bluuebunny/crossref_metadata_2025 huggingface dataset:
The impact of Illinois’ comprehensive handheld phone ban on talking on handheld and handsfree cellphones while driving
Authors: Benedetti Marco H. , Lu Bo , Kinnear Neale , Li Li , Delgado M. Kit , Zhu Motao
Published: April 2022

Introduction

Distracted driving has been linked to multiple driving decrements and is responsible for thousands of motor vehicle fatalities annually. Most US states have enacted restrictions on cellphone use while driving, the strictest of which prohibit any manual operation of a cellphone while driving. Illinois enacted such a law in 2014. To better understand how this law affected cellphone behaviors while driving, we estimated associations between Illinois’ handheld phone ban and self-reported talking on handheld, handsfree, and any cellphone (handheld or handsfree) while driving.

Methods

We leveraged data from annual administrations of the Traffic Safety Culture Index from 2012-2017 in Illinois and a set of control states. We cast the data into a difference-in-differences (DID) modeling framework, which compared Illinois to control states in terms of pre-to post-intervention changes in the proportion of drivers who self-reported the three outcomes. We fit separate models for each outcome, and fit additional models to the subset of drivers who talk on cellphones while driving.

Results

In Illinois, the pre-to post-intervention decrease in the drivers’ probability of self-reporting talking on a handheld phone was significantly more extreme than that of drivers in control states (DID estimate −0.22; 95% CI −0.31, −0.13). Among drivers who talk on cellphones while driving, those in Illinois exhibited a more extreme increase in the probability of talking on a handsfree phone while driving than those control states (DID estimate 0.13; 95% CI 0.03, 0.23).

Conclusions

Our results suggest that Illinois’ handheld phone ban reduced talking on handheld phones while driving and corroborated the hypothesis that the ban promoted harm-reduction via substitution from handheld to handsfree phones among drivers who talk on the phone while driving.

Practical Applications

Our findings should encourage other states to enact comprehensive handheld phone bans to improve traffic safety.
Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions
Authors: Zhao Yu , Coelho Camila , Hughes Amanda L. , Lazar-Stefanita Luciana , Yang Sandy , Brooks Aaron N. , Walker Roy S. K. , Zhang Weimin , Lauer Stephanie , Hernandez Cindy , Mitchell Leslie A. , Agmon Neta , Shen Yue , Sall Joseph , Fanfani Viola , Jalan Anavi , Rivera Jordan , Liang Feng-Xia , Stracquadanio Giovanni , Steinmetz Lars M. , Cai Yizhi Patrick , Boeke Jef D.
Published: April 2022

The Sc2.0 project is building a eukaryotic synthetic genome from scratch, incorporating thousands of designer features. A major milestone has been achieved with the assembly of all individual Sc2.0 chromosomes. Here, we describe the consolidation of multiple synthetic chromosomes using endoreduplication intercross to generate a strain with 6.5 synthetic chromosomes. Genome-wide chromosome conformation capture and long-read direct RNA sequencing were performed on this strain to evaluate the effects of designer modifications, such as loxPsym site insertion, tRNA relocation, and intron deletion, on 3D chromosome organization and transcript isoform profiles. To precisely map “bugs”, we developed a method, CRISPR Directed Biallelic URA3-assisted Genome Scan, or “CRISPR D-BUGS”, exploiting directed mitotic recombination in heterozygous diploids. Using this method, we first fine-mapped a synII defect resulting from two loxPsym sites in the 3’ UTR of SHM1. This approach was also used to map a combinatorial bug associated with synIII and synX, revealing a highly unexpected genetic interaction that links transcriptional regulation, inositol metabolism and tRNASerCGA abundance. “Starvation” for tRNASerCGA leads to insufficient levels of the key positive inositol biosynthesis regulator, Swi3, which contains tandem UCG codons. Finally, to expedite consolidation, we employed a new method, chromosome swapping, to incorporate the largest chromosome (synIV), thereby consolidating more than half of the Sc2.0 genome in a single strain.
Reduced affinity of calcium sensing-receptor heterodimers and reduced mutant homodimer trafficking combine to impair function in a mouse model of Familial Hypocalciuric Hypercalcemia Type 1
Authors: Wang Xiaohua , Lundblad James , Smith Stephen M.
Published: April 2022

Heterozygous loss-of-function mutation of the calcium sensing-receptor (CaSR), causes familial hypocalciuric hypercalcemia type 1 (FHH1), a typically benign condition characterized by mild hypercalcemia. In contrast, homozygous mutation of this dimer-forming G-protein coupled receptor manifests as the lethal neonatal severe hyperparathyroidism (NSHPT). To investigate the mechanisms by which CaSR mutations lead to these distinct disease states, we engineered wild-type (WT) and an exon 5-deficient disease-causing mutation, and transfected expression constructs into human embryonic kidney (HEK) cells. WT protein was mainly membrane-expressed whereas the mutant CaSR protein (mCaSR) was confined to the cytoplasm. Co-expression of WT CaSR directed mCaSR to the cell membrane. In assays of CaSR function, increases in extracellular [Ca2+] ([Ca2+]o) increased intracellular [Ca2+] ([Ca2+]i) in cells expressing WT CaSR while the response was reduced in cells coexpressingmutant and WT receptor. Untransfected cells or those expressing mCaSR alone, showed minimal, equivalent responses to increased [Ca2+]o. Immunoprecipitation experiments confirmed an association between mutant and wild-type CaSR. The affinity of the WT CaSR for calcium was three times greater than that of the heterodimer. The maximal functional response to [Ca]o was dependent on localization of CaSR to the membrane level and independent of homo- or heterodimerizations. In summary, these results suggest that heterodimerization of WT and mCaSR receptors, rescues the trafficking defect of the mutant receptors and also reduces the affinity of the WT-mutant heterodimer for [Ca]o. In contrast, the homozygous mutants do not produce functional receptors on cell membrane. These data indicate how substantial differences between signaling of hetero- and homodimeric mutants lead to profound differences in the severity of disease in heterozygous and homozygous carriers of these mutations.
Intradiscal Inflammatory Stimulation Induces Spinal Pain Behavior and Intervertebral Disc DegenerationIn Vivo
Authors: Lisiewski Lauren E. , Jacobsen Hayley E. , Viola Dan C. M. , Kenawy Hagar M. , Kiridly Daniel N. , Chahine Nadeen O.
Published: April 2022

Degeneration of the intervertebral disc (IVD) is known to occur naturally over time, with the severity of pain varying widely. Other components of the degenerative environment, including structural disruption and inflammatory cytokine levels, and their correlation with pain severity have been studied. However, the role of the inflammatory environment in activating degenerative changes that manifest as a pain phenotype has not been elucidated. Previous studies have aimed to recreate the sustained inflammatory environment exhibited during human disc degeneration in a rat model. Most commonly, a puncture injury has been used causing structural damage and only initiating an acute inflammatory response. This study utilized injection of lipopolysaccharide (LPS), a pro-inflammatory stimulus, into the rat discin vivoto create the desired sustained inflammatory environment independent of physical disruption. LPS injections resulted in upregulation of pro-inflammatory cytokines and an immunogenic response. The structural integrity of the IVD was also altered demonstrated by changes in histological score, disc height, and mechanical properties. Ultimately, a sustained inflammatory environment led to both local and radiating mechanical sensitivity, demonstrating that the pain phenotype experienced during disc degeneration can be initiated solely by a sustained inflammatory profile. Markers indicative of nerve ingrowth into the IVD were also expressed suggesting a potential mechanism for the pain exhibited by animals. This rat injury model will allow for future study of the direct relationship between inflammation and pain in the degenerative environment.
Sex-specific differences in rotarod performance and type 1 cannabinoid receptor levels in a rat model of traumatic brain injury treated with Δ9-tetrahydrocannabinol
Authors: Black Tallan , Zagoog Ayat , Roebuck Andrew J , Greba Quentin , Neary J. Patrick , Howland John G. , Laprairie Robert B.
Published: April 2022

Traumatic brain injuries (TBI) remain one of the leading causes of death and disability world-wide. One emerging area of TBI research is the involvement of the endocannabinoid system (ECS) in response to TBI. Endogenous cannabinoids modulate inflammation, pain, anxiety, and neurotransmitter release through the activation of the cannabinoid receptors CB1R and CB2R. CB1R and CB2R are activated by exogenous cannabinoids such as Δ9-tetrahydrocannabinol (THC) found inCannabis sativa. As public perceptions change in the wake ofCannabislegalization, research into the potential harmful and therapeutic effects of THC following TBI deserve exploration. In this preliminary study, we investigated sex differences in behavioral effects, CB1R abundance, and cytokine profiles in a rat model of moderate TBI treated with 1 mg·kg-1THC (i.p.). Neither TBI nor THC treatment altered catalepsy, body temperature, nociception, or spontaneous alternation as measured in the y-maze. TBI reduced male rotarod performance in both vehicle and THC-treated groups, and THC treatment decreased performance in Sham-TBI rats when compared to vehicle controls. Female rats that received a TBI and THC exhibited lower relative CB1R density when compared to the Sham-TBI+THC group. TBI was associated with reduced interleukin-4 in males; THC increased interleukin-6 in TBI males compared to Sham-TBI. These preliminary results highlight fundamental sex differences in the response of the ECS following TBI. Our results indicate the need for further investigation of the ECS and phytocannabinoids post-TBI in both acute and chronic phases.

Significance Statement

The endogenous cannabinoid system is a potential target in the pathophysiology and treatment of traumatic brain injury (TBI). In this study we observed TBI reduced rotarod performance in male rats only and performance was not affected by THC. Female rats the received THC and TBI displayed lower cortical cannabinoid receptor 1 levels. These early results showcase sex differences in rodent models of TBI and the endogenous cannabinoid system.
Genotypic and phenotypic diversity of the multidrug-resistant Mycobacterium tuberculosis strains from eastern India
Authors: Ghosh Arup , Bal Himadri , Biswas Viplov Kumar , Das Dasarathi , Pati Sanghmitra , Raghav Sunil
Published: April 2022

Mycobacterium tuberculosis (Mtb) poses a great challenge to human health and wellbeing and hinders economic growth of a region. India along with other south east Asian countries are known as high Tuberculosis burden countries. Adoption of whole genome sequencing in studying genetic diversity, evolution, transmission pattern and drug resistance development provided a great opportunity for developing and improving diagnostic and therapeutic approaches. In our study we have sequenced 118 Mtb whole genome from North East(NE) and Odisha as a representative of the diversity in eastern region of India for the first time. We observed high prevalence of multi-drug resistant(MDR) lineage-2(n=52) strains in NE whereas presence of mostly lineage-1(n=30) & 3 (n=11) strains in Odisha. The MDR strains from Sikkim demonstrated similar resistance profile of fluroquinolones and pair-wise SNP distances showed presence of local transmission clusters. We also detected significant enrichment of short INDELs in MDR samples in contrast to drug susceptible samples. This study provides molecular level insight into Mtb strains of eastern region in comparison with Indian and global perspective.
SARS-ANI: A Global Open Access Dataset of Reported SARS-CoV-2 Events in Animals
Authors: Nerpel Afra , Yang Liuhuaying , Sorger Johannes , Käsbohrer Annemarie , Walzer Chris , Desvars-Larrive Amélie
Published: April 2022

The zoonotic origin of SARS-CoV-2, the etiological agent of COVID-19, is not yet fully resolved. Although natural infections in animals are reported in a wide range of species, large knowledge and data gaps remain regarding SARS-CoV-2 animal hosts. We used two major health databases to extract unstructured data and generated a comprehensive global dataset of thoroughly documented SARS-CoV-2 events in animals. The dataset integrates relevant epidemiological and clinical data on each event and is readily usable for analytical purposes. We also share the code for technical and visual validation of the data and created a user-friendly dashboard for data exploration. Data on SARS-CoV-2 occurrence in animals is critical to adapt monitoring strategy, prevent the formation of animal reservoirs, and tailor future human and animal vaccination programs. The FAIRness and analytical flexibility of the data will support research efforts on SARS-CoV-2 at the human-animal-environment interface. We intend to update this dataset weekly for at least one year and, through collaborative processes, to develop the dataset further and expand its use.
Crosstalk between glucose metabolism and morphogen signalling specifies tonotopic identity in developing hair cells
Authors: O’Sullivan James DB , Blacker Thomas S , Scott Claire , Chang Weise , Ahmed Mohi , Yianni Val , Mann Zoe F
Published: April 2022

In vertebrates with elongated auditory organs, mechanosensory hair cells (HCs) are organised such that complex sounds are broken down into their component frequencies along the proximal-to-distal long (tonotopic) axis. Acquisition of frequency-specific morphologies at the appropriate positions along the chick cochlea, the basilar papilla (BP), requires that nascent HCs determine their tonotopic positions during development. The complex signalling within the auditory organ between the developing HC and its local niche along the axis is currently poorly understood. Here we apply NAD(P)H fluorescence lifetime imaging (FLIM) to reveal metabolic gradients along the tonotopic axis of the developing BP. Re-shaping these gradients during development, by inhibiting different branch points of cytosolic glucose catabolism, alters normal morphogen signalling and abolishes tonotopic patterning, normalising the graded differences in hair cell morphology along the BP. These findings highlight a causal link between morphogen signalling and metabolic reprogramming in specifying tonotopic identity in developing auditory HCs.
Quantitation of FGFR3 signaling via GRB2 recruitment on micropatterned surfaces
Authors: Hartl Ingrid , Brumovska Veronika , Striedner Yasmin , Yasari Atena , Schütz Gerhard J. , Sevcsik Eva , Tiemann-Boege Irene
Published: April 2022

Fibroblast growth factor receptors (FGFRs) initiate signal transduction via the RAS/MAPK pathway by their tyrosine-kinase activation known to determine cell-growth, tissue differentiation and apoptosis. Recently, many missense mutations have been reported for FGFR3, but we only know the functional effect for a handful of them. Some of these mutations result in aberrant FGFR3 signaling and are associated with various genetic disorders and oncogenic conditions. Here we employed micropatterned surfaces to specifically enrich fluorophore-tagged FGFR3 (mGFP-FGFR3) in certain areas of the plasma membrane of living cells. Receptor activation was then quantified via the recruitment of the downstream signal transducer GRB2 tagged with mScarlet (GRB2-mScarlet) to FGFR3 patterns. With this system, we tested the activation of FGFR3 upon ligand addition (fgf1 and fgf2) in the wildtype (WT), as well as in different FGFR3 mutants associated with congenital disorders (G380R, Y373C, K650Q, K650E). Our data showed that the addition of ligands increased GRB2 recruitment to WT FGFR3, with fgf1 having a stronger effect than fgf2. For all mutants, we found an increased basal receptor activity, and only for two of the four mutants (G380R and K650Q), activity was further increased upon ligand addition. Compared to previous reports, two mutant receptors (K650Q and K650E) had either an unexpectedly high or low activation state, respectively. This may be explained by the different receptor populations probed, since the micropatterning method specifically reports on signaling events at the plasma membrane.

Graphical Abstract

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Research Highlights

Quantification of FGFR3 signaling in live cells on micropatterned surfaces

Analysis of GRB2 recruitment to the mature receptor at the plasma membrane

Ligand-independent kinase activation of FGFR3 mutants

Activation of FGFR3 at the cell surface can be different than in bulk cell extracts
Broadly neutralizing antibodies target the coronavirus fusion peptide
Authors: Dacon Cherrelle , Tucker Courtney , Peng Linghang , Lee Chang-Chun D. , Lin Ting-Hui , Yuan Meng , Cong Yu , Wang Lingshu , Purser Lauren , Williams Jazmean K. , Pyo Chul-Woo , Kosik Ivan , Hu Zhe , Zhao Ming , Mohan Divya , Cooper Andrew , Peterson Mary , Skinner Jeff , Dixit Saurabh , Kollins Erin , Huzella Louis , Perry Donna , Byrum Russell , Lembirik Sanae , Zhang Yi , Yang Eun Sung , Chen Man , Leung Kwanyee , Weinberg Rona S. , Pegu Amarendra , Geraghty Daniel E. , Davidson Edgar , Douagi Iyadh , Moir Susan , Yewdell Jonathan W. , Schmaljohn Connie , Crompton Peter D. , Holbrook Michael R. , Nemazee David , Mascola John R. , Wilson Ian A. , Tan Joshua
Published: April 2022

The potential for future coronavirus outbreaks highlights the need to develop strategies and tools to broadly target this group of pathogens. Here, using an epitope-agnostic approach, we identified six monoclonal antibodies that bound to spike proteins from all seven human-infecting coronaviruses. Epitope mapping revealed that all six antibodies target the conserved fusion peptide region adjacent to the S2’ cleavage site. Two antibodies, COV44-62 and COV44-79, broadly neutralize a range of alpha and beta coronaviruses, including SARS-CoV-2 Omicron subvariants BA.1 and BA.2, albeit with lower potency than RBD-specific antibodies. In crystal structures of Fabs COV44-62 and COV44-79 with the SARS-CoV-2 fusion peptide, the fusion peptide epitope adopts a helical structure and includes the arginine at the S2’ cleavage site. Importantly, COV44-79 limited disease caused by SARS-CoV-2 in a Syrian hamster model. These findings identify the fusion peptide as the target of the broadest neutralizing antibodies in an epitope-agnostic screen, highlighting this site as a candidate for next-generation coronavirus vaccine development.

One-Sentence Summary

Rare monoclonal antibodies from COVID-19 convalescent individuals broadly neutralize coronaviruses by targeting the fusion peptide.
Short-course but not prolonged treatment with ATR inhibitor AZD6738 integrates with radiotherapy to generate a tumor antigen-specific CD8+ T cell expansion in the periphery
Authors: Vendetti Frank P. , Clump David A. , Schamus-Haynes Sandra , DiMayorca Maria , Islam Naveed , Chang Jina , Beumer Jan H. , Bakkenist Christopher J.
Published: April 2022

ATR kinase is a central regulator of the DNA damage response. While ATR kinase inhibitors (ATRi’s) are known to sensitize cancer cells to DNA damage, their effect on immune cells is not known. Here we show in mice that short-course AZD6738 (ATRi) on days 1-3 decreases proliferating T cells in the tumor and periphery and that cessation of ATRi causes a proliferative rebound. Integrating radiation on days 1-2 (RT) with ATRi on days 1-3 increases IFN-β in the tumor and activates tumor antigen-specific CD8+ T cells in the tumor-draining lymph node (DLN). RT with short-course ATRi induces an expansion of tumor antigen-specific CD8+ T cells in the DLN. In contrast, RT with prolonged daily ATRi blocks expansion of antigen-specific CD8+ T cells, despite increased IFN-β and activation of CD8+ T cells. Our data identifies critical schedule considerations for ATRi with RT, immunotherapy and genotoxic therapies.
Electrophysiological normative responses to emotional, neutral, and cigarette-related images
Authors: Versace Francesco , Sambuco Nicola , Deweese Menton M. , Cinciripini Paul M.
Published: April 2022

To create reproducible emotional probes, affective scientists rely on sets of standardized pictures that are normed using subjective ratings of valence and emotional arousal. Yet, to investigate psychophysiological emotional responses, it might be more appropriate to select pictures using normative neurophysiological responses rather than normative subjective ratings. Here, we provide electrophysiological normative responses for 323 emotional pictures (215 from the IAPS) covering a wide range of categories (erotica, romantic, appetizing foods, landscapes, people engaged in mundane activities, household objects, disgusting objects, accidents, sad people, violence, mutilations, and cigarette-related contents). Event-related potentials (ERPs) and subjective ratings of pleasure and emotional arousal were collected from 763 individuals (52% females, 41% white) aged between 18 and 65 (mean = 43). For each image, the mean amplitude of the late positive potential (LPP, an electrophysiological index of motivational relevance) and the mean subjective ratings of valence and arousal were calculated. We validated our procedure by showing that the subjective ratings of valence and arousal from this sample were highly correlated to the IAPS’ published norms (Pearson r=.97 for pleasure and r=.82 for emotional arousal). LPP responses and subjective ratings of emotional arousal also were correlated (Pearson r = .61), but some categories that participants reported being significantly more arousing than neutral (i.e., food, landscapes, and unpleasant objects) did not evoke LPPs significantly different from those evoked by neutral pictures. Researchers interested in probing the brain’s affective systems can use these electrophysiological normative responses to create emotional probes that evoke reliable neuroaffective responses.
Between-area communication through the lens of within-area neuronal dynamics
Authors: Gozel Olivia , Doiron Brent
Published: April 2022

A core problem in systems and circuits neuroscience is deciphering the origin of shared dynamics in neuronal activity: do they emerge through local network interactions, or are they inherited from external sources? We explore this question with large-scale networks of spatially ordered spiking neuron models where a downstream network receives input from an upstream sender network. We show that linear measures of the communication between the sender and receiver networks can discriminate between emergent or inherited population dynamics. Faithful communication requires a match in the dimensionality of the sender and receiver population activities, along with an alignment of their shared fluctuations. However, a nonlinear mapping between the sender – receiver activity or downstream emergent population-wide fluctuations can impair linear communication. Our work exposes the benefits and limitations of linear measures when analyzing between-area communication in circuits with rich population-wide neuronal dynamics.
Accurate Genome-Wide Phasing from IBD Data
Authors: Noto Keith , Ruiz Luong
Published: April 2022

As 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 summary

We 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

Amyloids 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

Earth’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

We 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.

SYNOPSIS

Methanogenic 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
Precise genotyping of circular mobile elements from metagenomic data uncovers human-associated plasmids with recent common ancestors
Authors: Shalon Nitan , Relman David A. , Yaffe Eitan
Published: April 2022

Mobile genetic elements with circular genomes play a key role in the evolution of microbial communities. Their circular genomes correspond to circular walks in metagenome graphs, and yet, assemblies derived from natural microbial communities produce graphs riddled with spurious cycles, complicating the accurate reconstruction of circular genomes. We present DomCycle, an algorithm that reconstructs likely circular genomes based on the identification of so-called “dominant” graph cycles. In the implementation, we leverage paired reads to bridge assembly gaps and scrutinize cycles through a nucleotide-level analysis, making the approach robust to misassembly artifacts. We validated the approach using simulated and real sequencing data. Application of DomCycle to 32 publicly available DNA shotgun sequence data sets from diverse natural environments led to the reconstruction of hundreds of circular mobile genomes. Clustering revealed 20 highly prevalent and cryptic plasmids that have clonal population structures with recent common ancestors. This method facilitates the study of microbial communities that evolve through horizontal gene transfer.
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

Purpose

The 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/approach

The 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.

Findings

The 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/value

The 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

Purpose

This 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/approach

This 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.

Findings

By 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/value

Even 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

Purpose

Although 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/approach

The 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.

Findings

This 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/implications

Our 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 implications

The 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/value

The 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

Purpose

The 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/approach

To 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.

Findings

Jharkhand 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/value

This 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

Trichophyton 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

Aim

The development of an evidence‐based algorithm for the clinical management of deviations in maternal temperature during labour and childbirth.

Population

Pregnant women at any stage of labour, with singleton, term (37–42 weeks) pregnancies at low risk of developing complications.

Setting

Health facilities in low‐ and middle‐income countries.

Search strategy

We 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 scenarios

Two 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.

Conclusions

We 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 abstract

An 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

Resistant 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.