bluuebunny/crossref_metadata_2025 huggingface dataset:
In situfilamentous communities from the Ediacaran (approx. 563 Ma) of Brazil
Authors: Becker-Kerber Bruno , de Barros Gabriel Eduardo Baréa , Paim Paulo Sergio Gomes , Prado Gustavo M. E. M. , da Rosa Ana Lucia Zucatti , El Albani Abderrazak , Laflamme Marc
Published: January 2021

Precambrian filamentous microfossils are common and diverse. Nevertheless, their taxonomic assignment can be difficult owing to their overall simple shapes typically lacking in diagnostic features. Here, we reportin situcommunities of well-preserved, large filamentous impressions from the Ediacaran Itajaí Basin (ca563 Ma) of Brazil. The filaments are uniserial (unbranched) and can reach up to 200 µm in width and up to 44 mm in length. They occur as both densely packed or sparsely populated surfaces, and typically show a consistent orientation. Although simple in shape, their preferred orientation suggests they were tethered to the seafloor, and their overall flexibility (e.g. bent, folded and twisted) supports a biological (rather than sedimentary) affinity. Biometric comparisons with modern filamentous groups further support their biological affinity, suggesting links with either large sulfide-oxidizing bacteria (SOB) or eukaryotes. Other morphological and palaeoecological characteristics further corroborates their similarities with modern large filamentous SOB. Their widespread occurrence and association with complex Ediacaran macrobiota (e.g. frondose organisms,Palaeopascichnus) suggest that they probably played an important role in the ecological dynamics of these early benthic communities by providing firm substrates for metazoans to inhabit. It is further hypothesized that the dynamic redox condition in the latest Ediacaran, with the non-continuous rise in oxygen concentration and periods of hypoxia, may have created ideal conditions for SOB to thrive.
The development of affiliative and coercive reproductive tactics in male chimpanzees
Authors: Reddy Rachna B. , Langergraber Kevin E. , Sandel Aaron A. , Vigilant Linda , Mitani John C.
Published: January 2021

Like many animals, adult male chimpanzees often compete for a limited number of mates. They fight other males as they strive for status that confers reproductive benefits and use aggression to coerce females to mate with them. Nevertheless, small-bodied, socially immature adolescent male chimpanzees, who cannot compete with older males for status nor intimidate females, father offspring. We investigated how they do so through a study of adolescent and young adult males at Ngogo in Kibale National Park, Uganda. Adolescent males mated with nulliparous females and reproduced primarily with these first-time mothers, who are not preferred as mating partners by older males. Two other factors, affiliation and aggression, also influenced mating success. Specifically, the strength of affiliative bonds that males formed with females and the amount of aggression males directed toward females predicted male mating success. The effect of male aggression toward females on mating success increased as males aged, especially when they directed it toward females with whom they shared affiliative bonds. These results mirror sexual coercion in humans, which occurs most often between males and females involved in close, affiliative relationships.
Multi-omic Evaluation of Metabolic Alterations in Multiple Sclerosis Identifies Shifts in Aromatic Amino Acid Metabolism
Authors: Fitzgerald Kathryn C. , Smith Matthew D. , Sotirchos Elias S. , Kornberg Michael D. , Douglas Morgan , Nourbakhsh Bardia , Graves Jennifer , Rattan Ramandeep , Poisson Laila , Cerghet Mirela , Mowry Ellen M. , Waubant Emmanuelle , Giri Shailendra , Calabresi Peter A. , Bhargava Pavan
Published: January 2021

The circulating metabolome is a product of interactions between the genome, epigenome, exposome and microbiome. The metabolome may be altered in people with multiple sclerosis (MS); however, existing metabolomics studies were relatively small or characterized a limited number of metabolites. Herein, we performed a multi-site study profiling the circulating metabolome to obtain relative abundances for 269 metabolites in a large cohort of MS patients and healthy controls. After adjusting for batch effects and extensive quality control, we created an overall metabolic dysfunction score, defined apriori sets of metabolites using known metabolic pathways, and derived novel networks of correlated metabolites using a weighted correlation network analysis (WGCNA). We assessed whether metabolic dysfunction, individual metabolites, metabolic pathways or WGCNA-identified module scores differed between people with MS versus healthy controls (HC) after adjusting for age, sex and race using generalized estimating equations (participants could provide multiple samples). In a subset of patients, information on disability status was also available. Similar models assessed the association between metabolites and metabolite sets with measures of disability. In people with MS, we identified striking abnormalities in a WGCNA-defined module enriched in aromatic amino acid (AAA) metabolites (FDR-adjusted p-value=2.77E-18) that are also strongly associated with disability (FDR-adjusted p-value for AAA module=1.01E-4). Consistent results were obtained using apriori-defined metabolite sets or in analyses of individual metabolites. The identified abnormalities likely relate to imbalances in gut microbial metabolism of AAAs resulting in reduced production of immunomodulatory metabolites and increased production of metabotoxins (indole acetate, phenylacetylglutamine, p-cresol sulfate, p-cresol glucuronide). Single cell RNA sequencing data analysis demonstrated altered AAA metabolism in CSF and blood derived monocyte cell populations, while treatment of human peripheral blood mononuclear cells with AAA-derived metabotoxins resulted in increased production of tumor necrosis factor-α. We identify novel metabolic alterations in people with MS potentially contributing to disease pathophysiology.
The social experience of participation in a COVID-19 vaccine trial: Subjects’ motivations, others’ concerns, and insights for vaccine promotion
Authors: Wentzell Emily , Racila Ana-Monica
Published: January 2021

Background

Vaccine hesitancy could undermine the effectiveness of COVID-19 vaccination programs. Knowledge about people’s lived experiences regarding COVID-19 vaccination can enhance vaccine promotion and increase uptake.

Aim

To use COVID-19 vaccine trial participants’ experiences to identify key themes in the lived experience of vaccination early in the vaccine approval and distribution process.

Methods

We interviewed 31 participants in the Iowa City, Iowa US site of the Pfizer/BioNTech COVID-19 vaccine phase 3 clinical trial. While trial participation differs from clinical receipt of an approved vaccine in key ways, it offers the first view of people’s lived experiences of potentially receiving a COVID-19 vaccine. The trial context is also useful since decision-making about vaccination and medical research participation often involve similar hopes and concerns, and because the public appears to view even approved COVID-19 vaccines as experimental given their novelty. Semi-structured interviews addressed subjects’ experiences, including decision-making and telling others about their trial participation. We analyzed verbatim transcripts of these interviews thematically and identified common themes relevant for vaccination decision-making.

Results

Participants across demographic groups, including age, sex/gender, race/ethnicity, and political affiliation, described largely similar experiences. Key motivations for participation included ending the pandemic/restoring normalcy, protecting oneself and others, doing one’s duty, promoting/modeling vaccination, and expressing aspects of identity like being a helper, career-related motivations, and support of science/vaccines. Participants often felt uniquely qualified to help via trial participation due to personal attributes like health, sex/gender or race/ethnicity. They reported hearing concerns about side effects and the speed and politicization of vaccine development. Participants responded by normalizing and contextualizing side effects, de-politicizing vaccine development, and explaining how the rapid development process was nevertheless safe.

Conclusion

These findings regarding participants’ reported motivations for trial participation and interactions with concerned others can be incorporated into COVID-19 vaccine promotion messaging aimed at similar populations.
Prediction of confirmed and death cases of Covid-19 in Chile through time series techniques: A comparative study
Authors: Barría-Sandoval Claudia , Ferreira Guillermo , Benz-Parra Katherine , López-Flores Pablo
Published: January 2021

(1)

Background

Chile has become one of the countries most affected by Covid-19, a pandemic that has generated a large number of cases worldwide, which if not detected and treated in time can cause multi-organic failure and even death. The social determinants of health such as education, work, social security, housing, environment, support networks and social cohesion are important aspects to consider for the control and intervention of this pathology. Therefore, it is essential to have information about the progress of the infections at the national level and thus apply effective public health interventions. In this paper, we compare different time series methodologies to predict the number of confirmed cases and deaths from Covid-19 in Chile and thus support the decisions of health agencies;

(2)

Methods

We modeled the confirmed cases and deaths from Covid-19 in Chile by using ARIMA models, exponential smoothing techniques, Poisson models for time-dependent counting data. In addition, we evaluated the accuracy of the predictions by using a training set and test set;

(3)

Results

The database used in this paper allows us to say that for the confirmed Covid-19 cases the best model corresponds to a well-known Autoregressive Integrated Moving Average (ARIMA) time-series model, whereas for deaths from Covid-19 in Chile the best model resulted in damped trend method;

(4)

Conclusion

ARIMA models are an alternative to model the behavior of the spread of Covid19, however, and depending on the characteristics of the data set, other methodologies can better capture the behavior of these records, for example, Holt-winter’s method and time-dependent counting models.
Ascertaining the initiation of epidemic resurgences: an application to the COVID-19 second surges in Europe and the Northeast United States
Authors: Vilar Jose M. G. , Saiz Leonor
Published: January 2021

Assessing a potential resurgence of an epidemic outbreak with certainty is as important as challenging. The low number of infectious individuals after a long regression, and the randomness associated with it, makes it difficult to ascertain whether the infectious population is growing or just fluctuating. We have developed an approach to compute confidence intervals for the switching time from decay to growth and to compute the corresponding supra-location aggregated quantities to increase the precision of the determination. We estimated the aggregate prevalence over time for Europe and the Northeast United States to characterize the COVID-19 second surge in these regions during year 2020. We find a starting date as early as July 3 (95% Confidence Interval (CI): July 1– July 6) for Europe and August 19 (95% CI: August 16 – August 23) for the Northeast; subsequent infectious populations that, as of December 31 have always increased or remained stagnant; and the resurgences being the collective effect of each overall region with no location dominating the regional dynamics by itself.
Pharmacokinetic modelling to estimate intracellular favipiravir ribofuranosyl-5’-triphosphate exposure to support posology for SARS-CoV-2
Authors: Pertinez Henry , Rajoli Rajith KR , Khoo Saye H , Owen Andrew
Published: January 2021

Background

The role of favipiravir as a treatment for COVID-19 is unclear, with discrepant activity against SARS-CoV-2in vitro, concerns about teratogenicity and pill burden, and an unknown optimal dose. In Vero-E6 cells, high concentrations are needed to inhibit SARS-CoV-2 replication. The purpose of this analysis was to use available data to simulate intracellular pharmacokinetics of favipiravir ribofuranosyl-5⍰-triphosphate (FAVI-RTP) to better understand the putative applicability as a COVID-19 intervention.

Methods

Previously publishedin vitrodata for the intracellular production and elimination of FAVI- RTP in MDCK cells incubated with parent favipiravir was fitted with a mathematical model to describe the time course of intracellular FAVI-RTP concentrations as a function of incubation concentration of parent favipiravir. Parameter estimates from this model fitting were then combined with a previously published population PK model for the plasma exposure of parent favipiravir in Chinese patients with severe influenza (the modelled free plasma concentration of favipiravir substituting forin vitroincubation concentration) to predict the human intracellular FAVI-RTP pharmacokinetics.

Results

In vitroFAVI-RTP data was adequately described as a function ofin vitroincubation media concentrations of parent favipiravir with an empirical model, noting that the model simplifies and consolidates various processes and is used under various assumptions and within certain limits. Parameter estimates from the fittings toin vitrodata predict a flatter dynamic range of peak to trough for intracellular FAVI-RTP when driven by a predicted free plasma concentration profile.

Conclusion

This modelling approach has several important limitations that are discussed in the main text of the manuscript. However, the simulations indicate that despite rapid clearance of the parent drug from plasma, sufficient intracellular FAVI-RTP may be maintained across the dosing interval because of its long intracellular half-life. Population average intracellular FAVI-RTP concentrations are estimated to maintain the Km for the SARS-CoV-2 polymerase for 3 days following 800 mg BID dosing and 9 days following 1200 mg BID dosing after a 1600 mg BID loading dose on day 1. Further evaluation of favipiravir as part of antiviral combinations for SARS-CoV-2 is warranted.
Genomic epidemiology of the SARS-CoV-2 epidemic in Zimbabwe: Role of international travel and regional migration in spread
Authors: Mashe Tapfumanei , Takawira Faustinos Tatenda , Martins Leonardo de Oliveira , Gudza-Mugabe Muchaneta , Chirenda Joconiah , Munyanyi Manes , Chaibva Blessmore V , Tarupiwa Andrew , Gumbo Hlanai , Juru Agnes , Nyagupe Charles , Phiri Isaac , Manangazira Portia , Goredema Alexander , Danda Sydney , Chabata Israel , Jonga Janet , Munharira Rutendo , Masunda Kudzai , Mukeredzi Innocent , Mangwanya Douglas ,   The COVID-19 Genomics UK (COG-UK) Consortium,   SARS-CoV-2 Research Group, Trotter Alex , Viet Thanh Le , Kay Gemma , Baker David , Thilliez Gaetan , Gutierrez Ana-Victoria , O’Grady Justin , Hove Maxwell , Mutapuri-Zinyowera Sekesai , Page Andrew J. , Kingsley Robert A. , Mhlanga Gibson
Published: January 2021

Zimbabwe reported its first case of SARS-Cov-2 infection in March 2020, and case numbers increased to more than 8,099 to 16th October 2020. An understanding of the SARS-Cov-2 outbreak in Zimbabwe will assist in the implementation of effective public health interventions to control transmission. Nasopharyngeal samples from 92,299 suspected and confirmed COVID-19 cases reported in Zimbabwe between 20 March and 16 October 2020 were obtained. Available demographic data associated with those cases identified as positive (8,099) were analysed to describe the national breakdown of positive cases over time in more detail (geographical location, sex, age and travel history). The whole genome sequence (WGS) of one hundred SARS-CoV-2-positive samples from the first 120 days of the epidemic in Zimbabwe was determined to identify their relationship to one another and WGS from global samples. Overall, a greater proportion of infections were in males (55.5%) than females (44.85%), although in older age groups more females were affected than males. Most COVID-19 cases (57 %) were in the 20-40 age group. Eight lineages, from at least 25 separate introductions into the region were found using comparative genomics. Of these, 95% had the D614G mutation on the spike protein which was associated with higher transmissibility than the ancestral strain. Early introductions and spread of SARS-CoV-2 were predominantly associated with genomes common in Europe and the United States of America (USA), and few common in Asia at this time. As the pandemic evolved, travel-associated cases from South Africa and other neighbouring countries were also recorded. Transmission within quarantine centres occurred when travelling nationals returning to Zimbabwe. International and regional migration followed by local transmission were identified as accounting for the development of the SARS-CoV-2 epidemic in Zimbabwe. Based on this, rapid implementation of public health interventions are critical to reduce local transmission of SARS-CoV-2. Impact of the predominant G614 strain on severity of symptoms in COVID-19 cases needs further investigation.
Reverse Transcriptase Loop Mediated Isothermal Amplification (RT-LAMP) for COVID-19 Diagnosis: A Systematic Review and Meta-Analysis
Authors: Subali Anita Dominique , Wiyono Lowilius
Published: January 2021

Background

Coronavirus Disease 2019 (COVID-19) has caused a severe outbreak and become a global public health priority. Rapid increment of infection number along with significant deaths have placed the virus as a serious threat to human health. Rapid, reliable, and simple diagnostic methods are critically essential for disease control. While Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) is the current diagnostic gold standard, Reverse Transcriptase Loop-Mediated Isothermal Amplification (RT-LAMP) appears as a compelling alternative diagnostic test due to its more simplicity, shorter time to result, and lower cost. This study examined RT-LAMP application for rapid identification of SARS-CoV-2 infection compared to RT-PCR assay.

Methods

A systematic review and meta-analysis (2020) was conducted in 6 scientific databases following the PRISMA Guideline. Original published studies on human clinical samples in English were included. Articles evaluated sensitivity and specificity of RT-LAMP relative to RT-PCR were considered eligible. Quality assessment of bias and applicability was examined based on QUADAS-2.

Results

A total of 351 studies were found based on the keywords and search queries. 14 eligible case control studies fitted the respective criteria. Quality assessment using QUADAS-2 indicated low risk bias in all included studies. All case studies, comprises 2,112 samples, had the cumulative sensitivity of 95.5% (CI 97.5%=90.8-97.9%) and cumulative specificity of 99.5% (CI 97.5%=97.7-99.9%).

Conclusion

RT-LAMP assay could be suggested as a reliable alternative COVID-19 diagnostic method with reduced cost and time compared to RT-PCR. RT-LAMP could potentially be utilized during the high-throughput and high-demand critical situations.
Socioeconomic and gender disparities in tobacco smoking among Jamaican adults from a national health survey
Authors: Bennett Nadia R , Ferguson Trevor S , Younger-Coleman Novie O , Francis Damian K , Anderson Simon G , Harris E. Nigel , MacLeish Marlene Y , Wilks Rainford J ,   U.S. Caribbean Alliance for Health Disparities Research Group (USCAHDR):
Published: January 2021

Objectives

Little is known of socioeconomic and gender disparities in tobacco use in the Caribbean. We evaluated education and occupation disparities in tobacco smoking prevalence in Jamaica.

Methods

Data on tobacco smoking, education attainment and usual occupation in adults 25-74 years in a national survey collected between 2007 and 2008 was analyzed. Using post stratification survey weights, Poisson regression models estimated sex-specific, age-adjusted prevalence estimates, prevalence differences and prevalence ratios.

Results

Analyses included 2299 participants (696 men, 1603 women), mean age 43 years. Current smoking prevalence was 26% in men and 8% in women (p<0.001). Among men, age adjusted prevalence of current smoking was highest in primary education (36.5%) and lowest in the post-secondary education groups (10.2%), (p= 0.003). Among women, prevalence was highest in junior secondary education (10.2%) and lowest in primary education groups (4.7%), (p = 0.014). Among men, for education, age-adjusted prevalence ratios for current smoking ranged from 2.6 to 3.6 using post-secondary education as the reference category (p<0.05). For occupation, age-adjusted prevalence ratios ranged from 1.7 to 4.1 using professionals and managers as the reference category. Among women, using the same reference categories age-adjusted prevalence ratios for education ranged from 1.4 to 2.2 and for occupation 0.6 to 2.2, neither were statistically significant.

Conclusion

In Jamaica, there are socioeconomic disparities in current tobacco smoking among men, where it is inversely associated with education attainment and occupation but in women is less clear. These findings suggest interventions to reduce smoking should consider these disparities.
Triglyceride Glucose Index Predicts Risk of Adverse Cardio-metabolic and Mortality Outcomes Among Chinese Adults: A Territory-Wide Longitudinal Study
Authors: Zhou Jiandong , Lee Sharen , Hui Jeremy , Wong Wing Tak , Leung Keith SK , Wai Abraham KC , Liu Tong , Yung Cheung Bernard Man , Tse Gary , Zhang Qingpeng
Published: January 2021

Background

The triglyceride glucose (TyG) index has been proposed to be a surrogate of insulin resistance. In the study, we aimed to examine the relationship between TyG index and the risk of new onset DM and secondary outcomes included atrial fibrillation (AF), heart failure (HF), acute myocardial infarction (AMI), ventricular tachycardia/fibrillation (VTF), cardiovascular mortality (CAD) and all-cause mortality.

Methods

The retrospective observational study analyzed patients recruited from 1st January 2000 to 31st December 2003 and followed up until 31st December 2019. Demographics, past comorbidities, medications and laboratory tests were extracted. At baseline and follow-up, DM was defined as 1) any occasion Hb1Ac ≥14 g/dL, 2) fasting glucose≥7 mmol/L on two occasions, or 3) with DM diagnosis. We excluded 1) patients with prior DM or with the use of antidiabetic medications; 2) patients with prior AMI/HF/AF or with the use of diuretic/beta blockers for HF were excluded. Univariate analysis and multivariate Cox analysis with adjustments on demographics, past comorbidities and medications were conducted to identify the significant risk predictors of primary and secondary outcomes. Optimal cutoffs of TyG index for the primary and secondary outcomes were found with maximally selected rank statistics approach.

Result

Lager TyG index is significantly associated with new onset DM (HR: 1.51, 95% CI: [1.47, 1.55], P vlaue<0.0001), new onset HF (HR: 1.27, 95% CI: [1.2, 1.34], P vlaue<0.0001), new onset AF (HR: 2.36, 95% CI: [2.26, 2.46], P vlaue<0.0001), new onset AMI (HR: 1.51, 95% CI: [1.42, 1.6], P vlaue<0.0001), new onset VTF (HR: 1.22, 95% CI: [1.13, 1.31], P vlaue<0.0001), new onset CAD (HR: 1.56, 95% CI: [1.45, 1.69], P value<0.0001) and all-cause mortality (HR: 1.21, 95% CI: [1.18, 1.25], P vlaue<0.0001). TyG index and its 3rd tertile remained significant after being adjusted with significant demographics, past comorbidities and medicactions in multivariate cox models (HR>1, P value<0.05). Optimal cut-off values of baseline TyG index and adjusted multivariate restricted cubic spline models further uncovered detailed associations of larger baseline TyG index with the primary and secondary outcome.

Conclusion

Higher TyG index remained significantly associated with the elevated risk of new onset DM, AF, HF, AMI, VTF, CAD and all-cause mortality after adjustments on demographics, past comorbidities, and medications.
Arrhythmic Outcomes in Catecholaminergic Polymorphic Ventricular Tachycardia
Authors: Lee Sharen , Zhou Jiandong , Jeevaratnam Kamalan , Lakhani Ishan , Wong Wing Tak , Kei Wong Ian Chi , Mak Chloe , Mok Ngai Shing , Liu Tong , Zhang Qingpeng , Tse Gary
Published: January 2021

Introduction

Catecholaminergic polymorphic ventricular tachycardia (CPVT) is a rare cardiac ion channelopathy. The aim of this study is to examine the genetic basis and identify pre-dictive factors for arrhythmic outcomes in CPVT patients from Hong Kong.

Methods

This was a territory-wide retrospective cohort study of consecutive patients diagnosed with CPVT at public hospitals or clinics in Hong Kong. The primary outcome was spontaneous ventricular tachycardia/ventricular fibrillation (VT/VF).

Results

A total of 16 (mean presentation age=11±4 years old) patients were included. All patients presented at or before 19 years of age. Fifteen patients (93.8%) were initially symptomatic. Ten patients had both premature ventricular complexes (PVCs) and VT/VF, whereas one patient had PVCs without VT/VF. Genetic tests were performed in 14 patients (87.5%). Eight (57.1%) tested positive for the RyR2 gene. Seven variants have been described else-where (c.14848G>A, c.12475C>A, c.7420A>G, c.11836G>A, c.14159T>C, c.10046C>T and c.7202G>A). c.14861C>G is a novel RyR2 variant that has not been reported outside this cohort. All patients were treated with beta-blockers, three patients received amiodarone and two received verapamil. Sympathectomy (n=8), ablation (n=1) and implantable-cardioverter defibrillator implantation (n=3) were performed. Over a median follow-up of 127 (IQR: 97-143) months, six patients suffered from incident VT/VF. No significant predictors were identified on Cox regression. Nevertheless, a random survival forest model identified initial VT/VF/sudden cardiac death, palpitations, QTc, initially symptomatic and heart rate as important variables for estimating the probability of developing incident VT/VF.

Conclusion

All CPVT patients who are from Hong Kong presented at or before 19 years of age. Clinical and electrocardiographic findings can be used to predict arrhythmic outcomes. A nonparametric machine learning survival analysis achieved high accuracy for predicting the probability of incident VT/VF.
IgA Potentiates NETosis in Response to Viral Infection
Authors: Stacey Hannah D. , Golubeva Diana , Posca Alyssa , Ang Jann C. , Novakowski Kyle E. , Zahoor Muhammad Atif , Kaushic Charu , Cairns Ewa , Bowdish Dawn M. E. , Mullarkey Caitlin E. , Miller Matthew S.
Published: January 2021

IgA is the second most abundant antibody present in circulation and is enriched at mucosal surfaces. As such, IgA plays a key role in protection against a variety of mucosal pathogens, including viruses. In addition to neutralizing viruses directly, IgA can also stimulate Fc-dependent effector functions via engagement of Fc alpha receptors (FcαRI) expressed on the surface of certain immune effector cells. Neutrophils are the most abundant leukocyte, express FcαRI, and are often the first to respond to sites of injury and infection. Here, we describe a novel function for IgA:virus immune complexes (ICs) during viral infections. We show that IgA:virus ICs potentiate NETosis – the programmed cell death pathway through which neutrophils release neutrophil extracellular traps (NETs). Mechanistically, IgA:virus ICs potentiated a suicidal NETosis pathway via engagement of FcαRI on neutrophils through a toll-like receptor (TLR)-independent, NADPH oxidase complex-dependent pathway. NETs also were capable of trapping and inactivating viruses, consistent with an antiviral function.
Mechanics of the cellular microenvironment as perceived by cellsin vivo
Authors: Mongera Alessandro , Pochitaloff Marie , Gustafson Hannah J. , Stooke-Vaughan Georgina A. , Rowghanian Payam , Campàs Otger
Published: January 2021

Tissue morphogenesis and repair, as well as organ homeostasis, require cells to constantly monitor their 3D microenvironment and adapt their behaviors in response to local biochemical and mechanical cues1-6.In vitrostudies have shown that substrate stiffness and stress relaxation are important mechanical parameters in the control of cell proliferation and differentiation, stem cell maintenance, cell migration7-11, as well as tumor progression and metastasis12,13. Yet, the mechanical parameters of the microenvironment that cells perceivein vivo, within 3D tissues, remain unknown. In complex materials with strain- and time-dependent material properties, the perceived mechanical parameters depend both on the strain and timescales at which the material is mechanically probed14. Here, we quantifyin vivoandin situthe mechanics of the cellular microenvironment that cells probe during vertebrate presomitic mesoderm (PSM) specification. By analyzing the magnitude and dynamics of endogenous, cell-generated strains, we show that individual cells preferentially probe the stiffness associated with deformations of the supracellular, foam-like tissue architecture. We reveal how stress relaxation leads to a perceived microenvironment stiffness that decreases over time, with cells probing the softest regime. While stress relaxation timescales are spatially uniform in the tissue, most mechanical parameters, including those probed by cells, vary along the anteroposterior axis, as mesodermal progenitors commit to different lineages. Understanding the mechanical parameters that cells probe in their native 3D environment is important for quantitative studies of mechanosensationin vivo2-4,6,15and can help design scaffolds for tissue engineering applications16-18.
Error Prediction Determines the Coordinate System Used for Novel Dynamics Representation
Authors: Leib Raz , Franklin David W.
Published: January 2021

Skillful object manipulation requires a representation of the object’s dynamics. Despite extensive research, previous studies have not been able to provide a consistent view of this representation in the motor system, with each study providing evidence favoring an extrinsic coordinate system, an intrinsic coordinate system, an object-based representation, or mixtures of these coordinate systems. In a series of experiments, we show that the motor system combines different representations based on their reliability. Specifically, since noise creates an error between planned and executed force production which depends on the arm state, the motor system will rely more on the representation for which the plan is less affected. In addition, we show that the error based weights predict the different results made about dynamics representation and thus explaining the discrepancy between influential past studies. Overall, we are able to reconcile all of the apparently disparate findings under a single cohesive model of dynamics representation.
An optimized ribodepletion approach forC. elegansRNA-sequencing libraries
Authors: Barrett Alec , McWhirter Rebecca , Taylor Seth R , Weinreb Alexis , Miller David M , Hammarlund Marc
Published: January 2021

A recent and powerful technique is to obtain transcriptomes from rare cell populations, such as single neurons inC. elegans,by enriching dissociated cells using fluorescent sorting. However, these cell samples often have low yields of RNA that present challenges in library preparation. This can lead to PCR duplicates, noisy gene expression for lowly expressed genes, and other issues that limit endpoint analysis. Further, some common resources, such as sequence specific kits for removing ribosomal RNA, are not optimized for non-mammalian samples. To optimize library construction for such challenging samples, we compared two approaches for building RNAseq libraries from less than 10 nanograms ofC. elegansRNA: SMARTSeq V4 (Takara), a widely used kit for selecting poly-adenylated transcripts; and SoLo Ovation (Tecan Genomics), a newly developed ribodepletion-based approach. For ribodepletion, we used a custom kit of 200 probes designed to matchC. elegansrRNA gene sequences. We found that SoLo Ovation, in combination with our customC. elegansprobe set for rRNA depletion, detects an expanded set of noncoding RNAs, shows reduced noise in lowly expressed genes, and more accurately counts expression of long genes. The approach described here should be broadly useful for similar efforts to analyze transcriptomics when RNA is limiting.
Cellular and Viral Determinants of HSV-1 Entry and Intracellular Transport towards Nucleus of Infected Cells
Authors: Musarrat Farhana , Chouljenko Vladimir , Kousoulas Konstantin G.
Published: January 2021

HSV-1 employs cellular motor proteins and modulates kinase pathways to facilitate intracellular virion capsid transport. Previously, we and others have shown that the Akt inhibitor miltefosine inhibited virus entry. Herein, we show that the protein kinase C inhibitors staurosporine (STS) and gouml inhibited HSV-1 entry into Vero cells, and that miltefosine prevents HSV-1 capsid transport toward the nucleus. We have reported that the HSV-1 UL37 tegument protein interacts with the dynein motor complex during virus entry and virion egress, while others have shown that the UL37/UL36 protein complex binds dynein and kinesin causing a saltatory movement of capsids in neuronal axons. Co-immoprecipitation experiments confirmed previous findings from our laboratory that the UL37 protein interacted with the dynein intermediate chain (DIC) at early times post infection. This UL37-DIC interaction was concurrent with DIC phosphorylation in infected, but not mock-infected cells. Miltefosine inhibited dynein phosphorylation when added before, but not after virus entry. Inhibition of motor accessory protein dynactins (DCTN2, DCTN3), the adaptor proteins EB1 and the Bicaudal D homolog 2 (BICD2) expression using lentiviruses expressing specific shRNAs, inhibited intracellular transport of virion capsids toward the nucleus of human neuroblastoma (SK-N-SH) cells. Co-immunoprecipitation experiments revealed that the major capsid protein Vp5 interacted with dynactins (DCTN1/p150 and DCTN4/p62) and the end-binding protein (EB1) at early times post infection. These results show that Akt and kinase C are involved in virus entry and intracellular transport of virion capsids, but not in dynein activation via phosphorylation. Importantly, both the UL37 and Vp5 viral proteins are involved in dynein-dependent transport of virion capsids to the nuclei of infected cells.

Importance

Herpes simplex virus type-1 enter either via fusion at the plasma membranes or endocytosis depositing the virion capsids into the cytoplasm of infected cells. The viral capsids utilize the dynein motor complex to move toward the nuclei of infected cells using the microtubular network. This work shows that inhibitors of the Akt kinase and kinase C inhibit not only viral entry into cells but also virion capsid transport toward the nucleus. In addition, the work reveals that the virion protein ICP5 (VP5) interacts with the dynein cofactor dynactin, while the UL37 protein interacts with the dynein intermediate chain (DIC). Importantly, neither Akt nor Kinase C was found to be responsible for phosphorylation/activation of dynein indicating that other cellular or viral kinases may be involved.
Associations between Stress and Child Verbal Abuse and Corporal Punishment during the COVID-19 Pandemic and Potential Effect Modification by Lockdown Measures
Authors: Jeharsae Rohani , Jae-noh Manusameen , Jae-a-lee Haneefah , Waeteh Suhaida , Nimu Nisuraida , Chewae Corliyoh , Yama Malinee , Dureh Nurin , Wichaidit Wit
Published: January 2021

Background

Child abuse appears to be on the increase during the COVID-19 pandemic, but the extent that lockdown measures modified the association between stress and abuses has not been systematically assessed.

Objectives

To assess: 1) the association between caregiver’s stress and self-reported verbal abuse and corporal punishment of a child in the household, and; 2) modification of the stated association by experienced COVID-19 lockdown measures.

Participants and settings

Caregivers residing in villages on lockdown in the Deep South of Thailand (n=466 participants)

Methods

We randomly sampled 12 villages in the study area, and 40 households per village. Trained enumerators who were residents of the sampled villages collected the data using phone-based interview. We measured stress level using the standard ST-5 questionnaire. We developed and pilot-tested questions for measurement of child abuse and lockdown experiences specifically for this study.

Results

Caregivers with moderate and higher levels of stress were more likely than caregivers with low level of stress to report verbal abuse (48% vs. 23%, respectively; Adj. OR = 3.12, 95% CI = 1.89, 5.15) and corporal punishment (28% vs. 8%, respectively; Adj. OR = 2.76, 95% CI = 1.41, 5.42). We found that COVID-19 lockdown experiences modified the associations between stress and verbal abuse and corporal punishment.

Conclusion

There were associations between stress and abuses, which were modified by lockdown experiences. However, social desirability, lack of details in the answers, and potential confounding by mental illness co-morbidities were notable limitations of the study. Caveat is advised in the interpretation of the study findings.
Analysis of 200,000 exome-sequenced UK Biobank subjects illustrates the contribution of rare genetic variants to hyperlipidaemia
Authors: Curtis David
Published: January 2021

A few genes have previously been identified in which very rare variants can have major effects on lipid levels. Weighted burden analysis of rare variants was applied to exome sequenced UK Biobank subjects with hyperlipidaemia as the phenotype, of whom 44,050 were designated cases and 156,578 controls, with the strength of association characterised by the signed log 10 p value (SLP). With principal components included as covariates there was a tendency for genes on the X chromosome to produce strongly negative SLPs, and this was found to be due to the fact that rare X chromosome variants were identified less frequently in males than females. The test performed well when both principal components and sex were included as covariates and strongly implicatedLDLR(SLP = 50.08) andPCSK9(SLP = -10.42) while also highlighting other genes previously found to be associated with lipid levels. Variants classified by SIFT as deleterious have on average a two-fold effect and their cumulative frequency is such that they are present in approximately 1.5% of the population. These analyses shed further light on the way that genetic variation contributes to risk of hyperlipidaemia and in particular that there are very many protein-altering variants which have on average moderate effects and whose effects can be detected when large samples of exome-sequenced subjects are available. This research has been conducted using the UK Biobank Resource.
Use of the FebriDx point-of-care assay as part of a triage algorithm for medical admissions with possible COVID-19
Authors: Houston Hamish , Deas Gavin , Naik Shivam , Shah Kamal , Patel Shiras , Dottori Maria Greca , Tay Michael , Filson Sarah , Biggin-Lamming James , Ross John , Vaughan Natalie , Vaid Nidhi , Rao Guduru Gopal , Amin Amit K , Gupta-Wright Ankur , John Laurence
Published: January 2021

Background

Patients admitted to hospital with COVID-19 need rapid identification and isolation to prevent nosocomial transmission. However, isolation facilities are often limited, and SARS-CoV-2 RT-PCR results are often not available when discharged from the emergency department. We evaluated a triage algorithm to isolate patients with suspected COVID-19 using simple clinical criteria and the FebriDx assay.

Design

Retrospective observational cohort

Setting

Large acute care hospital in London, UK

Participants

All medical admissions from the ED between 10th August 2020 and 4th November 2020 with valid SARS-CoV-2 RT-PCR.

Interventions

Medical admissions were triaged as likely, possible or unlikely COVID-19 based on clinical criteria. Patients triaged as possible COVID-19 underwent FebriDx lateral flow assay on capillary blood, and those positive for MxA were managed as likely COVID-19.

Primary Outcome measures

Diagnostic accuracy (sensitivity, specificity and predictive values) of the algorithm and the FebriDx assay compared to SARS-CoV-2 RT-PCR from nasopharyngeal swabs as the reference standard.

Results

4.0% (136/3,443) of medical admissions had RT-PCR confirmed COVID-19. Prevalence of COVID-19 was 45.7% (80/175) in those triaged as likely, 4.1% (50/1,225) in possible and 0.3% (6/2,033) in unlikely COVID-19. Compared to SARS-CoV-2 RT-PCR, clinical triage had sensitivity of 95.6% (95%CI: 90.5% - 98.0%) and specificity of 61.5% (95%CI: 59.8% - 63.1%), whilst the triage algorithm including FebriDx had sensitivity of 92.6% (95%CI: 86.8% - 96.0%) and specificity of 86.4% (95%CI: 85.2% - 87.5%). The triage algorithm reduced the need for 2,859 patients to be admitted to isolation rooms. Ten patients missed by the algorithm had mild or asymptomatic COVID-19.

Conclusions

A triage algorithm including FebriDx assay had good sensitivity and was useful to ‘rule-out’ COVID-19 among medical admissions to hospital.

STRENGTHS AND LIMITATIONS OF THIS STUDY

Pragmatic study including a large cohort of consecutive medical admissions providing routine clinical care.

A single SARS-CoV-2 RT-PCR is an imperfect reference standard for COVID-19. Multiple RT-PCR platforms used, with different PCR targets and performance.

A higher prevalence of COVID-19 or other respiratory pathogens might alter performance.

Criteria for likely and possible COVID-19 groups changed subtly during the study period.
Acceptability and efficacy of vaginal self-sampling for genital infection and bacterial vaginosis: A large, cross-sectional, non-inferiority trial
Authors: Claire Camus , Guillaume Penaranda , Hacène Khiri , Sabine Camiade , Lucie Molet , Melissa Lebsir , Anne Plauzolles , Laurent Chiche , Bernard Blanc , Edwin Quarello , Philippe Halfon
Published: January 2021

Objective

Screening for genital infection (GI), bacterial vaginosis (BV), sexually transmitted infection (STI) and asymptomatic carriage of group B streptococcus (GBS) in pregnant women is a common reason for medical appointments. Objectives were first to determine the non-inferiority of vaginal self-sampling compared with vaginal/cervical classical sampling to screen for GIs, bacterial vaginosis (BV), STIs, and GBS asymptomatic carriage in pregnant women; second to determine the feasibility of vaginal self-sampling.

Methods

Vaginal self-sampling (VSS) and vaginal/cervical classical sampling (VCS) of 1027 women were collected by health care professionals and simultaneously carried out on each patient. Bacterial infection, yeast infection, Chlamydia trachomatis, Neisseria gonorrhoea, Mycoplasma genitalium, Trichomonas vaginalis and Herpes simplex virus types were systematically screened in both paired VSS and VCS samples.

Results

Statistical tests supported the non-inferiority of VSS compared with VCS. Agreements between VCS and VSS remained high regardless of the type of studied infection. VSS had successful diagnostic performances, especially for Predictive negative value (PNV) (over 90%) for all studied infections. Most participants (84%) recommended the use of VSS.

Conclusions

This study remains the most exhaustive in screening for GI, BV, STI agents and asymptomatic GBS carriage. Given its efficacy and acceptability, VSS seems to be a viable alternative to classic physician sampling among women in the general population. This study provides evidence that vaginal self-sampling can be used as a universal specimen for detection of lower genital tract infections in women.

Study Identification number

ID-RCB 2014-A01250-4
Immunogenicity of an AAV-based, room-temperature stable, single dose COVID-19 vaccine in mouse and non-human primates
Authors: Zabaleta Nerea , Dai Wenlong , Bhatt Urja , Chichester Jessica A , Sanmiguel Julio , Estelien Reynette , Michalson Kristofer T , Diop Cheikh , Maciorowski Dawid , Qi Wenbin , Hudspeth Elissa , Cucalon Allison , Dyer Cecilia D , Pampena M. Betina , Knox James J. , LaRocque Regina C , Charles Richelle C , Li Dan , Kim Maya , Sheridan Abigail , Storm Nadia , Johnson Rebecca I , Feldman Jared , Hauser Blake M , Zinn Eric , Ryan Aisling , Kobayashi Dione T , Chauhan Ruchi , McGlynn Marion , Ryan Edward T , Schmidt Aaron G , Price Brian , Honko Anna , Griffiths Anthony , Yaghmour Sam , Hodge Robert , Betts Michael R. , Freeman Mason W , Wilson James M , Vandenberghe Luk H
Published: January 2021

The SARS-CoV-2 pandemic has affected more than 70 million people worldwide and resulted in over 1.5 million deaths. A broad deployment of effective immunization campaigns to achieve population immunity at global scale will depend on the biological and logistical attributes of the vaccine. Here, two adeno-associated viral (AAV)-based vaccine candidates demonstrate potent immunogenicity in mouse and nonhuman primates following a single injection. Peak neutralizing antibody titers remain sustained at 5 months and are complemented by functional memory T-cells responses. The AAVrh32.33 capsid of the AAVCOVID vaccine is an engineered AAV to which no relevant pre-existing immunity exists in humans. Moreover, the vaccine is stable at room temperature for at least one month and is produced at high yields using established commercial manufacturing processes in the gene therapy industry. Thus, this methodology holds as a very promising single dose, thermostable vaccine platform well-suited to address emerging pathogens on a global scale.
Integration of Protein Interactome Networks with Congenital Heart Disease Variants Reveals Candidate Disease Genes
Authors: Gonzalez-Teran Barbara , Pittman Maureen , Felix Franco , Richmond-Buccola Desmond , Thomas Reuben , Choudhary Krishna , Moroni Elisabetta , Colombo Giorgio , Alexanian Michael , Cole Bonnie , Samse-Knapp Kaitlen , McGregor Michael , Gifford Casey A. , Huttenhain Ruth , Gelb Bruce D. , Conklin Bruce R. , Black Brian L. , Bruneau Benoit G. , Krogan Nevan J. , Pollard Katherine S. , Srivastava Deepak
Published: January 2021

Congenital heart disease (CHD) is present in 1% of live births, yet identification of causal mutations remains a challenge despite large-scale genomic sequencing efforts. We hypothesized that genetic determinants for CHDs may lie in protein interactomes of GATA4 and TBX5, two transcription factors that cause CHDs. Defining their interactomes in human cardiac progenitors via affinity purification-mass spectrometry and integrating results with genetic data from thePediatric Cardiac Genomic Consortiumrevealed an enrichment ofde novovariants among proteins that interact with GATA4 or TBX5. A consolidative score that prioritized interactome members based on variant, gene, and proband features identified likely CHD-causing genes, including the epigenetic reader GLYR1. GLYR1 and GATA4 widely co-occupied cardiac developmental genes, resulting in co-activation, and the GLYR1 missense variant associated with CHD disrupted interaction with GATA4. This integrative proteomic and genetic approach provides a framework for prioritizing and interrogating the contribution of genetic variants in disease.