bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trio-binned genomes of the woodratsNeotoma bryantiandN. lepidareveal novel gene islands and rapid copy number evolution of xenobiotic metabolizing cytochrome p450 genes
Authors: Greenhalgh Robert , Holding Matthew L. , Orr Teri J. , Henderson James B. , Parchman Thomas L. , Matocq Marjorie D. , Shapiro Michael D. , Dearing M. Denise 
Published: March 2021

AbstractThe genomic architecture underlying the origins and maintenance of biodiversity is an increasingly accessible feature of species, due in large part to third-generation sequencing and novel analytical toolsets. Woodrats of the genusNeotomaprovide a unique opportunity to study how vertebrate herbivores respond to climate change, as two sister species (N. bryantiandN. lepida) independently achieved a major dietary feat – switching to the novel and toxic food source creosote bush (Larrea tridentata) – in the aftermath of a natural warming event. To better understand the genetic mechanisms underlying this ability, we employed a trio binning sequencing approach with aN. bryanti×N. lepidaF1hybrid, resulting in phased, chromosome-level, highly complete, haploid genome assemblies for each species from one individual. Using these new assemblies, we explored the genomic architecture of three cytochrome p450 subfamilies (2A, 2B, and 3A) that play key roles in the metabolism of naturally occurring toxic dietary compounds. We found that woodrats show expansions of all three p450 gene families, including the evolution of multiple novel gene islands within the 2B and 3A subfamilies. Our assemblies demonstrate that trio binning from an F1hybrid rodent effectively recovers parental genomes from species that diverged more than a million years ago. Turnover and novelty in detoxification gene islands in herbivores is widespread within distinct p450 subfamilies, and may have provided the crucial substrate for dietary adaptation during environmental change.
Mitochondrial variant enrichment from high-throughput single-cell RNA-seq resolves clonal populations
Authors: Miller Tyler E. , Lareau Caleb A. , Verga Julia A. , Ssozi Daniel , Ludwig Leif S. , Farran Chadi El , Griffin Gabriel K. , Lane Andrew A. , Bernstein Bradley E. , Sankaran Vijay G. , van Galen Peter 
Published: March 2021

AbstractReconstructing lineage relationships in complex tissues can reveal mechanisms underlying development and disease. Recent methods combine single-cell transcriptomics with mitochondrial DNA variant detection to establish lineage relationships in primary human cells, but are not scalable to interrogate complex tissues. To overcome this limitation, here we develop a technology for high-confidence detection of mitochondrial mutations from high-throughput single-cell RNA-sequencing. We use the new method to identify skewed immune cell expansions in primary human clonal hematopoiesis.
Segmentation of Tissues and Proliferating Cells in Light-Sheet Microscopy Images using Convolutional Neural Networks
Authors: Lo Vercio Lucas D. , Green Rebecca M. , Robertson Samuel , Guo Si Han , Dauter Andreas , Marchini Marta , Vidal-García Marta , Zhao Xiang , Marcucio Ralph S. , Hallgrímsson Benedikt , Forkert Nils D. 
Published: March 2021

AbstractBackground and ObjectiveA variety of genetic mutations are known to affect cell proliferation and apoptosis during organism development, leading to structural birth defects such as facial clefting. Yet, the mechanisms how these alterations influence the development of the face remain unclear. Cell proliferation and its relation to shape variation can be studied in high detail using Light-Sheet Microscopy (LSM) imaging across a range of developmental time points. However, the large number of LSM images captured at cellular resolution precludes manual analysis. Thus, the aim of this work was to develop and evaluate automatic methods to segment tissues and proliferating cells in these images in an accurate and efficient way.MethodsWe developed, trained, and evaluated convolutional neural networks (CNNs) for segmenting tissues, cells, and specifically proliferating cells in LSM datasets. We compared the automatically extracted tissue and cell annotations to corresponding manual segmentations for three specific applications: (i) tissue segmentation (neural ectoderm and mesenchyme) in nuclear-stained LSM images, (ii) cell segmentation in nuclear-stained LSM images, and (iii) segmentation of proliferating cells in Phospho-Histone H3 (PHH3)-stained LSM images.ResultsThe automatic CNN-based tissue segmentation method achieved a macro-average F-score of 0.84 compared to a macro-average F-score of 0.89 comparing corresponding manual segmentations from two observers. The automatic cell segmentation method in nuclear-stained LSM images achieved an F-score of 0.57, while comparing the manual segmentations resulted in an F-score of 0.39. Finally, the automatic segmentation method of proliferating cells in the PHH3-stained LSM datasets achieved an F-score of 0.56 for the automated method, while comparing the manual segmentations resulted in an F-score of 0.45.ConclusionsThe proposed automatic CNN-based framework for tissue and cell segmentation leads to results comparable to the inter-observer agreement, accelerating the LSM image analysis. The trained CNN models can also be applied for shape or morphological analysis of embryos, and more generally in other areas of cell biology.
A cross-cohort analysis of autosomal DNA methylation sex differences in the term placenta
Authors: Inkster Amy M. , Yuan Victor , Konwar Chaini , Matthews Allison M. , Brown Carolyn J. , Robinson Wendy P. 
Published: March 2021

ABSTRACTBackgroundHuman placental DNA methylation (DNAme) data is a valuable resource for studying sex differences during gestation, as DNAme profiles after delivery reflect the cumulative effects of gene expression patterns and exposures across gestation. Here, we present an analysis of sex differences in autosomal patterns of DNAme in the uncomplicated term placenta (n=343) using the Illumina 450K array.ResultsUsing a false discovery rate < 0.05 and a mean sex difference in DNAme beta value of > 0.10, we identified 162 autosomal CpG sites that were differentially methylated by sex, and that replicated in an independent cohort of samples (n=293). Several of these differentially methylated CpG sites were part of larger correlated regions of differential DNAme, and many also exhibited sex-specific DNAme variability. Although global DNAme levels did not differ by sex, the majority of significantly differentially methylated CpGs were more highly methylated in male placentae, the opposite of what is seen in differential methylation analyses of somatic tissues. Interestingly, patterns of autosomal DNAme at these significantly differentially methylated CpGs organized placental samples along a continuum, rather than into discrete male and female clusters, and sample position along the continuum was significantly associated with maternal age and newborn birthweight standard deviation.ConclusionsOur results provide a comprehensive analysis of sex differences in autosomal DNAme in the term human placenta. We report a list of high-confidence autosomal sex-associated differentially methylated CpGs, and identify several key features of these loci that suggest their relevance to sex differences observed in normative and complicated pregnancies.
A low-cost, long-term underwater camera trap network coupled with deep residual learning image analysis
Authors: Bilodeau Stephanie M. , Schwartz Austin W. H. , Xu Binfeng , Pauca V. Paúl , Silman Miles R. 
Published: March 2021

AbstractUnderstanding long-term trends in marine ecosystems requires accurate and repeatable counts of fishes and other aquatic organisms on spatial and temporal scales that are difficult or impossible to achieve with diver-based surveys. Long-term, spatially distributed cameras, like those used in terrestrial camera trapping, have not been successfully applied in marine systems due to limitations of the aquatic environment.Here, we develop methodology for a system of low-cost, long-term camera traps (DispersedEnvironmentAquaticCameras), deployable over large spatial scales in remote marine environments. We use machine learning to classify the large volume of images collected by the cameras. We present a case study of these combined techniques’ use by addressing fish movement and feeding behavior related to grazing halos, a well-documented benthic pattern in shallow tropical reefscapes.Cameras proved able to function continuously underwater at deployed depths (up to 7 m, with later versions deployed to 40 m) with no maintenance or monitoring for over five months, and collected time-lapse images during daylight hours for a total of over 100,000 images. Our ResNet-50-based deep learning model achieved 92.5% overall accuracy in sorting images with and without fish, and diver surveys revealed that the camera images accurately represented local fish communities.The cameras and machine learning classification represent the first successful method for broad-scale underwater camera trap deployment, and our case study demonstrates the cameras’ potential for addressing questions of marine animal behavior, distributions, and large-scale spatial patterns.
Sub-stoichiometric Hsp104 regulates the genesis and persistence of self-replicable amyloid seeds of a yeast prion protein
Authors: Mahapatra Sayanta , Sarbahi Anusha , Madhu Priyanka , Swasthi Hema M. , Mukhopadhyay Samrat 
Published: March 2021

AbstractThe prion-like self-perpetuating conformational conversion is involved in both transmissible neurodegenerative diseases and non-Mendelian inheritance traits. The transmissibility of amyloid-like aggregates is dependent on the stoichiometry of chaperones such as heat shock proteins. To provide the mechanistic underpinning of the generation and persistence of prefibrillar amyloid seeds that are critical for the prion-like propagation, we studied the effect of Hsp104 disaggregase on the assembly mechanism of a yeast prion determinant ofSaccharomyces cerevisiaeSup35. At low sub-stoichiometric concentrations, Hsp104 exhibits a dual role and considerably accelerates the formation of seeding-competent prefibrillar amyloids by shortening the lag phase but also prolongs their persistence by introducing unusual kinetic halts and delaying their conversion into matured fibers. Hsp104-mediated amyloid species comprise a more ordered packing and display an enhanced autocatalytic self-templating ability compare to amyloids formed without Hsp104. Our findings underscore the key functional and pathological roles of sub-stoichiometric chaperones in prion-like propagation.
A Scalable Screening ofE. coliStrains for Recombinant Protein Expression
Authors: Morão Luana G. , Manzine Lívia R. , Clementino Lívia Oliveira D. , Wrenger Carsten , Nascimento Alessandro S. 
Published: March 2021

AbstractStructural biology projects are highly dependent on the large-scale expression of soluble protein and, for this purpose, heterologous expression using bacteria or yeast as host systems is usually employed. In this scenario, some of the parameters to be optimized include (i) those related to the protein construct, such as the use of a fusion protein, the choice of an N-terminus fusion/tag or a C-terminus fusion/tag; (ii) those related to the expression stage, such as the concentration and selection of inducer agent and temperature expression and (iii) the choice of the host system, which includes the selection of a prokaryotic or eukaryotic cell and the adoption of a strain. The optimization of some of the parameters related to protein expression, stage (ii), is straightforward. On the other hand, the determination of the most suitable parameters related to protein construction requires a new cycle of gene cloning, while the optimization of the host cell is less straightforward. Here, we evaluated a scalable approach for the screening of host cells for protein expression in a structural biology pipeline. We evaluated fourEscherichia colistrains looking for the best yield of soluble heterologous protein expression using the same strategy for protein construction and gene cloning and comparing it to our standard strain, Rosetta 2 (DE3). Using a liquid handling device (robot),E. colipT-GroE, Lemo21(DE3), Arctic Express (DE3), and Rosetta Gami 2 (DE3) strains were screened for the maximal yield of soluble heterologous protein recovery. For the genes used in this experiment, the Arctic Express (DE3) strain resulted in better yields of soluble heterologous proteins. We propose that screening of host cell/strain is feasible, even for smaller laboratories and the experiment as proposed can easily be scalable to a high-throughput approach.
Rewriting deficit storylines: the positioning of one fourth-grader as comics expert
Authors: Reid Stephanie Francesca , Moses Lindsey 
Published: March 2021

PurposeThis study took place in an elementary English language arts classroom during a comics writers workshop unit and focused on one fourth-grade author. This paper aims to explain how a fourth-grade student receiving special education services positions himself and is positioned by others as an expert during a unit on comics. When students’ knowledge about multimodal composition is recognized and valued, the classroom community can become a place where students can author themselves into positions of power and authority.Design/methodology/approachInformed by sociocultural theory, social semiotics and positioning theory, the authors conducted a qualitative study to analyze the focal participant’s published comic, classroom interactions and interview data using open and in vivo coding systems.FindingsThe findings documented how the focal participant was positioned as an expert by others and how he positioned himself as an expert. The findings also explore how this fourth-grade comics expert left an authorial residue that extended beyond the boundaries of this particular comics unit, impacting his teachers and future iterations of the comics workshop.Originality/valueScholars have theorized multimodal approaches to reading and writing pedagogy as an equitable enterprise that values meaning-makers using a wide variety of semiotic resources. This study shows how incorporating an explicit multimodal composition opportunity allowed one fourth-grade author space to craft a comic and re-author traditional classroom positions of power.
Improving data quality for human-as-a-security-sensor. A process driven quality improvement approach for user-provided incident information
Authors: Vielberth Manfred , Englbrecht Ludwig , Pernul Günther 
Published: March 2021

Purpose
In the past, people were usually seen as the weakest link in the IT security chain. However, this view has changed in recent years and people are no longer seen only as a problem, but also as part of the solution. In research, this change is reflected in the fact that people are enabled to report security incidents that they have detected. During this reporting process, however, it is important to ensure that the reports are submitted with the highest possible data quality. This paper aims to provide a process-driven quality improvement approach for human-as-a-security-sensor information.

Design/methodology/approach
This work builds upon existing approaches for structured reporting of security incidents. In the first step, relevant data quality dimensions and influencing factors are defined. Based on this, an approach for quality improvement is proposed. To demonstrate the feasibility of the approach, it is prototypically implemented and evaluated using an exemplary use case.

Findings
In this paper, a process-driven approach is proposed, which allows improving the data quality by analyzing the similarity of incidents. It is shown that this approach is feasible and leads to better data quality with real-world data.

Originality/value
The originality of the approach lies in the fact that data quality is already improved during the reporting of an incident. In addition, approaches from other areas, such as recommender systems, are applied innovatively to the area of the human-as-a-security-sensor.
Access to precision medicine in Thailand: a comparative study
Authors: Jirawutkornkul Nisita , Patikorn Chanthawat , Anantachoti Puree 
Published: March 2021

PurposeThis study explored health insurance coverage of genetic testing and potential factors associated with precision medicine (PM) reimbursement in Thailand.Design/methodology/approachThe study employed a targeted review method. Thirteen PMs were selected to represent four PM categories: targeted cancer therapy candidate, prediction of adverse drug reactions (ADRs), dose adjustment and cancer risk prediction. Content analysis was performed to compare access to PMs among three health insurance schemes in Thailand. The primary outcome of the study was evaluating PM test reimbursement status. Secondary outcomes included clinical practice guidelines, PMs statement in FDA-approved leaflet and economic evaluation.FindingsCivil Servant Medical Benefits Scheme (CSMBS) provided more generous access to PM than Universal Coverage Scheme (UCS) and Social Security Scheme (SSS). Evidence of economic evaluations likely impacted the reimbursement decisions of SSS and UCS, while the information provided in FDA-approved leaflets seemed to impact the reimbursement decisions of CSMBS. Three health insurance schemes provided adequate access to PM tests for some cancer-targeted therapies, while gaps existed for access to PM tests for serious ADRs prevention, dose adjustment and cancer risk prediction.Originality/valueThis was the first study to explore the situation of access to PMs in Thailand. The evidence alerts public health insurance schemes to reconsider access to PMs. Development of health technology assessment guidelines for PM test reimbursement decisions should be prioritized.
Politics and new media in ex/communist states – the example of Montenegro
Authors: Scekic Radenko , Lakic Slobodan , Pejanovic Ana 
Published: March 2021

Purpose
This study aims to explore the use of evolutionary and institutionalization models to understand the technical progression of sustainability in political organizations and their contribution to sustainable effectiveness. It describes the evolution of mass media, political marketing, in the organization’s strategy and design and the methods it is using to institutionalize this political and transition change.

Design/methodology/approach
The study describes models of sustainability evolution and political and technical change, in political and social life in transition state Montenegro.

Findings
Online and internet presentations of political programs, political blogs, sites that promote the national history and culture of the desired perception – the achievements have already risen in Montenegro in the first decade of the new millennium and beyond. Internet presentation of political subjects are reduced mainly to a brief presentation of history and of political parties, and mostly during the current election campaign, serving to inform the public about the program and promotion announcements.

Originality/value
The findings of this study will help senior executives with responsibility for transition states. The aim of this paper is to show the transformation of the media during the transition period from one political system to another. With the use of descriptive methodological postulates and numerous case studies. With a wealth of facts and examples, which contributes to the originality and value of the article. The significance and originality of this research and article is reflected in a comprehensive and multidisciplinary approach to the transition process and quantitative and qualitative development of the media.
Design and optimization of projection stereolithography additive manufacturing system with multi-pass scanning
Authors: Qin Qin , Huang Jigang , Yao Jin , Gao Wenxiang 
Published: March 2021

Purpose
Scanning projection-based stereolithography (SPSL) is a powerful technology for additive manufacturing with high resolution as well as large building area. However, the surface quality of stitching boundary in an SPSL system has been rarely studied, and no positive settlement was proposed to address the poor stitching quality. This paper aims to propose an approach of multi-pass scanning and a compensation algorithm for multi-pass scanning process to address the issue of poor stitching quality in SPSL systems.

Design/methodology/approach
The process of multi-pass scanning is realized by scanning regions repeatedly, and the regions can be cured simultaneously because of the very short repeat exposure time and very fast scanning. Then, the poor stitching quality caused by the non-simultaneous curing can be eliminated. Also, a compensation algorithm is designed for multi-pass scanning to reduce the stitching errors. The validity of multi-pass scanning is verified by curing depth test, while the performance of multi-pass scanning as well as proposed compensation algorithm is demonstrated by comparing with that of a previous SPSL system.

Findings
The results lead to a conclusion that multi-pass scanning with its compensation algorithm is an effective approach to improve the stitching quality of an SPSL system.

Practical implications
This study can provide advice for researchers to achieve the satisfactory surface finish with SPSL technology.

Originality/value
The authors proposed a process of multi-pass scanning as well as a compensation algorithm for SPSL additive manufacturing (system to improve the stitching quality, which has rarely been studied in previous work.