bluuebunny/crossref_metadata_2025 huggingface dataset:
Introduction
Authors: Fleck Dieter
Published: March 2021

This introductory chapter provides an overview of international humanitarian law. During the past decades, international humanitarian law has been subject to a progressive development which culminated in the four 1949 Geneva Conventions, the 1977 Protocols Additional to these Conventions, the 1980 Weapons Convention, the 1993 Chemical Weapons Convention, and the 1998 Rome Statute of the International Criminal Court. While many efforts have been made by states to implement their obligations under international humanitarian law, much work remains to be done at international and national levels. This task poses a challenge to political decision-makers and to their legal and military advisers, many of whom must shoulder this workload in addition to other duties and in spite of the pressure of other priorities. Recent achievements of worldwide co-operation in this field are manifold: The interrelationship between humanitarian law and the protection of human rights in armed conflicts is largely accepted and better understood today than ever before. A progressive development of international criminal law has led to increased jurisprudence on war crimes and crimes against humanity by national courts, international ad hoc tribunals, and finally to the establishment of the International Criminal Court (ICC).
Protection of Civilians
Authors: Fleck Dieter
Published: March 2021

This chapter assesses the provisions of international law concerning the protection of civilians in armed conflict. The rules applicable in international armed conflict are highly developed and extensively codified. Of course, their scope of application is limited to conflicts of an international character, in particular armed clashes between states. Situations of foreign occupation are also international armed conflicts. The four Geneva Conventions, supplemented by their first 1977 Additional Protocol, constitute the heart of protections granted to civilians in international armed conflicts. Meanwhile, the law protecting civilians in non-international armed conflicts has been codified by Article 3 common to the four Geneva Conventions and the second 1999 Additional Protocol. Although these provisions are more summary in nature than the law on international armed conflicts, they contain important rules on the protection of civilians in an internal conflict. The chapter then considers the provisions concerning situations in which a party to an armed conflict comes into contact with civilians of the opposing side, especially with aliens on its own territory and with inhabitants of occupied territories.
Implementation and Enforcement of International Humanitarian Law
Authors: Fleck Dieter
Published: March 2021

This chapter deals with the most important and at the same time most challenging part of international humanitarian law, as it describes and evaluates national and international measures to ensure implementation and compliance with existing rules and to provide remedies for violations. One necessary condition for the effective implementation of humanitarian law is that its contents are known by persons involved in a conflict, especially the combatants, that those persons are aware that violations carry disciplinary or penal consequences, and that they realize that persistent breaches may lead to an escalation of the conflict. In this regard, compliance with humanitarian law is in the interest of every individual party to an armed conflict. Highlighting long-lasting legal developments which have eventually led to a strengthening of national and international criminal jurisdiction on war crimes and crimes against humanity, the chapter explores the legal obligations of states and international organizations and appropriate measures to implement existing obligations, to prevent any violations, and take effective action where breaches are committed. It also reflects on the continuing increase of relevant jurisprudence and policymaking by intergovernmental and other organizations in recent years.
Rights of the Reinsurer
Authors: Edelman Colin , Burns Andrew
Published: March 2021

This chapter details the rights of the reinsurer, one of which is the payment of premium. The premium is the consideration for the contract which proceeds from the reinsured to the reinsurer in return for coverage according to the policy terms. A reinsurer has the right to treat the contract of reinsurance as discharged upon non-payment of the premium if the contract contains an express right to cancel for non-payment of premium. In the absence of such an express clause, cancellation may be justified if it is an implied condition of the contract that the premium would be paid in advance or on the grounds that the reinsured has repudiated the contract by evincing an intention not to pay the premium. Meanwhile, a reinsurer can circumscribe the power of the reinsured to make settlements or other decisions which are binding on it by the use of a claims co-operation clause. A claims control clause gives a reinsurer even more influence in the handling of the original claim by the underlying insured. The chapter then looks at the right of the reinsurer to inspect the reinsured’s records; to declaratory relief; and to subrogation.
Structural phylogenetic analysis reveals lineage-specific RNA repetitive structural motifs in all coronaviruses and associated variations in SARS-CoV-2
Authors: Chen Shih-Cheng , Olsthoorn René C L , Yu Chien-Hung
Published: March 2021

In many single-stranded (ss) RNA viruses, the cis-acting packaging signal that confers selectivity genome packaging usually encompasses short structured RNA repeats. These structural units, termed repetitive structural motifs (RSMs), potentially mediate capsid assembly by specific RNA–protein interactions. However, general knowledge of the conservation and/or the diversity of RSMs in the positive-sense ssRNA coronaviruses (CoVs) is limited. By performing structural phylogenetic analysis, we identified a variety of RSMs in nearly all CoV genomic RNAs, which are exclusively located in the 5′-untranslated regions (UTRs) and/or in the inter-domain regions of poly-protein 1ab coding sequences in a lineage-specific manner. In all alpha- and beta-CoVs, except for Embecovirus spp, two to four copies of 5′-gUUYCGUc-3′ RSMs displaying conserved hexa-loop sequences were generally identified in Stem-loop 5 (SL5) located in the 5′-UTRs of genomic RNAs. In Embecovirus spp., however, two to eight copies of 5′-agc-3′/guAAu RSMs were found in the coding regions of non-structural protein (NSP) 3 and/or NSP15 in open reading frame (ORF) 1ab. In gamma- and delta-CoVs, other types of RSMs were found in several clustered structural elements in 5′-UTRs and/or ORF1ab. The identification of RSM-encompassing structural elements in all CoVs suggests that these RNA elements play fundamental roles in the life cycle of CoVs. In the recently emerged SARS-CoV-2, beta-CoV-specific RSMs are also found in its SL5, displaying two copies of 5′-gUUUCGUc-3′ motifs. However, multiple sequence alignment reveals that the majority of SARS-CoV-2 possesses a variant RSM harboring SL5b C241U, and intriguingly, several variations in the coding sequences of viral proteins, such as Nsp12 P323L, S protein D614G, and N protein R203K-G204R, are concurrently found with such variant RSM. In conclusion, the comprehensive exploration for RSMs reveals phylogenetic insights into the RNA structural elements in CoVs as a whole and provides a new perspective on variations currently found in SARS-CoV-2.
Illness Perceptions, Disabilities, and Quality of Life of Patients With Hand Injury: A Prospective Study
Authors: Chen Ying-Ying , Yang Cheng-San , Lee Bih-O
Published: March 2021

Background:

Few studies have tracked hand injury patients past the acute care period. Postdischarge tracking of hand injury patients may identify time points most patients require assistance, which can help direct interventions to reduce post–hand injury sequelae.

Objective:

To examine hand injury patients' experiences during early recovery to illness perceptions, disabilities, and quality of life and to identify predictors of quality of life at 1 month and 3 months after hospital discharge.

Methods:

This prospective observational study of hand injury patients was performed at a teaching hospital in Taiwan. Data were collected at patient discharge, 1 month, and 3 months after discharge, from January 2017 to October 2018. The variables measured included illness perceptions, disabilities, and quality of life.

Results:

A total of 117 patients participated in the study. The patients reported more positive illness perceptions at 3 months versus 1 month after discharge. The impact of disabilities on patient work was significantly greater at 1 month than at 3 months after discharge. Quality of life was better at 3 months than at 1 month after discharge. Predictors of quality of life after hospital discharge were demographic variables, clinical variables, and illness perceptions. Patients with lower education reported poorer psychological quality of life after discharge.

Conclusion:

Primary care providers should perform a comprehensive assessment of patients prior to their discharge. Patients should undergo regular follow-ups to reduce comorbidities and improve their outcomes.
Hearing Loss and Home Health
Authors: Pittman Corinne A. , Willink Amber , Nieman Carrie L.
Published: March 2021

The purpose of this study was to identify unmet hearing care needs among older adults receiving home healthcare as a potential method to reach a population unserved by clinic-based care. Cross-sectional analyses were used to identify hearing loss and hearing aid use among beneficiaries enrolled in home care, using data from the nationally representative 2017 Medicare Current Beneficiary Survey (MCBS). Survey participants who reported enrollment in home healthcare services in 2017 (n = 3,183,693) were included for the purposes of analyses. Home health and hearing status were assessed through MCBS questionnaires, reported by Medicare beneficiaries or an appointed proxy, along with hearing status evaluated at initial home care intake. Among older Medicare beneficiaries receiving home healthcare, 51.8% self-reported hearing concerns. Of this population, only 16.1% reported hearing aid use. Recipients with hearing difficulty received an average of 30 visits per year, totaling to $5,208.25 in expenditure. By self-report, 44% of older home care recipients with hearing difficulty were misclassified as having “adequate” hearing on initial assessment and 31% of initial assessments identified hearing loss among those who self-reported no difficulty hearing. Effective management of chronic health conditions is core to healthy aging, including sensory health. Hearing loss represents a largely unaddressed need among home care recipients and frequently goes unidentified. Home-based hearing services that integrate into existing assessments and practices may be an avenue in identifying hearing loss and extending care to older adults who have traditionally gone without access to hearing intervention.
A Look at 2021 Infusion Therapy Standards of Practice
Authors: Gorski Lisa A.
Published: March 2021

The Infusion Therapy Standards of Practice provide evidence-based recommendations as published by the Infusion Nurses Society every 5 years. This article provides a brief overview of the development process and short summaries of selected standards with attention to highlighting the relevance to home care agencies and nurses. The Standards should be reviewed by any home care organization that provides home infusion therapy.
The impact of paternal alcohol, tobacco, caffeine use and physical activity on offspring mental health: A systematic review and meta-analysis
Authors: Easey Kayleigh E , Sharp Gemma C
Published: March 2021

Background

There is some evidence that paternal health behaviours during and around pregnancy could be associated with offspring health outcomes. However, the impact that paternal health behaviours during pregnancy can have on offspring mental health is understudied and remains unclear.

Methods

We conducted a systematic review and meta-analysis of articles in PubMed describing studies of potentially modifiable paternal health behaviours (tobacco smoking, alcohol consumption, caffeine consumption and physical activity) in the prenatal period in relation to offspring mental health.

Results

Ten studies were included and categorized by paternal health behaviour and offspring mental health outcome investigated. The narrative synthesis provided evidence of association between paternal health behaviours around pregnancy and offspring mental health problems, with the strongest evidence shown for tobacco use. Grouped by analysis type, two separate meta-analyses showed evidence of paternal smoking during pregnancy being associated with greater odds of ADHD in offspring (OR 1.42, 95% CI 1.02 to 1.99; HR 1.28, 95% CI 1.19 to 1.39).

Conclusions

Our review suggests that paternal tobacco smoking and alcohol consumption in the prenatal period are associated with poorer offspring mental health, particularly hyperactivity/ADHD. Future investigation using methods that allow stronger causal inference is needed to further investigate if these associations are causal.
Maternal Levels of Acute Phase Proteins in Early Pregnancy and Risk of Autism Spectrum Disorders in Offspring
Authors: Brynge Martin , Gardner Renee M , Sjöqvist Hugo , Karlsson Håkan , Dalman Christina
Published: March 2021

Previous research supports a contribution of early-life immune disturbances in the etiology of autism spectrum disorders (ASD). Biomarker studies of the maternal innate (non-adaptive) immune status related to ASD risk have focused on one of the acute phase proteins (APP), C-reactive protein (CRP), with conflicting results. We evaluated levels of eight different APP in maternal serum samples drawn in first trimester, from 318 mothers to ASD-cases and 429 mothers to ASD-unaffected controls, nested within the register-based Stockholm Youth Cohort. Overall, we found no general trend of high levels of maternal APP being associated with increased risk of ASD. In contrast, maternal levels of CRP in the lowest compared to the middle tertile were associated with increased risk of ASD without ID or ADHD in offspring (OR = 2.15, 95 % CI 1.17-3.93). Further, levels of maternal ferritin in the lowest (OR = 1.82, 95 % CI 1.19-2.78) and highest (OR = 1.74, 95 % CI 1.16-2.60) tertiles were associated with increased risk of any ASD diagnosis in offspring, with stronger associations still between the lowest (OR = 3.58, 95 % CI 1.79-7.17) and highest (OR = 3.20, 95 % CI 1.62-6.29) tertiles of ferritin and risk of ASD with ID. The biological interpretation of lower CRP-levels among mothers to ASD-cases is not clear but might be related to the function of the maternal innate immune system. The finding of aberrant levels of ferritin conferring risk of ASD-phenotypes indicates a plausibly important role of iron during neurodevelopment.
Engineered SARS-CoV-2 receptor binding domain improves immunogenicity in mice and elicits protective immunity in hamsters
Authors: Dalvie Neil C. , Rodriguez-Aponte Sergio A. , Hartwell Brittany L. , Tostanoski Lisa H. , Biedermann Andrew M. , Crowell Laura E. , Kaur Kawaljit , Kumru Ozan , Carter Lauren , Yu Jingyou , Chang Aiquan , McMahan Katherine , Courant Thomas , Lebas Celia , Lemnios Ashley A. , Rodrigues Kristen A. , Silva Murillo , Johnston Ryan S. , Naranjo Christopher A. , Tracey Mary Kate , Brady Joseph R. , Whittaker Charles A. , Yun Dongsoo , Kar Swagata , Porto Maciel , Lok Megan , Andersen Hanne , Lewis Mark G. , Love Kerry R. , Camp Danielle L. , Silverman Judith Maxwell , Kleanthous Harry , Joshi Sangeeta B. , Volkin David B. , Dubois Patrice M. , Collin Nicolas , King Neil P. , Barouch Dan H. , Irvine Darrell J. , Love J. Christopher
Published: March 2021

Global containment of COVID-19 still requires accessible and affordable vaccines for low- and middle-income countries (LMICs).1Recently approved vaccines provide needed interventions, albeit at prices that may limit their global access.2Subunit vaccines based on recombinant proteins are suited for large-volume microbial manufacturing to yield billions of doses annually, minimizing their manufacturing costs.3These types of vaccines are well-established, proven interventions with multiple safe and efficacious commercial examples.4–6Many vaccine candidates of this type for SARS-CoV-2 rely on sequences containing the receptor-binding domain (RBD), which mediates viral entry to cells via ACE2.7,8Here we report an engineered sequence variant of RBD that exhibits high-yield manufacturability, high-affinity binding to ACE2, and enhanced immunogenicity after a single dose in mice compared to the Wuhan-Hu-1 variant used in current vaccines. Antibodies raised against the engineered protein exhibited heterotypic binding to the RBD from two recently reported SARS-CoV-2 variants of concern (501Y.V1/V2). Presentation of the engineered RBD on a designed virus-like particle (VLP) also reduced weight loss in hamsters upon viral challenge.
Characterization of the neurogenic niche in the aging dentate gyrus using iterative immunofluorescence imaging
Authors: Cole John Darby , del Castillo Jacobo Sarabia , Gut Gabriele , Gonzalez-Bohorquez Daniel , Pelkmans Lucas , Jessberger Sebastian
Published: March 2021

Advancing age causes reduced hippocampal neurogenesis, associated with age-related cognitive decline. The spatial relationship of age-induced alterations in neural stem cells (NSCs) and surrounding cells within the hippocampal niche remains poorly understood due to limitations of antibody-based cellular phenotyping. We established iterative indirect immunofluorescence imaging (4i) in tissue sections, allowing for simultaneous detection of 18 proteins to characterize NSCs and surrounding cells in young and aged mice. We show that reorganization of the DG niche already occurs in middle-aged mice, paralleling the decline in neurogenesis. Tissue 4i-based analysis of the DG identifies changes in cell-type contributions to the blood brain barrier and microenvironments surrounding NSCs to play a pivotal role to preserve neurogenic permissiveness. The data provided represent a resource to characterize the principles causing alterations of stem cell-associated plasticity within the aging DG and provide a blueprint to analyze somatic stem cell niches across lifespan in complex tissues.
Comparison of Chronic Wasting Disease Detection Methods and Procedures: Implications for Free-Ranging White-Tailed Deer (Odocoileus Virginianus) Surveillance and Management
Authors: Schwabenlander Marc D. , Rowden Gage R. , Li Manci , LaSharr Kelsie , Hildebrand Erik C. , Stone Suzanne , Seelig Davis M. , Jennelle Chris S. , Cornicelli Louis , Wolf Tiffany M. , Carstensen Michelle , Larsen Peter A.
Published: March 2021

Throughout North America, chronic wasting disease (CWD) has emerged as perhaps the greatest threat to wild cervid populations, including white-tailed deer (Odocoileus virginianus). White-tailed deer are the most sought after big game species across North America with populations of various subspecies in nearly all Canadian provinces, the contiguous USA, and Mexico. Documented CWD cases have dramatically increased across the white-tailed deer range since the mid-1990s, including in Minnesota. CWD surveillance in free-ranging white-tailed deer and other cervid populations mainly depends upon immunodetection methods (e.g., immunohistochemistry [IHC] and enzyme-linked immunosorbent assay [ELISA]) on medial retropharyngeal lymph nodes and obex. More recent technologies centered on prion protein amplification methods of detection have shown promise as more sensitive and rapid CWD diagnostic tools. Here, we used blinded samples to test the efficacy of real time quaking-induced conversion (RT-QuIC) in comparison to ELISA and IHC for screening tissues, blood, and feces collected in 2019 from white-tailed deer in southeastern Minnesota, where CWD has been routinely detected since 2016. Our results support previous findings that RT-QuIC is a more sensitive tool for CWD detection than current antibody-based methods. Additionally, a CWD testing protocol that includes multiple lymphoid tissues (medial retropharyngeal lymph node, parotid lymph node, and palatine tonsil) per animal may effectively identify a greater number of CWD detections in a white-tailed deer population than a single sample type (i.e., medial retropharyngeal lymph nodes). These results reveal that the variability of CWD pathogenesis, sampling protocol, and testing platform must be considered for the effective detection and management of CWD throughout North America.
Landscape connectivity alters the evolution of density-dependent dispersal during pushed range expansions
Authors: Dahirel Maxime , Bertin Aline , Calcagno Vincent , Duraj Camille , Fellous Simon , Groussier Géraldine , Lombaert Eric , Mailleret Ludovic , Marchand Anaël , Vercken Elodie
Published: March 2021

Abstract

As human influence reshapes communities worldwide, many species expand or shift their ranges as a result, with extensive consequences across levels of biological organization. Range expansions can be ranked on a continuum going from pulled dynamics, in which low-density edge populations provide the “fuel” for the advance, to pushed dynamics in which high-density rear populations “push” the expansion forward. While theory suggests that evolution during range expansions could lead pushed expansions to become pulled with time, empirical comparisons of phenotypic divergence in pushed vs. pulled contexts are lacking. In a previous experiment usingTrichogramma brassicaewasps as a model, we showed that expansions were more pushed when connectivity was lower. Here we used descendants from these experimental landscapes to look at how the range expansion process and connectivity interact to shape phenotypic evolution. Interestingly, we found no clear and consistent phenotypic shifts, whether along expansion gradients or between reference and low connectivity replicates, when we focused on low-density trait expression. However, we found evidence of changes in density-dependence, in particular regarding dispersal: populations went from positive to negative density-dependent dispersal at the expansion edge, but only when connectivity was high. As positive density-dependent dispersal leads to pushed expansions, our results confirm predictions that evolution during range expansions may lead pushed expansions to become pulled, but add nuance by showing landscape conditions may slow down or cancel this process. This shows we need to jointly consider evolution and landscape context to accurately predict range expansion dynamics and their consequences.
Cooperative regulation of coupled oncoprotein translation and stability in triple-negative breast cancer by EGFR and CDK12
Authors: Ang Hazel X. , Sutiman Natalia , Deng Xinyue L. , Bartelt Luke C. , Chen Qiang , Barrera Alejandro , Lin Jiaxing , Sheng Jeff , McDowell Ian C. , Reddy Timothy E. , Nicchitta Christopher V. , Wood Kris C.
Published: March 2021

Evidence has long suggested that epidermal growth factor receptor (EGFR) may play a prominent role in triple-negative breast cancer (TNBC) pathogenesis, but clinical trials of EGFR inhibitors have yielded disappointing results. Using a candidate drug screen, we discovered that inhibition of CDK12 dramatically sensitizes diverse models of TNBC to EGFR blockade. Instead of functioning through CDK12’s well-established roles proximal to transcription, this combination therapy drives cell death through the 4E-BP1-dependent suppression of the translation and consequent stability of driver oncoproteins, including MYC. A genome-wide CRISPR/Cas9 screen identified the CCR4-NOT complex as a major determinant of sensitivity to the combination therapy whose loss renders 4E-BP1 unresponsive to drug-induced dephosphorylation, rescuing MYC translational suppression and stability. The central roles of CCR4-NOT and 4E-BP1 in response to the combination therapy were further underscored by the observation of CNOT1 loss and rescue of 4E-BP1 phosphorylation in TNBC cells that naturally evolved therapy resistance. Thus, pharmacological inhibition of CDK12 reveals a long proposed EGFR dependence in TNBC that functions through the cooperative regulation of translation-coupled oncoprotein stability.
Spt4 Facilitates the Movement of RNA Polymerase II through the +2 Nucleosomal Barrier
Authors: Uzun Ülkü , Brown Thomas , Fischl Harry , Angel Andrew , Mellor Jane
Published: March 2021

Spt4 is a transcription elongation factor, with homologues in organisms with nucleosomes. Structural andin vitrostudies implicate Spt4 in transcription through nucleosomes, yet thein vivofunction of Spt4 is unclear. Here we assessed the precise position of Spt4 during transcription and the consequences of loss of Spt4 on RNA polymerase II (RNAPII) dynamics and nucleosome positioning inSaccharomyces cerevisiae. In the absence of Spt4, the spacing between gene-body nucleosomes increases and RNAPII accumulates upstream of the nucleosomal dyad, most dramatically at nucleosome +2. Spt4 associates with elongating RNAPII early in transcription and its association dynamically changes depending on nucleosome positions. Together, our data show that Spt4 regulates early elongation dynamics, participates in co-transcriptional nucleosome positioning, and promotes RNAPII movement through the gene-body nucleosomes, especially the +2 nucleosome.
Joint identification of sex and sex-linked scaffolds in non-model organisms using low depth sequencing data
Authors: Nursyifa Casia , Brüniche-Olsen Anna , Erill Genis Garcia , Heller Rasmus , Albrechtsen Anders
Published: March 2021

Being able to assign sex to individuals and identify autosomal and sex-linked scaffolds are essential in most population genomic analyses. Non-model organisms often have genome assemblies at scaffold level and lack characterization of sex-linked scaffolds. Previous methods to identify sex and sex-linked scaffolds have relied on e.g. sequence similarity between the non-model organism and a closely related species or prior knowledge about the sex of the samples to identify sex-linked scaffolds. In the latter case, the difference in depth of coverage between the autosomes and the sex chromosomes are used. Here we present ‘Sex Assignment Through Coverage’ (SATC), a method to identify sample sex and sex-linked scaffolds from NGS data. The method only requires a scaffold level reference assembly and sampling of both sexes with whole genome sequencing (WGS) data. We use the sequencing depth distribution across scaffolds to jointly identify: i) male and female individuals and ii) sex-linked scaffolds. This is achieved through projecting the scaffold depths into a low-dimensional space using principal component analysis (PCA) and subsequent Gaussian mixture clustering. We demonstrate the applicability of our method using data from five mammal species and a bird species complex. The method is open source and freely available athttps://github.com/popgenDK/SATC
COVID Seroprevalence, Symptoms and Mortality During the First Wave of SARS-CoV-2 in Canada
Authors:   Action to beat coronavirus/Action pour battre le coronavirus (Ab-C) Study Investigators, Jha Prabhat
Published: March 2021

Background

Efforts to stem Canada’s SARS-CoV-2 pandemic can benefit from direct understanding of the prevalence, infection fatality rates (IFRs), and information on asymptomatic infection.

Methods

We surveyed a representative sample of 19,994 adult Canadians about COVID symptoms and analyzed IgG antibodies against SARS-CoV-2 from self-collected dried blood spots (DBS) in 8,967 adults. A sensitive and specific chemiluminescence ELISA detected IgG to the spike trimer. We compared seroprevalence to deaths to establish IFRs and used mortality data to estimate infection levels in nursing home residents.

Results

The best estimate (high specificity) of adult seroprevalence nationally is 1.7%, but as high as 3.5% (high sensitivity) depending on assay cut-offs. The highest prevalence was in Ontario (2.4-3.9%) and in younger adults aged 18-39 years (2.5-4.4%). Based on mortality, we estimated 13-17% of nursing home residents became infected. The first viral wave infected 0.54-1.08 million adult Canadians, half of whom were <40 years old. The IFR outside nursing homes was 0.20-0.40%, but the COVID mortality rate in nursing home residents was >70 times higher than that in comparably-aged adults living in the community. Seropositivity correlated with COVID symptoms, particularly during March. Asymptomatic adults constituted about a quarter of definite seropositives, with a greater proportion in the elderly.

Interpretation

Canada had relatively low infection prevalence and low IFRs in the community, but not in nursing homes, during the first viral wave. Self-collected DBS for antibody testing is a practicable strategy to monitor the ongoing second viral wave and, eventually, vaccine-induced immunity among Canadian adults.
A modeling framework for determining modulation of neural-level tuning from non-invasive human fMRI data
Authors: Sadil Patrick , Cowell Rosemary A. , Huber David E.
Published: March 2021

Many neuroscience theories assume that tuning modulation of individual neurons underlies changes in human cognition. However, non-invasive fMRI lacks sufficient resolution to visualize this modulation. To address this limitation, we developed an analysis framework called Inferring Neural Tuning Modulation (INTM) for “peering inside” voxels. Precise specification of neural tuning from the BOLD signal is not possible. Instead, INTM compares theoretical alternatives for the form of neural tuning modulation that might underlie changes in BOLD across experimental conditions. The most likely form is identified via formal model comparison, with assumed parametric Normal tuning functions, followed by a non-parametric check of conclusions. We validated the framework by successfully identifying a well-established form of modulation: visual contrast-induced multiplicative gain for orientation tuned neurons. INTM can be applied to any experimental paradigm testing several points along a continuous feature dimension (e.g., direction of motion, isoluminant hue) across two conditions (e.g., with/without attention, before/after learning).
Self-supervised learning of probabilistic prediction through synaptic plasticity in apical dendrites: A normative model
Authors: Rao Arjun , Legenstein Robert , Subramoney Anand , Maass Wolfgang
Published: March 2021

Sensory information is processed by the brain not in a simple feedforward fashion. Rather, bottom-up inputs are combined in pyramidal cells of sensory cortices with top-down information from higher brain areas that arrives through synapses in apical dendrites. The exact functional role of these top-down inputs has remained unknown. A promising abstract model posits that they provide probabilistic priors for bottom-up sensory inputs. We show that this hypothesis is consistent with a large number of experimental about synaptic plasticity in apical dendrites, in particular with the prominent role of NMDA-spikes. We identify conditions under which this synaptic plasticity could approximate the gold standard for self-supervised learning of probabilistic priors: logistic regression. Furthermore, this perspective suggests an additional functional role for the complex structure of the dendritic arborization plays: It enables the neuron to learn substantially more complex landscapes of probabilistic priors.
Discovery and validation of novel human genomic safe harbor sites for gene and cell therapies
Authors: Aznauryan Erik , Yermanos Alexander , Kinzina Elvira , Kapetanovic Edo , Milanova Denitsa , Church George M. , Reddy Sai T.
Published: March 2021

Existing approaches for the integration and expression of genes of interest in a desired human cellular context are marred by the safety concerns related to either the random nature of viral-mediated integration or unpredictable pattern of gene expression in currently employed targeted genomic integration sites. Disadvantages of these methods lead to their limited use in clinical practice, thus encouraging future research in identifying novel human genomic sites that allow for predictable and safe expression of genes of interest. We conducted a bioinformatic search followed by experimental validation of novel genomic sites and identified two that demonstrated stable expression of integrated reporter and therapeutic genes without detrimental changes to cellular transcriptome. The cell-type agnostic criteria used in our bioinformatic search suggest wide-scale applicability of our sites for engineering of a diverse range of tissues for therapeutic as well as enhancement purposes, including modified T-cells for cancer therapy and engineered skin to ameliorate inherited diseases and aging. Additionally, the stable and robust levels of gene expression from identified sites allow for their use in industry-scale biomanufacturing of desired proteins in human cells.
Bovine milk somatic cell transcriptomic response toStaphylococcus aureusis dependent on strain genotype
Authors: Niedziela Dagmara A. , Cormican Paul , Foucras Gilles , Leonard Finola C. , Keane Orla M.
Published: March 2021

Background

Mastitis is an economically important disease of dairy cows with Staphylococcus aureus a major cause worldwide. Challenge of Holstein-Friesian cows demonstrated that S. aureus strain MOK124, which belongs to Clonal Complex (CC)151, caused clinical mastitis, while strain MOK023, belonging to CC97, caused mild or subclinical mastitis. The aim of this study was to elucidate the molecular mechanisms of the host immune response utilising a transcriptomic approach. Milk somatic cells were collected from cows infected with either S. aureus MOK023 or MOK124 at 0, 24, 48, 72 and 168 hours post-infection (hpi) and analysed for differentially expressed (DE) genes in response to each strain.

Results

In response to MOK023, 1278, 2278, 1986 and 1750 DE genes were found at 24, 48, 72 and 168 hpi, respectively, while 2293, 1979, 1428 and 1544 DE genes were found in response to MOK124 at those time points. Genes involved in milk production (CSN1, CSN10, CSN1S2, CSN2, a-LACTA and PRLR) were downregulated in response to both strains, with a more pronounced decrease in the MOK124 group. Immune response pathways such as NF-κB and TNF signalling were overrepresented in response to both strains at 24 hpi. These immune pathways continued to be overrepresented in the MOK023 group at 48 and 72 hpi, while the Hippo signalling, extracellular matrix interaction (ECM) and tight junction pathways were overrepresented in the MOK124 group between 48 and 168 hpi. Cellular composition analysis demonstrated that a neutrophil response was predominant in response to MOK124, while M1 macrophages were the main milk cell type post-infection in the MOK023 group.

Conclusions

A switch from immune response pathways to pathways involved in maintaining the integrity of the epithelial cell layer was observed in the MOK124 group from 48 hpi, which coincided with the occurrence of clinical signs in the infected animals. The higher proportion of M1 macrophages in the MOK023 group and lack of substantial neutrophil recruitment in response to MOK023 may indicate immune evasion by this strain. The results of this study highlight that the somatic cell transcriptomic response to S. aureus is dependent on the genotype of the infecting strain.
Smartphone deprivation alters cortical sensorimotor processing of the hand
Authors: Ghosh Arko
Published: March 2021

Brain areas representing the body can change in response to behavioral alterations. This idea is firmly established for the adult cortex in response to extraordinary alterations such as traumatic amputation or casting of the limb. Here we address how adult cortical sensorimotor processing alters in response to a subtle perturbation in the form of smartphone deprivation lasting for ~7 days. We quantified the sensorimotor processes associated with the fingertips before and after the deprivation in right-handed smartphone users. The measurements were contrasted with those of a control group with unperturbed smartphone behavior. First, smartphone tapping speed in daily life became slower after the deprivation. Second, according to reaction time tests conducted in the laboratory the asymmetrically superior performance of the right vs. left thumb was eroded by the deprivation. Third, according to EEG measurements at physical rest, tactile stimulation at the right thumb tip resulted in smaller signal amplitudes after the deprivation. Moreover, the EEG measurements during smartphone use revealed larger signal amplitudes for tactile stimulation at the right little fingertip after the deprivation. We show that cortical plasticity can occur by merely disengaging from a common day-to-day behavior. We suggest that in daily life the adult brain continuously and selectively updates its sensorimotor processing according to recent experience.
NPAS4 in the medial prefrontal cortex mediates chronic social defeat stress-induced anhedonia and dendritic spine loss
Authors: Hughes Brandon W , Siemsen Benjamin M , Berto Stefano , Kumar Jaswinder , Cornbrooks Rebecca G , Akiki Rose Marie , Carter Jordan S , Scofield Michael D , Cowan Christopher W , Taniguchi Makoto
Published: March 2021

Chronic stress can produce reward system deficits (i.e. anhedonia) and other common symptoms associated with depressive disorders, as well as neural circuit hypofunction in the medial prefrontal cortex (mPFC). However, the molecular mechanisms by which chronic stress promotes depressive-like behavior and hypofrontality remain unclear. We show here that the neuronal activity-regulated transcription factor, NPAS4, in the mPFC is regulated by chronic social defeat stress (CSDS), and it’s required in this brain region for CSDS-induced changes in sucrose preference and natural reward motivation. Interestingly, NPAS4 is not required for CSDS-induced social avoidance or anxiety-like behavior. We also find that mPFC NPAS4 is required for CSDS-induced reduction of pyramidal cell dendritic spine density, revealing a relationship between mPFC dendritic spine changes and anhedonia-like behavior, but not social avoidance behavior. Finally, transcriptomic analysis from the mPFC revealed that NPAS4 influences expression of numerous genes linked to glutamatergic synapses and ribosomal function, as well as many dysregulated genes observed in common neuropsychiatric disorders, including depression. Together our findings reveal an essential role for the activity-regulated transcription factor, NPAS4, in chronic stress-induced mPFC hypofunction and anhedonia.
Glucagon-like peptide 1 receptor-mediated stimulation of a GABAergic projection from the bed nucleus of the stria terminalis to the hypothalamic paraventricular nucleus
Authors: Povysheva Nadya , Zheng Huiyuan , Rinaman Linda
Published: March 2021

We previously reported that GABAergic neurons within the ventral anterior lateral bed nucleus of the stria terminalis (alBST) express glucagon-like peptide 1 receptor (GLP1R) in rats, and that virally-mediated “knock-down” of GLP1R expression in the alBST prolongs the hypothalamic-pituitary-adrenal axis response to acute stress. Given other evidence that a GABAergic projection pathway from ventral alBST serves to limit stress-induced activation of the HPA axis, we hypothesized that GLP1 signaling promotes activation of GABAergic ventral alBST neurons that project directly to the paraventricular nucleus of the hypothalamus (PVN). After PVN microinjection of fluorescent retrograde tracer followed by preparation ofex vivorat brain slices, whole-cell patch clamp recordings were made in identified PVN-projecting neurons within the ventral alBST. Bath application of Exendin-4 (a specific GLP1R agonist) indirectly depolarized PVN-projecting neurons in the ventral alBST and adjacent hypothalamic parastrial nucleus (PS) via circuit-mediated effects that increased excitatory synaptic inputs and decreased inhibitory synaptic inputs to the PVN-projecting neurons; these effects were occluded by prior bath application of a GLP1R antagonist. Additional retrograde tracing experiments combined within situhybridization confirmed that PVN-projecting neurons within the ventral alBST/PS are GABAergic, and do not express GLP1R mRNA. Conversely, GLP1 mRNA is expressed by a subset of GABAergic neurons within the oval subnucleus of the dorsal alBST that project into the ventral alBST. Our novel findings reveal a potential GLP1R-mediated mechanism through which the alBST exerts inhibitory control over the endocrine HPA axis.
Paucimyces polynucleatusgen. nov, sp. nov., a novel polycentric genus of anaerobic gut fungi from the feces of a wild blackbuck antelope
Authors: Hanafy Radwa A. , Youssef Noha H. , Elshahed Mostafa
Published: March 2021

The anaerobic gut fungi (AGF, phylum Neocallimastigomycota) reside in the alimentary tracts of herbivores. Multiple novel, yet-uncultured AGF taxa have recently been identified in culture-independent diversity surveys. Here, we report on the isolation and characterization of the first representative of the RH5 lineage from fecal samples of a wild blackbuck (Indian Antelope) from Sutton County, Texas, USA. The isolates displayed medium sized (2-4 mm) compact circular colonies on agar roll tubes and thin loose biofilm-like growth in liquid medium. Microscopic examination revealed monoflagellated zoospores and polycentric thalli with highly branched nucleated filamentous rhizomycelium, a growth pattern encountered in a minority of described AGF genera so far. The obtained isolates are characterized by formation of spherical vesicles at the hyphal tips from which multiple sporangia formed either directly on the spherical vesicles or at the end of sporangiophores. Phylogenetic analysis using the D1/D2 regions of the large ribosomal subunit (D/D2 LSU) and the ribosomal internal transcribed spacer 1 (ITS1) revealed sequence similarities of 93.5%, and 81.3%, respectively, to the closest cultured relatives (Orpinomyces joyoniistrain D3A (D1/D2 LSU), andJoblinomyces apicalisstrain GFH681 (ITS1). Substrate utilization experiments using the type strain (BB-3) demonstrated growth capabilities on a wide range of mono-, oligo-, and polysaccharides, including glucose, xylose, mannose, fructose, cellobiose, sucrose, maltose, trehalose, lactose, cellulose, xylan, starch, and raffinose. We propose accommodating these novel isolates in a new genus and species, for which the namePaucimyces polynucleatusis proposed. The type species is strain BB-3.
Efficient generative modeling of protein sequences using simple autoregressive models
Authors: Trinquier Jeanne , Uguzzoni Guido , Pagnani Andrea , Zamponi Francesco , Weigt Martin
Published: March 2021

Generative models emerge as promising candidates for novel sequence-data driven approaches to protein design, and for the extraction of structural and functional information about proteins deeply hidden in rapidly growing sequence databases. Here we propose simple autoregressive models as highly accurate but computationally extremely efficient generative sequence models. We show that they perform similarly to existing approaches based on Boltzmann machines or deep generative models, but at a substantially lower computational cost. Furthermore, the simple structure of our models has distinctive mathematical advantages, which translate into an improved applicability in sequence generation and evaluation. Using these models, we can easily estimate both the model probability of a given sequence, and the size of the functional sequence space related to a specific protein family. In the case of response regulators, we find a huge number of ca. 1068sequences, which nevertheless constitute only the astronomically small fraction 10-80of all amino-acid sequences of the same length. These findings illustrate the potential and the difficulty in exploring sequence space via generative sequence models.
Molecular strategies for antibody binding and escape of SARS-CoV-2 and its mutations
Authors: Hendy Mohamed , Kaufman Samuel , Ponga Mauricio
Published: March 2021

The COVID19 pandemic, caused by SARS-CoV-2, has infected more than 100 million people worldwide. Due to the rapid spreading of SARS-CoV-2 and its impact, it is paramount to find effective treatments against it. Human neutralizing antibodies are an effective method to fight viral infection. However, the recent discovery of new strains that substantially change the S-protein sequence has raised concern about vaccines and antibodies’ effectiveness. Here, we investigated the binding mechanisms between the S-protein and several antibodies. Multiple mutations were included to understand the strategies for antibody escape in new variants. We found that the combination of mutations K417N and E484K produced higher binding energy to ACE2 than the wild type, suggesting higher efficiency to enter host cells. The mutations’ effect depends on the antibody class. While Class I enhances the binding avidity in the presence of N501Y mutation, class II antibodies showed a sharp decline in the binding affinity. Our simulations suggest that Class I antibodies will remain effective against the new strains. In contrast, Class II antibodies will have less affinity to the S-protein, potentially affecting these antibodies’ efficiency.
Direct molecular evidence for an ancient, conserved developmental toolkit controlling post-transcriptional gene regulation in land plants
Authors: Jia Haiyan , Aadland Kelsey , Kolaczkowski Oralia , Kolaczkowski Bryan
Published: March 2021

RNA interference (RNAi) plays important roles in organism development through post-transcriptional regulation of specific target mRNAs. Target specificity is largely controlled by base-pair complementarity between micro-RNA (miRNA) regulatory elements and short regions of the target mRNA. The pattern of miRNA production in a cell interacts with the cell’s mRNA transcriptome to generate a specific network of post-transcriptional regulation that can play critical roles in cellular metabolism, differentiation, tissue/organ development and developmental timing. In plants, miRNA production is orchestrated in the nucleus by a suite of proteins that control transcription of the pri-miRNA gene, post-transcriptional processing and nuclear export of the mature miRNA. In the model plant, Arabidopsis thaliana, post-transcriptional processing of miRNAs is controlled by a pair of physically-interacting proteins, HYL1 and DCL1. However, the evolutionary history of the HYL1-DCL1 interaction is unknown, as is its structural basis. Here we use ancestral sequence reconstruction and functional characterization of ancestral HYL1 in vitro and in vivo to better understand the origin and evolution of the HYL1-DCL1 interaction and its impact on miRNA production and plant development. We found the ancestral plant HYL1 evolved high affinity for both double-stranded RNA (dsRNA) and its DCL1 partner very early in plant evolutionary history, before the divergence of mosses from seed plants (~500 Ma), and these high-affinity interactions remained largely conserved throughout plant evolutionary history. Structural modeling and molecular binding experiments suggest that the second of two double-stranded RNA-binding motifs (DSRMs) in HYL1 may interact tightly with the first of two C-terminal DCL1 DSRMs to mediate the HYL1-DCL1 physical interaction necessary for efficient miRNA production. Transgenic expression of the nearly 200 Ma-old ancestral flowering-plant HYL1 in A. thaliana was sufficient to rescue many key aspects of plant development disrupted by HYL1− knockout and restored near-native miRNA production, suggesting that the functional partnership of HYL1-DCL1 originated very early in and was strongly conserved throughout the evolutionary history of terrestrial plants. Overall, our results are consistent with a model in which miRNA-based gene regulation evolved as part of a conserved plant ‘developmental toolkit’; its role in generating developmental novelty is probably related to the relatively rapid evolution of miRNA genes.