bluuebunny/crossref_metadata_2025_split huggingface dataset:
Brief report: Attentional Bias towards Social Interactions during Viewing of Naturalistic Scenes
Authors: Skripkauskaite Simona , Mihai Ioana , Koldewyn Kami 
Published: February 2021

AbstractHuman visual attention is readily captured by the social information in scenes. Multiple studies have shown that social areas of interest (AOIs) such as faces and bodies attract more attention than non-social AOIs (e.g. objects or background). However, whether this attentional bias is moderated by the presence (or absence) of a social interaction remains unclear. Here, the gaze of 70 young adults was tracked during the free viewing of 60 naturalistic scenes. All photographs depicted two people, who were either interacting or not. Analyses of dwell time revealed that more attention was spent on human than background AOIs in the interactive pictures. In non-interactive pictures, however, dwell time did not differ between AOI type. In the time-to-first-fixation analysis, humans always captured attention before other elements of the scene, although this difference was slightly larger in interactive than non-interactive scenes. These findings confirm the existence of a bias towards social information in attentional capture, and suggest that the presence of social interaction may be important in inducing a similar social bias in attentional engagement. Together with previous research using less naturalistic stimuli, these findings suggest that social interactions carry additional social value that guides one’s perceptual system.
Gene regulatory networks for compatible versus incompatible grafts identify a role for SlWOX4 during junction formation
Authors: Thomas Hannah , Van den Broeck Lisa , Spurney Ryan , Sozzani Rosangela , Frank Margaret 
Published: February 2021

AbstractGraft incompatibility is a poorly understood phenomenon that presents a serious agricultural challenge. Unlike immediate incompatibility that results in rapid death, delayed incompatibility can take months or even years to manifest, creating a significant economic burden for perennial crop production. To gain insight into the genetic mechanisms underlying this phenomenon, we developed a model system withSolanum lycopersicum‘tomato’ andCapsicum annuum‘pepper’ heterografting, which expresses signs of anatomical junction failure within the first week of grafting. By generating a detailed timeline for junction formation we were able to pinpoint the cellular basis for this delayed incompatibility. Furthermore, we infer gene regulatory networks for compatible self-grafts versus incompatible heterografts based on these key anatomical events, which predict core regulators for grafting. Finally, we delve into the role of vascular development in graft formation and validate SlWOX4 as a regulator for grafting in tomato. Notably, SlWOX4 is the first gene to be functionally implicated in vegetable crop grafting.
Dual targeting of salt inducible kinases and CSF1R uncouples bone formation and bone resorption
Authors: Tang Cheng-Chia , Castro Andrade Christian D. , Omeara Maureen J. , Yoon Sung-Hee , Brooks Daniel J. , Bouxsein Mary L. , da Silva Martins Janaina , Wang Jinhua , Gray Nathanael S. , Misof Barbara M. , Roschger Paul , Blouin Stéphane , Klaushofer Klaus , Veldhuis-Vlug Annegreet , Vegting Yosta , Rosen Clifford J. , O’Connell Daniel J. , Sundberg Thomas B. , Xavier Ramnik J. , Ung Peter M.U. , Schlessinger Avner , Kronenberg Henry M. , Berdeaux Rebecca , Foretz Marc , Wein Marc N. 
Published: February 2021

AbstractBone formation and resorption are typically coupled, such that the efficacy of anabolic osteoporosis treatments may be limited by bone destruction. The multi-kinase inhibitor YKL-05-099 potently inhibits salt inducible kinases (SIKs) and may represent a promising new class of bone anabolic agents. Here we report that YKL-05-099 increases bone formation in hypogonadal female mice without increasing bone resorption. Postnatal mice with inducible, global deletion of SIK2 and SIK3 show increased bone mass, increased bone formation, and, distinct from the effects of YKL-05-099, increased bone resorption. No cell-intrinsic role of SIKs in osteoclasts was noted. In addition to blocking SIKs, YKL-05-099 also binds and inhibits CSF1R, the receptor for the osteoclastogenic cytokine M-CSF. Modeling reveals that YKL-05-099 binds to SIK2 and CSF1R in a similar manner. Dual targeting of SIK2/3 and CSF1R induces bone formation without concomitantly increasing bone resorption and thereby may overcome limitations of most current anabolic osteoporosis therapies.
High-throughput functional analysis of natural variants in yeast
Authors: Yeh Chiann-Ling C. , Tsouris Andreas , Schacherer Joseph , Dunham Maitreya J. 
Published: February 2021

AbstractHow natural variation affects phenotype is difficult to determine given our incomplete ability to deduce the functional impact of the polymorphisms detected in a population. Although current computational and experimental tools can predict and measure allele function, there has previously been no assay that does so in a high-throughput manner while also representing haplotypes derived from wild populations. Here, we present such an assay that measures the fitness of hundreds of natural alleles of a given gene without site-directed mutagenesis or DNA synthesis. With a large collection of diverseSaccharomyces cerevisiaenatural isolates, we piloted this technique using the geneSUL1, which encodes a high-affinity sulfate permease that, at increased copy number, can improve the fitness of cells grown in sulfate-limited media. We cloned and barcoded all alleles from a collection of over 1000 natural isolatesen masseand matched barcodes with their respective variants using PacBio long-read sequencing and a novel error-correction algorithm. We then transformed the reference S288C strain with this library and used barcode sequencing to track growth ability in sulfate limitation of lineages carrying each allele. We show that this approach allows us to measure the fitness conferred by each allele and stratify functional and nonfunctional alleles. Additionally, we pinpoint which polymorphisms in both coding and noncoding regions are detrimental to fitness or are of small effect and result in intermediate phenotypes. Integrating these results with a phylogenetic tree, we observe how often loss-of-function occurs and whether or not there is an evolutionary pattern to our observable phenotypic results. This approach is easily applicable to other genes. Our results complement classic genotype-phenotype mapping strategies and demonstrate a high-throughput approach for understanding the effects of polymorphisms across an entire species which can greatly propel future investigations into quantitative traits.
VCFCons: a versatile VCF-based consensus sequence generator for small genomes
Authors: Tseng Elizabeth , Zeng Qiandong , Iyer Lax 
Published: February 2021

AbstractWe had developed VCFCons to address urgent need for a robust consensus sequence generator for SARS-CoV-2 viral surveillance, which presented several unique requirements, including: (a) low coverage areas should be noted with ‘N’s, (b) low frequency or suspicious variant calls need to be filtered. We have found that, while some existing tools such as bcftools can generate the desired consensus sequence, it required multiple filtering steps and additional scripting. VCFCons can generate consensus sequences based on variant calls in a VCF format with versatile filtering criteria based on coverage and estimated variant frequency. We applied VCFCons to the Labcorp SARS-CoV-2 sequencing data and showed that it generated correct consensus sequences that were successfully submitted to GISAID and NCBI. We hope the community will find value in this tool and aim to continue developing VCFCons to handle more complex viral data in the future.
High and low expression of the hyperpolarization activated current (Ih) in mouse CA1 stratum oriens interneurons
Authors: Hewitt Lauren T. , Ordemann Gregory J. , Brager Darrin H. 
Published: February 2021

AbstractInhibitory interneurons are among the most diverse cell types in the brain; the hippocampus itself contains more than 28 different inhibitory interneurons. Interneurons are typically classified using a combination of physiological, morphological and biochemical observations. One broad separator is action potential firing: low threshold, regular spiking vs. higher threshold, fast spiking. We found that spike frequency adaptation (SFA) was highly heterogeneous in low threshold interneurons in the mouse stratum oriens region of area CA1. Analysis with a k-means clustering algorithm parsed the data set into two distinct clusters based on a constellation of physiological parameters and reliably sorted strong and weak SFA cells into different groups. Interneurons with strong SFA fired fewer action potentials across a range of current inputs and had lower input resistance compared to cells with weak SFA. Strong SFA cells also had higher sag and rebound in response to hyperpolarizing current injections. Morphological analysis shows no difference between the two cell types and the cell types did not segregate along the dorsal-ventral axis of the hippocampus. Strong and weak SFA cells were labeled in hippocampal slices from SST:cre Ai14 mice suggesting both cells express somatostatin. Voltage-clamp recordings showed hyperpolarization activated current Ihwas significantly larger in strong SFA cells compared to weak SFA cells. We suggest that the strong SFA cell represents a previously uncharacterized type of CA1 stratum oriens interneuron. Due to the combination of physiological parameters of these cells, we will refer to them asLowThresholdHigh Ih(LTH) cells.Key PointsSpike frequency adaptation (SFA) was highly variable among stratum oriens interneuronsAdapting stratum oriens interneurons were separated into two cell groups using multiple subthreshold and action potential parameters by cluster analysisCells with strong SFA fired fewer action potentials for a given current injection, had lower input resistance and more sag and rebound compared to weak SFA cellsThe physiological differences were not correlated with neuron morphology, location in stratum oriens, or anatomical location along the dorsal-ventral axis of the hippocampusVoltage-clamp recordings revealed that strong SFA cells had higher density of the hyperpolarization activated current Ihcompared to weak SFA cells
NiftyTorch: A Deep Learning framework for NeuroImaging
Authors: Subramanian Adithya , Lan Haoyu , Govindarajan Sankareswari , Viswanathan Lavanya , Choupan Jeiran , Sepehrband Farshid 
Published: February 2021

AbstractWe present NiftyTorch a Deep Learning Framework for NeuroImaging. The motivation behind the development of such a library is that there are scant amount of centralized tool for deploying 3D deep learning for NeuroImaging. In addition, most of the existing tools require expert technical knowledge in Deep Learning or programming, creating a barrier for entry. The goal is to provide a one stop package using which the users can perform classification tasks, Segmentation tasks and Image Transformation tasks. The intended audience are the members of NeuroImaging who would like to explore deep learning but have no background in coding. In this article we explore the capabilities of the framework, the performance of the framework and the future work for the framework.
Amplicon sequence variants artificially split bacterial genomes into separate clusters
Authors: Schloss Patrick D. 
Published: February 2021

AbstractAmplicon sequencing variants (ASVs) have been proposed as an alternative to operational taxonomic units (OTUs) for analyzing microbial communities. ASVs have grown in popularity, in part, because of a desire to reflect a more refined level of taxonomy since they do not cluster sequences based on a distance-based threshold. However, ASVs and the use of overly narrow thresholds to identify OTUs increase the risk of splitting a single genome into separate clusters. To assess this risk, I analyzed the intragenomic variation of 16S rRNA genes from the bacterial genomes represented in arrncopy number database, which contained 20,427 genomes from 5,972 species. As the number of copies of the 16S rRNA gene increased in a genome, the number of ASVs also increased. There was an average of 0.58 ASVs per copy of the 16S rRNA gene for full length 16S rRNA genes. It was necessary to use a distance threshold of 5.25% to cluster full length ASVs from the same genome into a single OTU with 95% confidence for genomes with 7 copies of the 16S rRNA, such asE. coli. This research highlights the risk of splitting a single bacterial genome into separate clusters when ASVs are used to analyze 16S rRNA gene sequence data. Although there is also a risk of clustering ASVs from different species into the same OTU when using broad distance thresholds, those risks are of less concern than artificially splitting a genome into separate ASVs and OTUs.
Downsizing in plants - UV induces pronounced morphological changes in cucumber in the absence of stress
Authors: Qian Minjie , Rosenqvist Eva , Prinsen Els , Pescheck Frauke , Flygare Ann-Marie , Kalbina Irina , Jansen Marcel A.K. , Strid Åke 
Published: February 2021

AbstractUltraviolet (UV)-A- or UV-B-enrichment of growth light resulted in a stocky cucumber (Cucumis sativusL.) phenotype exhibiting decreased stem and petiole lengths and leaf area. Effects were larger in plants grown in UV-B- than in UV-A-enriched light. In plants grown in UV-A-enriched light, decreases in stem and petiole lengths were similar independently of tissue age. In the presence of UV-B radiation, stems and petioles were progressively shorter the younger the tissue. Also, plants grown under UV-A-enriched light significantly reallocated photosynthate from shoot to root and also had thicker leaves with decreased specific leaf area. Our data therefore imply different morphological plant regulatory mechanisms under UV-A and UV-B radiation. There was no evidence of stress in the UV-exposed plants, neither in photosynthetic parameters, total chlorophyll content, nor in accumulation of damaged DNA (cyclobutane pyrimidine dimers). The ABA content of the plants also was consistent with non-stress conditions. Parameters such as total leaf antioxidant activity, leaf adaxial epidermal flavonol content and foliar total UV-absorbing pigment levels revealed successful UV acclimation of the plants. Thus, the stocky UV-phenotype was displayed by healthy cucumber plants, implying a strong morphological response and regulatory adjustment as part of UV acclimation processes involving UV-A and/or UV-B photoreceptors.
Structural basis of substrate recognition and translocation by human ABCA4
Authors: Xie Tian , Zhang Zike , Du Bowen , Fang Qi , Gong Xin 
Published: February 2021

AbstractHuman ATP-binding cassette (ABC) subfamily A (ABCA) transporters mediate the transport of various lipid compounds across the membrane. Mutations in human ABCA transporters have been described to cause severe hereditary disorders associated with impaired lipid transport. However, little is known about the mechanistic details of substrate recognition and translocation by ABCA transporters. Here, we present three cryo-EM structures of human ABCA4, a retinal-specific ABCA transporter, in distinct functional states at resolutions of 3.3-3.4 Å. In the nucleotide-free state, the two transmembrane domains (TMDs) exhibited a lateral-opening conformation, allowing the lateral entry of substrate from the lipid bilayer. N-retinylidene-phosphatidylethanolamine (NRPE), the physiological lipid substrate of ABCA4, is sandwiched between the two TMDs in the luminal leaflet and is further stabilized by an extended loop from extracellular domain 1. In the ATP-bound state, the two TMDs displayed an unprecedented closed conformation, which precludes the substrate binding. Our study provides a molecular basis to understand the mechanism of ABCA4-mediated NRPE recognition and translocation, and suggests a common ‘lateral access and extrusion’ mechanism for ABCA-mediated lipid transport.
Co-design in the architectural process
Authors: Combrinck Carin , Porter Caitlin Jane 
Published: February 2021

PurposeDespite the proven importance of co-design as a way of improving the social relevance of architecture, there is a lack of opportunity for meaningful co-design processes in the current professional Master of Architecture programme in South Africa as it is largely modelled on the professional work stages of the South African Council for the Architecture Profession (SACAP), which are based on the assumption of primary authorship and authority of the architect.Design/methodology/approachThis problem has been investigated by way of ten workshops with high school learners in the Mamelodi East township in South Africa, as part of a professional master’s degree in architecture.FindingsThe findings of the workshops indicate that the initial stages of design could benefit directly from the participation processes and could be critiqued constructively. However, increased resistance to the process by crit panels was experienced once the sketch design phase was completed and the expectation of primary authorship increased. Engagement of the learners in the latter part of the design decision-making process also diminished as levels of experience in spatial design became evidently further removed from the expected outcomes.Research limitations/implicationsIn terms of co-design discourse and the evident value of participatory skills in practice, it is evident that the initial work stages of concept, brief and ideation are fairly easily assimilated into the pedagogical requirements of the degree programme and as such could enable a more socially relevant and responsive approach to professional practice.Practical implicationsThe South African standard of practising architecture leaves little space for the process of co-design, even within the educational environment. The value of co-design within this context lies predominantly in the values and conversations generated rather than the aesthetics of the end product. The process of co-design opens up the opportunity for new dialogues to emerge and for relationships to form.Social implicationsCo-design illustrates how architectural intelligence can be exercised in a much broader spatial field that acknowledges more than just the building itself but social, global, ecological and virtual networks, thereby changing how the authors design, what the authors design and who designs it.Originality/valueIt is in the realm of co-design that the beauty of architecture oscillates between strangeness and the ordinary. If the authors embrace the power of the collective and collaborative thinking, the authors are able to conceive new ways in the making of architecture. In order to arrive at this, however, the straightjacketed approach of modelling the master’s programme on professional work stages and outcomes needs to be challenged so that true transformation of the profession can be enabled through its pedagogical instruments.
Contemporary academic library users in Kenya: their needs and preferences in access and use of information resources
Authors: Ombogo Tandy M. , Namande Ben W. 
Published: February 2021

Purpose
The purpose of this study is to assess the influence of generations on information behavior and needs to access and use of library resources and how well academic libraries in Kenya are simultaneously serving both generations. From literature reviewed, a study on the Kenyan scenario on generational behavior and needs was not identified and this study sought to fill that gap.

Design/methodology/approach
Data collected were done through mixed-methods research using observation, structured interviews and questionnaires. The sample included 143 students and faculty within different generations, and three library staffs at The United States International University-Africa’s Library. Quantitative data were analyzed through SPSS and Excel, while qualitative data were analyzed according to the theme of this study. Likert-scale responses were used to measure information behavior of users’ needs and preferences.

Findings
Findings showed that the library is serving two distinct generations with different needs: out of a mean score of 5.00 of sample surveyed; digital immigrants need information resources mainly for research at an aggregate 3.93 while digital natives need information resources mainly for examinations at an aggregate 4.01. Both generations need to use technology to access and use information resources at 94% of digital immigrants and an aggregate 81.5% of digital natives surveyed. The library is training both user groups accordingly. This answered the research problem this study sought to assess.

Research limitations/implications
The generation of users was known only after administering the questionnaires. Consequently, the researcher targeted them using the status of respondents, faculty or student, to maximize sampling for each generation. Undergraduate and master’s students were used to target digital natives, while the faculty was used to target digital immigrants. PhD students were used to target both digital immigrants and digital natives. This study was done only in one location, USIU-Africa’s Library.

Originality/value
This study assessed how different generations within academic libraries in Kenya could be guided to effectively and efficiently adapt to global changes. This study assessed generational influence on needs and preferences in access and use of information resources, and assessed how academic libraries are concurrently and successfully serving variant user needs in Kenya,