bluuebunny/crossref_metadata_2025 huggingface dataset:
United States military fatalities during Operation New Dawn
Authors: Kotwal Russ S. , Mazuchowski Edward L. , Janak Jud C. , Howard Jeffrey T. , Harcke Howard T. , Holcomb John B. , Eastridge Brian J. , Gurney Jennifer M. , Shackelford Stacy A.
Published: May 2021

BACKGROUND

Military operations vary by scope, purpose, and intensity, each having unique forces and actions to execute a mission. Evaluation of military operation fatalities guides current and future casualty care.

METHODS

A retrospective study was conducted of all US military fatalities from Operation New Dawn in Iraq, 2010 to 2011. Data were obtained from autopsies and other records. Population characteristics, manner of death, cause of death, and location of death were analyzed. All fatalities were evaluated for concomitant evidence of underlying atherosclerosis. Nonsuicide trauma fatalities were also reviewed for injury severity, mechanism of death, injury survivability, death preventability, and opportunities for improvement.

RESULTS

Of 74 US military Operation New Dawn fatalities (median age, 26 years; male, 98.6%; conventional forces, 100%; prehospital, 82.4%) the leading cause of death was injury (86.5%). The manner of death was primarily homicide (55.4%), followed by suicide (17.6%), natural (13.5%), and accident (9.5%). Fatalities were divided near evenly between combatants (52.7%) and support personnel (47.3%), and between battle injury (51.4%) and disease and nonbattle injury (48.6%). Natural and suicide death was higher (p < 0.01, 0.02) among support personnel who were older (p = 0.05) with more reserve/national guard personnel (p = 0.01). Total population prevalence of underlying atherosclerosis was 18.9%, with more among support personnel (64.3%). Of 46 nonsuicide trauma fatalities, most died of blast injury (67.4%) followed by gunshot wound (26.1%) and multiple/blunt force injury (6.5%). The leading mechanism of death was catastrophic tissue destruction (82.6%). Most had nonsurvivable injuries (82.6%) and nonpreventable deaths (93.5%).

CONCLUSION

Operation New Dawn fatalities were exclusively conventional forces divided between combatants and support personnel, the former succumbing more to battle injury and the latter to disease and nonbattle injury including self-inflicted injury. For nonsuicide trauma fatalities, none died from a survivable injury, and 17.4% died from potentially survivable injuries. Opportunities for improvement included providing earlier blood products and surgery.

LEVEL OF EVIDENCE

Therapeutic, level V and epidemiological, level IV.
MAGEC3 is a prognostic biomarker in ovarian and kidney cancers
Authors: Ellegate James , Mastri Michalis , Isenhart Emily , Krolewski John J. , Chatta Gurkamal , Kauffman Eric , Moffitt Melissa , Eng Kevin H.
Published: May 2021

Rare variants in MAGEC3, members of the melanoma antigen gene family, are associated with BRCA-independent early onset ovarian cancers, while somatic mutations of this gene have been associated with kidney cancers. In this report, we quantified normal and tumor protein expression of MAGEC3 via immunohistochemistry in N=394 ovarian cancers and N=220 renal cell carcinomas. MAGEC3 protein levels fell into two categories – normal MAGEC3 and MAGEC3 loss – characterized by expression equivalent to normal tissue or significantly lower than normal tissue, respectively. Interestingly, cases with MAGEC3 loss demonstrated better overall survival in both ovarian cancers and renal cell carcinomas, which resembles patient outcomes with BRCA2 loss. MAGEC3 protein expression was associated with upregulation of pathways regulating G2/M checkpoint (NES: 4.13, FDR<0.001) and mitotic spindle formation (NES: 2.84, FDR<0.001). Increased CD8+ cell infiltration, coordinate expression of other cancer testis antigens, and tumor mutational burden were also associated with MAGEC3 expression. To emphasize the impact of these results, we built a prognostic RNA-based model using N=180 cancers of an independent cohort with matching transcriptomic data and tested its performance in two large public cohorts (N=282 ovary and N=606 kidney). Results based on predicted protein scores within these patients validated those discovered in patients with directly measured MAGEC3 protein. The RNA model was reproduced in independent cohorts implying a broader potential for MAGEC3-driven disease etiology and relevance to potential treatment selection.

STATEMENT OF TRANSLATIONAL RELEVANCE

MAGEC3 protein is expressed in multiple tissues and is dysregulated in cancer. In this work, we show that ovarian and kidney cancer patients with loss of MAGEC3 protein have favorable prognosis, indicating that MAGEC3 protein level may be used as a prognostic biomarker. Integrative genomic analysis of patients spanning more than nine cancer types showed an association between MAGEC3 protein and genes affecting stress response, including those involved in cell cycle and DNA damage repair. Additionally, it is correlated with tumor mutational burden in patients with mutated oncogenes. These associations suggest that MAGEC3 protein levels may be used to identify patients with deficient DNA damage repair mechanisms that can be targeted by PARP inhibitors. To operationalize this idea, we use machine learning to predict MAGEC3 protein levels from RNA sequencing data which can facilitate the identification of patients for treatment stratification according to their MAGEC3 status.
ROCCA study protocol and interim analysis on safety of Sputnik V vaccine (Gam-COVID-Vac) in the Republic of San Marino: an observational study using active surveillance
Authors: Montalti Marco , Soldà Giorgia , Di Valerio Zeno , Salussolia Aurelia , Lenzi Jacopo , Forcellini Marcello , Barvas Edoardo , Guttman Susanna , Messina Rossella , Poluzzi Elisabetta , Raschi Emanuel , Riccardi Rossano , Fantini Maria Pia , Fauci Giusy La , Gori Davide ,   for the San Marino Republic COVID ROCCA Group
Published: May 2021

OBJECTIVE

To assess the safety of the Sputnik V (Gam-COVID-Vac) COVID-19 vaccine through participant-based active surveillance from the Republic of San Marino vaccination campaign.

DESIGN AND SETTING

This is a nation-wide cohort study in the Republic of San Marino to monitor any Adverse Events Following Immunisation (AEFI) with the Sputnik V.

PARTICIPANTS

Adults aged 18-89 years who had at least one dose of Sputnik V administered and who responded or accessed to an e-questionnaire sent via email, QR-code or were live/phone interviewed about the 7 days after the first vaccine dose (n=2,558) and 7 days after the second dose (n=1,288). Exclusion criteria were inability to understand nor to answer the questionnaire properly.

MAIN OUTCOME MEASURES

Rates of overall AEFI short-term and long-term (3 months). Secondary outcomes focus on subgroups of the population presenting specific comorbidities. Being this an interim analysis, long-term data (3 months) is still being collected, especially for vulnerable populations, including subjects with comorbidities and the youngest age groups.

RESULT

The median age of participants was 68 years. 56% were females. After the first dose, vaccine recipients described both local and systemic reactions in 16.4% of cases, 25.8% reported systemic reactions only, and 10.2% reported local symptoms only. After the second dose, both local and systemic reactions were reported in 31.9% of cases, 18.5% reported systemic reactions only, and 16.1% reported local symptoms only. Main symptoms were local pain (24.8% for first dose and 43.8% for the second), asthenia (23.8% and 31.9%), headache (18.5% and 21.0%), and joint pain (16.5% and 21.9%). In the population over 60, recipients having reported AEFI after the first dose could be a predictor of AEFI recurrence after the second dose (p<0.001). 81.8% of those reporting second-dose AEFI, reported AEFI after the first dose, while amongst those not having reported any AEFI after the first dose, 18.2% reported AEFI after the second dose.

CONCLUSION

The ROCCA interim analysis confirmed a good tolerability profile in the over 60 years age group after both doses regarding short-term solicited AEFI to Sputnik V (Gam-COVID-Vac).
Describing the burden of the COVID-19 pandemic in people with psoriasis: findings from a global cross-sectional study
Authors: Mahil SK , Yates M , Yiu ZZN , Langan SM , Tsakok T , Dand N , Mason KJ , McAteer H , Meynell F , Coker B , Vincent A , Urmston D , Vesty A , Kelly J , Lancelot C , Moorhead L , Bachelez H , Capon F , Contreras CR , De La Cruz C , Meglio P Di , Gisondi P , Jullien D , Lambert J , Naldi L , Norton S , Puig L , Spuls P , Torres T , Warren RB , Waweru H , Weinman J , Brown MA , Galloway JB , Griffiths CM , Barker JN , Smith CH
Published: May 2021

Background

Indirect excess morbidity has emerged as a major concern in the COVID-19 pandemic. People with psoriasis may be particularly vulnerable to this because of prevalent anxiety and depression, multimorbidity and therapeutic use of immunosuppression.

Objective

Characterise the factors associated with worsening psoriasis in the COVID-19 pandemic, using mental health status (anxiety and depression) as the main exposure of interest.

Methods

Global cross-sectional study using a primary outcome of self-reported worsening of psoriasis. Individuals with psoriasis completed an online self-report questionnaire (PsoProtectMe; Psoriasis Patient Registry for Outcomes, Therapy and Epidemiology of COVID-19 Infection Me) between May 2020 and January 2021. Each individual completed a validated screen for anxiety (Generalized Anxiety Disorder-2) and depression (Patient Health Questionnaire-2). Odds ratios (OR) and 95% confidence intervals (CI) were estimated using multivariable logistic regression.

Results

4,043 people with psoriasis (without COVID-19) from 86 countries self-reported to PsoProtectMe (mean age 47.2 years [SD 15.1]; mean BMI 27.6kg/m2 [SD 6.0], 2,684 [66.4%] female and 3,016 [74.6%] of white European ethnicity). 1,728 (42.7%) participants (1322 [77%] female) reported worsening of their psoriasis in the pandemic. A positive screen for anxiety or depression associated with worsening psoriasis in age and gender adjusted (OR 2.04, 95% CI 1.77-2.36), and fully adjusted (OR 2.01, 95% CI 1.72-2.34) logistic regression models. Female sex, obesity, shielding behaviour and systemic immunosuppressant non-adherence also associated with worsening psoriasis. The commonest reason for non-adherence was concern regarding complications related to COVID-19.

Conclusions

These data indicate an association between poor mental health and worsening psoriasis in the pandemic. Access to holistic care including psychological support may mitigate potentially long-lasting effects of the pandemic on health outcomes in psoriasis. The study also highlights an urgent need to address patient concerns about immunosuppressant-related risks, which may be contributing to non-adherence.
Covid-19 and the South Asian Countries: factors ruling the pandemic
Authors: Biswas Tannishtha , Mondal Madhura , Bhattacharya Srijan , Sarkar Moitrayee , Dhara Bikram , Mitra Arup Kumar , Chandra Ayan
Published: May 2021

The novel corona virus causing Covid-19 was first detected in the city of Wuhan, China in December, 2019. In matter of months Covid-19 was declared a pandemic by the World Health Organization. The focus of this research includes the probable factors that might have played an important role in the spread of this infection causing a global threat. In this study we dealt with the South Asian countries namely Bangladesh, Bhutan, India, Maldives, Nepal, Pakistan. Data on the demography of the countries, the climatic and geographical conditions, the socio-economic statuses, GDP being in the forefront, was collected and compared with Covid-19 related data such as total number of positive, recovered and death cases, etc. to determine if there was any significant correlation. The wide range of correlations observed can curve the path for the future research to understand the factors behind the spread of the communicable disease, analyzing the dynamics of the future biological threats to mankind and design the precautionary or preventive methods accordingly.
SARS-CoV-2 infection and reinfection in a seroepidemiological workplace cohort in the United States
Authors: Finch Emilie , Lowe Rachel , Fischinger Stephanie , de St Aubin Michael , Siddiqui Sameed M. , Dayal Diana , Loesche Michael A. , Rhee Justin , Berger Samuel , Hu Yiyuan , Gluck Matthew J. , Mormann Benjamin , Hasdianda Mohammad A. , Musk Elon R. , Alter Galit , Menon Anil S. , Nilles Eric J. , Kucharski Adam J.
Published: May 2021

Identifying the extent of SARS-CoV-2 reinfection is crucial for understanding possible long-term epidemic dynamics. We analysed longitudinal PCR and serological testing data from a prospective cohort of 4411 US employees in four states between April 2020 and February 2021. We conducted a multivariable logistic regression investigating the association between baseline serological status and subsequent PCR test result in order to calculate an odds ratio for reinfection. We estimated an adjusted odds ratio of 0.09 (95% CI: 0.005 – 0.48) for reinfection, implying that the presence of SARS-CoV-2 antibodies at baseline is associated with around 91% reduced odds of a subsequent PCR positive test. This suggests that primary infection with SARS-CoV-2 provides protection against reinfection in the majority of individuals, at least over a sixth month time period. We also highlight two major sources of bias and uncertainty to be considered when estimating reinfection risk, confounders and the choice of baseline time point, and show how to account for both in our analysis.
Asynchronous glutamate exocytosis is enhanced in low release probability synapses and is widely dispersed across the active zone
Authors: Mendonça Philipe R. F. , Tagliatti Erica , Langley Helen , Kotzadimitriou Dimitrios , Zamora-Chimal Criseida G. , Timofeeva Yulia , Volynski Kirill E.
Published: May 2021

The balance between fast synchronous and delayed asynchronous release of neurotransmitters has a major role in defining computational properties of neuronal synapses and regulation of neuronal network activity. However, how it is tuned at the single synapse level remains poorly understood. Here, using the fluorescent glutamate sensor SF-iGluSnFR, we image quantal vesicular release in tens to hundreds of individual synaptic outputs (presynaptic boutons) from single pyramidal cells in culture with 4 millisecond temporal resolution, and localise vesicular release sites with ~ 75 nm spatial resolution. We find that the ratio between synchronous and asynchronous synaptic vesicle exocytosis varies extensively among presynaptic boutons supplied by the same axon, and that asynchronous release fraction is elevated in parallel with short-term facilitation at synapses with low release probability. We further demonstrate that asynchronous exocytosis sites are more widely distributed within the presynaptic release area than synchronous sites. These findings are consistent with a model in which functional presynaptic properties are regulated via a synapsespecific adjustment of the coupling distance between presynaptic Ca2+channels and releaseready synaptic vesicles. Together our results reveal a universal relationship between the two major functional properties of synapses – the timing and the overall probability of neurotransmitter release.
Imaging Nanoscale Nuclear Structures with Expansion Microscopy
Authors: Faulkner Emma L. , Pike Jeremy A. , Densham Ruth M. , Garlick Evelyn , Thomas Steven G. , Neely Robert K. , Morris Joanna R.
Published: May 2021

Commonly applied super-resolution light microscopies have provided insight into subcellular processes at the nanoscale. However, imaging depth, speed, throughput and cost remain significant challenges, reducing the numbers of three-dimensional, nanoscale processes that can be investigated and the number of laboratories able to undertake such analysis. Expansion microscopy solves many of these limitations but its application to imaging nuclear processes has been constrained by concerns of unequal nuclear expansion.

Here we demonstrate the conditions for isotropic expansion of the nucleus. Using DNA damage response proteins, BRCA1, 53BP1 and RAD51 as exemplars we quantitatively describe the three-dimensional nanoscale organisation of over 50,000 DNA damage response structures. We demonstrate the ability to assess chromatin regulated events and show the simultaneous assessment of four elements. This study thus provides the means by which expansion microscopy can contribute to the investigation of nanoscale nuclear processes.
A natural transdifferentiation event involving mitosis is empowered by integrating signaling inputs with conserved plasticity factors
Authors: Riva Claudia , Hajduskova Martina , Gally Christelle , Ahier Arnaud , Jarriault Sophie
Published: May 2021

Transdifferentiation, or direct cell reprogramming, is the direct conversion of one fully differentiated cell type into another. Whether core mechanisms are shared between different transdifferentiation events, which can occur naturally in presence or in absence of cell division, is unclear. Our lab has previously characterized the Y-to-PDA natural transdifferentiation inCaenorhabditis elegans, which occurs without cell division and requires orthologs of vertebrates’ reprogramming factors. In this study, focusing on another transdifferentiation process, the K rectal cell-to-DVB GABAergic neuron, we report that the Y-to-PDA reprogramming factor SEM-4/SALL, SOX-2, CEH-6/POU are required for K-to-DVB transdifferentiation to allow the erasure of the rectal identity. In addition, cell division is necessary but not sufficient for this transdifferentiation event while the Wnt signaling plays distinct functions during the process including the selection of the daughter cell with a different fate, loss of the rectal identity and imposition of the specific neuronal subtype identity. We provide evidence that both the Wnt signaling and Y-to-PDA reprogramming factor SEM-4/SALL, SOX-2, CEH-6/POU act in parallel for the rectal identity erasure. Our results further support a model where antagonistic activities of SOX-2 and POP-1 and decreasing SOX-2 levels over time provide a timer for the acquisition of the final identity. In addition, the different levels of SOX-2 provide a mechanism for the integration of Wnt opposite dedifferentiation and re-differentiation functions during K-to-DVB transdifferentiation.
RF-Net 2: Fast Inference of Virus Reassortment and Hybridization Networks
Authors: Markin Alexey , Wagle Sanket , Anderson Tavis K. , Eulenstein Oliver
Published: May 2021

Motivation

A phylogenetic network is a powerful model to represent entangled evolutionary histories with both divergent (speciation) and convergent (e.g., hybridization, reassortment, recombination) evolution. The standard approach to inference of hybridization networks is to (i) reconstruct rooted gene trees and (ii) leverage gene tree discordance for network inference. Recently, we introduced a method calledRF-Netfor accurate inference of virus reassortment and hybridization networks from input gene trees in the presence of errors commonly found in phylogenetic trees. While RF-Net demonstrated the ability to accurately infer networks with up to four reticulations from erroneous input gene trees, its application was limited by the number of reticulations it could handle in a reasonable amount of time. This limitation is particularly restrictive in the inference of the evolutionary history of segmented RNA viruses such as influenza A virus (IAV), where reassortment is one of the major mechanisms shaping the evolution of these pathogens.

Results

Here we expand the functionality of RF-Net that makes it significantly more applicable in practice. Crucially, we introduce a fast extension to RF-Net, calledFast-RF-Net, that can handle large numbers of reticulations without sacrificing accuracy. Additionally, we develop automatic stopping criteria to select the appropriate number of reticulations heuristically and implement a feature for RF-Net to output error-corrected input gene trees. We then conduct a comprehensive study of the original method and its novel extensions and confirm their efficacy in practice using extensive simulation and empirical influenza A virus evolutionary analyses.

Availability

RF-Net 2is available athttps://github.com/flu-crew/rf-net-2.
Population analysis ofVibrio choleraein aquatic reservoirs reveals a novel sister species(Vibrio paracholeraesp. nov.) with a history of association with human infections
Authors: Islam Mohammad Tarequl , Nasreen Tania , Kirchberger Paul , Liang Kevin Y. H. , Orata Fabini , Johura Fatema-Tuz , Im Monica S. , Tarr Cheryl L. , Alam Munirul , Boucher Yann F.
Published: May 2021

Most efforts to understand the biology ofVibrio choleraehave focused on a single group, the pandemic-generating lineage harbouring the strains responsible for all known cholera pandemics. Consequently, little is known about the diversity of this species in its native aquatic environment. To understand the differences in theV. choleraepopulations inhabiting in regions with varying history of cholera cases and how that might influence the abundance of pandemic strains, a comparative analysis of population composition was performed. Little overlap was found in lineage compositions between those in Dhaka (cholera endemic) located in the Ganges delta, and of Falmouth (no known history of cholera), a small coastal town on the US East Coast. The most striking difference was the presence of a group of related lineages at high abundance in Dhaka which was completely absent from Falmouth. Phylogenomic analysis revealed that these lineages form a cluster at the base of the phylogeny ofV. choleraespecies, sufficiently differentiated genetically and phenotypically to form a novel species. Strains from this species have been anecdotally isolated from around the world and were isolated as early as 1916 from a British soldier in Egypt suffering from choleraic diarrhoea. In 1935 Gardner and Venkatraman unofficially referred to a member of this group asVibrio paracholerae. In recognition of this earlier designation, we propose the nameVibrio paracholerae, sp. nov. for this bacterium. Genomic analysis suggests a link with human populations for this novel species and substantial interaction with its better-known sister species.

Importance

Cholera continues to remain a major public health threat around the globe. Understanding the ecology, evolution and environmental adaptation of the causative agentVibrio choleraeand tracking the emergence of novel lineages with pathogenic potential are essential to combat the problem. In this study, we investigated the population dynamics ofVibrio choleraein an inland locality which is known as endemic for cholera and compared with that of a cholera free coastal location. We found the consistent presence of the pandemic generatingV. choleraein cholera-endemic Dhaka and an exclusive presence of a lineage phylogenetically distinct from otherV. cholerae. Our study suggests that this lineage represents a novel species having pathogenic potential and a human link to its environmental abundance. The possible association with human population, co-existence and interaction with toxigenicV. choleraein the natural environment make this potential human pathogen an important subject for future studies.
Evaluation of wound healing effects of ginsenoside Rg1 and red ginseng extract in STZ-induced diabetic wound model: an in vivo pilot study
Authors: Lim Ji Yun , Suk Choi Young , Lee Hye Rim , Min An Hye , Lee Young Koo
Published: May 2021

Red ginseng is an immune-enhancing compound that exhibits anti-inflammatory action. The ginsenoside Rg1, an ingredient of red ginseng, has been shown to play an important role in tumor suppression, wound healing, and angiogenesis. This study evaluated the effects of red ginseng extract and Rg1 in a diabetic wound model. Diabetes was induced with streptozotocin (STZ) in 8-week-old male Institute of Cancer Research (ICR) mice weighing 30–35 g. A full-thickness skin defect was treated by applying a dressing every 3 days. The mice were divided into three groups. Group 1 was administered an extract of red ginseng (10 mg/kg/d,n= 27, oral) and group 2 was administered Rg1 (10 mg/kg/d,n= 27, oral). Group 3 was a control group treated with phosphate-buffered saline (0.3 mL/kg/d,n= 27, oral). Red ginseng extract and Rg1 were orally administered to mice daily for 10 days following injury in groups 1 and 2, respectively. Both increased mRNA and protein levels of vascular endothelial growth factor (VEGF) and transforming growth factor (TGF)-β1 compared to controls. In addition, the wounds of animals in the Rg1 group were significantly smaller between days 7 and 10 (p< 0.05). VEGF and TGF-β1 were not expressed in diabetic mice in the control group. Both red ginseng extract and Rg1 promoted the production of VEGF and TGF-β1, which are important in wound healing. Our results for Rg1 suggest its potential to promote diabetic wound healing by stimulating the production or activity of VEGF and TGF-β1 factors involved in the wound healing process.
Influence of GdVO4:Eu3+nanocrystals on growth, germination, root cell viability and oxidative stress of wheat (Triticum aestivumL.) seedlings
Authors: Ekner-Grzyb Anna , Chmielowska-Bąk Jagna , Szczeszak Agata
Published: May 2021

Increasing application of lanthanide-doped nanocrystals (LDNCs) entails a risk of a harmful impact on the natural environment. Therefore, in the presented study the influence of gadolinium orthovanadates doped with Eu3+nanocrystals on wheat (Triticum aestivumL.), chosen as a model plant species, was investigated. The seeds were grown in Petri dishes filled with colloids of LDNCs at the concentrations of: 0, 10, 50 and 100 µg/ml. The plants’ growth endpoints (number of roots, roots length, roots mass, hypocotyl length and hypocotyl mass) and germination rate were found to be not significantly changed after the exposure to GdVO4:Eu3+nanocrystals at all used concentrations. The presence of LDNCs also had no effect on oxidative stress intensity determined on the basis of the amount of lipid peroxidation product (thiobarbituric acid reactive substances; TBARS) of the roots. Similarly, TTC (tetrazolium chloride) assay did not show any differences in cells’ viability. However, root cells of the treated seedlings contained less amount of Evans Blue (EB) when compared to the control.
Phylogenetic profiling in eukaryotes: The effect of species, orthologous group, and interactome selection on protein interaction prediction
Authors: Deutekom Eva S. , van Dam Teunis J.P. , Snel Berend
Published: May 2021

Phylogenetic profiling in eukaryotes is of continued interest to study and predict the functional relationships between proteins. This interest is likely driven by the increased number of available diverse genomes and computational methods to infer orthologies. The evaluation of phylogenetic profiles has mainly focussed on reference genome selection in prokaryotes. However, it has been proven to be challenging to obtain high prediction accuracies in eukaryotes. As part of our recent comparison of orthology inference methods for eukaryotic genomes, we observed a surprisingly high performance for predicting interacting orthologous groups. This high performance, in turn, prompted the question of what factors influence the success of phylogenetic profiling when applied to eukaryotic genomes.

Here we analyse the effect of species, orthologous group and interactome selection on protein interaction prediction using phylogenetic profiles. We select species based on the diversity and quality of the genomes and compare this supervised selection with randomly generated genome subsets. We also analyse the effect on the performance of orthologous groups defined to be in the last eukaryotic common ancestor of eukaryotes to that of orthologous groups that are not. Finally, we consider the effects of reference interactome set filtering and reference interactome species.

In agreement with other studies, we find an effect of genome selection based on quality, less of an effect based on genome diversity, but a more notable effect based on the amount of information contained within the genomes. Most importantly, we find it is not merely selecting the correct genomes that is important for high prediction performance. Other choices in meta parameters such as orthologous group selection, the reference species of the interaction set, and the quality of the interaction set have a much larger impact on the performance when predicting protein interactions using phylogenetic profiles. These findings shed light on the differences in reported performance amongst phylogenetic profiles approaches, and reveal on a more fundamental level for which types of protein interactions this method has most promise when applied to eukaryotes.
1H,13C and15N resonance assignment of the SARS-CoV-2 full-length nsp1 protein and its mutants reveals its unique secondary structure features in solution
Authors: Agback Tatiana , Dominguez Francisco , Frolov Ilya , Frolova Elena I. , Agback Peter
Published: May 2021

Structural characterization of the SARS-CoV-2 full length nsp1 protein will be an essential tool for developing new target-directed antiviral drugs against SARS-CoV-2 and for further understanding of intra- and intermolecular interactions of this protein. As a first step in the NMR studies of the protein, we report the1H,13C and15N resonance backbone assignment as well as the Cβ of the apo form of the full-lengthSARS-CoV-2 nsp1 including folded domain together with the flaking N- and C-terminal intrinsically disordered fragments. The 19.8 kD protein was characterized by high-resolution NMR. Validation of assignment have been done by using two different mutants, H81P and K129E/D48E as well as by amino acid specific experiments. According to the obtained assignment, the secondary structure of the folded domain in solution was almost identical to its previously published X-ray structure, but some discrepancies have been detected. In the solution SARS-CoV-2 nsp1 exhibited disordered, flexible N- and C-termini with different dynamic characteristics. The short peptide in the beginning of the disordered C-terminal domain adopted two different conformations distinguishable on the NMR time scale. We propose that the disordered and folded nsp1 domains are not fully independent units but are rather involved in intramolecular interactions. Studies of the structure and dynamics of the SARS-CoV-2 mutant in solution are on-going and will provide important insights into the molecular mechanisms underlying these interactions.
Combination Respiratory Vaccine Containing Recombinant SARS-CoV-2 Spike and Quadrivalent Seasonal Influenza Hemagglutinin Nanoparticles with Matrix-M Adjuvant
Authors: Massare Michael J , Patel Nita , Zhou Bin , Maciejewski Sonia , Flores Rhonda , Guebre-Xabier Mimi , Tian Jing-Hui , Portnoff Alyse D. , Fries Louis , Shinde Vivek , Ellingsworth Larry , Glenn Gregory , Smith Gale
Published: May 2021

The 2019 outbreak of a severe respiratory disease caused by an emerging coronavirus, SARS-CoV-2, has spread globally with high morbidity and mortality. Co-circulating seasonal influenza has greatly diminished recently, but expected to return with novel strains emerging, thus requiring annual strain adjustments. We have developed a recombinant hemagglutinin (HA) quadrivalent nanoparticle influenza vaccine (qNIV) produced using an established recombinant insect cell expression system to produce nanoparticles. Influenza qNIV adjuvanted with Matrix-M was well-tolerated and induced robust antibody and cellular responses, notably against both homologous and drifted A/H3N2 viruses in Phase 1, 2, and 3 trials. We also developed a full-length SARS-CoV-2 spike protein vaccine which is stable in the prefusion conformation (NVX-CoV2373) using the same platform technology. In phase 3 clinical trials, NVX-CoV2373 is highly immunogenic and protective against the prototype strain and B.1.1.7 variant. Here we describe the immunogenicity and efficacy of a combination quadrivalent seasonal flu and COVID-19 vaccine (qNIV/CoV2373) in ferret and hamster models. The combination qNIV/CoV2373 vaccine produces high titer influenza hemagglutination inhibiting (HAI) and neutralizing antibodies against influenza A and B strains. The combination vaccine also elicited antibodies that block SARS-CoV-2 spike protein binding to the human angiotensin converting enzyme-2 (hACE2) receptor. Significantly, hamsters immunized with qNIV/CoV2373 vaccine and challenged with SARS-CoV-2 were protected against weight loss and were free of replicating SARS-CoV-2 in the upper and lower respiratory tract with no evidence of viral pneumonia. This study supports evaluation of qNIV/CoV2373 combination vaccine as a preventive measure for seasonal influenza and CoVID-19.

Highlights

Combination qNIV/CoV2373 vaccine induced protective hemagglutination inhibition (HAI) responses to seasonal influenza A and B unchanged when formulated with recombinant spike.

Combination qNIV/CoV2373 vaccine maintained clinical and virologic protection against experimental challenge with SARS-CoV-2.

Combination qNIV/CoV2373 vaccine showed no clinical or histological sign of enhanced disease following experimental challenge with SARS-CoV-2.

Combination qNIV/CoV2373 vaccine induced antibodies against SARS-CoV-2 neutralizing epitopes common between US-WA and B.1.352 variant.
Structural basis of RNA polymerase recycling by the Swi2/Snf2 ATPase RapA inEscherichia coli
Authors: Qayyum M. Zuhaib , Molodtsov Vadim , Renda Andrew , Murakami Katsuhiko S.
Published: May 2021

After transcription termination, cellular RNA polymerases (RNAPs) are occasionally trapped on DNA, impounded in an undefined Post-Termination Complex (PTC), limiting free RNAP pool and making transcription inefficient. InEscherichia coli, a Swi2/Snf2 ATPase RapA is involved in countering such inefficiency through RNAP recycling. To understand its mechanism of RNAP recycling, we have determined the cryo-electron microscopy (cryo-EM) structures of two sets ofE. coliRapA-RNAP complexes along with RNAP core enzyme and elongation complex (EC). The structures revealed the large conformational changes of RNAP and RapA upon their association implicated in the hindrance in PTC formation. Our study reveals that although RapA binds away from the DNA binding channel of RNAP, it can close the RNAP clamp allosterically thereby preventing its non-specific DNA binding. Together with DNA binding assays, we propose that RapA acts as a guardian of RNAP by which prevents non-specific DNA binding of RNAP without affecting the sigma factor binding to RNAP core enzyme, thereby enhancing RNAP recycling.
A lipid-based parallel processor for chemical signals
Authors: Cazimoglu Idil , Booth Michael J. , Bayley Hagan
Published: May 2021

A key goal of bottom-up synthetic biology is to construct cell- and tissue-like structures. Underpinning cellular life is the ability to process several external chemical signals, often in parallel. Until now, however, cell- and tissue-like structures have only been constructed with one signalling pathway. Here, we construct a dual-signal processor from the bottom up in a modular fashion. The processor comprises three aqueous compartments bounded by lipid bilayers and operates in an aqueous environment. It can receive two chemical signals from the external environment, process them orthogonally, and then produce a distinct output for each signal. It is suitable for both sensing and enzymatic processing of environmental signals with fluorescence and molecular outputs. In the future, such processors could serve as smart drug delivery vehicles or as modules within synthetic tissues to control their behaviour in response to external chemical signals.
Mechanistic Insights of High Temperature-Interfered Meiosis in AutotetraploidArabidopsis thaliana
Authors: Fu Huiqi , Yang Ke , Zhang Xiaohong , Zhao Jiayi , Elesawi Ibrahim Eid , Liu Hong , Xia Jing , Yu Guanghui , Chen Chunli , Wang Chong , Liu Bing
Published: May 2021

Environmental temperature has a huge impact on multiple meiosis processes in flowering plants. Polyploid plants derived from whole genome duplication are believed to have an enhanced abiotic stress tolerance. In this study, the impact of high temperatures on male meiosis in autotetraploidArabidopsis thalianawas investigated. We found that autotetraploid Columbia (Col-0) plants generate a subpopulation of aberrant meiotic products under normal temperature, which is significantly increased under heat stress. Cytological studies revealed that, as the case in diploidArabidopsis thaliana, assembly of microtubular cytoskeleton network, pairing and segregation of homologous chromosomes, and meiotic recombination in autotetraploid Arabidopsis are compromised under the high temperatures. Immunostaining of ɤH2A.X and recombinase DMC1 suggested that heat stress inhibits formation of DNA double-strand breaks; additionally, it specifically destabilizes ASY1 and ASY4, but not SYN1 on chromosomes. The loading defects of ASY1 and ASY4 overlap in thesyn1mutant, which supports that the building of lateral element of synaptonemal complex occurs downstream of a SYN1-ASY4-ASY3 stepwise assembly of axis. Remarkably, heat-induced abnormalities of ASY1 and ASY4 co-localize on chromosomes of both diploid and autotetraploid Arabidopsis, suggesting that high temperatures interfere with ASY1-associated SC via an impacted stability of chromosome axis. Furthermore, ZYP1-dependent transverse filament of SC is disrupted by heat stress. Taken together, these findings suggest that polyploidization negatively contributes to instability of chromosome axis and meiotic recombination inArabidopsis thalianaunder heat stress.
DNA methylation calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation
Authors: Liu Yang , Rosikiewicz Wojciech , Pan Ziwei , Jillette Nathaniel , Wang Ping , Taghbalout Aziz , Foox Jonathan , Mason Christopher , Carroll Martin , Cheng Albert , Li Sheng
Published: May 2021

Background

Nanopore long-read sequencing technology greatly expands the capacity of long-range single-molecule DNA-modification detection. A growing number of analytical tools have been actively developed to detect DNA methylation from Nanopore sequencing reads. Here, we examine the performance of different methylation calling tools to provide a systematic evaluation to guide practitioners for human epigenome-wide research.

Results

We compare five analytic frameworks for detecting DNA modification from Nanopore long-read sequencing data. We evaluate the association between genomic context, CpG methylation-detection accuracy, CpG sites coverage, and running time using Nanopore sequencing data from natural human DNA. Furthermore, we provide an online DNA methylation database (https://nanome.jax.org) with which to display genomic regions that exhibit differences in DNA-modification detection power among different methylation calling algorithms for nanopore sequencing data.

Conclusions

Our study is the first benchmark of computational methods for mammalian whole genome DNA-modification detection in Nanopore sequencing. We provide a broad foundation for cross-platform standardization, and an evaluation of analytical tools designed for genome-scale modified-base detection using Nanopore sequencing.
QSMxT: Robust Masking and Artefact Reduction for Quantitative Susceptibility Mapping
Authors: Stewart Ashley Wilton , Robinson Simon Daniel , O’Brien Kieran , Jin Jin , Widhalm Georg , Hangel Gilbert , Walls Angela , Goodwin Jonathan , Eckstein Korbinian , Tourell Monique , Morgan Catherine , Narayanan Aswin , Barth Markus , Bollmann Steffen
Published: May 2021

Purpose

Quantitative Susceptibility Mapping (QSM) is a post-processing technique applied to gradient-echo phase data. QSM algorithms require a signal mask to delineate regions with reliable phase signal for subsequent susceptibility estimation. Existing masking techniques used in QSM have limitations that introduce artefacts, exclude anatomical detail, and rely on parameter tuning and anatomical priors that narrow their application. Here, a robust masking and reconstruction procedure is presented to overcome these limitations and enable automated QSM processing for a wide range of use-cases implemented in an open-source software framework:QSMxT.

Methods

A robust masking technique that automatically separates reliable from less reliable phase regions was developed and combined with a two-pass reconstruction procedure that operates on the separated sources before combination, extracting more information while reducing the influence of artefacts.

Result

Compared with standard masking and reconstruction procedures, the two-pass inversion reduces streaking artefacts caused by unreliable phase and high dynamic ranges of susceptibility sources. QSMxT is robust across a range of datasets at 3 T in healthy volunteers and phantoms, at 7 T in tumour patients, and in the QSM challenge 2.0 simulated brain dataset, with significant artefact and error reductions, greater anatomical detail, and minimal parameter tuning.

Conclusion

QSMxT generates masks for QSM that separate reliable from less reliable phase regions, enables a more accurate QSM reconstruction that mitigates artefacts, operates without anatomical priors, and requires minimal parameter tuning. QSMxT makes QSM processing more accessible, reliable and reproducible.
Cell-envelope synthesis is required for surface-to-mass coupling, which determines dry-mass density inBacillus subtilis
Authors: Kitahara Yuki , Oldewurtel Enno R. , Wilson Sean , Sun Yingjie , Garner Ethan C. , van Teeffelen Sven
Published: May 2021

Cells must increase their volumes in response to biomass growth to maintain intracellular mass density, the ratio of dry mass to cell volume, within physiologically permissive bounds. To increase volume, bacteria enzymatically expand their cell envelopes and insert new envelope material. Recently, we demonstrated that the Gram-negative bacteriumEscherichia coliexpands cell-surface area rather than volume in proportion to mass. Here, we investigate the regulation of cell-volume growth in the evolutionarily distantBacillus subtilis. First, we demonstrate that the coupling of surface growth to mass growth is conserved inB. subtilis. Therefore, mass density changes with cell shape at the single-cell level. Interestingly, mass density varies by more than 30% when we systematically change cell width by modulation of cell-wall insertion, without any effect on mass-growth rate. Second, we demonstrate that the coupling of surface- and mass growth is broken if peptidoglycan or membrane synthesis are inhibited. Once transient perturbations are relieved, the surface-to-mass ratio is rapidly restored. In conclusion, we demonstrate that surface-to-mass coupling is a conserved principle for volume regulation in bacteria, and that envelope synthesis provides an important link between surface growth and biomass growth inB. subtilis.
Somatic genetics analysis of sleep in adult mice
Authors: Wang Guodong , Li Qi , Xu Junjie , Zhao Shuai , Zhou Rui , Chen Zhenkang , Jiang Wentong , Gao Xue , Zhou Shuang , Chen Zhiyu , Sun Quanzhi , Ma Chengyuan , Chen Lin , Shi Bihan , Guo Ying , Wang Haiyan , Wang Xia , Li Huaiye , Cai Tao , Wang Yibing , Chen Zhineng , Wang Fengchao , Liu Qinghua
Published: May 2021

Classical forward and reverse mouse genetics approaches require germline mutations and, thus, are unwieldy to study sleep functions of essential genes or redundant pathways. It is also time-consuming to conduct electroencephalogram/electromyogram-based mouse sleep screening owning to labor-intensive surgeries and genetic crosses. Here, we describe a highly accurate SleepV (video) system and adeno-associated virus (AAV)-based adult brain chimeric (ABC)- expression/knockout (KO) platform for somatic genetics analysis of sleep in adult mice. A pilot ABC-expression screen identifies CREB and CRTC1, of which constitutive or inducible expression significantly reduces quantity and quality of non-rapid eye movement sleep. Whereas ABC-KO of exon 13 ofSik3by AAV-Cre injection inSik3-E13flox/floxadult mice phenocopiesSleepy (Sik3Slp/+)mice, ABC-CRISPR ofSlp/Sik3reverses hypersomnia ofSleepymice, indicating a direct role of SLP/SIK3 kinase in sleep regulation. Multiplex ABC-CRISPR of both orexin/hypocretin receptors causes narcolepsy-like episodes, enabling one-step analysis of redundant genes in adult mice. Finally, ABC-expression/KO screen identifies Ankrd63 and NR1 as two potentially new sleep regulators. Therefore, this somatic genetics approach should facilitate high-throughput analysis of sleep regulatory genes, especially for essential or redundant genes, in adult mice by skipping the mouse development and genetic crosses.
Mechanical collaboration between the embryonic brain and the surrounding scalp tissues
Authors: Tsujikawa Koichiro , Saito Kanako , Nagasaka Arata , Miyata Takaki
Published: May 2021

During brain enlargement between embryonic day (E) 11 and E13, within the limited mouse cranial space enclosed by the scalp consisting of epidermal and preosteogenic mesenchymal layers, the angle between the pons and the medulla decreases. This raises the possibility that the scalp, upon being pushed outwardly by the brain and stretched, in return inwardly recoils to confine and fold the brain. Our stress-releasing tests showed that the scalp recoiled to shrink more extensively at E12~13 than at E15~16 and that thein vivopre-stretch prerequisite for this recoil response depended physically on the brain (pressurization at 77~93 Pa) and on actomyosin and elastin within the scalp layers. Under non-stretched conditions, scalp cell proliferation declined, while re-stretching of the shrunken scalp rescued proliferation. In scalp-removed heads, pons–medulla folding was reduced, and the spreading of ink from the lateral ventricle to the spinal cord that occurred in scalp-intact embryos (with >5 μl injection) was lost, suggesting that the scalp plays roles in brain morphogenesis and cerebrospinal fluid homeostasis. Thus, the brain and the scalp mechanically interact and collaborate.
Unbiased lexicometry analyses illuminate plague dynamics during the second pandemic
Authors: Barbieri Rémi , Nodari Riccardo , Signoli Michel , Epis Sara , Raoult Didier , Drancourt Michel
Published: May 2021

Knowledge of the second plague pandemic that swept over Europe during the 14th-19th centuries, mainly relies on the exegesis of contemporary texts, prone to interpretive bias. Leveraging bioinformatic tools routinely used in biology, we here developed a quantitative lexicography of 32 texts describing two major plague outbreaks using contemporary plague-unrelated texts as negative controls. Nested, network and category analyses of a 207-word pan-lexicome over-represented in plague-related texts, indicated that “buboes” and “carbuncles” words were significantly associated with plague, signaling ectoparasite- borne plague. Moreover, plague-related words were associated with the words “merchandise”, “movable”, “tatters”, “bed” and “clothes”, while no association was found with rats and fleas. These results support the hypothesis that during the second plague pandemic, human ectoparasites were the major drivers of plague. Analyzing ancient texts using here reported method would certify plague-related historical records and indicate particularities of each plague outbreak, including sources of the causativeYersinia pestis.