bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accurate Genome-Wide Phasing from IBD Data
Authors: Noto Keith , Ruiz Luong 
Published: April 2022

AbstractAs genotype databases increase in size, so too do the number of detectable segments of identity by descent (IBD): segments of the genome where two individuals share an identical copy of one of their two parental haplotypes, due to shared ancestry. We show that given a large enough genotype database, these segments of IBD collectively overlap entire chromosomes and can be used to phase them accurately. Furthermore, primarily using instances of IBD that span multiple chromosomes, we can accurately phase an entire genome.We are able to separate the DNA inherited from each parent completely, across the entire genome, with 98% median accuracy in a test set of 30,000 individuals. We estimate the IBD data requirements for accurate phasing, and we propose a method for estimating confidence in the resulting phase. We show that our methods do not require the genotypes of close family, and that they are robust to genotype errors and missing data. In fact, our method can impute missing data accurately and correct genotype errors.Author summaryWe present a method for phasing, separating the DNA inherited from each parent, of an entire genome using short segments of DNA that are shared between the genome of the person we wish to phase and those of distant cousins. Essentially, if we have enough of these distant cousins’ genotypes available, we can piece together overlapping segments until we have phased the entire genome.We have developed a method that can phase large numbers of individuals, and that makes special considerations for potential close family and potential genotype errors in data.We report results on experiments phasing 30,000 individuals. We analyze how many such segments are required to phase accurately, and propose a model-based method to estimate accuracy. We also show that our method can accurately impute missing data and correct genotype errors.
A Rapidin vivoPipeline to Identify Small Molecule Inhibitors of Amyloid Aggregation
Authors: Kamal Muntasir , Knox Jessica , Horne Robert I. , Tiwari Om Shanker , Burns Andrew R. , Han Duhyun , Bar-Yosef Dana Laor , Gazit Ehud , Vendruscolo Michele , Roy Peter J. 
Published: April 2022

AbstractAmyloids are associated with over 50 human diseases and have inspired significant effort to identify small molecule remedies. Here, we present a novelin vivoplatform that efficiently yields small molecule disruptors of amyloid formation. We previously identified small molecules that kill the nematodeC. elegansby forming membrane-piercing crystals in the pharynx cuticle, which is rich in amyloid-like material. We show here that many of these molecules are known amyloid-binders whose crystal-formation in the pharynx can be blocked by amyloid-binding dyes. Furthermore, we found that amyloid fibrils can seed small molecule crystal formationin vitro. These observations suggest that small molecule crystals are seeded by the cuticle’s amyloid-like material. We asked whether this phenomenon could be exploited to identify additional molecules that interfere with the ability of amyloids to seed higher-order structures. We screened 2560 compounds and identified 85 crystal suppressors, which we found to be 10-fold enriched in known amyloid disruptors relative to a random set. Of the uncharacterized suppressors, we found 25% to inhibit Ab42 fibril nucleation and/or extensionin vitro, which is a hit rate that far exceeds other screening methodologies. Hence, screens for suppressors of crystal formation can efficiently reveal small molecules with amyloid-disrupting potential.
Low-cost genomics enable high-throughput isolate screening and strain-level microbiome profiling
Authors: Sanders Jon G. , Yan Weiwei , Moeller Andrew H. 
Published: April 2022

AbstractEarth’s environments harbor complex consortia of microbial lineages that affect processes ranging from host health to biogeochemical cycles. However, understanding the evolution and function of these microbiota has been limited by an inability to isolate individual microbial constituents and assemble their complete genomes in a high-throughput manner. Here, we present a workflow for bacterial isolation and whole-genome sequencing from complex microbiota using open-source labware and the OpenTrons automated liquid handling robotics platform. Our approach circumvents the need for isolate screening (e.g., through 16S rDNA sequencing or mass spectrometry analyses) by reducing the costs of genome-sequencing to ~$10 per bacterium. Applying the workflow, we quantified genomic diversity within 45 bacterial species in the chimpanzee gut microbiota. Results revealed hotspots of recombination in bacterial genomes and elevated transmission of plasmids between distantly related bacterial species within individual chimpanzee hosts. This study develops and applies an approach for high-throughput bacterial isolation and genome sequencing, enabling population genetic analyses of bacterial strains within complex communities not currently possible with metagenomic data alone.
Transient Oxygen Exposure Causes Profound and Lasting Changes to a Benzene-Degrading Methanogenic Community
Authors: Guo Shen , Toth Courtney R. A. , Luo Fei , Chen Xu , Xiao Johnny , Edwards Elizabeth A. 
Published: April 2022

ABSTRACTWe investigated the impact of oxygen on a strictly anaerobic, methanogenic benzene-degrading enrichment culture derived decades ago from oil-contaminated sediment. The culture includes a benzene fermenter from Deltaproteobacteria Candidate clade Sva0485 (referred to as ORM2) and methanogenic archaea. A relatively small one-time injection of air, simulating a small leak into a batch culture bottle, had no measurable impact on benzene degradation rates, although retrospectively, a tiny enrichment of aerobic taxa was detected. A subsequent 100 times larger injection of air stalled methanogenesis and caused drastic perturbation of the microbial community. A benzene-degrading Pseudomonas became highly enriched and consumed benzene and all available oxygen. Anaerobic benzene-degrading ORM2 cell numbers plummeted during this time; re-growth and associated recovery of methanogenic benzene degradation took almost one year. These results highlight the oxygen-sensitivity of this methanogenic culture and confirm that the mechanism for anaerobic biotransformation of benzene is independent of oxygen, fundamentally different from established aerobic pathways, and is carried out by distinct microbial communities. The study further highlights the importance of including microbial decay in characterizing and modelling and mixed microbial communities.SYNOPSISMethanogenic benzene degradation in a highly enriched anaerobic consortium was inhibited for a year after transient exposure to oxygen, causing mass decay of benzene-fermenting bacteria.GRAPHIC FOR ABSTRACT ART
Faculty perceptions of the implementation of the United Arab Emirate's qualifications framework (QF Emirates) in federal higher education institutions
Authors: Elhakim Ahmed , Alhosani Mohamed 
Published: April 2022

PurposeThe purpose of this study is to examine faculty perceptions of the aim/structure of the United Arab Emirate's Qualifications Framework (QF Emirates) and its impact on academic practices in order to support policymakers on how to better implement the framework.Design/methodology/approachThe study applied a mixed-methods approach to obtain quantitative and qualitative feedback from faculty members from two of the largest higher education institutions in the United Arab Emirates (UAE), namely the UAE University (UAEU) and the Higher Colleges of Technology (HCT). A questionnaire was used to capture broad insight from a sample of 788 faculty members from both institutions. In addition, semistructured interviews were conducted with 20 faculty members to offer more in-depth analysis of how to improve QF Emirates strategies in light of the current challenges and future aspirations.FindingsThe study revealed that faculty members have an overall “average” to “high” perceptions of the general aim/structure of the QF Emirates and its impact on teaching, learning and assessment. Moreover, the study revealed that faculty from the HCT have a significantly higher perception of the QF Emirates implementation compared to faculty from the UAEU. The study concluded with proposing a number of solutions to support in improving the QF Emirates implementation, including raising awareness across stakeholders, identifying and communicating faculty roles in the process, and developing polices, guidelines and systems to support consistent integration of QF Emirates into academic practices.Originality/valueThe outcomes of this study would add to the existing body of knowledge pertaining to the role of stakeholders (e.g. faculty members) in the implementation of the national qualifications framework. It addition, it can drive future professional development activities and add to the discourse around the conceptual framework of NQFs. Outcomes of the study could also provide additional information on the use of the QF Emirates as a supporting instrument. Last but not least, this work could provide insight to policymakers in regard to institutional support that would promote effective adoption of the QF Emirates.
Housing affordability in a resource rich economy: the case of Kuwait
Authors: Alfalah Abdullah , Stevenson Simon , Heinig Steffen , D’Arcy Eamonn 
Published: April 2022

PurposeThis paper aims to improve the housing affordability by measuring the housing affordability in a resource-rich economy and studying the impact of implementing new policies.Design/methodology/approachThis paper seeks to test the impact of new policies introduced to the Kuwaiti housing market to improve affordability. In 2008, the Kuwaiti parliament introduced two policies: a tax on empty lands and, forbidding companies to own or develop residential lands or houses.FindingsBy constructing the housing affordability index and the price-to-income multiplier using observations from 2004 until 2017, it has been found that affordability has worsened over time regardless of the new policies introduced in 2008. Housing in Kuwait became “severely unaffordable” (equivalent to London in the UK, San Diego in USA and Toronto in Canada).Originality/valueEven with its unique condition, as a rich country, small population and availability of white land and other resources, the affordability worsened over time. Introducing new policies without solving the central issue of housing supply challenges seems not worth it. This paper is the first of its kind on the Kuwait housing market, and it provides a valuable foundation for future research on this market and similar markets in the region.
Psychological impact of domestic violence on women in India due to COVID-19
Authors: Tripathi Priyanka , Dwivedi Prabha S. , Sharma Shreya 
Published: April 2022

Purpose
The COVID-19 outbreak has significant psychological effects because of reduced support system and social quarantine, making women the worst-hit population of shadow pandemic, i.e. domestic violence. While food shortages, unemployment and increased domestic-work burdens are the immediate effects of the lockdown, women at home have to bear its far-reaching impacts in the long term in the form of domestic abuse, making the study of the psychological impact of domestic violence against women imperative. This paper aims to identify the factors and causes responsible for domestic violence and its psychological impacts on women in different aspects. This paper further focuses on the reasons behind an escalation in psychological violence against women.

Design/methodology/approach
This paper is based on extrapolating data from various journal articles, Indian Government reports, newspaper articles and other printed materials that are recent, relevant and discuss domestic violence and mental stress during the COVID-19 pandemic. Researchers use Indian National Commission for Women’s (NCW) data on complaints received regarding violence against women and domestic abuse in the year 2020 and 15 journal articles that discuss domestic violence against women during the COVID-19 period in different countries to discuss social inequalities and power relations impact on women’ mental health.

Findings
The findings suggest that economic instability during the pandemic and social and cultural norms of India ignited psychological abuse against women during the pandemic. The number of monthly complaints of dowry death, dowry harassment and protection of women against domestic violence reflect on increased registered complaints in the postlockdown period in the year 2020. The number of monthly complaints received by the NCW from January 2020 to December 2020 in India represents that WhatsApp chat is a powerful tool for reporting domestic violence.

Originality/value
The pandemic lockdown has an adverse psychological impact on women, making them suffer from posttraumatic symptoms, substance abuse, panic attacks, depressions, hallucinations, eating disorders, self-harm, etc. This paper strives to reflect upon mitigation strategies to curb domestic violence in India.
Performance measurement and management systems for dealing with strategies in uncertain ecosystems
Authors: Gomes Leonardo Augusto de Vasconcelos , Hourneaux Junior Flavio , Facin Ana Lucia Figueiredo , Leal Lorenna Fernandes 
Published: April 2022

PurposeAlthough there is a growing research stream on Performance Measurement and Management Systems (PMMS) in Ecosystems literature, current research offers limited theoretical insights into how PMMS deal with two types of strategies in uncertain ecosystems: ecosystem-based strategy – EBS (at the focal firm level) and ecosystem strategy – ES (at the ecosystem level). This study aims at identifying how PMMS are employed to deal with different types of strategies in uncertain ecosystems.Design/methodology/approachThe authors employed an inductive, rich multiple case approach in five focal firms with platform ecosystems. Data collection involved multiple sources of information (primary and secondary data), combing retrospective and longitudinal perspectives. Data analysis combined replication and comparison logic with coding.FindingsThis study identifies four major distinctive dimensions of Ecosystem PMMS under uncertainty: (1) Integrative Performance (considering the different ecosystem actors’ performance), (2) Interdependence Performance (mutual, yet not necessarily convergent amongst ecosystem partners), (3) Regulative Performance (paradoxical in nature, having to cope with both flexibility and stability) and finally (4) Phased Learning Performance (non-linear).Research limitations/implicationsOur primary contribution is a new framework for PMMS literature: a performance measurement and management system for dealing with strategies in ecosystems. This framework enables managing performance regarding both types of strategies (EBS and ES) and their interplay in uncertain ecosystems.Practical implicationsThe ecosystem management requires focal firms to measure and manage the overall ecosystem’s performance, and it varies according to the type of strategy adopted in each case. Our framework provides dimensions that guide firms to build and implement PMMS for an ecosystem consistent with the ES. Therefore, it may improve performance, especially in uncertain business contexts.Originality/valueThe findings enrich PMMS literature in an ecosystem context related to the ES in uncertain environments.
Water Poverty Index and its changing trend in India
Authors: Pandey Suchitra , Mohapatra Geetilaxmi , Arora Rahul 
Published: April 2022

PurposeThe purpose of this paper is to provide a picture of the water situation of the states of India and to identify key areas in which intervention is necessary for sustainable development and poverty elevation.Design/methodology/approachTo understand the trend and situation of water across the states, Water Poverty Index (WPI) has been constructed. WPI has been computed for the years 2012 and 2018 to get a picture of temporal change happening in the region. Further, descriptive statistics were used to show the required changes.FindingsJharkhand and Rajasthan continue to be the worst performer in both time periods. Water poverty was the least in the states of Goa and Chandigarh for both time periods. Although owing to improvement in access and capacity component, the water status of India as a whole improved from 2012 to 2018 but few states have witnessed a decline in their water situation mainly due to deterioration in the environment and resource components.Originality/valueThis paper adds to the relatively scarce literature on the water situation conducted for the states of India. The findings of the paper provide insights into the lacking areas responsible for the deterioration in water poverty status. The results can be utilized for framing proper policies to combat the water woes of the country.
Genotyping ofTrichophyton tonsuransstrains isolated between 2016 and 2020, and terbinafine susceptibility of the species in Japan
Authors: Futatsuya Taketoshi , Taga Fumiaki , Sakata Yuichi , Takeda Kiminobu , Anzawa Kazushi , Mochizuki Takashi , Shimizu Akira 
Published: April 2022

AbstractTrichophyton tonsuransis the most prevalent fungus which causes dermatophytosis among contact sports players in Japan. We previously surveyed the epidemic ofT. tonsuransin Japan from early 2000, and determined the genotypes of isolates by analysis of restriction enzyme fragment length polymorphisms in the non‐transcription spacer (NTS) region of ribosomal RNA gene, which enabled discrimination of eight genotypes, namely NTS I to NTS VIII. In the present study, we performed genotyping ofT. tonsuransisolated between 2016 and 2020, and investigated the trend of the epidemic and resistance of the pathogen to antibiotic terbinafine (TBF). Regardless of which contact sport they played, the genotype of all 123 strains ofT. tonsuransisolated from athletes was NTS I. Genotypes NTS II and III, which were isolated in considerable numbers mainly from wrestlers between 2000 and 2015, were conspicuously absent. TBF susceptibility was screened in 237T. tonsuransstrains isolated between 2000 and 2020 with 28 of these further assessed for minimum inhibitory concentration of TBF and squalene epoxidase gene sequences. None of the strains showed TBF resistance. TBF may still be effective to control the epidemic ofT. tonsurans.
Clinical management of deviations in maternal temperature during labour and childbirth: an evidence‐based intrapartum care algorithm
Authors: Blennerhassett A , Dunlop C , Lissauer D ,   the WHO Intrapartum Care Algorithms Working Group
Published: April 2022

AimThe development of an evidence‐based algorithm for the clinical management of deviations in maternal temperature during labour and childbirth.PopulationPregnant women at any stage of labour, with singleton, term (37–42 weeks) pregnancies at low risk of developing complications.SettingHealth facilities in low‐ and middle‐income countries.Search strategyWe searched for international guidelines and prioritised WHO guidelines. In addition, we searched for other sources of evidence in the Cochrane Database of Systematic Reviews, EMBASE, MEDLINE and CINAHL until June 2020. Studies were prioritised according to the hierarchy of evidence.Case scenariosTwo case scenarios were identified: maternal hyperthermia and hypothermia. We developed a single algorithm including both, due to commonalities in diagnosis, monitoring and management of underlying causes. The underlying conditions covered in the pathway include maternal sepsis and infection, chorioamnionitis, pyelonephritis, lower urinary tract and respiratory infections. Key decision points in the algorithm are suspicion of condition, definition, differential diagnosis, monitoring and management.ConclusionsWe present an evidence‐based algorithm to assist healthcare professionals in making decisions about appropriate clinical management of deviations in maternal temperature. Research is needed to assess the views of healthcare professionals and women accessing healthcare on the feasibility of implementing the algorithm.Tweetable abstractAn evidence‐based intrapartum care algorithm to support management of deviations in maternal temperature in labour and childbirth. #sepsis #maternitycare.
Acid‐treated high‐amylose corn starch suppresses high‐fat diet‐induced steatosis
Authors: Yoshida Ryutaro , Yano Yoshihiko , Hoshi Namiko , Okamoto Norihiro , Sui Yunlong , Yamamoto Atsushi , Asaji Naoki , Shiomi Yuuki , Yasutomi Eiichiro , Hatazawa Yuri , Hayashi Hiroki , Ueda Yoshihide , Kodama Yuzo 
Published: April 2022

ABSTRACTResistant starch (RS) has been reported to improve steatosis as well as obesity. Type 4 resistant starch (RS4), a chemically modified starch, is particularly hard to digest and suggesting higher efficacy. However, because the effects of RS4 on steatosis are not yet fully understood, the effects of RS4 on steatosis were examined using a murine high‐fat diet model. Seven‐week‐old male mice were divided into three groups and fed a normal diet, a high‐fat diet (HFD), or a high‐fat diet with added RS (HFD + RS). Amylofiber SH® produced from acid‐treated corn starch was used as the dietary RS. At 22 weeks old, hepatic steatosis and short chain fatty acid (SCFA) content and gut microbiota in cecum stool samples were analyzed. The ratio of body weight to 7 weeks was significantly suppressed in the HFD + RS group compared to the HFD group (132.2 ± 1.4% vs. 167.2 ± 3.9%, p = 0.0076). Macroscopic and microscopic steatosis was also suppressed in the HFD + RS group. Analysis of cecum stool samples revealed elevated SCFA levels in the HFD + RS group compared with the HFD group. Metagenome analysis revealed that Bifidobacterium (17.9 ± 1.9% vs. 3.6 ± 0.7%, p = 0.0019) and Lactobacillus (14.8 ± 3.4% vs. 0.72 ± 0.23%, p = 0.0045), which degrade RS to SCFA, were more prevalent in the HFD + RS group than the HFD group. In conclusion, RS4 suppressed steatosis, and increased Bifidobacterium and Lactobacillus, and SCFAs. RS4 may prevent steatosis by modulating the intestinal environment.
Accounting for R&D: Evidence and Implications*
Authors: Canace Thomas G. , Jackson Scott B. , Ma Tao , Zimbelman Aaron 
Published: April 2022

ABSTRACTAccounting rules require that certain R&D expenditures be capitalized, but academic research often states that all R&D expenditures must be immediately expensed. An accurate understanding of actual R&D accounting practices is critical because that understanding influences research questions and design choices. To examine the competing R&D accounting perspectives, we survey 184 experienced financial officers. Our survey reveals that R&D capitalization is common and extensive in practice. Over 90% of respondents indicate that their firm capitalizes at least some R&D expenditures, and our evidence shows that about 22% of annual R&D expenditures are capitalized. When facing an earnings shortfall, respondents indicate that firms are often willing to cut R&D expense. However, respondents also indicate an unwillingness to cut types of R&D expenses that cause long‐term harm—for example, laying off scientists or delaying the execution of trials—and they often redirect the freed‐up R&D resources to R&D expenditures that are capitalized. Using archival data, we also corroborate our survey finding about the pervasiveness of capitalized R&D, and we demonstrate its empirical implications. Our study helps to align the characterization of R&D accounting rules in the academic literature with the authoritative professional literature and provides a more nuanced understanding of firms’ R&D response to an earnings shortfall.