bluuebunny/crossref_metadata_2025 huggingface dataset:
Pregnancy outcomes from a restorative infertility treatment model: a single centre case series
Authors: James Gabriel , Mclindon Lucas A. , Hatch Joshua , Mol Ben W. , Turner Joseph V.
Published: April 2021

Background

Infertility is a significant problem with multiple causes and a corresponding array of therapeutic options. In an era of increasing assisted reproductive treatments, few studies examine the role of conventional non-assisted reproductive treatments to address underlying behavioural, lifestyle and medical issues.

Aim

To assess outcomes from a conventional or non-assisted reproductive treatment approach

Materials and Methods

Retrospective case series of 162 couples that attended an Australian, hospital-based, multidisciplinary fertility clinic between 2005 and 2010.

Results

There were 58 live births for all couples giving a crude live birth rate of 35.4% over a 24-month analysis period. When adjusted by Kaplan-Meier method, a 57.4% cumulative live birth rate (CLBR) was achieved. Couples had a median 33.9 months duration of infertility and the median female age was 33.7. For the 74 couples with an unexplained infertility diagnosis, 32 achieved a live birth at a crude rate of 43.2% or 71.2% CLBR when adjusted by Kaplan-Meier method.

Conclusions

This observational data indicates that reproductive medicine should have a personalized approach in which alternatives for immediate IVF are considered.
The impact of real-time whole genome sequencing in controlling healthcare-associated SARS-CoV-2 outbreaks
Authors: Francis Rodric V. , Billam Harriet , Clarke Mitch , Yates Carl , Tsoleridis Theocharis , Berry Louise , Mahida Nikunj , Irving William L. , Moore Christopher , Holmes Nadine , Ball Jonathan , McClure C. Patrick , Loose Matthew
Published: April 2021

Background

Nosocomial infections have posed a significant problem during the COVID-19 pandemic, affecting bed capacity and patient flow in hospitals. Effective infection control measures and identifying areas of highest risk is required to reduce the risk of spread to patients who are admitted with other illnesses. This is the first pandemic where whole genome sequencing (WGS) has been readily available. We demonstrate how WGS can be deployed to help identify and control outbreaks.

Aims & Methods

Swabs performed on patients to detect SARS-CoV-2 underwent RT-PCR on one of multiple different platforms available at Nottingham University Hospitals NHS Trust. Positive samples underwent WGS on the GridION platform using the ARTIC amplicon sequencing protocol at the University of Nottingham.

Results

Phylogenetic analysis from WGS and epidemiological data was used to identify an initial transmission that occurred in the admissions ward. It also showed high prevalence of asymptomatic staff infection with genetically identical viral sequences which may have contributed to the propagation of the outbreak. Actions were taken to help reduce the risk of nosocomial transmission by the introduction of rapid point of care testing in the admissions ward and introduction of portable HEPA14 filters. WGS was also used in two instances to exclude an outbreak by discerning that the phylotypes were not identical, saving time and resources.

Conclusions

In conjunction with accurate epidemiological data, timely WGS can identify high risk areas of nosocomial transmission, which would benefit from implementation of appropriate control measures. Conversely, WGS can disprove nosocomial transmission, validating existing control measures and maintaining clinical service, even where epidemiological data is suggestive of an outbreak.
Declines in life expectancy following the COVID-19 pandemic in provinces of Spain
Authors: Trias-Llimós Sergi , Blanes Amand , Franco Manuel , Bilal Usama , Riffe Tim
Published: April 2021

The COVID-19 pandemic has impacted population health on a global scale. Most of the studies on mortality impacts are at national level, while broad evidence exists on heterogeneous COVID-19 incidence across regions and within countries. Using Spanish data for 2020, we estimate life expectancy changes in 2020 compared with the 2017-19 period in 50 Spanish provinces. We visualize longer-term trends (1990-2020), and compare the robustness of our province-specific results with cumulative COVID-19 incidence using regional data from the Spanish ENECOVID seroprevalence study. In 2020 there was a 1.2 and 1.1 year drop in life expectancy for men and women in Spain, but this impact was heterogeneous across regions. For men these losses were highest in the province of Segovia (−3.5 years decline), while for women the highest drop was observed in Salamanca (−2.8 years decline). Life expectancy actually increased in Santa Cruz de Tenerife (+1.1 and +0.6 years for men and women, respectively). Declines in life expectancy in 2020 were also highly correlated with the cumulative seroprevalence through November 2020 (ρ=0.80 and 0.77 in men and women, respectively). Monitoring regional life expectancy dynamics provide valuable and granular information on the heterogeneous impacts of the pandemic on health at the population level. Similar exercises in other European countries may reveal insightful geographic patterns in mortality impacts in COVID-19 pandemic years.
Using rapid (point-of-care) tests for COVID-19: A decision analysis comparing the expected benefit of two screening strategies
Authors: Baillargeon Raymond H. , Seyer Xavier , Bernard-Bédard Éricka
Published: April 2021

Background

Rapid tests for COVID-19 could be used to augment the otherwise limited laboratory-based testing capacity, but there are concerns that their utility may be compromised by their limited accuracy. The objective of this article is to compare the expected benefit (EB) of two screening strategies, one with rapid tests (SwRT) and another one without rapid tests.

Methods

We performed a decision analysis, with the overall EB defined as the proportion of correctly identified individuals minus the proportion of incorrectly identified individuals. Accordingly, the SwRT strategy will be deemed a better screening strategy if its lesser EB for COVID-19 free individuals is more than compensated by its greater EB for COVID-19 individuals. Otherwise, it will not.

Results

As expected, the EB for COVID-19 individuals was greater for the SwRT strategy, with a far superior ability to rule out the presence of COVID-19. In fact, under the scenario of interest (i.e., 8000 ID Now rapid tests in addition to 28185 lab-based RT-PCR tests), it identified almost 16% more COVID-19 individuals than thestrategy. In addition, the EB for COVID-19 free individuals was the same for both strategies, with a perfect ability at ruling in the presence of COVID-19.

Conclusion

The SwRT strategy identified more COVID-19 individuals and this gain was not obtained at the detriment of COVID-19 free individuals who were equally well identified by both strategies. Hence, the SwRT strategy is a better screening strategy for COVID-19. It represents an opportunity to curtail the spread of SARS-CoV-2 that we may not afford to miss with new more contagious variants becoming more and more common in Canada.
Evaluating implementation of LEAPS, a youth-led early childhood care and education intervention in rural Pakistan: protocol for a stepped-wedge cluster randomized trial
Authors: Yousafzai Aisha K. , Sudfeld Christopher R. , Franchett Emily E. , Siyal Saima , Rehmani Karima , Bhamani Shelina , Dai Quanyi , Reyes Chin R. , Fink Günther , Ponguta Liliana A.
Published: April 2021

Background

The Sustainable Development Goals (SDGs) highlight the importance of investments in early childhood care and education (ECCE) for young children and youth development. Given Pakistan’s large young population, and gender and urban-rural inequalities in access to education, training and employment, such investments offer opportunities. LEAPS is a youth-led ECCE program that trains female youth, 18-24 years, as Community Youth Leaders (CYLs) to deliver high-quality ECCE for children, 3.5-5.5 years, in rural Sindh, Pakistan.

Methods

We use a stepped-wedge cluster randomized trial to evaluate implementation of LEAPS. Ninety-nine clusters will be randomized to receive the intervention in one of three seven-month steps (33 clusters/step). Primary outcomes are children’s school readiness (measured with the International Development and Early Learning Assessment) and executive functions. Secondary outcomes are youth personal and professional development, depressive symptoms, and executive functions. Data is collected in cross-sectional surveys of 1,089 children (11 children/cluster from 99 clusters) aged 4.5-5.5 years at four time points (baseline and at the end of each step). We will enroll three youth participant open cohorts, one per step (33 CYLs: 66 comparison youth per cohort; 99:198 in total). Youth cohorts will be assessed at enrollment and every six to seven months thereafter (i.e., once per consecutive Step). A school cohort of 330 LEAPS students (10 students/cluster from 33 clusters) will be enrolled and assessed during Step 1 after intervention rollout and at endline. The quality of the learning environment will be assessed in each LEAPS ECCE center and in a comparison center at two time points midway following rollout and at endline. A concurrent mixed-methods implementation evaluation will assess program fidelity and quality, as well as the extent to which a technical support strategy is successful in strengthening systems for program expansion. A cost evaluation will assess cost-per-beneficiary. Data collection for implementation and cost evaluations will occur in Step 3.

Discussion

Youth-led models for ECCE offer a promising approach to support young children and youth; however, there is little empirical evidence on real-world implementation. This study will contribute to the evidence as a means to promote sustainable human development across multiple SDG targets.

Trial Registration

ClinicalTrials.gov:NCT03764436. Registered December 5th, 2018,https://clinicaltrials.gov/ct2/show/NCT03764436.
Comparison of Accelerated Resolution Therapy (ART) for Post-Traumatic Stress Disorder (PTSD) Between Veterans With and Without Prior PTSD Treatment
Authors: Pang Tiantian , Murn Lindsay , Williams Dana , Lawental Maayan , Abhayakumar Anya , Kip Kevin E.
Published: April 2021

Background

Post-traumatic stress disorder (PTSD) is a psychiatric disorder commonly caused by a traumatic event(s) and prevalent among service members and veterans. Accelerated Resolution Therapy (ART) is an emerging “mind-body” psychotherapy for PTSD that is generally briefer and less expensive than current first-line treatments, such as cognitive processing therapy (CPT) and prolonged exposure (PE) therapy.

Objective

This study aimed to examine the results of ART for treatment of military-related PTSD, with stratification by prior history of PTSD treatment, including refractory PTSD following receipt of guideline-driven first-line psychotherapy.

Methods

The study compares the PTSD treatment results of ART between (military service members and/or) veterans with a prior history of PTSD treatment (medication only, n=40; first-line psychotherapy, n=33; other psychotherapy, n=42) and a treatment-naïve group (n=33). Participants were assessed at baseline, post-treatment, and 3- or 6-month follow-up using PCL-M scores (PTSD checklist).

Results

Mean age was 43.8 years, 95% male, 84% white race. The treatment completion rate was 72% with a mean of 3.5 treatment sessions. Within-group standardized effect sizes for pre-to-post changes in PTSD scores (PCL-M) were large at 1.11, 1.88, 1.03, and 1.48 for the medication only, first-line psychotherapy, other psychotherapy, and treatment-naïve groups, respectively (p=0.02 for between-group comparison). Similar results were observed for measures of depression and anxiety, and baseline to follow-up results was generally similar.

Conclusions

In a brief treatment period, ART appears to result in substantial reductions in symptoms of PTSD among veterans, including those previously treated (unsuccessfully) with first-line psychotherapies endorsed by the U.S. Department of Defense (DoD) and Veterans Affairs (VA). These results suggest that ART be considered as a treatment modality for veterans with refractory PTSD.

Highlights

Accelerated Resolution Therapy (ART) is a potentially acceptable psychological intervention for treatment-refractory PTSD.
Evaluating Vaccine Efficacy Against SARS-CoV-2 Infection
Authors: Lin Dan-Yu , Gu Yu , Zeng Donglin , Janes Holly E. , Gilbert Peter B.
Published: April 2021

Although interim results from several large placebo-controlled phase 3 trials demonstrated high vaccine efficacy (VE) against symptomatic COVID-19, it is unknown how effective the vaccines are in preventing people from becoming asymptomatically infected and potentially spreading the virus unwittingly. It is more difficult to evaluate VE against SARS-CoV-2 infection than against symptomatic COVID-19 because infection is not observed directly but rather is known to occur between two antibody or RT-PCR tests. Additional challenges arise as community transmission changes over time and as participants are vaccinated on different dates because of staggered enrollment or crossover before the end of the study. Here, we provide valid and efficient statistical methods for estimating potentially waning VE against SARS-CoV-2 infection with blood or nasal samples under time-varying community transmission, staggered enrollment, and blinded or unblinded crossover. We demonstrate the usefulness of the proposed methods through numerical studies mimicking the BNT162b2 phase 3 trial and the Prevent COVID U study. In addition, we assess how crossover and the frequency of diagnostic tests affect the precision of VE estimates.

We show how to estimate potentially waning efficacy of COVID-19 vaccines against SARS-CoV-2 infection using blood or nasal samples collected periodically from clinical trials with staggered enrollment of participants and crossover of placebo recipients.
GPR171 Agonist Reduces Chronic Neuropathic and Inflammatory Pain in Male, but not in Female Mice
Authors: Ram Akila , Edwards Taylor , McCarty Ashley , Afrose Leela , McDermott Max V. , Bobeck Erin N.
Published: April 2021

Chronic pain is a growing public health crisis that requires exigent and efficacious therapeutics. GPR171 is a promising therapeutic target that is widely expressed through the brain, including within the descending pain modulatory regions. Here, we explore the therapeutic potential of the GPR171 agonist, MS15203, in its ability to alleviate chronic pain in male and female mice using a once-daily systemic dose (10mg/kg, i.p.) of MS15203 over the course of 5 days. We found that in our models of Complete Freund’s Adjuvant (CFA)-induced inflammatory pain and chemotherapy-induced peripheral neuropathy (CIPN), MS15203 did not reduce thermal hypersensitivity and allodynia, respectively, in female mice. On the other hand, MS15203 treatment decreased the duration of thermal hyper-sensitivity in CFA-treated male mice following 3 days of once-daily administration. MS15203 treatment also produced an improvement in allodynia in male mice, but not female mice, in neuropathic pain after 5 days of treatment. Gene expression of GPR171 and that of its endogenous ligand BigLEN, encoded by the gene PCSK1N, were unaltered within the periaqueductal gray in both male and female mice following inflammatory and neuropathic pain. However, following neuropathic pain in male mice, the protein levels of GPR171 were decreased in the periaqueductal gray. Treatment with MS15203 then rescued the protein levels of GPR171 in the periaqueductal gray of these mice. Taken together, our results identify GPR171 as a GPCR that displays sexual dimorphism in alleviation of chronic pain. Further, our results suggest that GPR171 and MS15203 have demonstrable therapeutic potential in the treatment of chronic pain.
Genomic Skimming and Nanopore Sequencing Uncover Cryptic Hybridization in One of World’s Most Threatened Primates
Authors: Malukiewicz Joanna , Cartwright Reed A , Dergam Jorge A , Igayara Claudia S , Nicola Patricia A , Pereira Luiz MC , Ruiz-Miranda Carlos R , Stone Anne C , Silva Daniel L , de Fátima Rodrigues da Silva Fernanda , Varsani Arvind , Walter Lutz , Wilson Melissa A , Zinner Dietmar , Roos Christian
Published: April 2021

The Brazilian buffy-tufted-ear marmoset (Callithrix aurita), one of the world’s most endangered primates, is threatened by anthropogenic hybridization with exotic, invasive marmoset species. As there are few genetic data available forC. aurita, we developed a PCR-free protocol with minimal technical requirements to rapidly generate genomic data with genomic skimming and portable nanopore sequencing. With this direct DNA sequencing approach, we successfully determined the complete mitogenome of a marmoset that we initially identified asC. aurita. The obtained nanopore-assembled sequence was highly concordant with a Sanger sequenced version of the same mitogenome. Phylogenetic analyses unexpectedly revealed that our specimen was a cryptic hybrid, with aC. auritaphenotype andC. penicillatamitogenome lineage. We also used publicly available mitogenome data to determine diversity estimates forC. auritaand three other marmoset species. Mitogenomics holds great potential to address deficiencies in genomic data for endangered, non-model species such asC. aurita. However, we discuss why mitogenomic approaches should be used in conjunction with other data for marmoset species identification. Finally, we discuss the utility and implications of our results and genomic skimming/nanopore approach for conservation and evolutionary studies ofC. auritaand other marmosets.
YhcB coordinates peptidoglycan and LPS biogenesis with phospholipid synthesis duringEscherichia colicell growth
Authors: Goodall Emily C. A. , Isom Georgia L. , Rooke Jessica L. , Icke Christopher , Pullela Karthik , Zhang Bing , Rae James , Tan Wee Boon , Winkle Matthias , Delhaye Antoine , Heinz Eva , Collet Jean-Francois , Cunningham Adam F. , Blaskovich Mark A. , Parton Robert G. , Cole Jeff A. , Chng Shu-Sin , Vollmer Waldemar , Bryant Jack A. , Henderson Ian R.
Published: April 2021

The cell envelope is essential for viability in all kingdoms of life. It retains enzymes and substrates within a confined space while providing a protective barrier to the external environment. Destabilising the envelope of bacterial pathogens is a common strategy employed by antimicrobial treatment. However, even in one of the most well studied organisms,Escherichia coli, there remain gaps in our understanding of how the synthesis of the successive layers of the cell envelope are coordinated during growth and cell division. Here, we used a whole genome phenotypic screen to identify mutants with a defective cell envelope. We report that loss ofyhcB, a conserved gene of unknown function, results in loss of envelope stability, increased cell permeability and dysregulated control of cell size. Using whole genome transposon mutagenesis strategies we report the complete genetic interaction network ofyhcB, revealing all genes with a synthetic negative and a synthetic positive relationship. These genes include those previously reported to have a role in cell envelope biogenesis. Surprisingly, we identified genes previously annotated as essential that became non-essential in a ΔyhcBbackground. Subsequent analyses suggest that YhcB sits at the junction of several envelope biosynthetic pathways coordinating the spatiotemporal growth of the cell, highlighting YhcB as an as yet unexplored antimicrobial target.
Direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mapping (CasKAS)
Authors: Marinov Georgi K. , Kim Samuel H. , Bagdatli S. Tansu , Trevino Alexandro E. , Tycko Josh , Wu Tong , Bintu Lacramioara , Bassik Michael C. , He Chuan , Kundaje Anshul , Greenleaf William J.
Published: April 2021

Detecting and mitigating off-target activity is critical to the practical application of CRISPR-mediated genome and epigenome editing. While numerous methods have been developed to map Cas9 binding specificity genome-wide, they are generally time-consuming and/or expensive, and not applicable to catalytically dead CRISPR enzymes. We have developed a rapid, inexpensive, and facile assay for identifying off-target CRISPR enzyme binding and cleavage by chemically mapping the unwound single-stranded DNA structures formed upon binding of a sgRNA-loaded Cas9 protein (“CasKAS”). We demonstrate this method in bothin vitroandin vivocontexts.
Generative AAV capsid diversification by latent interpolation
Authors: Sinai Sam , Jain Nina , Church George M , Kelsic Eric D
Published: April 2021

Adeno-associated virus (AAV) capsids have shown clinical promise as delivery vectors for gene therapy. However, the high prevalence of pre-existing immunity against natural capsids poses a challenge for widespread treatment. The generation of diverse capsids that are potentially more capable of immune evasion is challenging because introducing multiple mutations often breaks capsid assembly. Here we target a representative, immunologically relevant 28-amino-acid segment of the AAV2 capsid and show that a low-complexity Variational Auto-encoder (VAE) can interpolate in sequence space to produce diverse and novel capsids capable of packaging their own genomes. We first train the VAE on a 564-sample Multiple-Sequence Alignment (MSA) of dependo-parvoviruses, and then further augment this dataset by adding 22,704 samples from a deep mutational exploration (DME) on the target region. In both cases the VAE generated viable variants with many mutations, which we validated experimentally. We propose that this simple approach can be used to optimize and diversify other proteins, as well as other capsid traits of interest for gene delivery.
Engineering single pan-specific ubiquibodies for targeted degradation of all forms of endogenous ERK protein kinase
Authors: Stephens Erin A. , Ludwicki Morgan B. , Meksiriporn Bunyarit , Li Mingji , Ye Tianzheng , Monticello Connor , Forsythe Katherine J. , Kummer Lutz , Plückthun Andreas , DeLisa Matthew P.
Published: April 2021

Ubiquibodies (uAbs) are a customizable proteome editing technology that utilizes E3 ubiquitin ligases genetically fused to synthetic binding proteins to steer otherwise stable proteins of interest (POIs) to the proteasome for degradation. The ability of engineered uAbs to accelerate the turnover of exogenous or endogenous POIs in a posttranslational manner offers a simple yet robust tool for dissecting diverse functional properties of cellular proteins as well as for expanding the druggable proteome to include tumorigenic protein families that have yet-to-be successfully drugged by conventional inhibitors. Here, we describe the engineering of uAbs comprised of a highly modular human E3 ubiquitin ligase, human carboxyl terminus of Hsc70-interacting protein (CHIP), tethered to different designed ankyrin repeat proteins (DARPins) that bind to nonphosphorylated (inactive) and/or doubly phosphorylated (active) forms of extracellular signal-regulated kinase 1 and 2 (ERK1/2). Two of the resulting uAbs were found to be global ERK degraders, pan-specifically capturing all endogenous ERK1/2 protein forms and redirecting them to the proteasome for degradation in different cell lines, including MCF7 breast cancer cells. Taken together, these results demonstrate how the substrate specificity of an E3 ubiquitin ligase can be reprogrammed to generate designer uAbs against difficult-to-drug targets, enabling a modular platform for remodeling the mammalian proteome.
Genomic Stability and Genetic Defense Systems inDolosigranulum pigruma Candidate Beneficial Bacterium from the Human Microbiome
Authors: Ramos Stephany Flores , Brugger Silvio D. , Escapa Isabel Fernandez , Skeete Chelsey A. , Cotton Sean L. , Eslami Sara M. , Gao Wei , Bomar Lindsey , Tran Tommy H. , Jones Dakota S. , Minot Samuel , Roberts Richard J. , Johnston Christopher D. , Lemon Katherine P.
Published: April 2021

Dolosigranulum pigrumis positively associated with indicators of health in multiple epidemiological studies of human nasal microbiota. Knowledge of the basic biology ofD. pigrumis a prerequisite for evaluating its potential for future therapeutic use; however, such data are very limited. To gain insight intoD. pigrum’s chromosomal structure, pangenome and genomic stability, we compared the genomes of 28D. pigrumstrains that were collected across 20 years. Phylogenomic analysis showed closely related strains circulating over this period and closure of 19 genomes revealed highly conserved chromosomal synteny. Gene clusters involved in the mobilome and in defense against mobile genetic elements (MGEs) were enriched in the accessory genome versus the core genome. A systematic analysis for MGEs identified the first candidateD. pigrumprophage and insertion sequence. A systematic analysis for genetic elements that limit the spread of MGEs, including restriction modification (RM), CRISPR-Cas, and deity-named defense systems, revealed strain-level diversity in host defense systems that localized to specific genomic sites including one RM system hotspot. Analysis of CRISPR spacers pointed to a wealth of MGEs against whichD. pigrumdefends itself. These results reveal a role for horizontal gene transfer and mobile genetic elements in strain diversification while highlighting that inD. pigrumthis occurs within the context of a highly stable chromosomal organization protected by a variety of defense mechanisms.

IMPORTANCE

Dolosigranulum pigrumis a candidate beneficial bacterium with potential for future therapeutic use. This is based on its positive associations with characteristics of health in multiple studies of human nasal microbiota across the span of human life. For example, high levels ofD. pigrumnasal colonization in adults predicts the absence ofStaphylococcus aureusnasal colonization. Also,D. pigrumnasal colonization in young children is associated with healthy control groups in studies of middle ear infections. Our analysis of 28 genomes revealed a remarkable stability ofD. pigrumstrains colonizing people in the U.S. across a 20-year span. We subsequently identified factors that can influence this stability, including genomic stability, phage predators, the role of MGEs in strain-level variation and defenses against MGEs. Finally, theseD. pigrumstrains also lacked predicted virulence factors. Overall, these findings add additional support to the potential forD. pigrumas a therapeutic bacterium.
A fastMyhsuper enhancer dictates adult muscle fiber phenotype through competitive interactions with the fastMyhgenes
Authors: Santos Matthieu Dos , Backer Stéphanie , Auradé Frédéric , Wong Matthew , Wurmser Maud , Pierre Rémi , Langa Francina , Cruzeiro Marcio Do , Schmitt Alain , Concordet Jean-Paul , Sotiropoulos Athanassia , Dilworth Jeffrey , Noordermeer Daan , Relaix Frédéric , Sakakibara Iori , Maire Pascal
Published: April 2021

The contractile properties of adult myofibers are shaped by their Myosin heavy chain (MYH) isoform content. We identify by snATAC-seq a 42kb super-enhancer (SE) at the locus regrouping the fastMyh(fMyh) genes. By 4C-seq we show that active fMyhpromoters interact with the SE by DNA looping, leading to the activation of a single promoter per nucleus. A rainbow mouse transgenic model of the locus including the SE recapitulates the endogenous spatio-temporal expression of adult fMyhgenes.In situdeletion of the SE by CRISPR/Cas9 editing demonstrates its major role in the control of associated fMyhgenes, and deletion of two fMyhgenes at the locus reveals an active competition of the promoters for the shared SE. Last, by disrupting the organization of fMyh, we uncover positional heterogeneity within limb skeletal muscles that may underlie selective muscle susceptibility to damage in certain myopathies.
Precision Genome and Base Editing by Regulating mRNA Nuclear Export Using Selective Inhibitors of Nuclear Export (SINEs)
Authors: Cui Yan-ru , Wang Shao-jie , Ma Tiancheng , Yu Peihong , Chen Jun , Guo Taijie , Meng Genyi , Jiang Biao , Dong Jiajia , Liu Jia
Published: April 2021

CRISPR-based genome engineering tools are associated with off-target effects that constitutively active Cas9 protein may instigate. In the present study, we screened for irreversible small molecule off-switches of CRISPR-Cas9 and discovered that selective inhibitors of nuclear export (SINEs) could inhibit the cellular activity of CRISPR-Cas9 by interfering with the nuclear export of Cas9 mRNA. We subsequently found that SINEs, including an FDA-approved anticancer drug KPT330, could improve the specificities of CRISPR-Cas9-based genome and base editing tools in human cells.
NeuroMechFly, a neuromechanical model of adultDrosophila melanogaster
Authors: Ríos Victor Lobato , Ramalingasetty Shravan Tata , Özdil Pembe Gizem , Arreguit Jonathan , Ijspeert Auke Jan , Ramdya Pavan
Published: April 2021

Animal behavior emerges from a seamless interaction between neural network dynamics, musculoskeletal properties, and the physical environment. Accessing and understanding the interplay between these intertwined elements requires the development of integrative and morphologically realistic neuromechanical simulations. Until now, there has been no such simulation framework for the widely studied model organism,Drosophila melanogaster. Here we present NeuroMech-Fly, a data-driven model of the adult female fly within a physics-based simulation environment. NeuroMechFly combines a series of independent computational modules including a biomechanical exoskeleton with articulating body parts−legs, halteres, wings, abdominal segments, head, proboscis, and antennae−muscle models, and neural network controllers. To enable illustrative use cases, we first define minimal leg degrees-of-freedom by analyzing real 3D kinematic measurements during realDrosophilawalking and grooming. Then, we show how, by replaying these behaviors using NeuroMechFly’s biomechanical exoskeleton in its physics-based simulation environment, one can predict otherwise unmeasured torques and contact reaction forces. Finally, we leverage NeuroMechFly’s full neuromechanical capacity to discover neural networks and muscle parameters that enable locomotor gaits optimized for speed and stability. Thus, NeuroMechFly represents a powerful testbed for building an understanding of how behaviors emerge from interactions between complex neuromechanical systems and their physical surroundings.
Profiling the molecular signature of Satellite Glial Cells at the single cell level reveals high similarities between rodent and human
Authors: Avraham Oshri , Chamessian Alexander , Feng Rui , Yang Lite , Halevi Alexandra E. , Moore Amy M. , Gereau Robert W. , Cavalli Valeria
Published: April 2021

Peripheral sensory neurons located in dorsal root ganglia relay sensory information from the peripheral tissue to the brain. Satellite glial cells (SGC) are unique glial cells that form an envelope completely surrounding each sensory neuron soma. This organization allows for close bi-directional communication between the neuron and it surrounding glial coat. Morphological and molecular changes in SGC have been observed in multiple pathological conditions such as inflammation, chemotherapy-induced neuropathy, viral infection and nerve injuries. There is evidence that changes in SGC contribute to chronic pain by augmenting neuronal activity in various rodent pain models. SGC also play a critical role in axon regeneration. Whether findings made in rodent model systems are relevant to human physiology have not been investigated. Here we present a detailed characterization of the transcriptional profile of SGC in mouse, rat and human at the single cell level. Our findings suggest that key features of SGC in rodent models are conserved in human. Our study provides the potential to leverage rodent SGC properties and identify potential targets in humans for the treatment of nerve injuries and alleviation of painful conditions.
The ChvG–ChvI and NtrY–NtrX two-component systems coordinately regulate growth ofCaulobacter crescentus
Authors: Stein Benjamin J. , Fiebig Aretha , Crosson Sean
Published: April 2021

Two-component signaling systems (TCSs) are comprised of a sensory histidine kinase and a response regulator protein. In response to environmental changes, sensor kinases directly phosphorylate their cognate response regulator to affect gene expression. Bacteria typically express multiple TCSs that are insulated from one another and regulate distinct physiological processes. There are certainly examples of cross-regulation between TCSs, but this phenomenon remains relatively unexplored. We have identified regulatory links between the ChvG–ChvI (ChvGI) and NtrY–NtrX (NtrYX) TCSs, which control important and often overlapping processes in α-proteobacteria, including maintenance of the cell envelope. Deletion ofchvGandchvIinCaulobacter crescentuslimited growth in defined medium and a selection for genetic suppressors of this growth phenotype uncovered interactions amongchvGI, ntrYX, andntrZ, which encodes a previously uncharacterized periplasmic protein. Significant overlap in the experimentally-defined ChvI and NtrX transcriptional regulons provided support for the observed genetic connections betweenntrYXandchvGI. Moreover, we present evidence that the growth defect of strains lackingchvGIis influenced by the phosphorylation state of NtrX and, to some extent, by levels of the TonB-dependent receptor ChvT. Measurements of NtrX phosphorylationin vivoindicated that NtrZ is an upstream regulator of NtrY, and that NtrY primarily functions as an NtrX phosphatase. We propose a model in which NtrZ functions in the periplasm to inhibit NtrY phosphatase activity; regulation of phosphorylated NtrX levels by NtrZ and NtrY provides a mechanism to modulate and balance expression of the NtrX and ChvI regulons under different growth conditions.

Importance

Two-component signaling systems (TCSs) enable bacteria to regulate gene expression in response to physiochemical changes in their environment. The ChvGI and NtrYX TCSs regulate diverse pathways associated with pathogenesis, growth, and cell envelope function in many α-proteobacteria. We usedCaulobacter crescentusas a model to investigate regulatory connections between ChvGI and NtrYX. Our work defined the ChvI transcriptional regulon inC. crescentusand revealed a genetic interaction between ChvGI and NtrYX, whereby modulation of NtrYX signaling affects the survival of cells lacking ChvGI. In addition, we identified NtrZ as a periplasmic inhibitor of NtrY phosphatase activityin vivo. Our work establishesC. crescentusas an excellent model to investigate multi-level regulatory connections between ChvGI and NtrYX in α-proteobacteria.
Evidence for a Nuclear Role forDrosophilaDlg as a Regulator of the NURF Complex
Authors: Sharp Katherine A. , Khoury Mark J. , Wirtz-Peitz Frederick , Bilder David
Published: April 2021

Scrib, Dlg, and Lgl are basolateral regulators of epithelial polarity and tumor suppressors whose molecular mechanisms of action remain unclear. We used proximity biotinylation to identify proteins localized near Dlg in theDrosophilawing imaginal disc epithelium. In addition to expected membrane- and cytoskeleton-associated protein classes, nuclear proteins were prevalent in the resulting mass spectrometry data set, including all four members of the NURF chromatin remodeling complex. Subcellular fractionation demonstrated a nuclear pool of Dlg and proximity ligation confirmed its position near the NURF complex. Genetic analysis showed that NURF activity is also required for the overgrowth ofdlgtumors, and this growth suppression correlated with a reduction in Hippo pathway gene expression. Together, these data suggest a nuclear role for Dlg in regulating chromatin and transcription through a more direct mechanism than previously thought.

Highlight Summary

Proximity proteomics is used as an entry point towards identifying partners of the polarity-regulating tumor suppressor Dlg. A nuclear pool of the protein associated with NURF chromatin remodelers is revealed, along with evidence of functional interactions during growth regulation.
Same Action, Different Meaning: Neural substrates of Semantic Goal Representation
Authors: Aberbach Shahar , Buaron Batel , Mudrik Liad , Mukamel Roy
Published: April 2021

Accurate control over everyday goal-directed actions is mediated by sensory-motor predictions of intended consequences and their comparison with actual outcomes. Such online comparisons of the expected and re-afferent, immediate, sensory feedback are conceptualized as internal forward models. Current predictive coding theories describing such models typically address the processing ofimmediatesensory-motor goals, yet voluntary actions are also oriented towardslong-termconceptual goals and intentions, for which the sensory consequence is sometimes absent or cannot be fully predicted. Thus, the neural mechanisms underlying actions with distal conceptual goals is far from being clear. Specifically, it is still unknown whether sensory-motor circuits also encode information regarding the global meaning of the action, detached from the immediate, movement-related goal. Therefore, using fMRI and behavioral measures, we examined identical actions (either right or left-hand button presses) performed for two different semantic intentions (‘yes’/‘no’ response to questions regarding visual stimuli). Importantly, actions were devoid of differences in the immediate sensory outcome. Our findings revealed voxel patterns differentiating the two semantic goals in the frontoparietal cortex and visual pathways including the Lateral-occipital complex, in both hemispheres. Behavioral results suggest that the results cannot be explained by kinetic differences such as force. To the best of our knowledge, this is the first evidence showing that semantic meaning is embedded in the neural representation of actions independent of immediate sensory outcome and kinetic differences.

Significance statement

A standing question in neuroscience concerns the nature of neural circuits representing conceptual information. Previous studies indicate that regions traditionally associated with movement kinematics, also encode symbolic action categories regardless of their specific motor scheme. However, it is currently unclear whether these sensory-motor circuits also play a role in the representation of the intention, for which an action was initiated. Our results demonstrate that an action’s intention, such as its semantic goal, can be discriminated based on neural activity patterns in motor and sensory regions. Moreover, our findings suggest that semantic goals are embedded in sensorimotor regions in a hand-dependent manner.
Activity-dependent alteration of early myelin ensheathment in a developing sensory circuit
Authors: Chorghay Zahraa , MacFarquhar David , Li Vanessa J. , Aufmkolk Sarah , Schohl Anne , Wiseman Paul W. , Káradóttir Ragnhildur Thora , Ruthazer Edward S.
Published: April 2021

Adaptive myelination has been reported in response to experimental manipulations of neuronal activity, but the links between sensory experience, corresponding neuronal activity, and resultant alterations in myelination require investigation. To study this, we used theXenopus laevistadpole, which is a classic model for studies of visual system development and function because it is translucent and visually responsive throughout the formation of this retinotectal system. Here, we report the timecourse of early myelin ensheathment in theXenopusretinotectal system using immunohistochemistry of myelin basic protein (MBP) along with third-harmonic generation (THG) microscopy, a label-free structural imaging technique. Characterization of the myelination progression revealed an appropriate developmental window to address the effects of early patterned visual experience on myelin ensheathment. To alter patterned activity, we showed tadpoles stroboscopic stimuli and measured the calcium responses of retinal ganglion cell axon terminals. We identified strobe frequencies that elicited robust versus dampened calcium responses, reared animals in these strobe conditions for 7 d, and subsequently observed differences in the amount of early myelin ensheathment at the optic chiasm. This study provides evidence that it is not just the presence but also to the specific temporal properties of sensory stimuli that are important for myelin plasticity.
Perioperative acute kidney injury and urine output in lower limb arthroplasties
Authors: Nikkinen Okke , Jämsä Elias , Aaltonen Toni , Alahuhta Seppo , Ohtonen Pasi , Vakkala Merja
Published: April 2021

Background

This study aimed to evaluate the occurrence and perioperative risk factors of acute kidney injury (AKI) in primary elective hip and knee and emergency hip arthroplasty patients. We also aimed to assess the effect of urine output (UOP) as a diagnostic criterion in addition to serum creatinine (sCr) levels. We hypothesized that emergency arthroplasties are prone to AKI and that UOP is an underrated marker of AKI.

Methods

This retrospective, register‐based study assessed 731 patients who underwent primary elective knee or hip arthroplasty and 170 patients who underwent emergency hip arthroplasty at Oulu University Hospital, Finland, between January 2016 and February 2017.

Results

Of the elective patients, 18 (2.5%) developed AKI. The 1‐year mortality rate was 1.5% in elective patients without AKI and 11.1% in those with AKI (P = .038). Of the emergency patients, 24 (14.1%) developed AKI. The mortality rate was 16.4% and 37.5% in emergency patients without and with AKI, respectively (P = .024). In an AKI subgroup analysis of the combined elective and emergency patients, the mortality rate was 31.3% (n = 5) in the sCr group (n = 16), 23.5% (n = 4) in the UOP group (n = 17), and 22.2% (n = 2) in AKI patients who met both the sCr and UOP criteria (n = 9).

Conclusion

Emergency hip arthroplasty is associated with an increased risk of AKI. Since AKI increases mortality in both elective and emergency arthroplasty, perioperative oliguria should also be considered as a diagnostic criterion for AKI. Focusing solely on sCr may overlook many cases of AKI.
Functional neurological disorder in the emergency department
Authors: Finkelstein Sara A. , Cortel‐LeBlanc Miguel A. , Cortel‐LeBlanc Achelle , Stone Jon
Published: April 2021

We provide a narrative review of functional neurological disorder (FND, or conversion disorder) for the emergency department (ED). Diagnosis of FND has shifted from a “rule‐out” disorder to one now based on the recognition of positive clinical signs, allowing the ED physician to make a suspected or likely diagnosis of FND. PubMed, Google Scholar, academic books, and a hand search through review article references were used to conduct a literature review. We review clinical features and diagnostic pitfalls for the most common functional neurologic presentations to the ED, including functional limb weakness, functional (nonepileptic) seizures, and functional movement disorders. We provide practical advice for discussing FND as a possible diagnosis and suggestions for initial steps in workup and management plans.
CEO religious university affiliation and financial reporting quality
Authors: Chen Yu , Chu Xiaoyan , Park Jung Chul , Soileau Jared S.
Published: April 2021

Utilising a novel proxy for CEO religiosity that is based on graduation from a religious university, we document evidence that a CEO’s religiosity improves financial reporting quality. This effect is more pronounced when the firm is located in an area with higher geographical religiosity or more social capital, suggesting that a favourable environment facilitates the CEO religiosity effect. We also find that analyst forecasts are more accurate for firms led by a religious CEO, and that fewer analysts follow such firms, consistent with the view that there is less need for analyst service if the firm provides high‐quality information. We develop a series of tests to alleviate endogeneity concerns, including a reverse causality test, a difference‐in‐differences test based on a sample of exogenous CEO turnovers, and a placebo test. Our evidence suggests a causal explanation of the effect of CEO religiosity on financial reporting quality.
Vitamin B3 levels in women who experience first‐trimester miscarriage
Authors: Yakob Nurul A. , Peek Michael J. , Quinlivan Julie A.
Published: April 2021

Miscarriage is the most common complication in early pregnancy. It was recently reported in mice that miscarriage can be prevented through the administration of niacin. We conducted a prospective, exploratory pilot study involving 24 women who were less than 14 weeks pregnant. Neither niacin intake (P = 0.24) nor urinary vitamin B3 measured as the 1‐methyl‐5‐carboxylamide‐2‐pyridone/N‐1‐methylnicotinamide (2‐pyr/MNA) ratio (P = 1.00) predicted miscarriage. However, the difference in mean 2‐pyr/MNA ratios between women who miscarried and controls suggests there may be a threshold niacin level protective in miscarriage prevention warranting further investigation.
Allergens and their associated small molecule ligands—their dual role in sensitization
Authors: Chruszcz Maksymilian , Chew Fook Tim , Hoffmann‐Sommergruber Karin , Hurlburt Barry K. , Mueller Geoffrey A. , Pomés Anna , Rouvinen Juha , Villalba Mayte , Wöhrl Birgitta M. , Breiteneder Heimo
Published: April 2021

Many allergens feature hydrophobic cavities that allow the binding of primarily hydrophobic small‐molecule ligands. Ligand‐binding specificities can be strict or promiscuous. Serum albumins from mammals and birds can assume multiple conformations that facilitate the binding of a broad spectrum of compounds. Pollen and plant food allergens of the family 10 of pathogenesis‐related proteins bind a variety of small molecules such as glycosylated flavonoid derivatives, flavonoids, cytokinins, and steroids in vitro. However, their natural ligand binding was reported to be highly specific. Insect and mammalian lipocalins transport odorants, pheromones, catecholamines, and fatty acids with a similar level of specificity, while the food allergen β‐lactoglobulin from cow's milk is notably more promiscuous. Non‐specific lipid transfer proteins from pollen and plant foods bind a wide variety of lipids, from phospholipids to fatty acids, as well as sterols and prostaglandin B2, aided by the high plasticity and flexibility displayed by their lipid‐binding cavities. Ligands increase the stability of allergens to thermal and/or proteolytic degradation. They can also act as immunomodulatory agents that favor a Th2 polarization. In summary, ligand‐binding allergens expose the immune system to a variety of biologically active compounds whose impact on the sensitization process has not been well studied thus far.
Low‐affinity but high‐avidity interactions may offer an explanation for IgE‐mediated allergen cross‐reactivity
Authors: Chang Xinyue , Zha Lisha , Wallimann Alexandra , Mohsen Mona O. , Krenger Pascal , Liu Xuelan , Vogel Monique , Bachmann Martin F.
Published: April 2021

Background

Allergy is a global disease with overall frequencies of >20%. Symptoms vary from irritating local itching to life‐threatening systemic anaphylaxis. Even though allergies are allergen‐specific, there is a wide range of cross‐reactivities (eg apple and latex) that remain largely unexplained. Given the abilities of low‐affinity IgG antibodies to inhibit mast cells activation, here we elucidate the minimal affinity of IgE antibodies to induce type I hypersensitivity.

Methods

Three mature (high‐affinity) IgE antibodies recognizing three distinct epitopes on Fel d 1, the major cat allergen, were back‐mutated to germline conformation, resulting in binding to Fel d 1 with low affinity. The ability of these IgE antibodies to activate mast cells in vitro and in vivo was tested.

Results

We demonstrate that affinities as low as 10−7 M are sufficient to activate mast cells in vitro and drive allergic reactions in vivo. Low‐affinity IgE antibodies are able to do so, since they bind allergens bivalently on the surface of mast cells, leading to high‐avidity interactions.

Conclusions

These results suggest that the underlying mechanism of allergen cross‐reactivity may be low‐affinity but high‐avidity binding between IgE antibodies and cross‐reactive allergen.