bluuebunny/crossref_metadata_2025 huggingface dataset:
Distribution of Panama’s narrow-range trees: are there hot-spots?
Authors: Tokarz Elizabeth , Condit Richard
Published: February 2021

Background

Tree species with narrow ranges are a conservation concern because heightened extinction risk accompanies their small populations. Assessing risks for these species is challenging, however, especially in tropical flora where their sparse populations seldom appear in traditional plots and inventories. Here, we utilize instead large scale databases that combine tree records from many sources to test hypotheses about where the narrow-range tree species of Panama are concentrated.

Methods

All individual records were collected from public databases, and the range size of each tree species found in Panama was estimated as a polygon around all its locations. Rare species were defined as those with ranges < 20,000 km2. We divided Panama into geographic regions and elevation zones and counted the number of individual records and the species richness in each, separating rare species from all other species.

Results

The proportion of rare species peaked at elevations above 2000 m, reaching 17.3% of the species recorded. At lower elevation across the country, the proportion was 6-11%, except in the dry Pacific region, where it was 1.5%. Wet forests of the Caribbean coast had 8.4% rare species, slightly higher than other regions. The total number of rare species, however, peaked at mid-elevation, not high elevation, because total species richness was highest there.

Conclusions

High elevation forests of west Panama have higher endemicity of trees than all low-elevation regions. Dry forests had the lowest endemicity. This supports the notion that montane forests of Central America should be a conservation focus, however, given generally higher diversity at low- to mid-elevation, lowlands are also important habitats for rare species.
Functional Near Infrared Spectroscopy (fNIRS) based Odor Detection and Classification using Functional Data Analysis
Authors: Moradi Faezeh , Moein Shima T. , Zakeri Issa , Pourrezaei Kambiz
Published: February 2021

An objective approach for odor detection is to analyze the brain activity using imaging techniques during the odor stimulation. In this study, Functional Near Infrared Spectroscopy (fNIRS) is used to record hemodynamic response from the frontal region of the brain by using a 4-channel fNIRS system. The fNIRs data is collected during the odor detection task in which the subjects were asked to press a button when they detect the given odor. Functional Data Analysis (FDA) was applied on fNIRs data to convert discrete measured samples of data to continuous smooth curves. The FDA method enables us to use the bases coefficients of fNIRS smoothed curves for features that represent the shape of the raw fNIRS signal. With the learning algorithm that we proposed, these features were used to train the support vector machine classifier. We evaluated the odor detection problem, in two binary classification cases: odorantvs. non-odorant and odorantvs. fingertapping. The model achieved a classification accuracy of 94.12% and 97.06% over the stimulus condition in the two cases, respectively. Moreover to find the actual predictors we used the extracted defined features (slope, standard deviation, and delta) to train our classifier. We achieved an average accuracy of 91.18 % on classifying odorantvs. non-odorant and an accuracy of 94.12% for odorantvs. fingertapping on the stimulus condition. The results determined that fNIRs signals of odorant and non-odorant are distinguishable without being affected by the motor activity during the experiment.

These findings suggest that fNIRs measurement on the forehead could be potentially used for objective and comparably inexpensive assessment of odor detection in cases that the subjective report is unreliable.
Impact of January 2021 curfew measures on SARS-CoV-2 B.1.1.7 circulation in France
Authors: Di Domenico Laura , Sabbatini Chiara E. , Pullano Giulia , Lévy-Bruhl Daniel , Colizza Vittoria
Published: February 2021

Facing B.1.1.7 variant, social distancing was strengthened in France in January 2021. Using a 2-strain mathematical model calibrated on genomic surveillance, we estimated that curfew measures allowed hospitalizations to plateau, by decreasing transmission of the historical strain while B.1.1.7 continued to grow. School holidays appear to have further slowed down progression in February. Without progressively strengthened social distancing, a rapid surge of hospitalizations is expected, despite the foreseen increase in vaccination rhythm.
Reinfection Rates among Patients who Previously Tested Positive for COVID-19: a Retrospective Cohort Study
Authors: Sheehan Megan M. , Reddy Anita J. , Rothberg Michael B.
Published: February 2021

Objectives

To evaluate reinfection rates and protective effectiveness of prior disease among patients with coronavirus disease 2019 (COVID-19) infection in the United States.

Design

Retrospective cohort study

Setting

One multi-hospital health system in Ohio and Florida

Participants

All 150,325 patients who were tested for COVID-19 infection via PCR from March 12, 2020 to August 30, 2020. Testing performed up to January 7, 2021 in these patients was included for analysis. Healthcare workers were excluded.

Main outcome measures

The main outcome was reinfection, defined as infection ≥ 90 days after initial testing. Secondary outcomes were symptomatic infection and protective effectiveness of prior infection.

Results

Of 150,325 patients tested for COVID-19 prior to August 30, 8,845 (5.9%) tested positive and 141,480 (94.1%) tested negative. 974 (11%) of the positive patients were retested after 90 days, and 56 had possible reinfection. Of those, 26 (46.4 %) were symptomatic. Of those with initial negative testing, 4,163 (12.9%) were subsequently positive and 2,460 of those (59.1%) were symptomatic. Protective effectiveness of prior infection was 78.5% (95% confidence interval 72.0 to 83.5), and against symptomatic infection was 83.1% (95% confidence interval 75.1 to 88.5). Protective effectiveness increased over time.

Conclusions

Prior infection in patients with COVID-19 was highly protective against reinfection and symptomatic disease. Protective effectiveness increased over time, suggesting that viral shedding or ongoing immune response may persist beyond 90 days and may not represent true reinfection. As vaccine supply is a limited resource around the world, patients with known history of COVID-19 could delay early vaccination to allow for the most vulnerable to access the vaccine and slow transmission.
Workplace measures against COVID-19 during the winter third wave in Japan: company size-based differences
Authors: Ishimaru Tomohiro , Nagata Masako , Hino Ayako , Yamashita Satoshi , Tateishi Seiichiro , Tsuji Mayumi , Ogami Akira , Matsuda Shinya , Fujino Yoshihisa ,   for the CORoNaWork Project
Published: February 2021

Objectives

Little is known about workplace measures against coronavirus disease 2019 (COVID-19) in Japan after the first state of emergency period, especially in micro-, small-, and medium-sized enterprises (MSMEs). This study aimed to provide an overview of the current situation of anti-COVID-19 measures in Japanese enterprises, considering company size.

Methods

This study was an Internet-based nationwide cross-sectional study. Data were collected using an online self-administered questionnaire in December 2020 during the third wave of COVID-19. The chi-squared test for trend was performed to calculate the p-value for trend for each workplace measure across company sizes.

Results

For the 27,036 participants, across company sizes, the most prevalent workplace measure was encouraging mask wearing at work, followed by requesting that employees refrain from going to work when ill and restricting work-related social gatherings and entertainment. These measures were implemented by approximately 90% of large-scale enterprises and by more than 40% of micro- and small-scale enterprises. In contrast, encouraging remote working and restricting eating and drinking at personal workspaces were implemented by less than half of large-scale enterprises and by around 15% of micro- and small-scale enterprises. There were statistically significant differences in all workplace measures by company size (all p-values < .001).

Conclusions

We found that various responses to COVID-19 had been taken in workplaces. However, some measures, including remote working, were still not well implemented, especially in smaller enterprises. The findings suggest that occupational health support for MSMEs is urgently needed to mitigate the current wave of COVID-19.
Genetic and gene expression analysis of flowering time regulation by light quality in lentil
Authors: Yuan Hai Ying , Caron Carolyn T. , Ramsay Larissa , Fratini Richard , Pérez de la Vega Marcelino , Vandenberg Albert , Weller James L. , Bett Kirstin E.
Published: February 2021

Flowering time is important due to its roles in adaptation to different environments and subsequent formation of crop yield. Changes in light quality affect a range of developmental processes including flowering time, however little is known about light quality induced flowering time control in lentil. This study aims to investigate the genetic basis for differences in flowering response to light quality in lentil.

We explored variation in flowering time caused by changes in red/far-red related light quality environments of a lentil interspecific recombinant inbred line population developed from a cross betweenLens culinariscv. Lupa andL. orientalisaccession BGE 016880. A genetic linkage map was constructed and then used for identifying QTL associated with flowering time regulation under different light quality environments. Differential gene expression analysis through transcriptomic study and RT-qPCR were used to identify potential candidate genes.

QTL mapping located 13 QTLs controlling flower time under different light quality environments, with phenotypic variance explained ranging from 1.7 to 62.9%. Transcriptomic profiling and gene expression analysis for both parents of this interspecific RIL population identified flowering-related genes showing environment-specific differential expression (flowering DEGs). One of these, a member of the florigen gene family FTa1 (LcFTa1) was located close to 3 major QTLs. Furthermore, gene expression results suggests two other florigen genes (LcFTb1andLcFTb2), MADS-box transcription factors likeLcAGL6/13d, LcSVPb, LcSOC1bandLcFULb, as well as bHLH transcription factorLcPIF6and Gibberellin 20 oxidaseLcGA20oxC,G, may be involved in the light quality response as well.

Our results show that a major component of flowering time sensitivity to light quality is tightly linked toLcFTa1and associated with changes in its expression. This work provides a foundation for crop improvement of lentil with better adaptation to variable light environments.
Fast Numerical Optimization for Genome Sequencing Data in Population Biobanks
Authors: Li Ruilin , Chang Christopher , Tanigawa Yosuke , Narasimhan Balasubramanian , Hastie Trevor , Tibshirani Robert , Rivas Manuel A.
Published: February 2021

We develop two efficient solvers for optimization problems arising from large-scale regularized regressions on millions of genetic variants sequenced from hundreds of thousands of individuals. These genetic variants are encoded by the values in the set {0, 1, 2,NA}. We take advantage of this fact and use two bits to represent each entry in a genetic matrix, which reduces memory requirement by a factor of 32 compared to a double precision floating point representation. Using this representation, we implemented an iteratively reweighted least square algorithm to solve Lasso regressions on genetic matrices, which we namesnpnet-2.0. When the dataset contains many rare variants, the predictors can be encoded in a sparse matrix. We utilize the sparsity in the predictor matrix to further reduce memory requirement and computational speed. Our sparse genetic matrix implementation uses both the compact 2-bit representation and a simplified version of compressed sparse block format so that matrix-vector multiplications can be effectively parallelized on multiple CPU cores. To demonstrate the effectiveness of this representation, we implement an accelerated proximal gradient method to solve group Lasso on these sparse genetic matrices. This solver is namedsparse-snpnet, and will also be included as part ofsnpnetR package. Our implementation is able to solve group Lasso problems on sparse genetic matrices with more than 1, 000, 000 columns and almost 100, 000 rows within 10 minutes and using less than 32GB of memory.
Long-reads are revolutionizing 20 years of insect genome sequencing
Authors: Hotaling Scott , Sproul John S. , Heckenhauer Jacqueline , Powell Ashlyn , Larracuente Amanda M. , Pauls Steffen U. , Kelley Joanna L. , Frandsen Paul B.
Published: February 2021

The first insect genome (Drosophila melanogaster) was published two decades ago. Today, nuclear genome assemblies are available for a staggering 601 insect species representing 20 orders. In this study, we analyzed the most-contiguous assembly for each species and provide a “state of the field” perspective, emphasizing taxonomic representation, assembly quality, gene completeness, and sequencing technologies. Relative to species richness, genomic efforts have been biased towards four orders (Diptera, Hymenoptera, Collembola, and Phasmatodea), Coleoptera are underrepresented, and 11 orders still lack a publicly available genome assembly. The average insect genome assembly is 439.2 megabases in length with 87.5% of single-copy benchmarking genes intact. Most notable has been the impact of long-read sequencing; assemblies that incorporate long-reads are ~48x more contiguous than those that do not. We offer four recommendations as we collectively continue building insect genome resources: (1) seek better integration between independent research groups and consortia, (2) balance future sampling between filling taxonomic gaps and generating data for targeted questions, (3) take advantage of long read sequencing technologies, and (4) expand and improve gene annotations.

Significance statement

Since the first insect genome was sequenced ~20 years ago, sequencing technologies and the availability of insect genome assemblies have both advanced dramatically. In this study, we curated, analyzed, and summarized the field of insect genomics in terms of taxonomic representation, assembly quality, gene completeness, and sequencing technology. We show that 601 insect species have genome assemblies available, with some groups heavily overrepresented (e.g., Diptera) relative to others (e.g., Coleoptera). The major takeaway of our study is that genome assemblies produced with long reads are ~48x more contiguous than short read assemblies.
Expanding theMECP2network using comparative genomics reveals potential therapeutic targets for Rett syndrome
Authors: Unterman Irene , Bloch Idit , Cazacu Simona , Kazimirsky Gila , Berman Benjamin P. , Ben-Zeev Bruria , Brodie Chaya , Tabach Yuval
Published: February 2021

Inactivating mutations in the Methyl-CpG Binding Protein 2 (MECP2) gene are the main cause of Rett syndrome (RTT). Despite extensive research into MECP2 function, no treatments for RTT are currently available. Here we use an evolutionary genomics approach to construct an unbiased MECP2 gene network, using 1,028 eukaryotic genomes to prioritize proteins with strong co-evolutionary signatures with MECP2. Focusing on proteins targeted by FDA approved drugs led to three promising candidates, two of which were previously linked to MECP2 function (IRAK, KEAP1) and one that was not (EPOR). We show that each of these compounds has the ability to rescue different phenotypes of MECP2 inactivation in cultured human neural cell types, and appear to act on Nuclear Factor Kappa B (NF-κB) signaling in inflammation. This study highlights the potential of comparative genomics to accelerate drug discovery, and yields potential new avenues for the treatment of RTT.

Abstract Figure
c-Rel is required for IL-33-dependent activation of ILC2s
Authors: Zaini Aidil , Fulford Thomas S. , Grumont Raelene J. , Runting Jessica , Rodrigues Grace , Ng Judy , Gerondakis Steve , Zaph Colby , Scheer Sebastian
Published: February 2021

Group 2 innate lymphoid cells (ILC2s) are emerging as important cellular regulators of homeostatic and disease-associated immune processes. The cytokine interleukin-33 (IL-33) promotes ILC2-dependent inflammation and immunity, with IL-33 having been shown to activate NF-κB in a wide variety of cell types. However, it is currently unclear which NF-κB members play an important role in IL-33-dependent ILC2 biology. Here, we identify the NF-κB family member c-Rel as a critical component of the IL-33-dependent activation of ILC2s. Although c-Rel is dispensable for ILC2 development, it is critical for ILC2 function in the lung, with c-Rel-deficient (c-Rel–/–) mice resistant to papain- and IL-33-induced lung inflammation. We also show that the absence of c-Rel reduces the IL-33-dependent expansion of ILC2 precursors and lower levels of IL-5 and IL-13 cytokine production by mature ILC2s in the lung. Together, these results identify the IL-33-c-Rel axis as a central control point of ILC2 activation and function.
Effects of kinship correction on inflation of genetic interaction statistics in commonly used mouse populations
Authors: Tyler Anna L. , El Kassaby Baha , Kolishovski Georgi , Emerson Jake , Wells Ann , Mahoney J. Matthew , Carter Gregory W.
Published: February 2021

It is well understood that variation in relatedness among individuals, or kinship, can lead to false genetic associations. Multiple methods have been developed to adjust for kinship while maintaining power to detect true associations. However, relatively unstudied, are the effects of kinship on genetic interaction test statistics. Here we performed a survey of kinship effects on studies of six commonly used mouse populations. We measured inflation of main effect test statistics, genetic interaction test statistics, and interaction test statistics reparametrized by the Combined Analysis of Pleiotropy and Epistasis (CAPE). We also performed linear mixed model (LMM) kinship corrections using two types of kinship matrix: an overall kinship matrix calculated from the full set of genotyped markers, and a reduced kinship matrix, which left out markers on the chromosome(s) being tested. We found that test statistic inflation varied across populations and was driven largely by linkage disequilibrium. In contrast, there was no observable inflation in the genetic interaction test statistics. CAPE statistics were inflated at a level in between that of the main effects and the interaction effects. The overall kinship matrix overcorrected the inflation of main effect statistics relative to the reduced kinship matrix. The two types of kinship matrices had similar effects on the interaction statistics and CAPE statistics, although the overall kinship matrix trended toward a more severe correction. In conclusion, we recommend using a LMM kinship correction for both main effects and genetic interactions and further recommend that the kinship matrix be calculated from a reduced set of markers in which the chromosomes being tested are omitted from the calculation. This is particularly important in populations with substantial population structure, such as recombinant inbred lines in which genomic replicates are used.
Community end-of-life care during the COVID-19 pandemic: Initial findings of a UK primary care survey
Authors: Mitchell Sarah , Oliver Phillip , Gardiner Clare , Chapman Helen , Khan Dena , Boyd Kirsty , Dale Jeremy , Barclay Stephen , Mayland Catriona
Published: February 2021

Background

Thousands of people in the UK have required end-of-life care in the community during the COVID-19 pandemic. Primary healthcare teams (general practice and community nursing services) have provided the majority of this care, alongside specialist colleagues. There is a need to learn from this experience in order to inform future service delivery and planning.

Aim

To understand the views of general practitioners and community nurses providing end-of-life care during the first wave of the COVID-19 pandemic.

Design and Setting

A web-based, UK-wide questionnaire survey circulated via professional general practice and community nursing networks during September and October 2020.

Method

Responses were analysed using descriptive statistics and an inductive thematic analysis.

Results

Valid responses were received from 559 individuals (387 community nurses, 156 General Practitioners (GPs) and 16 unspecified role), from all regions of the UK. The majority reported increased involvement in providing community end-of-life care. Contrasting and potentially conflicting roles emerged between GPs and community nurses. There was increased use of remote consultations, particularly by GPs. Community nurses took greater responsibility in most aspects of end-of-life care practice, particularly face-to-face care, but reported feeling isolated. For some GPs and community nurses, there has been considerable emotional distress.

Conclusion

Primary healthcare services are playing a critical role in meeting increased need for end-of-life care in the community during the COVID-19 pandemic. They have adapted rapidly, but the significant emotional impact, especially for community nurses, needs addressing alongside rebuilding trusting and supportive team dynamics.

How this fits in (4 sentences)

This study provides insights into experiences of delivering end-of-life care in the community during the first wave of the COVID-19 pandemic from the perspectives of UK general practitioners (GPs) and community nurses.

Services have changed and adapted rapidly to meet increased need in terms of both volume and complexity, with community nurses taking greater responsibility for most areas of palliative care clinical practice, and GPs undertaking more care planning conversations.

While GPs and specialist palliative care services conducted more remote consultations, community nurses carried out face-to-face end-of-life care and reported a feeling of isolation.

As the pandemic progresses, and the increased need for end-of-life care in the community persists, more effective service models and multi-disciplinary teamwork in primary care are urgently needed.
Anterior eye development in the brown anole,Anolis sagrei
Authors: Rasys Ashley M. , Pau Shana H. , Irwin Katherine E. , Luo Sherry , Menke Douglas B. , Lauderdale James D.
Published: February 2021

Background

Anterior eye development has been explored in different vertebrate species ranging from fish to mammals. However, missing from this diverse group is a representative of reptiles. A promising candidate to fill this void is the brown anole,Anolis sagrei, which is easily raised in the laboratory and for which genome editing techniques exist. Here we provide a detailed histological analysis of the development of the anterior structures of the eye inA. sagrei, which include the cornea, iris, ciliary body, lens, trabecular meshwork, and sclera ossicles.

Results

Development of the anterior segment in Anoles proceeds as for other vertebrates with the lens forming first followed by the cornea, then the iris, ciliary body, trabecular meshwork, and sclera ossicles. The onset of these latter structures occurs first temporally than nasally. Unlike the eyes of mammals and birds, anoles possess a remarkably thin cornea, flat ciliary body, and a trabecular meshwork that lacks an obvious Schlemm’s canal.

Conclusions

This study highlights several features present in anoles and represents an important step towards understanding reptile eye development.

Key Findings

The anole cornea epithelium is thin, composed mainly of a single basal cell layer.

The ciliary body lacks a ciliary process.

Iris and ciliary body formation occur in a spatiotemporal fashion, developing first temporally then nasally.

The anole trabecular meshwork is composed of a spongiform tissue and lacks a Schlemm’s canal.
Parasite co-opts a ubiquitin receptor to induce a plethora of developmental changes
Authors: Huang Weijie , MacLean Allyson M. , Sugio Akiko , Maqbool Abbas , Busscher Marco , Cho Shu-Ting , Kamoun Sophien , Kuo Chih-Horng , Immink Richard G.H. , Hogenhout Saskia A.
Published: February 2021

Obligate parasites can induce complex and substantial phenotypic changes in their hosts in ways that favour their transmission to other trophic levels. However, mechanisms underlying these changes remain largely unknown. Here, we demonstrate how SAP05 protein effectors from insect-vectored plant pathogenic phytoplasmas take control of several plant developmental processes to simultaneously prolong host lifespan and induce witch’s broom-like proliferations of leaf and sterile shoots, organs colonized by phytoplasmas and vectors. SAP05 acts by mediating the concurrent degradation of SPL and GATA developmental regulators via a process that uniquely relies on hijacking the plant ubiquitin receptor RPN10 independently of substrate lysine ubiquitination. RPN10 is highly conserved among eukaryotes, but SAP05 does not bind insect vector RPN10. A two-amino-acid substitution within plant RPN10 generates a functional variant that is resistant to SAP05 activities. Therefore, one effector protein enables obligate parasitic phytoplasmas to induce a plethora of developmental phenotypes in their hosts.
Comparative Analysis of common alignment tools for single cell RNA sequencing
Authors: Brüning Ralf Schulze , Tombor Lukas , Schulz Marcel H. , Dimmeler Stefanie , John David
Published: February 2021

With the rise of single cell RNA sequencing new bioinformatic tools became available to handle specific demands, such as quantifying unique molecular identifiers and correcting cell barcodes. Here, we analysed several datasets with the most common alignment tools for scRNA-seq data. We evaluated differences in the whitelisting, gene quantification, overall performance and potential variations in clustering or detection of differentially expressed genes.

We compared the tools Cell Ranger 5, STARsolo, Kallisto and Alevin on three published datasets for human and mouse, sequenced with different versions of the 10X sequencing protocol.

Striking differences have been observed in the overall runtime of the mappers. Besides that Kallisto and Alevin showed variances in the number of valid cells and detected genes per cell. Kallisto reported the highest number of cells, however, we observed an overrepresentation of cells with low gene content and unknown celtype. Conversely, Alevin rarely reported such low content cells.

Further variations were detected in the set of expressed genes. While STARsolo, Cell Ranger 5 and Alevin released similar gene sets, Kallisto detected additional genes from the Vmn and Olfr gene family, which are likely mapping artifacts. We also observed differences in the mitochondrial content of the resulting cells when comparing a prefiltered annotation set to the full annotation set that includes pseudogenes and other biotypes.

Overall, this study provides a detailed comparison of common scRNA-seq mappers and shows their specific properties on 10X Genomics data.

Key messages

Mapping and gene quantifications are the most resource and time intensive steps during the analysis of scRNA-Seq data.

The usage of alternative alignment tools reduces the time for analysing scRNA-Seq data.

Different mapping strategies influence key properties of scRNA-SEQ e.g. total cell counts or genes per cell

A better understanding of advantages and disadvantages for each mapping algorithm might improve analysis results.
The social cerebellum: A large-scale investigation of functional and structural specificity and connectivity
Authors: Metoki Athanasia , Wang Yin , Olson Ingrid R.
Published: February 2021

The cerebellum has been traditionally disregarded in relation to non-motor functions, but recent findings indicate it may be involved in language, affective processing, and social functions. Mentalizing is the ability to infer mental states of others and this skill relies on a distributed network of brain regions. Here, we leveraged large-scale multimodal neuroimaging data to elucidate the structural and functional role of the cerebellum in mentalizing. We used functional activations to determine whether the cerebellum has a domain-general or domain-specific functional role, and effective connectivity and probabilistic tractography to map the cerebello-cerebral mentalizing network. We found that the cerebellum is organized in a domain-specific way and that there is a left cerebellar effective and structural lateralization, with more and stronger effective connections from the left cerebellar hemisphere to the right cerebral mentalizing areas, and greater cerebello-thalamo-cortical (CTC) and cortico-ponto-cerebellar (CPC) streamline counts from and to the left cerebellum. Our study provides novel insights to the network organization of the cerebellum, an overlooked brain structure, and mentalizing, one of humans’ most essential abilities to navigate the social world.
Effect of aging-related network changes on unimanual sensorimotor learning – a simultaneous EEG-fMRI study
Authors: Chettouf Sabrina , Triebkorn Paul , Daffertshofer Andreas , Ritter Petra
Published: February 2021

Sensorimotor coordination requires orchestrated network activity mediated by inter- and intra-hemispheric, excitatory and inhibitory neuronal interactions. Aging-related structural changes may alter these interactions. Disbalancing strength and timing of excitation and inhibition may limit motor performance. This is particularly true during motor coordination tasks that have to be learned through practice. To investigate this, we simultaneously acquired electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) in two groups of healthy adults (young N=13: 20-25y and elderly N=14: 59-70y), while they were practicing a unimanual motor task. Both groups learned the task during brain scanning, which was confirmed by a 24h follow-up retention test. On average, quality of performance of older participants stayed significantly below that of the younger ones. Accompanying decreases in motor-event-related EEG-source beta band power (β, 15-30 Hz) were lateralized in both groups towards the contralateral side, albeit more so in younger participants. In the latter, the mean β-power during motor learning in bilateral pre-motor cortex (PM1) was significantly higher than in the older group. Combined EEG/fMRI analysis revealed positive correlations between fMRI signals and source-reconstructed β-amplitude time courses in contralateral and ipsilateral M1, and negative correlations in bilateral PM1 for both groups. The β-positive fMRI response in bilateral M1 might be explained by an increased cross-talk between hemispheres during periods of pronounced β-activity. During learning, the Rolandic β-power relative to rest was higher in bilateral PM1 in younger participants, suggesting less task-related beta band desynchronization in this (better performing) group. We also found positive correlations between Rolandic β-amplitude and fMRI-BOLD in bilateral M1 and negative correlations bilateral in PM1. This indicates that increased β-amplitudes are associated with increased M1 “activity” (positive BOLD response) and decreased PM1 “activity” (negative BOLD response). Our results point at decreased pre-motor inhibitory inputs to M1 as possible source for increased interhemispheric crosstalk and an aging-related decline in motor performance.

Highlights

Sensorimotor coordination performance decreases with increasing age.

During motor learning the β-power in pre-motor areas is reduced with age.

EEG/fMRI points at less effective inhibitory inputs from PM1 to ipsilateral M1 in older adults.
Id4 is required for normal ependymal cell development
Authors: Rocamonde Brenda , Herranz-Pérez Vicente , Garcia-Verdugo Jose-Manuel , Huillard Emmanuelle
Published: February 2021

Ependymal cells are radial glia-derived multiciliated cells lining the lateral ventricles of the brain and spinal cord. Correct development and coordinated cilia beating is essential for proper cerebrospinal fluid flow (CSF) and neurogenesis modulation. Dysfunctions of ependymal cells were associated with transcription factor deregulation. Here we provide evidence that the transcriptional regulator Id4 is involved in ependymal cell development and maturation. We observed thatId4-deficient mice display altered ependymal cytoarchitecture, decreased ependymal cell number, altered CSF flow and enlarged ventricles. Our findings open the way for a potential role of Id4 in ependymal cell development and/or motor cilia function.
Different evolutionary trends form the twilight zone of the bacterial pan-genome
Authors: Horesh Gal , Taylor-Brown Alyce , McGimpsey Stephanie , Lassalle Florent , Corander Jukka , Heinz Eva , Thomson Nicholas R.
Published: February 2021

The pan-genome is defined as the combined set of all genes in the gene pool of a species. Pan-genome analyses have been very useful in helping to understand different evolutionary dynamics of bacterial species: an open pan-genome often indicates a free-living lifestyle with metabolic versatility, while closed pan-genomes are linked to host-restricted, ecologically specialised bacteria. A detailed understanding of the species pan-genome has also been instrumental in tracking the phylodynamics of emerging drug resistance mechanisms and drug resistant pathogens. However, current approaches to analyse a species’ pan-genome do not take the species population structure into account, nor do they account for the uneven sampling of different lineages, as is commonplace due to over-sampling of clinically relevant representatives. Here we present the application of a population structure-aware approach for classifying genes in a pan-genome based on within-species distribution. We demonstrate our approach on a collection of 7,500E. coligenomes, one of the most-studied bacterial species used as a model for an open pan-genome. We reveal clearly distinct groups of genes, clustered by different underlying evolutionary dynamics, and provide a more biologically informed and accurate description of the species’ pan-genome.
Topoisomerase VI is a chirally-selective, preferential DNA decatenase
Authors: McKie Shannon J. , Desai Parth , Seol Yeonee , Maxwell Anthony , Neuman Keir
Published: February 2021

DNA topoisomerase VI (topo VI) is a type IIB DNA topoisomerase found predominantly in archaea and some bacteria, but also in plants and algae. Since its discovery, topo VI has been proposed to be a DNA decatenase, however robust evidence and a mechanism for its preferential decatenation activity was lacking. Using single-molecule magnetic tweezers measurements and supporting ensemble biochemistry, we demonstrate thatMethanosarcina mazeitopo VI preferentially unlinks, or decatenates, DNA crossings, in comparison to relaxing supercoils, through a preference for certain DNA crossing geometries. In addition, topo VI demonstrates a dramatic increase in ATPase activity, DNA binding and rate of strand passage, with increasing DNA writhe, providing further evidence that topo VI is a DNA crossing sensor. Our study strongly suggests that topo VI has evolved an intrinsic preference for the unknotting and decatenation of interlinked chromosomes by sensing and preferentially unlinking DNA crossings with geometries close to 90°.
massiveGenesetsTest: a web tool to run enrichment analysis
Authors: Cerulo Luigi , Pagnotta Stefano Maria
Published: February 2021

Motivation

Inferring biological phenotypes from genomic data and sample clusters is a routinely task usually performed with Gene-Set Enrichment Analysis (GSEA), a tool that queries gene-profiles. In previous work, we scrutinized the approach based on Mann-Witney for Gene-Sets test. We highlighted the Mann-Witney test-statistics sensitivity to uncover weak signals and the drastic decreasing of time complexity.

Results

We propose web implementation of the Gene-sets testing based on the Mann-Witney procedure. The test-procedure has reshaped to decrease the computational expense, now about tens of seconds, even if a large collection of gene-sets queries the same gene-profile. The probabilistic interpretation of the normalized test-statistic has been investigated to a better understanding of the enrichment results. A novel prioritization method across enrichment-scores, gene-set dimensions, and p-values, draws attention to relevant gene-sets. The web tool provides both tabular and graphical enrichment results. A complimentary R function allows integrating the enrichment procedure in a complex context.

Contact

pagnotta@unisannio.it

Supplementary information

Example data and guidelines are included in the supporting material of the web-site.
Shared genetic influences on resting-state functional networks of the brain
Authors: Guimaraes JPOFT , Sprooten E , Beckmann CF , Franke B , Bralten J
Published: February 2021

The amplitude of activation in brain resting state networks (RSNs), measured with resting-state functional MRI, is heritable and genetically correlated across RSNs, indicating pleiotropy. Recent univariate genome-wide association studies (GWAS) explored the genetic underpinnings of individual variation in RSN activity. Yet univariate genomic analyses do not describe the pleiotropic nature of RSNs. In this study we used a novel multivariate method called genomic SEM to model latent factors that capture the shared genomic influence on RSNs and to identify SNPs and genes driving this pleiotropy. Using summary statistics from GWAS of 21 RSNs reported in UK Biobank (N = 31,688), the genomic latent factor analysis was first conducted in a discovery sample (N = 21,081), and then tested in an independent sample from the same cohort (N = 10,607). In the discovery sample, we show that the genetic organization of RSNs can be best explained by two distinct but correlated genetic factors that divide multimodal association networks and sensory networks. Eleven of the 17 factor loadings were replicated in the independent sample. With the multivariate GWAS, we found and replicated nine independent SNPs associated with the joint architecture of RSNs. Further, by combining the discovery and replication samples, we discovered additional SNP and gene associations with the two factors of RSN amplitude. We conclude that modelling the genetic effects on brain function in a multivariate way is a powerful approach to learn more about the biological mechanisms involved in brain function.
How to achieve a higher selection plateau in forest tree breeding? Fostering Heterozygote x Homozygote relationships in Optimal Contribution Selection in the case study of Populus nigra
Authors: Tiret Mathieu , Pégard Marie , Sánchez Leopoldo
Published: February 2021

In breeding, Optimal Contribution Selection (OCS) is one of the most effective strategies to balance short- and long-term genetic responses, by maximizing genetic gain and minimizing global coancestry. Considering genetic diversity in the selection dynamic – through coancestry – is undoubtedly the reason for the success of OCS, as it avoids initial loss of favorable alleles. Originally formulated with the pedigree relationship matrix, global coancestry can nowadays be assessed with one of the possible formulations of the realized genomic relationship matrix. Most formulations were optimized for genomic evaluation, but few for the management of coancestry. We introduce here an alternative formulation specifically developed for Genomic OCS (GOCS), intended to better control heterozygous loci, and thus better account for Mendelian sampling. We simulated a multi-generation breeding program with mate allocation and under GOCS for twenty generations, solved with quadratic programming. With the case study ofPopulus nigra, we have shown that, although the dynamic was mainly determined by the trade-off between genetic gain and genetic diversity, better formulations of the genomic relationship matrix, especially those fostering individuals carrying multiple heterozygous loci, can lead to better short-term genetic gain and a higher selection plateau.
SARS-CoV2 envelop proteins reshape the serological responses of COVID-19 patients
Authors: Martin Sophie , Heslan Christopher , Jégou Gwénaële , Eriksson Leif A. , Le Gallo Matthieu , Thibault Vincent , Chevet Eric , Godey Florence , Avril Tony
Published: February 2021

The SARS-CoV-2 pandemic has elicited a unique international mobilization of the scientific community to better understand this coronavirus and its associated disease and to develop efficient tools to combat infection. Similar to othercoronavirae, SARS-CoV-2 hijacks the host cell complex secretory machinery to produce properly folded viral proteins that will compose the nascent virions; including Spike, Envelope and Membrane proteins, the most exposed membrane viral proteins to the host immune system. Antibody response is part of the anti-viral immune arsenal that infected patients develop to fight viral particles in the body. Herein, we investigate the immunogenic potential of Spike (S), Envelope (E) and Membrane (M) proteins using a human cell-based system to mimic membrane insertion and N-glycosylation. We show that both S and M proteins elicit the production of specific IgG, IgM and IgA in SARS-CoV-2 infected patients. Elevated Ig responses were observed in COVID+ patients with moderate and severe forms of the disease. Finally, when SARS-CoV-2 Spike D614 and G614 variants were compared, reduced Ig binding was observed with the Spike G614 variant. Altogether, this study underlines the needs for including topological features in envelop proteins to better characterize the serological status of COVID+ patients, points towards an unexpected immune response against the M protein and shows that our assay could represent a powerful tool to test humoral responses against actively evolving SARS-CoV-2 variants and vaccine effectiveness.
A farewell to EQ: A new brain size measure for comparative primate cognition
Authors: van Schaik Carel P. , Triki Zegni , Bshary Redouan , Heldstab Sandra Andrea
Published: February 2021

Both absolute and relative brain size vary greatly among and within the major vertebrate lineages. Scientists have long debated how larger brains in primates and hominins translate into greater cognitive performance, and in particular how to control for the relationship between the non-cognitive functions of the brain and body size. One solution to this problem is to establish the slope of cognitive equivalence, that is the line connecting organisms with an identical bauplan but different body sizes. Here, we suggest that intraspecific slopes provide the best available estimate of this measure. This approach was abandoned because slopes were too low by an unknown margin due to estimation error. We control for the error problem by focusing on highly dimorphic primate species with large sample sizes and fitting a line through the mean values for adult females and males. We obtain the best estimate for the slope of ca 0.27, a value much lower than those constructed using all mammal species, and close to the value expected based on the genetic correlation between brain size and body size. We also find that the estimate of cognitive brain size based on cognitive equivalence fits empirical cognitive studies better than the encephalization quotient (EQ), which should therefore be avoided in future studies on primates, and presumably mammals and birds in general. The use of residuals from the line of cognitive equivalence may change conclusions concerning the cognitive abilities of extant and extinct primate species, including hominins.
Molecular epidemiology of human respiratory syncytial virus with severe acute respiratory infection in Huzhou from 2016 to 2019
Authors: Xu Deshun , Ji Lei , Wu Xiaofang , Yan Wei , Chen Liping
Published: February 2021

Background

Human respiratory syncytial virus (HRSV) is one of the major cause of acute lower respiratory infection in infants, the elderly and people with low immunity worldwide. Based on antigenic and genetic variations, Human respiratory syncytial virus is divided into two subgroups (A and B). Each of the subgroups is further categorized into genotypes based on the phylogenetic analyses of the sequences of the second hypervariable region.

Methods

Nasopharyngeal swabs (NPSs) were collected from patients of the First People’s Hospital in Huzhou from January 2016 to December 2019. Real-time RT-PCR (qPCR) was performed using double nucleic acid detection kit for respiratory syncytial virus (A\B) (Shenzhen shengkeyuan) with the ABI Q7 (Applied Biosystems). For genotyping, the primer set A-F/A-R was used to amplify the G protein of HRSV-A. Primer set B-F/B-R was used to amplify the G protein of HRSV-B. The phylogenetic analysis was constructed using the neighbor-joining algorithm with the Kimura two-parameter model and supported statistically by bootstrapping with 1000 replicates with MEGA software (version 7.0) with 1000 bootstrap replicates.

Results

A total of 973 nasopharyngeal swab samples were collected from January 2016 to December 2019, and 63 samples were positive for RSV nucleic acid, with the detection rate of 6.47%. Of the positive specimens, 28 were belonged to HRSV-A, and 35 were belonged to HRSV-B. Infection with RSV was found in all age groups tested, with the 0-1 year age group having the highest detection rate 15.2%. The detection rate was high from November to next March. Phylogenetic analysis clustered HRSV-A strains identified in Huzhou into ON1genotype. All 17 of the HRSV-B strains belonged to BA9 genotype.

Conclusions

We analyzed the HRSV strains circulation in Huzhou from January 2016 to December 2019 in Huzhou, China. This is the first molecular analysis on HRSV in Huzhou. We found Subgroup A and B of RSV were co-circulating and the 0-1 year age group having the highest infection rate.
Hybrid Support Vector Regression Model and K-Fold Cross Validation for Water Quality Index Prediction in Langat River, Malaysia
Authors: Mamat Naeimah , Hamzah Firdaus Mohamad , Jaafar Othman
Published: February 2021

Water quality analysis is an important step in water resources management and needs to be managed efficiently to control any pollution that may affect the ecosystem and to ensure the environmental standards are being met. The development of water quality prediction model is an important step towards better water quality management of rivers. The objective of this work is to utilize a hybrid of Support Vector Regression (SVR) modelling and K-fold cross-validation as a tool for WQI prediction. According to Department of Environment (DOE) Malaysia, a standard Water Quality Index (WQI) is a function of six water quality parameters, namely Ammoniacal Nitrogen (AN), Biochemical Oxygen Demand (BOD), Chemical Oxygen Demand (COD), Dissolved Oxygen (DO), pH, and Suspended Solids (SS). In this research, Support Vector Regression (SVR) model is combined with K-fold Cross Validation (CV) method to predict WQI in Langat River, Kajang. Two monitoring stations i.e., L15 and L04 have been monitored monthly for ten years as a case study. A series of results were produced to select the final model namely Kernel Function performance, Hyperparameter Kernel value, K-fold CV value and sets of prediction model value, considering all of them undergone training and testing phases. It is found that SVR model i.e., Nu-RBF combined with K-fold CV i.e., 5-fold has successfully predicted WQI with efficient cost and timely manner. As a conclusion, SVR model and K-fold CV method are very powerful tools in statistical analysis and can be used not limited in water quality application only but in any engineering application.