bluuebunny/crossref_metadata_2025_split huggingface dataset:
Young chicks rely on perceptual grouping to discriminate prime numbers
Authors: Loconsole Maria , De Agrò Massimo , Regolin Lucia 
Published: March 2021

AbstractGrouping sets of elements into smaller, equal-sized, subsets constitutes a perceptual strategy employed by humans and other animals to enhance cognitive performance. We hypothesized that asymmetrical grouping, a characteristic of prime numbers, could provide visual cues enabling discrimination of prime from non-prime numerosities. Newborn chicks were habituated to even numerosities (as sets of elements presented on a screen), and then tested for their spontaneous choice among a prime and a non-prime odd numerosity. Chicks discriminated and preferred the prime over the composite set of elements. We discuss this result in terms of novelty preference. By employing different contrasts (i.e., 7vs.9, 11vs.9, and 13vs.15) we investigated the limits of such mechanism showing that induced grouping positively affects chicks’ performance.
Positional SHAP (PoSHAP) for Interpretation of Machine Learning Models Trained from Biological Sequences
Authors: Dickinson Quinn , Meyer Jesse G. 
Published: March 2021

AbstractMachine learning with multi-layered artificial neural networks, also known as “deep learning,” is effective for making biological predictions. However, model interpretation is challenging, especially for sequential input data used with recurrent neural network architectures. Here, we introduce a framework called “Positional SHAP” (PoSHAP) to interpret models trained from biological sequences by utilizing SHapely Additive exPlanations (SHAP) to generate positional model interpretations. We demonstrate this using three long short-term memory (LSTM) regression models that predict peptide properties, including binding affinity to major histocompatibility complexes (MHC), and collisional cross section (CCS) measured by ion mobility spectrometry. Interpretation of these models with PoSHAP reproduced MHC class I (rhesus macaque Mamu-A1*001 and human A*11:01) peptide binding motifs, reflected known properties of peptide CCS, and provided new insights into interpositional dependencies of amino acid interactions. PoSHAP should have widespread utility for interpreting a variety of models trained from biological sequences.
Haplotype-aware variant calling enables high accuracy in nanopore long-reads using deep neural networks
Authors: Shafin Kishwar , Pesout Trevor , Chang Pi-Chuan , Nattestad Maria , Kolesnikov Alexey , Goel Sidharth , Baid Gunjan , Eizenga Jordan M. , Miga Karen H. , Carnevali Paolo , Jain Miten , Carroll Andrew , Paten Benedict 
Published: March 2021

AbstractLong-read sequencing has the potential to transform variant detection by reaching currently difficult-to-map regions and routinely linking together adjacent variations to enable read based phasing. Third-generation nanopore sequence data has demonstrated a long read length, but current interpretation methods for its novel pore-based signal have unique error profiles, making accurate analysis challenging. Here, we introduce a haplotype-aware variant calling pipeline PEPPER-Margin-DeepVariant that produces state-of-the-art variant calling results with nanopore data. We show that our nanopore-based method outperforms the short-read-based single nucleotide variant identification method at the whole genome-scale and produces high-quality single nucleotide variants in segmental duplications and low-mappability regions where short-read based genotyping fails. We show that our pipeline can provide highly-contiguous phase blocks across the genome with nanopore reads, contiguously spanning between 85% to 92% of annotated genes across six samples. We also extend PEPPER-Margin-DeepVariant to PacBio HiFi data, providing an efficient solution with superior performance than the current WhatsHap-DeepVariant standard. Finally, we demonstratede novoassembly polishing methods that use nanopore and PacBio HiFi reads to produce diploid assemblies with high accuracy (Q35+ nanopore-polished and Q40+ PacBio-HiFi-polished).
Induction ofBdnffrom promoter I following electroconvulsive seizures contributes to structural plasticity in neurons of the piriform cortex
Authors: Ramnauth Anthony D. , Maynard Kristen R. , Kardian Alisha S. , Phan BaDoi , Tippani Madhavi , Rajpurohit Sumita , Hobbs John W. , Page Stephanie Cerceo , Jaffe Andrew E. , Martinowich Keri 
Published: March 2021

ABSTRACTThe efficacy of electroconvulsive therapy (ECT) as a treatment for psychiatric disorders, including major depressive disorder (MDD) is hypothesized to depend on induction of molecular and cellular events that trigger structural plasticity in neurons. Electroconvulsive seizures (ECS) in animal models can help to inform our understanding of how electroconvulsive therapy (ECT) impacts the brain. ECS induces structural plasticity in neuronal dendrites in many brain regions, including the piriform cortex, a highly epileptogenic region that has also been implicated in depression. ECS-induced structural plasticity is associated with differential expression of unique isoforms encoding the neurotrophin, brain-derived neurotrophic factor (BDNF), but the functional significance of these transcripts in dendritic plasticity is not clear. Here, we demonstrate that differentBdnfisoforms are expressed non-stochastically across neurons of the piriform cortex following ECS. Specifically, cells expressingBdnfexon 1-containing transcripts show a unique spatial recruitment pattern in response to ECS. We further demonstrate thatBdnfEx1 expression in these cells is necessary for ECS-induced dendritic spine plasticity.
IgM+and IgM-memory B cells represent heterogeneous populations capable of producing class-switched antibodies and germinal center B cells upon re-challenge withP. yoelii
Authors: Brown Susie L. , Bauer Jonathan J. , Lee Juhyung , Ntirandekura Enatha , Stumhofer Jason S. 
Published: March 2021

AbstractMemory B cells (MBCs) are essential for maintaining long-term humoral immunity to infectious organisms, includingPlasmodium. MBCs are a heterogeneous population whose function can be dictated by isotype or expression of particular surface proteins. Here, aided by antigen-specific B-cell tetramers, MBC populations were evaluated to discern their phenotype and function in response to infection with a non-lethal strain ofP. yoelii. Infection of mice withP. yoelii17X resulted in the production of two predominant MBC populations: somatically hypermutated isotype-switched (IgM-) and IgM+MBCs that co-expressed CD73 and CD80 that produced antigen-specific antibodies in response to secondary infection. Re-challenge experiments indicated that IgG-producing cells dominated the recall response over the induction of IgM-secreting cells, with both populations expanding with similar timing during the secondary response. Furthermore, using ZsGreen1 expression as a surrogate for activation-induced cytidine deaminase expression alongside CD73 and CD80 co-expression, ZsGreen1+CD73+CD80+IgM+MBCs gave rise to class-switched IgG-producing plasmablasts that induced comparable titers of Ag-specific Abs as their IgM-counterparts after adoptive transfer and infection withP. yoelii. Moreover, ZsGreen1+CD73+CD80+IgM+and IgM-MBCs differentiated into B cells with a germinal center phenotype after adoptive transfer. A third population of B cells (ZsGreen1-CD73-CD80-IgM-) that emerges after infection responded poorly to reactivation in vitro and in vivo, indicating that these cells do not represent a population of MBCs. Together these data indicated that MBC function is not defined by immunoglobulin isotype, nor does co-expression of key surface markers limit the potential fate of MBCs after recall.SummaryIgM+and IgM-MBCs that co-express CD73 and CD80 can differentiate into plasmablasts and GC B cells after re-challenge withP. yoelii.
Structural insights into plasticity and discovery of remdesivir metabolite GS-441524 binding in SARS-CoV-2 macrodomain
Authors: Ni Xiaomin , Schröder Martin , Olieric Vincent , Sharpe May E. , Olmos Victor , Proschak Ewgenij , Merk Daniel , Knapp Stefan , Chaikuad Apirat 
Published: March 2021

ABSTRACTThe nsP3 macrodomain is a conserved protein interaction module that plays essential regulatory roles in host immune response by recognizing and removing posttranslational ADP-ribosylation sites during SARS-CoV-2 infection. Thus, targeting this protein domain may offer a therapeutic strategy to combat the current and future virus pandemics. To assist inhibitor development efforts, we report here a comprehensive set of macrodomain crystal structures complexed with diverse naturally-occurring nucleotides, small molecules as well as nucleotide analogues including GS-441524 and its phosphorylated analogue, active metabolites of remdesivir. The presented data strengthen our understanding of the SARS-CoV-2 macrodomain structural plasticity and it provides chemical starting points for future inhibitor development.
Large-scale placenta DNA methylation mega-analysis reveals fetal sex-specific differentially methylated CpG sites and regions
Authors: Andrews Shan V. , Yang Irene J. , Froehlich Karolin , Oskotsky Tomiko , Sirota Marina 
Published: March 2021

AbstractAlthough male-female differences in placental structure and function have been observed, little is understood about their molecular underpinnings. Here, we present a mega-analysis of 14 publicly available placenta DNA methylation (DNAm) microarray datasets to identify individual CpGs and regions associated with fetal sex. In the discovery dataset of placentas from full term pregnancies (N = 532 samples), 5,212 CpGs met genome-wide significance (p < 1E-8) and were enriched in pathways such as keratinization (FDR p-value = 7.37E-14), chemokine activity (FDR p-value = 1.56E-2), and eosinophil migration (FDR p-value = 1.83E-2). Nine differentially methylated regions were identified (fwerArea < 0.1) including a region in the promoter ofZNF300that showed consistent differential DNAm in samples from earlier timepoints in pregnancy and appeared to be driven predominately by effects in the trophoblast cell type. We describe the largest study of fetal sex differences in placenta DNAm performed to date, revealing genes and pathways characterizing sex-specific placenta function and health outcomes later in life.
A genetic screen for regulators of muscle morphogenesis inDrosophila
Authors: Ou Tiffany , Huang Gary , Wilson Beth , Gontarz Paul , Skeath James B. , Johnson Aaron N. 
Published: March 2021

AbstractThe mechanisms that determine the final topology of skeletal muscles remain largely unknown. We have been developingDrosophilabody wall musculature as a model to identify and characterize the pathways that control muscle size, shape, and orientation during embryogenesis (Johnson et al., 2013; Williams et al., 2015; Yang et al., 2020a; Yang et al., 2020b). Our working model argues muscle morphogenesis is regulated by (1) extracellular guidance cues that direct muscle cells toward muscle attachment sites, and (2) contact dependent interactions between muscles and tendons. While we have identified several pathways that regulate muscle morphogenesis, our understanding is far from complete. Here we report the results of a recent EMS-based forward genetic screen that identified a myriad of loci not previously associated with muscle morphogenesis. We recovered new alleles of known muscle morphogenesis genes, includingbsd, kon, ths, andtum, arguing our screening strategy was effective and efficient. We also identified and sequenced new alleles ofsalm,barr, andptcthat presumably disrupt independent pathways directing muscle morphogenesis. Equally as important, our screen shows that at least 11 morphogenetic loci remain to be identified. This screen has developed exciting new tools to study muscle morphogenesis, which may provide future insights into the mechanisms that determine skeletal muscle topology.
Localised expression ofOsIAA29suggests a key role for auxin in regulating development of the dorsal aleurone of early rice grains
Authors: Basunia Mafroz A. , Nonhebel Heather M. , Backhouse David , McMillan Mary 
Published: March 2021

AbstractEndosperm of rice and other cereals accumulates high concentrations of the predominantin plantaauxin, indole-3-acetic acid (IAA) during early grain development. However, IAA signalling and function during endosperm development are poorly understood. Here, we report thatOsYUC12(an auxin biosynthesis gene) andOsIAA29(encoding a non-canonical AUX/IAA) are both expressed exclusively in grains, reaching a maximum 5 to 6 days after pollination.OsYUC12expression is localized in the aleurone, sub-aleurone and embryo, whereasOsIAA29expression is restricted to a narrow strip in the dorsal aleurone, directly under the vascular bundle. Although rice has been reported to lack endosperm transfer cells (ETCs), this region of the aleurone is enriched with sugar transporters and is likely to play a key role in apoplastic nutrient transfer, analogous to ETCs in other cereals.OsIAA29has orthologues only in grass species; expression of which is also specific to early grain development.OsYUC12andOsIAA29are temporally co-expressed with two genes(AL1andOsPR602)previously linked to the development of dorsal aleurone or ETCs. Also up regulated at the same time are a cluster of MYB-related genes (designatedOsMRPLs)homologous toZmMRP-1,which regulates maize ETC development. Wheat homologues ofZmMRP-1are also expressed in ETCs. Although previous work has suggested that other cereals do not have orthologues of ZmMRP-1, our work suggests OsIAA29 and OsMRPLs and their homologues in other grasses are part of an auxin-regulated, conserved signalling network involved in the differentiation of cells with ETC-like function in developing cereal grains.Main ConclusionNon-canonical AUX/IAA protein, OsIAA29, and ZmMPR-1 homologues, OsMRPLs, are part of an auxin-related signalling cascade operating in the dorsal aleurone during early rice grain development.
Compound- and fiber type-selective requirement of AMPKγ3 for insulin-independent glucose uptake in skeletal muscle
Authors: Rhein Philipp , Desjardins Eric M. , Rong Ping , Ahwazi Danial , Bonhoure Nicolas , Stolte Jens , Santos Matthieu D. , Ovens Ashley J. , Ehrlich Amy M. , Garcia José L. Sanchez , Ouyang Qian , Kjolby Mads F. , Membrez Mathieu , Jessen Niels , Oakhill Jonathan S. , Treebak Jonas T. , Maire Pascal , Scott John W. , Sanders Matthew J. , Descombes Patrick , Chen Shuai , Steinberg Gregory R. , Sakamoto Kei 
Published: March 2021

ABSTRACTObjective:The metabolic master-switch AMP-activated protein kinase (AMPK) mediates insulin-independent glucose uptake in muscle and regulates the metabolic activity of brown and beige adipose tissue (BAT). The regulatory AMPKγ3 isoform is uniquely expressed in skeletal muscle and also potentially in BAT. Here, we investigated the role that AMPKγ3 plays in mediating skeletal muscle glucose uptake and whole-body glucose clearance in response to small-molecule activators that act on AMPK via distinct mechanisms. We also assessed if γ3 plays a role in adipose thermogenesis and browning.Methods:Global AMPKγ3 knockout (KO) mice were generated. A systematic whole-body, tissue and molecular phenotyping linked to glucose homeostasis was performed in γ3 KO and wild type (WT) mice. Glucose uptake in glycolytic and oxidative skeletal muscleex vivo,as well as blood glucose clearance in response to small molecule AMPK activators that target nucleotide-binding domain of γ subunit (AICAR) and allosteric drug and metabolite (ADaM) site located at the interface of the α and β subunit (991, MK-8722) were assessed. Oxygen consumption, thermography, and molecular phenotyping with a β3-adrenergic receptor agonist (CL-316,243) treatment were performed to assess BAT thermogenesis, characteristics and function.Results:Genetic ablation of γ3 did not affect body weight, body composition, physical activity, and parameters associated with glucose homeostasis under chow or high fat diet. γ3 deficiency had no effect on fiber-type composition, mitochondrial content and components, or insulin-stimulated glucose uptake in skeletal muscle. Glycolytic muscles in γ3 KO mice showed a partial loss of AMPKα2 activity, which was associated with reduced levels of AMPKα2 and β2 subunit isoforms. Notably, γ3 deficiency resulted in a selective loss of AICAR-, but not MK-8722-induced blood glucose-loweringin vivoand glucose uptake specifically in glycolytic muscleex vivo. We detected γ3 in BAT and found that it preferentially interacts with α2 and β2. We observed no differences in oxygen consumption, thermogenesis, morphology of BAT and inguinal white adipose tissue (iWAT), or markers of BAT activity between WT and γ3 KO mice.Conclusions:These results demonstrate that γ3 plays a key role in mediating AICAR- but not ADaM site binding drug-stimulated blood glucose clearance and glucose uptake specifically in glycolytic skeletal muscle. We also showed that γ3 is dispensable for thermogenesis and browning of iWAT.
Open space and sense of community of older adults: a study in a residential area in Hong Kong
Authors: Yu Andrew 
Published: March 2021

PurposeThis study examines the relationship between quality and quantity of open space in residential areas and the sense of community of Chinese older adults in Hong Kong.Design/methodology/approachA survey was conducted with 257 adults aged 55 and over in Kwun Tong, Hong Kong. The quality of open space was assessed from four dimensions: social and recreational facilities, entrance, location and environment. Geographic information system (GIS) was used to evaluate the quantity of open space in terms of size and amount.FindingsThe result shows that the environment has a strong influence on the sense of community, while the quantity of open space does not. The results provide urban planners with evidence for open space planning in the future. Urban planners should consider building more people-oriented environment; such as green areas instead of merely increasing the size, amount and facilities of open space. The Hong Kong Government also needs to review the current standardised planning guideline in order to maximise the social connection of older adults.Originality/valueThis cross-sectional study tried to understand the relationship between the quality and quantity of open spaces and sense of community in Chinese older adults in Hong Kong. It is one of the few studies to simultaneously examine both the quality and quantity of open spaces when studying its relationship with sense of community.
Identification and ordering of safety performance indicators using fuzzy TOPSIS: a case study in Indian construction company
Authors: Singh Arpit , Misra Subhas C. , Kumar Vinod , Kumar Uma 
Published: March 2021

PurposeThe purpose of this paper is to propose a practical framework to measure the safety performance of workers in the Indian construction industry. The key safety performance indicators are identified and ordered on the premise that the higher order assignment of an indicator implies a strong indication of an effective safety performance.Design/methodology/approachVarious indicators of safety performance in the construction industry were identified from extant literature review combined with author's personal viewpoint. The identified variables were inquired for appropriateness for the Indian construction scenario by consultation with experts. Fuzzy Technique for order preference by similarity to ideal solution (TOPSIS) technique was considered for the ranking of the indicators from most to least important.FindingsThe most important highlight of the study was the importance of the role of management by participating in informing workers about the safety rules and compliance toward safety measures. Proper and timely safety training to the workers and equipping them with sophisticated safety equipment for daily activities is perceived to be highly important in ensuring a safe and healthy workplace environment. Controlling the absenteeism rate reduces the burden of extra work on the employees, thereby, encouraging safe work-related behavior.Originality/valueSenior management should make safety induction programs compulsory at the time of joining of the employees. The guidelines for safety practices, rules and information about the safety equipment should be properly documented and arranged in safety manuals. Periodical drills involving visual demonstration of the safety practices should be followed to ensure safety at workplace.
Occupational choices in art and agriculture – a mixed-method web scraping approach
Authors: Mann Stefan 
Published: March 2021

PurposeEmpirical studies on occupational choice have typically concentrated on a specific sector. The purpose of this study is to compare two sectors wherein there are grounds to hypothesise that lifestyle reasons play a key role for occupational choice.Design/methodology/approachArguing that the potential for qualitative web scraping is still underused, the hypothesis is tested through qualitative web scraping for occupational choices.FindingsIt is shown that incomes for farmers are both documented in a better way and higher than in arts. The central roles played by farmers in the provision of basic needs and in powerful value chains are possible reasons for this difference. As a common factor between the sectors, two-thirds of both farmers and artists choose their profession for reasons of self-realisation or societal motives.Originality/valueThis study is the first to show both common grounds and differences in occupational choices of two different sectors.
Failure learning and entrepreneurial resilience: the moderating role of firms’ knowledge breadth and knowledge depth
Authors: Yao Kai , Li Xiaolin , Liang Bang 
Published: March 2021

PurposeDrawing on the knowledge-based view, the purpose of this study is to investigate the differential effects of failure normalization (FN) and failure analysis (FA) on entrepreneurial resilience (ER) and examines how firms’ knowledge breadth (KB) and knowledge depth (KD) moderate these effects in distinctive ways.Design/methodology/approachThe study uses a mixed-methods approach, including a two-wave survey study among 226 entrepreneurial high-tech firms in China and a qualitative study.FindingsThe findings reveal that FA has a stronger positive effect on ER than FN. KB enhances the effect of FA on ER, whereas KD enhances the effect of FN on ER but buffers the effect of FA on ER.Practical implicationsThe study advocates that entrepreneurs need to be aware of the importance of ER and strengthen the reflection on failure. Additionally, the study suggests that entrepreneurs should match FN and FA with firms’ knowledge characteristics. With this match, KB and KD can exert greater impacts on the effect of failure learning on ER.Originality/valueKnowledge can influence the effect of learning on firm capability. However, such an effect in entrepreneurial firms linking to ER remains to be explored. This study contributes to ER from the failure learning perspective and extends knowledge management theory in the entrepreneurship context.
The Challenges of Implementing Anti‐Money Laundering Regulation: An Empirical Analysis
Authors: Zavoli Ilaria , King Colin 
Published: March 2021

AbstractFor over three decades, money laundering has been an area of concern for policymakers and law enforcement, with significant efforts undertaken at national and international levels to combat it. Recently, laundering of criminal proceeds using real property has attracted increased attention amongst policymakers. Various efforts are now being undertaken to tackle money laundering in the UK property market, but there are still significant difficulties in its practical implementation. Drawing upon semi‐structured interviews with estate agents and compliance officials, this study identifies critical aspects of AML compliance that are particularly problematic for those involved in it. In so doing, this article delivers a new perspective, by analysing data gathered with the first empirical study on the implementation of AML obligations in practice (in the UK property market) since the introduction of the 2017 Money Laundering Regulations.