bluuebunny/crossref_metadata_2025_split huggingface dataset:
Revisiting a ‘simple’ fungal metabolic pathway reveals redundancy, complexity and diversity
Authors: Chroumpi Tania , Peng Mao , Aguilar‐Pontes Maria Victoria , Müller Astrid , Wang Mei , Yan Juying , Lipzen Anna , Ng Vivian , Grigoriev Igor V. , Mäkelä Miia R. , de Vries Ronald P. 
Published: March 2021

SummaryNext to d‐glucose, the pentoses l‐arabinose and d‐xylose are the main monosaccharide components of plant cell wall polysaccharides and are therefore of major importance in biotechnological applications that use plant biomass as a substrate. Pentose catabolism is one of the best‐studied pathways of primary metabolism of Aspergillus niger, and an initial outline of this pathway with individual enzymes covering each step of the pathway has been previously established. However, although growth on l‐arabinose and/or d‐xylose of most pentose catabolic pathway (PCP) single deletion mutants of A. niger has been shown to be negatively affected, it was not abolished, suggesting the involvement of additional enzymes. Detailed analysis of the single deletion mutants of the known A. niger PCP genes led to the identification of additional genes involved in the pathway. These results reveal a high level of complexity and redundancy in this pathway, emphasizing the need for a comprehensive understanding of metabolic pathways before entering metabolic engineering of such pathways for the generation of more efficient fungal cell factories.
EigenGWAS: An online visualizing and interactive application for detecting genomic signatures of natural selection
Authors: Qi Guo‐An , Zheng Yuan‐Ting , Lin Feng , Huang Xin , Duan Li‐Wen , You Yue , Liu Hailan , Wang Ying , Xu Hai‐Ming , Chen Guo‐Bo 
Published: March 2021

AbstractDetecting genetic regions under selection in structured populations is of great importance in ecology, evolutionary biology and breeding programmes. We recently proposed EigenGWAS, an unsupervised genomic scanning approach that is similar to but does not require grouping information of the population, for detection of genomic regions under selection. The original EigenGWAS is designed for the random mating population, and here we extend its use to inbred populations. We also show in theory and simulation that eigenvalues, the previous corrector for genetic drift in EigenGWAS, are overcorrected for genetic drift, and the genomic inflation factor is a better option for this adjustment. Applying the updated algorithm, we introduce the new EigenGWAS online platform with highly efficient core implementation. Our online computational tool accepts plink data in a standard binary format that can be easily converted from the original sequencing data, provides the users with graphical results via the R‐Shiny user‐friendly interface. We applied the proposed method and tool to various data sets, and biologically interpretable results as well as caveats that may lead to an unsatisfactory outcome are given. The EigenGWAS online platform is available at www.eigengwas.com, and can be localized and scaled up via R (recommended) or docker.
Habitats determining local frog assemblages within aquatic macrophyte meadows in Amazonia, through species traits filtering
Authors: Ganança Pedro Henrique Salomão , Santos Alfredo P. , Kawashita‐Ribeiro Ricardo A. , de Vasconcelos Neto Lourival Baía , dos Santos Júnior Ivan Alves , Guedes Daniel de Sousa , de Fraga Rafael 
Published: March 2021

AbstractInvestigating non‐random assemblages emerging in response to environmental gradients is relevant to understand mechanisms and processes affecting biodiversity. Species may be filtered from fractions of environmental gradients that limit dispersal, survival or ontogenetic development, which ultimately leads to biotic complementarities among sites. Non‐random assemblages as a response to environmental filtering have been widely demonstrated in Amazonian forests, but are rarely assessed in non‐forest ecosystems such as macrophyte meadows covering lakes. In this study, we sampled 50 plots (50 m long, 6 m wide) along continuous macrophyte meadows in a lake system in the lower Amazon River. Our main goal is to test the effects of distance from the lake bank, macrophyte height and composition (frequency of morphotype occurrence), air temperature and physicochemical properties of water (pH, dissolved oxygen, depth and temperature) on frog α and β‐diversity estimates, and frequency of species traits occurrence (abundance‐weighted body size, toe pads, foot webbing and tadpole habit). We found 16 species, for which local assemblages quantified by α and β‐diversity estimates were not random, but predicted by macrophyte height, morphotype composition and water depth. We have explicitly shown that species are filtered from fractions of these gradients through ecomorphological relationships, since morphological traits and tadpole habits were also selected by the vertical stratification provided by the vegetation cover and water depth. Overall, we present an investigation of assemblage ecology that is relevant to conservation, because the results suggest biotic complementarities within habitats that are rarely considered as distinct biogeographic units from the surrounding várzea forests.Abstract in Portuguese is available with online material.
Potential functional variants in AHR signaling pathways are associated with age at puberty in swine
Authors: Nonneman Dan , Lents Clay A. , Rempel Lea A. , Rohrer Gary A. 
Published: March 2021

SummaryPuberty in female pigs is defined as age at first estrus and gilts that have an earlier age at puberty are more likely to have greater lifetime productivity. Because age at puberty is predictive for sow longevity and lifetime productivity, but not routinely measured in commercial herds, it would be beneficial to use genomic or marker‐assisted selection to improve these traits. A GWAS at the US Meat Animal Research Center (USMARC) identified several loci associated with age at puberty in pigs. Candidate genes in these regions were scanned for potential functional variants using sequence information from the USMARC swine population founder animals and public databases. In total, 135 variants (SNP and insertion/deletions) in 39 genes were genotyped in 1284 phenotyped animals from a validation population sired by Landrace and Yorkshire industry semen using the Agena MassArray system. Twelve variants in eight genes were associated with age at puberty (P < 0.005) with estimated additive SNP effects ranging from 1.6 to 5.3 days. Nine of these variants were non‐synonymous coding changes in AHR, CYP1A2, OR2M4, SDCCAG8, TBC1D1 and ZNF608, two variants were deletions of one and four codons in aryl hydrocarbon receptor, AHR, and the most significant SNP was near an acceptor splice site in the acetyl‐CoA carboxylase alpha, ACACA. Several of the loci identified have a physiological and a genetic role in sexual maturation in humans and other animals and are involved in AHR‐mediated pathways. Further functional validation of these variants could identify causative mutations that influence age at puberty in gilts and possibly sow lifetime productivity.
Able and Mostly Willing: An Empirical Anatomy of Information's Effect on Voter‐Driven Accountability in Senegal
Authors: Bhandari Abhit , Larreguy Horacio , Marshall John 
Published: March 2021

AbstractPolitical accountability may be constrained by the reach and relevance of information campaigns in developing democracies and—upon receiving information—voters' ability and will to hold politicians accountable. To illuminate voter‐level constraints and information relevance absent dissemination constraints, we conducted a field experiment around Senegal's 2017 parliamentary elections to examine the core theoretical steps linking receiving different types of incumbent performance information to electoral and nonelectoral accountability. Voters immediately processed information as Bayesians, found temporally benchmarked local performance outcomes particularly informative, and updated their beliefs for at least a month. Learning that incumbents generally performed better than expected, voters durably requested greater politician contact after elections while incumbent vote choice increased among likely voters and voters prioritizing local projects when appraising incumbents. In contrast, information about incumbent duties did not systematically influence beliefs or accountability. These findings suggest voters were able and mostly willing to use relevant information to hold politicians to account.
Tree encroachment impacts on seed predator selection and seedling establishment in degraded pine woodlands
Authors: Willis John L. , Schnake David K. , DePerno Christopher S. , Lashley Marcus A. , Wetzstein Branson , Yow Justin 
Published: March 2021

AbstractQuestionsWhile much is known about the impact of tree encroachment on flammability in degraded pine woodlands, little is known about how encroachment is impacting other important ecosystem functions. We investigated how the availability of seed from four encroaching tree species and the presence of a midstorey and litter layer affect seed predator selection. Additionally, we investigated how seed predators, the midstorey, overstorey basal area, substrate availability, and vegetation cover affect germination for a foundational species (Pinus palustris) compared to an encroaching species (Pinus taeda).LocationSandhills Ecoregion, NC, USA (35°3′34.6932″ N, 79°22′22.0872″ W).MethodsWe measured seed depredation of Pinus palustris, Pinus taeda, Liquidambar styraciflua, Acer rubrum, and Quercus nigra in cafeteria trials. Each trial was held within a 2 × 2 factorial involving vertebrate seed predator exclusion and midstorey and litter layer removal across a gradient of overstorey basal area (6–25 m2). Additionally, we measured Pinus palustris and Pinus taeda germination within each treatment and correlated germinant density to substrate and understorey vegetation cover.ResultsGranivory generally varied inversely with seed size, with small‐seeded Liquidambar styraciflua experiencing the highest (27%) and large‐seeded Quercus nigra (7%) and Acer rubrum (6%) the lowest depredation pressure. Pinus palustris and Pinus taeda germinant density was significantly highest where vertebrate seed predators were excluded and the midstorey and litter layer were removed. For both pine species, this result corresponded with a significant positive association with mineral soil and negative associations with hardwood and pine litter where vertebrate predators were excluded. Basal area did not affect granivory or germination for any species.ConclusionsOur results demonstrate that granivores did not select Pinus palustris, and that large‐seeded species encroachment was less inhibited by seed predators. Pinus palustris and Pinus taeda are depredated at comparable rates and germinate best under similar understorey conditions.
Barter markets, indivisibilities, and Markovian core
Authors: Fujishige Satoru , Yang Zaifu 
Published: March 2021

AbstractWe study a general barter market where every agent is endowed with several heterogeneous indivisible items and wishes to exchange. There is no medium of exchange like money. Agents have general preferences over their interested bundles of items and may acquire several items. We propose a practical and sensible solution called a Markovian core, generalizing the classical notion of the core. A Markovian core allocation is individually rational, Pareto‐efficient, and stable against any coalition deviation by comparison with their current assignments instead of their initial endowments and is shown to be a natural outcome of a decentralized market process.
Geographical sampling bias on the assessment of endemism areas for marine meiobenthic fauna
Authors: Garraffoni André , Sørensen Martin V. , Worsaae Katrine , Di Domenico Maikon , Sales Lilian P. , Santos Jessie , Lourenço Anete 
Published: March 2021

AbstractSpecies distribution patterns are constrained by historical and ecological processes in space and time, but very often the species range sizes are geographical sampling biases resulting from unequal sampling effort. One of the most common definitions of endemism is based on the “congruence of distributional areas” criterion, when two or more species have the same distributional limits. By acknowledging that available data of marine meiobenthic species are prone to geographical sampling bias and that can affect the accuracy of the biogeographical signals, the present study combines analyses of inventory incompleteness and recognition of spatial congruence of Gastrotricha, Kinorhyncha, meiobenthic Annelida and Tardigrada in order to better understand the large‐scale distribution of these organisms in coastal and shelf areas of the world. We used the marine bioregionalization framework for geographical operative units to quantify the inventory incompleteness effect (by modelling spatial predictions of species richness) and to recognize areas of endemism. Our models showed that the difference between observed and expected species richness in the Southern Hemisphere is much higher than in the Northern Hemisphere. Parsimony Analysis of Endemicity delimited 20 areas of endemism, most found in the Northern Hemisphere. Distribution patterns of meiobenthic species are shown to respond to events of geographical barriers and abiotic features, and their distribution is far from homogeneous throughout the world. Also, our data show that ecoregions with distinct biotas have at least some cohesion over evolutionary time. However, we found that inventory incompleteness may significantly affect the explanatory power of areas of endemism delimitation in both hemispheres. Yet, whereas future increases in sampling efforts are likely to change the spatial congruence ranges in the Southern Hemisphere, patterns for the Northern Hemisphere may prove to be relatively more resilient.
Government economic policy uncertainty and corporate debt contracting
Authors: Tran Dung T. T. , Phan Hieu V. 
Published: March 2021

AbstractWe examine the relation between government economic policy uncertainty and debt contracting of U.S. public firms. We find that policy uncertainty is associated with more stringent debt terms, such as shorter debt maturity, higher cost of debt, and more restrictive debt covenants, and these relations are concentrated in financially constrained firms. Further analysis indicates that the negative real effects of policy uncertainty documented in the literature are more pronounced for financially constrained firms. Overall, our evidence suggests that policy uncertainty dampens external financing and exacerbates firms' financial constraints, leading to their investment delays.
Microclimate and habitat heterogeneity as important drivers of soil Collembola in a karst collapse doline in the temperate zone
Authors: Marcin Michal , Raschmanová Natália , Miklisová Dana , Kováč Ľubomír 
Published: March 2021

AbstractChanges in well‐delimited Collembola communities along a steep microclimatic gradient at the entrance of Silická ľadnica Ice Cave, Slovakia, were investigated after 10 years (2007, 2017). We focused on the occurrence of psychrophilic and endemic species occupying this unique karst collapse doline and their response to climatic singularities in the given years as well as the increasing trend in regional air temperature. The soil temperature means at sites across the doline slope corresponded with climatic trends in the periods 2006–2007 and 2016–2017. Significantly lower average soil temperatures but significantly higher mean abundances, species richness, and diversity indices of the collembolan communities were recorded at sites during the second study period, which was characterized by more favorable soil microclimatic conditions (temperature and moisture content) compared to the first period. The dominance structure and community composition of the studied assemblages appeared to be relatively constant after 10 years, indicating stable collembolan communities, especially at cold sites at the bottom of the doline. Redundancy ordination analysis documented a clear delimitation of the communities in relation to the soil temperature, pH, and C:N ratio in both periods. Long‐term (30‐year) regional climatic data showed an increasing trend of annual air temperature means and precipitation. However, an increase in the number and abundance of xerothermophilous species and a decline in psychrophilic species (mostly endemic) along the gradient as a potential response of the increasing regional temperature were not observed, suggesting the high resilience of these communities. Microclimate and habitat heterogeneity are probably major drivers of soil Collembola communities along the steep microclimatic gradient of a karst collapse doline, which was observed by the repeated sampling after 10 years. Karst dolines as potentially important local sources of ɑ‐diversity will likely become increasingly indispensable refugia for local biodiversity under ongoing global warming, thus deserving reliable conservation.
Identification of hub genes associated with neutrophils infiltration in colorectal cancer
Authors: Su Hao , Cai Tianyi , Zhang Sen , Yan Xialin , Zhou Leqi , He Zirui , Xue Pei , Li Jianwen , Zheng Minhua , Yang Xiao , Feng Bo 
Published: March 2021

AbstractColorectal cancer (CRC) is the leading cause of cancer‐related mortality in the world. Accumulating evidence indicate that tumour infiltrating immune cells participated in cancer progression. Among them, tumour infiltrating neutrophils (TINs) are reported to play crucial role in various cancers. In this study, we used CIBERSORTx, a digital cytometry tool to evaluate the neutrophils infiltration in CRC based on gene expression data of CRC tissues from GSE39582 data set and The Cancer Genome Atlas data set (TCGA‐COAD and TCGA‐READ). Weighted gene co‐expression network analysis (WGCNA) was conducted in GSE39582 data set to identify hub genes associated with neutrophil infiltration. The association of hub gene and neutrophils was then validated in TCGA cohorts and an independent RJ cohort. Functional analysis was performed to investigate the molecular mechanisms of the interested hub gene. We found that neutrophil infiltration is elevated in CRC tissues, and it is related to a poorer prognosis. A total of 18 gene modules are identified by WGCNA in GSE39582 data set, among which lightcyan module is significantly correlated with neutrophils infiltration. Furthermore, Superoxide Dismutase 2 (SOD2) in lightcyan module was proved to correlated with neutrophils infiltration in various cancer types. In addition, SOD2 expression is highly associated with several chemokines, including CXCL8, a neutrophils‐related attractant, and functional analysis revealed that SOD2 is involved in neutrophils recruitment biological process. These results indicate that an ‘SOD2‐CXCL8‐neutrophil recruitment’ axis plays a potential role in colorectal cancer progression.
The rural identity scale: Development and validation
Authors: Oser Carrie B. , Strickland Justin , Batty Evan J. , Pullen Erin , Staton Michele 
Published: March 2021

AbstractPurposeThe purpose of this study was to conduct a psychometric evaluation of a new 35‐item survey developed in the United States to measure rural identity.MethodsFactor structure, reliability, convergent validity, and incremental validity of the Rural Identity Scale (RIS) were examined using two datasets. Study 1 examined RIS psychometric properties using survey data collected from substance use treatment counselors in a southeastern state (n = 145), while Study 2 used data collected from women incarcerated in rural jails (n = 400).FindingsA one‐factor structure containing 15 items was identified in the RIS, with acceptable internal reliability (α = .72–.83). In Study 1, participants from rural counties had significantly higher RIS scores than their urban counterparts. In both studies, convergent validity was evaluated and the RIS scores were significantly associated with other measures relevant to identity and rurality at the bivariate level. Incremental validity was supported in multivariable models as the RIS scores were significantly and uniquely associated with primary rural place variables in each sample.ConclusionsThis study is an initial step toward a reliable, valid scale measuring rural identity. RIS may be especially beneficial to health research as a methodological tool that can contextualize health behaviors among rural populations and highlight potential interventions to promote health equity.
Behavioural biometrics: Using smartphone keyboard activity as a proxy for rest–activity patterns
Authors: Druijff‐van de Woestijne Gerrieke B. , McConchie Hannah , de Kort Yvonne A. W. , Licitra Giovanni , Zhang Chao , Overeem Sebastiaan , Smolders Karin C. H. J. 
Published: March 2021

SummaryRest–activity patterns are important aspects of healthy sleep and may be disturbed in conditions like circadian rhythm disorders, insomnia, insufficient sleep syndrome, and neurological disorders. Long‐term monitoring of rest–activity patterns is typically performed with diaries or actigraphy. Here, we propose an unobtrusive method to obtain rest–activity patterns using smartphone keyboard activity. The present study investigated whether this proposed method reliably estimates rest and activity timing compared to daily self‐reports within healthy participants. First‐year students (n = 51) used a custom smartphone keyboard to passively and objectively measure smartphone use behaviours and completed the Consensus Sleep Diary for 1 week. The time of the last keyboard activity before a nightly absence of keystrokes, and the time of the first keyboard activity following this period were used as markers. Results revealed high correlations between these markers and user‐reported onset and offset of resting period (r ranged from 0.74 to 0.80). Linear mixed models could estimate onset and offset of resting periods with reasonable accuracy (R2 ranged from 0.60 to 0.66). This indicates that smartphone keyboard activity can be used to estimate rest–activity patterns. In addition, effects of chronotype and type of day were investigated. Implementing this method in longitudinal studies would allow for long‐term monitoring of (disturbances to) rest–activity patterns, without user burden or additional costly devices. It could be particularly interesting to replicate these findings in studies amongst clinical populations with sleep‐related problems, or in populations for whom disturbances in rest–activity patterns are secondary complaints, such as neurological disorders.
Projecting Religious Demographics: The Case of Jews in the United States
Authors: Pinker Edieal J. 
Published: March 2021

AbstractDrawing upon the comprehensive survey of the American Jewish population conducted in 2013 by the Pew Research Center, we estimate the trajectory of the population and its denominational segments, 50 years into the future. Our analysis relies upon estimates of the population in 2013, fertility rates, marriage behaviors, and denominational switching patterns as inputs into a model of population demographics. We project that over the next 50 years, the demographics of U.S. Jews are likely to change dramatically, with the share of the population that is Orthodox rising from 12 percent to 29 percent, with their share of the child population increasing from 22 percent to 51 percent. Among Reform and Conservative Jews, the number of 30‐ to 69‐year‐olds is projected to drop by approximately 46 percent over this period. We also project a slight drop in the total Jewish population followed by a recovery propelled by the growing Orthodox population.