom in the ocean depends on the juxtaposition of two depth horizons: the mixed-layer depth and the critical depth. Mixed-layer depth shallower than the critical depth favours phytoplankton growth in the layer and vice versa. However, mathematically, Sverdrup left the problem unsolved in the form of a transcendental equation. In spite of the high number of citations that this paper has garnered, the solution to this equation has not been found, until now. In this work, we present an analytical solution for the critical depth, as originally defined by Sverdrup. The paper opens with the definition of the critical depth and the description of the Lambert W function. The analytical solution for critical depth follows. Sverdrup’s original model is extended to include the effect of light attenuation by phytoplankton and the analytical solution for steady-state biomass in the mixed layer is derived. The expression for mixed-layer production at steady state is also presented. Two novel variants of the critical depth are defined: the optically uncoupled critical depth and the optically coupled critical depth. It is demonstrated that at steady state the optically coupled critical depth equals the mixed-layer depth and that the irradiance at the base of the mixed layer equals the irradiance at the optically uncoupled critical depth. Competitive exclusion is demonstrated to hold and the optically uncoupled critical depth is linked to the critical light intensity in multi-species competition. Finally, a conservation principle for the critical depth is found.

Description: Fishery bycatch poses a serious threat to seabird populations globally. Traditional haul-only post-capture observations are inadequate and inefficient to document seabird bycatch due to the substantial bycatch loss known to occur. Pre-capture observations offer an alternative by documenting seabird interactions leading up to captures. Based on the long-term large-scale dedicated field observations, this study revealed significant risk factors for the pre-capture stages of the seabird bycatch process in pelagic longline fisheries using Bayesian methods. Rough sea conditions were found to correlate with more seabirds following fishing vessels. Species identity, density effect, inter-species effect, and sea condition were found to significantly affect how frequently seabirds aggregated around a fishing vessel engage in bait-taking interactions. Intra-species competition was found to be the dominant type of density effect. Moreover, a web of inter-species interactions was identified to facilitate the bait-taking of superior competitors at the expense of inferior ones. The findings of this study are relevant to fishery managers in updating current data collection protocols to alleviate data issues caused by bycatch loss, to conservation biologists in quantifying bycatch risks for susceptible seabird populations, and in aiding the design and evaluation of bycatch mitigation measures.

Description: Fishing and translocation of marine species for use in aquaculture is widespread. Corkwing, goldsinny, and ballan wrasse (Symphodus melops, Ctenolabrus rupestris, and Labrus bergylta) are fished on the Swedish west coast for use as cleaner-fish in Norwegian salmon farms. Here, we aim to provide knowledge and recommendations to support ecosystem-based management for wrasse fisheries in Sweden. We compared fished and non-fished areas to test if current fishery levels have led to stock depletion. To gain insight on the role of wrasse in the algal belt trophic chain, we analysed the gut contents of goldsinny and corkwing using metabarcoding. Finally, we analysed the trophic interactions of wrasse and potential prey in a mesocosm study. We could not detect any signs of stock depletion or altered size structure in fished areas compared to the protected control area. Gut analyses confirmed both goldsinny and corkwing as non-specialized, omnivorous opportunists and revealed, with 189 prey taxa detected, a broader spectrum of prey than previously known. Common prey items included mesoherbivores such as small gastropods and crustaceans, but also insects and algae. We conclude that there are no visible signs of stock depletion at the current removal level of wrasses by the fishery. However, this emerging fishery should be closely monitored for potential cascading effects on the algal belt ecosystem, and our study could provide a baseline for future monitoring.

Description: In this era of big data, breeding programs are producing ever larger amounts of data. This necessitates access to efficient management systems to keep track of cross, performance, pedigree, geographical and image-based data, as well as genotyping data. In this article, we report the progress on the Breeding Information Management System (BIMS), a free, secure and online breeding management system that allows breeders to store, manage, archive and analyze their private breeding data. BIMS is the first publicly available database system that enables individual breeders to integrate their private phenotypic and genotypic data with public data and, at the same time, have complete control of their own breeding data along with access to tools such as data import/export, data analysis and data archiving. The integration of breeding data with publicly available genomic and genetic data enhances genetic understanding of important traits and maximizes the marker-assisted breeding utility for breeders and allied scientists. BIMS incorporates the use of the Android App Field Book, open-source phenotype data collection software for phones and tablets that allows breeders to replace hard copy field books, thus alleviating the possibility of transcription errors while providing faster access to the collected data. BIMS comes with training materials and support for individual or small group training and is currently implemented in the Genome Database for Rosaceae, CottonGEN, the Citrus Genome Database, the Pulse Crop Database, and the Genome Database for Vaccinium. Database URLs: (https://www.rosaceae.org/), (https://www.cottongen.org/), (https://www.citrusgenomedb.org/), (https://www.pulsedb.org/) and (https://www.vaccinium.org/)

Description: Contactin 4 (CNTN4) is a crucial synaptic adhesion protein that belongs to the contactin superfamily. Evidence from both human genetics and mouse models suggests that synapse formation and structural deficits strongly correlate with neurodevelopmental disorders, including autism. In addition, several lines of evidence suggest that CNTN4 is associated with the risk of autism. However, the biological functions of CNTN4 in neural development and disease pathogenesis are poorly understood. In this study, we investigated whether and how CNTN4 is autonomously involved in the development of dendrites and dendritic spines in cortical neurons. Disruption of Cntn4 decreased the number of excitatory synapses, which led to a reduction in neural activity. Truncated proteins lacking the signal peptide, FnIII domains, or GPI domain lacked the ability to regulate dendritic spine formation, indicating that CNTN4 regulates dendritic spine density through a mechanism dependent on FnIII domains. Importantly, we revealed that autism-related variants lacked the ability to regulate spine density and neural activity. In conclusion, our study suggests that CNTN4 is essential for promoting dendrite growth and dendritic spine formation and that disruptive variants of CNTN4 interfere with abnormal synapse formation and may increase the risk of autism.

Description: This paper explores methods for constructing low multipole temperature and polarization likelihoods from maps of the cosmic microwave background anisotropies that have complex noise properties and partial sky coverage. We use Planck 2018 High Frequency Instrument (HFI) and updated SRoll2 temperature and polarization maps to test our methods. We present three likelihood approximations based on quadratic cross spectrum estimators: (i) a variant of the simulation-based likelihood (SimBaL) techniques used in the Planck legacy papers to produce a low multipole EE likelihood; (ii) a semi-analytical likelihood approximation (momento) based on the principle of maximum entropy; (iii) a density-estimation ‘likelihood-free’ scheme (delfi). Approaches (ii) and (iii) can be generalized to produce low multipole joint temperature-polarization (TTTEEE) likelihoods. We present extensive tests of these methods on simulations with realistic correlated noise. We then analyse the Planck data and confirm the robustness of our method and likelihoods on multiple inter- and intra-frequency detector set combinations of SRoll2 maps. The three likelihood techniques give consistent results and support a low value of the optical depth to reoinization, τ, from the HFI. Our best estimate of τ comes from combining the low multipole SRoll2momento (TTTEEE) likelihood with the CamSpec high multipole likelihood and is $au = 0.0627^{+0.0050}_{-0.0058}$. This is consistent with the SRoll2 team’s determination of τ, though slightly higher by ∼0.5σ, mainly because of our joint treatment of temperature and polarization.

Description: X-ray flares in gamma-ray bursts (GRBs) are believed to be generated by the late activities of central engine, and thus provide an useful tool to diagnose the properties of central objects. In this paper, we work on a GRB X-ray flare sample whose bulk Lorentz factors are constrained by two different methods and the jet opening angles are determined by the jet breaks in afterglow light curves. Considering a hyperaccreting stellar-mass black hole (BH) as the central engine of GRBs and the Blandford & Znajek process (BZ) as the jet production mechanism, we constrain the parameters of central engine by using the X-ray flare data. We find that the BZ mechanism is so powerful making it possible to interpret both GRB prompt emissions and bright X-ray flares. The wind parameter (p) and accreted mass (Md) fall into reasonable ranges. Our result is also applied to GRB 170817A. The late X-ray flare in GRB 170817A, if it is true, might not be a BH origin.

Description: Young neutron stars (NSs) have magnetic fields in the range 1012–1015 G, believed to be generated by dynamo action at birth. We argue that such a dynamo is actually too inefficient to explain the strongest of these fields. Dynamo action in the mature star is also unlikely. Instead we propose a promising new precession-driven dynamo and examine its basic properties, as well as arguing for a revised mean-field approach to NS dynamos. The precession-driven dynamo could also play a role in field generation in main-sequence stars.

Description: We report the discovery of a rare close binary system, SMSS J160639.78−100010.7, comprising a magnetic white dwarf with a field of about 30 MG and a brown dwarf. We measured an orbital period of 92 min which is consistent with the photometric period. Minimum and maximum light occur at the orbital quadratures Φ = 0.25 and 0.75, respectively, and cannot be caused by reflection on the brown dwarf, but, instead, by a spot on the synchronously rotating magnetic white dwarf. The brown dwarf does not fill its Roche lobe and the system may be in a low-accretion state or, more likely, in a detached state following episodes of mass transfer. SMSS J160639.78−100010.7 is the nearest known magnetic white dwarf plus brown dwarf system.

Description: In this work, we expand and test the capabilities of our recently developed superresolution (SR) model to generate high-resolution (HR) realizations of the full phase-space matter distribution, including both displacement and velocity, from computationally cheap low-resolution (LR) cosmological N-body simulations. The SR model enhances the simulation resolution by generating 512 times more tracer particles, extending into the deeply nonlinear regime where complex structure formation processes take place. We validate the SR model by deploying the model in 10 test simulations of box size 100 h−1 Mpc, and examine the matter power spectra, bispectra, and two-dimensional power spectra in redshift space. We find the generated SR field matches the true HR result at per cent level down to scales of k ∼ 10 h  Mpc−1. We also identify and inspect dark matter haloes and their substructures. Our SR model generates visually authentic small-scale structures that cannot be resolved by the LR input, and are in good statistical agreement with the real HR results. The SR model performs satisfactorily on the halo occupation distribution, halo correlations in both real and redshift space, and the pairwise velocity distribution, matching the HR results with comparable scatter, thus demonstrating its potential in making mock halo catalogues. The SR technique can be a powerful and promising tool for modelling small-scale galaxy formation physics in large cosmological volumes.