bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigation of the evolution and control of fractures in surrounding rock under different pressure relief and support measures in mine roadways prone to rockburst events
Authors: He Yongliang , Gao Mingshi , Xu Dong , Yu Xin
Published: March 2021

This paper studies the evolution and control of surrounding rock under different pressure relief support conditions in mine roadways in which rockburst events have occurred. The evolution of fractures in the surrounding rock was determined from borehole images obtained with a digital panoramic borehole camera, and the surface displacement due to the rockburst events in the mine roadway was measured. According to the existing problems of the original support system of the roadway, a new coupled support system to prevent rockburst events in mine roadways was proposed, resolving both the pressure relief and support of the roadway. Field measurements indicate that the effect on the roadway under the coupled method of pressure relief and support was more satisfactory than that under the original support system. With the coupled support method, the surface displacement of the roadway was approximately 0.6 m, fractures were distributed only in the soft structures and bolt anchorage areas, and the maximum depth of the fractures was 2.95 m. By contrast, under the original support system, fractures were distributed throughout the roadway surrounding rock, and the maximum depth of fractures was 6.75 m. This coupled roadway support technology of pressure relief and support effectively maintains the stability of the rock surrounding the roadway and ensures the safety of the working face. The research results can provide a reference for damage prevention and support of mine roadways prone to rockburst events.
Effect of urea concentration on properties of peanut protein isolate, arachin and conarachin-based adhesives during urea-epichlorohydrin modification
Authors: Chen Chen , Du Yan , Chen Fusheng
Published: March 2021

To lay a theoretical basis for the preparation of peanut protein-based adhesives and promote the sustainable development of the adhesive industry, properties of peanut protein isolate (PPI), arachin and conarachin-based adhesives modified by urea and epichlorohydrin (ECH) were investigated under different urea concentrations. When the urea concentration was 2 mol l
−1
, the wet shear strength of the PPI-based adhesive was 1.24 MPa with the best water resistance. With the increase of urea concentration from 0 to 4 mol l
−1
, the apparent viscosity of the PPI-based adhesive increased from 3.87 to 136.80 Pa s and the solid content increased from 18.11% to 31.11%. Compared with conarachin-based adhesive, the properties of arachin-based adhesive were improved more obviously during the combined modification. Scanning electron microscopy images illustrated that when the urea concentration was 2 mol l
−1
, the surface of the PPI-based adhesive was more compact and smoother, which was beneficial to the improvement of water resistance and related to the structure changes of arachin and conarachin components. Fourier-transform infrared spectroscopy results indicated that different urea concentrations caused the change of ester and ether bonds in the PPI-based adhesive, which was mainly related to arachin component. Thermogravimetry results suggested that when the urea concentration was 2 mol l
−1
, the decomposition temperature of protein skeleton in the PPI-based adhesive reached a maximum of 314°C exhibiting the highest thermal stability. The improvement of the thermal stability of conarachin was greater than that of arachin during the combined modification.
On habit and habitat
Authors: Vadasz Peter , Vadasz Alisa S.
Published: March 2021

Scientific theories based on mathematical models are frequently used in sciences to reveal natural behaviour of systems and eventually to be able in predicting such behaviour once the system's parameters and relevant conditions are known and can be specified. The integration of accumulated theoretical as well as experimental knowledge allows us to present such a unifying theory underlying the equivalence between habit and habitat in population growth. While the focus of the initial development was derived from microorganisms, the theory is extended to other population types too. The biological interpretation of ‘inertia’ or ‘habit’-based processes is provided as a consequence of this theory, and its relationship to the population ‘resource utilization’ available in the ‘habitat’ is derived. This paper focuses on the link between the ‘resource utilization’, which is related to the ‘habitat’, and ‘biological inertia’, which is related to population ‘habit’. This link extends the context of population growth and predictive modelling of microorganisms.
Evolutionary loss of a signalling colour is linked to increased response to conspecific chemicals
Authors: Romero-Diaz Cristina , Pruett Jake A. , Campos Stephanie M. , Ossip-Drahos Alison G. , Zúñiga-Vega J. Jaime , Vital-García Cuauhcihuatl , Hews Diana K. , Martins Emília P.
Published: March 2021

Behavioural responses to communicative signals combine input from multiple sensory modalities and signal compensation theory predicts that evolutionary shifts in one sensory modality could impact the response to signals in other sensory modalities. Here, we conducted two types of field experiments with 11 species spread across the lizard genus
Sceloporus
to test the hypothesis that the loss of visual signal elements affects behavioural responses to a chemical signal (conspecific scents) or to a predominantly visual signal (a conspecific lizard), both of which are used in intraspecific communication. We found that three species that have independently lost a visual signal trait, a colourful belly patch, responded to conspecific scents with increased chemosensory behaviour compared to a chemical control, while species with the belly patch did not. However, most species, with and without the belly patch, responded to live conspecifics with increased visual displays of similar magnitude. While aggressive responses to visual stimuli are taxonomically widespread in
Sceloporus
, our results suggest that increased chemosensory response behaviour is linked to colour patch loss. Thus, interactions across sensory modalities could constrain the evolution of complex signalling phenotypes, thereby influencing signal diversity.
Bitter taste receptors of the common vampire bat are functional and show conserved responses to metal ionsin vitro
Authors: Ziegler Florian , Behrens Maik
Published: March 2021

The bitter taste sensation is important to warn mammals of the ingestion of potentially toxic food compounds. For mammals, whose nutrition relies on highly specific food sources, such as blood in the case of vampire bats, it is unknown if bitter sensing is involved in prey selection. By contrast to other bat species, vampire bats exhibit numerous bitter taste receptor pseudogenes, which could point to a decreased importance of bitter taste. However, electrophysiological and behavioural studies suggest the existence of functional bitter taste transmission. To determine the agonist spectra of the three bitter taste receptors that are conserved in all three vampire bat species, we investigated thein vitroactivation ofDesmodus rotundusT2R1, T2R4 and T2R7. Using a set of 57 natural and synthetic bitter compounds, we were able to identify agonists for all three receptors. Hence, we confirmed a persisting functionality and, consequently, a putative biological role of bitter taste receptors in vampire bats. Furthermore, the activation of the human TAS2R7 by metal ions is shown to be conserved inD. rotundus.
Attitudes toward COVID-19 illness and COVID-19 vaccination among pregnant women: a cross-sectional multicenter study during August-December 2020
Authors: Battarbee Ashley N. , Stockwell Melissa S. , Varner Michael , Newes-Adeyi Gabriella , Daugherty Michael , Gyamfi-Bannerman Cynthia , Tita Alan , Vorwaller Kelly , Vargas Celibell , Subramaniam Akila , Reichle Lawrence , Galang Romeo , Powers Emily , Lucca-Susana Miriam , Parks Mickey , Chen Tiffany J. , Razzaghi Hilda , Dawood Fatimah S.
Published: March 2021

Objective

Evaluate pregnant women’s attitudes toward COVID-19 illness and vaccination and identify factors associated with vaccine acceptability.

Study Design

Cross-sectional survey among pregnant women enrolled in a prospective COVID-19 cohort study in Salt Lake City, UT, Birmingham, AL, and New York, NY, August 9– December 10, 2020. Women were eligible if they were 18-50 years old and <28 weeks of gestation. Upon enrollment, women completed surveys regarding concerns about COVID-19 illness and likelihood of getting COVID-19 vaccine if one were available during pregnancy. Vaccine acceptability was defined as a response of “very likely” or “somewhat likely” on a 4-point Likert scale. Factors associated with vaccine acceptability were assessed with multivariable logistic regression.

Results

Of 939 pregnant women eligible for the main cohort study, 915 (97%) consented to participate. Among these 915 women, 39% self-identified as White, 23% Black, 33% Hispanic, and 4% Other. Sixty-two percent received an influenza vaccine last season. Seventy-two percent worried about getting sick with COVID-19. If they were to get sick, 92% worried about harm to their pregnancy and 80% about harm to themselves. Only 41% reported they would get a vaccine. Of women who were unlikely to get vaccinated, the most frequently cited concern was vaccine safety for their pregnancy (82%). Non-Hispanic Black and Hispanic women had lower odds of accepting a vaccine compared with non-Hispanic White women (adjusted odds ratios (aOR) 0.4, 95%CI 0.2–0.6 for both). Receipt of influenza vaccine during the previous season was associated with higher odds of vaccine acceptability (aOR 2.1, 95%CI 1.5-3.0).

Conclusion

Although most pregnant women worried about COVID-19 illness, <50% were willing to get vaccinated during pregnancy. Racial and ethnic disparities in plans to accept COVID-19 vaccine highlight the need to prioritize strategies to address perceived barriers among groups at high risk for COVID-19.
Non-Invasive Scale Measurement of Cardiac Output Compared with the Gold-Standard Direct Fick Method: A Feasibility Study
Authors: Yazdi Daniel , Patel Sarin , Sridaran Suriya , Wilson Evan , Smith Sarah , Centen Corey , Gillon Leah , Kapur Sunil , Tracy Julie A. , Lewine Katherine , Systrom David M. , MacRae Calum A.
Published: March 2021

Background

Objective markers of cardiac function are limited in the outpatient setting and may be beneficial for monitoring patients with chronic cardiac conditions.

Objective

We assess the accuracy of a scale, with the ability to capture ballistocardiography, electrocardiography, and impedance plethysmography signals from a patient’s feet while standing on the scale, in measuring stroke volume and cardiac output compared to the gold-standard direct Fick method.

Methods

Thirty-two patients with unexplained dyspnea undergoing level 3 invasive cardiopulmonary exercise test at a tertiary medical center were included in the final analysis. We obtained scale and direct Fick measurements of stroke volume and cardiac output before and immediately after invasive cardiopulmonary exercise test.

Results

Stroke volume and cardiac output from a cardiac scale and the direct Fick method correlated with r = 0.81 and r = 0.85, respectively (P < 0.001 each). The mean absolute error of the scale estimated stroke volume was -1.58 mL, with a 95% limits of agreement (LOA) of -21.97 mL to 18.81 mL. The mean error for the scale estimated cardiac output was -0.31 L/min, with a 95% LOA of -2.62 L/min to 2.00 L/min. The change in stroke volume and cardiac output before and after exercise were 78.9% and 96.7% concordant, respectively between the two measuring methods.

Conclusions

This novel scale with cardiac monitoring abilities may allow for non-invasive, longitudinal measures of cardiac function. Using the widely accepted form factor of a bathroom scale, this method of monitoring can be easily integrated into a patient’s lifestyle.
Efficacy and safety of convalescent plasma and intravenous immunoglobulin in critically ill COVID-19 patients. A controlled clinical trial
Authors: Gonzalez Jose Lenin Beltran , González Gámez Mario , Mendoza Enciso Emmanuel Antonio , Esparza Maldonado Ramiro Josue , Palacios Daniel Hernández , Campos Samuel Dueñas , Robles Itzel Ovalle , Macías Guzmán Mariana Jocelyn , García Díaz Andrea Lucia , Gutiérrez Peña César Mauricio , Reza-Escalera Ana Lilian , Tiscareño Gutierrez Maria Teresa , Galvan-Guerra Elva , Dorantes Morales Maria del Rocio , Medina Lucila Martínez , Monroy Colin Victor Antonio , Jose Manuel Arreola Guerra
Published: March 2021

Background

The proportion of critically ill COVID-19 patients has collapsed hospital care worldwide. The need for alternative therapies for this group of patients is imperative. This study aims to compare the safety and efficacy of convalescent plasma (CP) compared with human immunoglobulin (IVIg) in patients requiring the administration of high oxygen levels or mechanical ventilation.

Methods

This is a controlled, randomized, open clinical trial of patients with pneumonia secondary to SARS-CoV-2 infection, that fulfilled criteria for severe or critical disease. They were randomized in a 1:2 ratio; group 1 was administered IVIg at a dose of 0.3 grams per kilogram of ideal weight, in an 8-hour infusion every 24 hours, for 5 days. Group 2 was administered 200 ml of CP infused in 2 hours, for 2 days. The primary outcomes were duration of hospitalization and mortality at 28 days.

Results

One hundred and ninety (190) patients were randomized; 130 to the CP group, and 60 to the IVIg group. Their average age was 58 years (IQR 47 – 72), and most were male (n= 119, 62.6 %). On inclusion, 85.2 % of patients (n=162) were on invasive mechanical ventilation therapy. Overall mortality in all included patients was 53 % (n= 102), with a median follow-up of 14 days (IQI 8 – 26). Mortality at 28 days was 45.2 % (n=86). In the intention-to-treat analysis, there was no difference between groups neither in mortality on follow-up (53.8 vs. 53.3, p =1.0) nor at 28 days (46.2 vs 43 %, p=0.75, Log Rank p = 0.83). Per-protocol analysis between treatment groups revealed no difference in mortality throughout hospitalization (51.5 vs 51.4 %, p=1.0) nor after 28 days (42.1 vs 42.87 %, p=0.92 Log Rank p = 0.54). Only 23 patients in the CP group received plasma with detectable anti-SARS-CoV-2 antibodies.

Conclusions

In critically ill patients or on invasive mechanical ventilation for treatment of Covid-19, the use of CP is not superior to IVIg in terms of hospitalization duration or mortality. The use of CP is based on complex logistics and requires an assured level of antibodies if used therapeutically. IVIg does not appear to be useful in this group of patients.

clinicaltrials.gov identifier:NCT04381858.
Rapid genomic surveillance of SARS-CoV-2 in a dense urban community using environmental (sewage) samples
Authors: Napit Rajindra , Manandhar Prajwol , Chaudhary Ashok , Shrestha Bishwo , Poudel Ajit , Raut Roji , Pradhan Saman , Raut Samita , Mathema Sujala , Rajbhandari Rajesh , Dixit Sameer , Schwind Jessica S. , Johnson Christine K , Mazet Jonna K , Karmacharya Dibesh
Published: March 2021

Understanding disease burden and transmission dynamics in resource-limited, developing countries like Nepal is often challenging due to a lack of adequate surveillance systems. These issues are exacerbated by limited access to diagnostic and research facilities throughout the country. Nepal has one of the highest COVID-19 case rates (915 cases per 100,000 people) in South Asia, with densely-populated Kathmandu experiencing the highest number of cases. Swiftly identifying case clusters and introducing effective intervention programs is crucial to mounting an effective containment strategy. The rapid identification of circulating SARS-CoV-2 variants can also provide important information on viral evolution and epidemiology. Genomic-based environmental surveillance can help in the early detection of outbreaks before clinical cases are recognized, and identify viral micro-diversity that can be used for designing real-time risk-based interventions. This research aimed to develop a genomic-based environmental surveillance system by detecting and characterizing SARS-CoV-2 in sewage samples of Kathmandu using portable next-generation DNA sequencing devices. Out of 20 selected sites in the Kathmandu Valley, sewage samples from 16 (80%) sites had detectable SARS-CoV-2. A heat-map was created to visualize transmission activity in the community based on viral load intensity and corresponding geospatial data. Further, 41 mutations were observed in the SARS-CoV-2 genome. Some detected mutations (n=9, 2%) were novel and yet to be reported in the global database, with one indicating a frameshift deletion in the spike gene. We also observed more transition than transversion on detected mutations, indicating rapid viral evolution in the host. Our study has demonstrated the feasibility of rapidly obtaining vital information on community transmission and disease dynamics of SARS-CoV-2 using genomic-based environmental surveillance.
Pediatric household transmission of SARS-CoV-2 infection
Authors: Paul Lauren A. , Daneman Nick , Schwartz Kevin L. , Science Michelle , Brown Kevin A. , Whelan Michael , Chan Ellen , Buchan Sarah A.
Published: March 2021

BACKGROUND

As a result of low numbers of pediatric cases early in the COVID-19 pandemic, pediatric household transmission of SARS-CoV-2 remains an understudied topic. This study sought to determine whether there are differences in the odds of household transmission for younger children compared to older children.

METHODS

We assembled a cohort of all individuals in Ontario, Canada with laboratory-confirmed SARS-CoV-2 infection between June 1 and December 31, 2020. The cohort was restricted to individuals residing in private households (N=132,232 cases in 89,191 households), identified through an address matching algorithm. Analysis focused on households in which the index case was aged <18 years. Logistic regression models were fit to estimate the association between age group of pediatric index cases (0-3, 4-8, 9-13, and 14-17 years) and odds of household transmission.

RESULTS

A total of 6,280 households had pediatric index cases, and 1,717 (27.3%) experienced secondary transmission. Children aged 0-3 years had the highest odds of household transmission compared to children aged 14-17 years (model adjusted for gender, month of disease onset, testing delay, and average family size: 1.43, 95% CI: 1.17-1.75). This association was similarly observed in sensitivity analyses defining secondary cases as 2-14 days or 4-14 days after the index case, and stratified analyses by presence of symptoms, association with a school/childcare outbreak, or school/childcare reopening. Children aged 4-8 years and 9-13 years also had increased odds of transmission (4-8: 1.40, 95% CI: 1.18-1.67; 9-13: 1.13, 95% CI: 0.97-1.32).

CONCLUSIONS

This study suggests that younger children are more likely to transmit SARS-CoV-2 infection compared to older children, and the highest odds of transmission was observed for children aged 0-3 years. Differential infectivity of pediatric age groups has implications for infection prevention controls within households, as well as schools/childcare, to minimize risk of household secondary transmission.
Nonpharmaceutical Interventions Remain Essential to Reducing COVID-19 Burden Even in a Well-Vaccinated Society: A Modeling Study
Authors: León Tomás M. , Vargo Jason , Pan Erica S. , Jain Seema , Shete Priya B.
Published: March 2021

Vaccination and non-pharmaceutical interventions (NPIs) reduce transmission of SARS-CoV-2 infection, but their effectiveness depends on coverage and adherence levels. We used scenario modeling to evaluate their effects on cases and deaths averted and herd immunity. NPIs and vaccines worked synergistically in different parts of the pandemic to reduce disease burden.
Migration of households from New York City and the Second Peak in Covid-19 cases in New Jersey, Connecticut and New York Counties
Authors: Schulman Adam , Bhanot Gyan
Published: March 2021

The five boroughs of New York City (NYC) were early epicenters of the Covid-19 pandemic in the United States, with over 380,000 cases by May 31. High caseloads were also seen in nearby counties in New Jersey (NJ), Connecticut (CT) and New York (NY). The pandemic started in the area in March with an exponential rise in the number of daily cases, peaked in early April, briefly declined, and then, showed clear signs of a second peak in several counties. We will show that despite control measures such as lockdown and restriction of movement during the exponential rise in daily cases, there was a significant net migration of households from NYC boroughs to the neighboring counties in NJ, CT and NY State. We propose that the second peak in daily cases in these counties around NYC was due, in part, to the movement of people from NYC boroughs to these counties. We estimate the movement of people using “Change of Address” (CoA) data from the US Postal Service, provided under the “Freedom of Information Act” of 1967. To identify the timing of the second peak and the number of cases in it, we use a previously proposed SIR model, which accurately describes the early stages of the coronavirus pandemic in European countries. Subtracting the model fits from the data identified, we establish the timing and the number of cases, NCS, in the second peak. We then related the number of cases in the second peak to the county population density, P, and the excess Change of Address, ECoA, into each county using the simple model which fits the data very well with α = 0.68, β = 0.31 (R2 = 0.74, p = 1.3e-8). We also find that the time between the first and second peaks was proportional to the distance of the county seat from NY Penn Station, suggesting that this migration of households and disease was a directed flow and not a diffusion process. Our analysis provides a simple method to use change of address data to track the spread of an infectious agent, such as SARS-Cov-2, due to migrations away from epicenters during the initial stages of a pandemic.
The unbiased estimation ofr2between two sets of noisy neural responses
Authors: Pospisil Dean A. , Bair Wyeth
Published: March 2021

The Pearson correlation coefficient squared,r2, is often used in the analysis of neural data to estimate the relationship between neural tuning curves. Yet this metric is biased by trial-to-trial variability: as trial-to-trial variability increases, measured correlation decreases. Major lines of research are confounded by this bias, including the study of invariance of neural tuning across conditions and the similarity of tuning across neurons. To address this, we extend the estimator,, developed for estimating model-to-neuron correlation to the neuron-to-neuron case. We compare the estimator to a prior method developed by Spearman, commonly used in other fields but widely overlooked in neuroscience, and find that our method has less bias. We then apply our estimator to the study of two forms of invariance and demonstrate how it avoids drastic confounds introduced by trial-to-trial variability.

Significant Statement

Quantifying the similarity between two sets of averaged neural responses is fundamental to the analysis of neural data. A ubiquitous metric of similarity, the correlation coefficient, is attenuated by trial-to-trial variability that depends on a variety of irrelevant factors. Spearman recognized this problem and proposed corrected methods that have been extended over a century. We show this method has large asymptotic biases and derive a novel estimator to overcome this. Despite the frequent use of the correlation coefficient in neuroscience, consensus on how to address this fundamental statistical issue has not been reached. We both explicate this issue in a neuroscience setting while at the same time making major strides in addressing it.
ALOHA: Aggregated local extrema splines for high-throughput dose-response analysis
Authors: Davidson Sarah E. , Wheeler Matthew W. , Auerbach Scott S. , Sivaganesan Siva , Medvedovic Mario
Published: March 2021

Computational methods for genomic dose-response integrate dose-response modeling with bioinformatics tools to evaluate changes in molecular and cellular functions related to pathogenic processes. These methods use parametric models to describe each gene’s dose-response, but such models may not adequately capture expression changes. Additionally, current approaches do not consider gene co-expression networks. When assessing co-expression networks, one typically does not consider the dose-response relationship, resulting in ‘co-regulated’ gene sets containing genes having different dose-response patterns. To avoid these limitations, we develop an analysis pipeline called Aggregated Local Extrema Splines for High-throughput Analysis (ALOHA), which computes individual genomic dose-response functions using a flexible class Bayesian shape constrained splines and clusters gene co-regulation based upon these fits. Using splines, we reduce information loss due to parametric lack-of-fit issues, and because we cluster on dose-response relationships, we better identify co-regulation clusters for genes that have co-expressed dose-response patterns from chemical exposure. The clustered pathways can then be used to estimate a dose associated with a pre-specified biological response, i.e., the benchmark dose (BMD), and approximate a point of departure dose corresponding to minimal adverse response in the whole tissue/organism. We compare our approach to current parametric methods and our biologically enriched gene sets to cluster on normalized expression data. Using this methodology, we can more effectively extract the underlying structure leading to more cohesive estimates of gene set potency.
Perception of effort during an isometric contraction is influenced by prior muscle lengthening or shortening
Authors: Kozlowski Benjamin , Pageaux Benjamin , Hubbard Emma F. , St. Peters Benjamin , Millar Philip J. , Power Geoffrey A.
Published: March 2021

Purpose

Following a shortening or lengthening muscle contraction, the torque produced in the isometric steady state is distinctly lower (residual torque depression; rTD) or higher (residual torque enhancement; rTE), respectively, compared to a purely isometric contraction at the same final muscle length and level of activation. This is referred to as the history dependence of force. When matching a given torque level, there is greater muscle activation (electromyography; EMG) following shortening and less activation following lengthening. Owing to these differences in neuromuscular activation, it is unclear whether perception of effort is altered by the history dependence of force.

Methods

Experiment 1 tested whether perception of effort differed between the rTD and rTE state when torque was matched. Experiment 2 tested whether perception of effort differed between the rTD and rTE state when EMG was matched. Finally, experiment 3 tested whether EMG differed between the rTD and rTE state when perception of effort was matched.

Results

When torque was matched, both EMG and perception of effort were higher in the rTD compared to rTE state. When EMG was matched, torque was lower in the rTD compared to rTE state while perception of effort did not differ between the two states. When perception of effort was matched, torque was lower in the rTD compared to rTE state and EMG did not differ between the two states.

Conclusion

The combined results from these experiments indicate that the history dependence of force alters one’s perception of effort, dependent on the level of motor command.
The truncate soft-shell clam,Mya truncata, as a biomonitor of municipal wastewater exposure and historical anthropogenic impacts in the Canadian Arctic
Authors: Schaefer Christina M , Deslauriers David , Jeffries Ken M
Published: March 2021

Municipal wastewater is a large source of pollution to Canadian waters, yet its effects on Arctic marine ecosystems remains relatively unknown. We characterized the impacts of municipal wastewater from a growing northern community, Iqaluit, Nunavut on the Arctic truncate soft-shell clam,Mya truncata. Clams were sampled from six locations that varied in proximity to the wastewater treatment plant and shell biogeochemical analysis revealed that clams nearest the wastewater treatment plant had slower growth rates, lower carbon and oxygen stable isotope ratios, and elevated concentrations of copper and lead. A parallel analysis on mRNA expression profiles characterizedM. truncata’s physiological response to wastewater effluent. Clams nearest the wastewater treatment plant had significantly lower mRNA expression of genes associated with metabolism, antioxidants, molecular chaperones, and phase I and II detoxification, but had heightened mRNA expression in genes coding for enzymes that bind and remove contaminants. These results demonstrated a biological response to Iqaluit’s wastewater effluent and highlightM. truncata’s potential to act as a biomonitor of municipal wastewater along Canadian Arctic coastlines.
Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes
Authors: Kleiner Manuel , Kouris Angela , Jensen Marlene , D’Angelo Grace , Liu Yihua , Korenek Abigail , Tolić Nikola , Sachsenberg Timo , McCalder Janine , Lipton Mary S. , Strous Marc
Published: March 2021

Stable isotope probing (SIP) approaches are a critical tool in microbiome research to determine associations between species and substrates. The application of these approaches ranges from studying microbial communities important for global biogeochemical cycling to host-microbiota interactions in the intestinal tract. Current SIP approaches, such as DNA-SIP or nanoSIMS, are limited in terms of sensitivity, resolution or throughput. Here we present an ultra-sensitive, high-throughput protein-based stable isotope probing approach (Protein-SIP), which cuts cost for labeled substrates by ∼90% as compared to other SIP and Protein-SIP approaches and thus enables isotope labeling experiments on much larger scales and with higher replication. It allows for the determination of isotope incorporation into microbiome members with species level resolution using standard metaproteomics LC-MS/MS measurements. The analysis has been implemented as an open-source application (https://sourceforge.net/projects/calis-p/). We demonstrate sensitivity, precision and accuracy using bacterial cultures and mock communities with different labeling schemes. Furthermore, we benchmark our approach against two existing Protein-SIP approaches and show that in the low labeling range used our approach is the most sensitive and accurate. Finally, we measure translational activity using 18O heavy water labeling in a 63-species community derived from human fecal samples grown on media simulating two different diets. Activity could be quantified on average for 27 species per sample, with 9 species showing significantly higher activity on a high protein diet, as compared to a high fiber diet. Surprisingly, among the species with increased activity on high protein were severalBacteroidesspecies known as fiber consumers. Apparently, protein supply is a critical consideration when assessing growth of intestinal microbes on fiber, including fiber based prebiotics. In summary, we demonstrate that our Protein-SIP approach allows for the ultra-sensitive (0.01% to 10% label) detection of stable isotopes of elements found in proteins, using standard metaproteomics data.
Non-severe SARS-CoV-2 infection is characterised by very early T cell proliferation independent of type 1 interferon responses and distinct from other acute respiratory viruses
Authors: Chandran Aneesh , Rosenheim Joshua , Nageswaran Gayathrie , Swadling Leo , Pollara Gabriele , Gupta Rishi K , Guerra-Assuncao Jose Afonso , Woolston Annemarie , Ronel Tahel , Pade Corrina , Gibbons Joseph , De Estrada Blanca Sanz-Magallon Duque , de Massy Marc Robert , Whelan Matthew , Semper Amanda , Brooks Tim , Altmann Daniel M , Boyton Rosemary J , McKnight Áine , Manisty Charlotte , Treibel Thomas Alexander , Moon James , Tomlinson Gillian S , Maini Mala K , Chain Benjamin M , Noursadeghi Mahdad ,   COVIDsortium Investigators
Published: March 2021

The correlates of natural protective immunity to SARS-CoV-2 in the majority who experience asymptomatic infection or non-severe disease are not fully characterised, and remain important as new variants emerge. We addressed this question using blood transcriptomics, multiparameter flow cytometry and T cell receptor (TCR) sequencing spanning the time of incident infection. We identified a type 1 interferon (IFN) response common to other acute respiratory viruses, and a cell proliferation response that discriminated SARS-CoV-2 from other viruses. These responses peaked by the time the virus was first detected, and in some preceded virus detection. Cell proliferation was most evident in CD8 T cells and associated with rapid expansion of SARS-CoV-2 reactive TCRs. We found an equally rapid increase in immunoglobulin transcripts, but circulating virus-specific antibodies lagged by 1-2 weeks. Our data support a protective role for rapid induction of type 1 IFN and CD8 T cell responses to SARS-CoV-2.
Prevalence and risk factors of internet gaming disorder and problematic internet use before and during the COVID-19 pandemic: A large online survey of Japanese adults
Authors: Oka Taiki , Hamamura Toshitaka , Miyake Yuka , Kobayashi Nao , Honjo Masaru , Kawato Mitsuo , Kubo Takatomi , Chiba Toshinori
Published: March 2021

Internet gaming disorder (IGD) and problematic internet use (PIU) are becoming increasingly detrimental in modern society, with serious consequences for daily functioning. IGD and PIU may be exacerbated by lifestyle changes imposed by the coronavirus 2019 (COVID-19) pandemic. This study investigated changes in IGD and PIU during the pandemic and risk factors for them. This study is a part of a larger online study on problematic smartphone use in Japan, originally planned in 2019, and expanded in August 2020 to include the impact of COVID-19. 51,246 adults completed an online survey during the pandemic (August 2020), in Japan. Of these, 3,938 had also completed the survey before the onset of the pandemic (December, 2019) and were used as the study population to determine how the pandemic has influenced IGD and PIU. IGD was assessed using the Internet Gaming Disorder Scale (IGDS). PIU was measured using the Compulsive Internet Use Scale (CIUS). The prevalence of probable IGD during COVID-19 was 4.1% [95%CI, 3.9% to 4.2%] overall (N=51,246), and 8.6% among younger people (age < 30), higher than reported before the pandemic (1 - 2.5%). Probable PIU was 7.8% [95%CI, 7.6% to 8.1%] overall, and 17.0% [95%CI, 15.9% to 18.2%] among younger people, also higher than reported before the pandemic (3.2 - 3.7%). Comparisons before and during the pandemic, revealed that probable IGD prevalence has increased 1.6 times, and probable PIU prevalence by 1.5 times (IGD:t3937= 5.93,p< .001, PIU:t3937= 6.95,p< .001). Youth (age < 30) and COVID-19 infection were strongly associated with IGD exacerbation (odds ratio, 2.10 [95%CI, 1.18 to 3.75] and 5.67 [95%CI, 1.33 to 24.16]). Internet gaming disorder and problematic internet use appear to be aggravated by the pandemic. In particular, younger persons and people infected with COVID-19 are at higher risk for Internet Gaming Disorder. Prevention of these problems is needed.
Primary Care for Homeless Veterans: A Systematic Review of the Homeless Patient Aligned Care Team (HPACT)
Authors: Rosenthal David , Howell Benjamin A. , Johnson Erin , Frumento Katherine Stemmer , Tsai Jack
Published: March 2021

Background

In 2011, the Veterans Health Administration (VHA) implemented homeless-tailored primary care medical home models, called the Homeless Patient Aligned Care Teams (HPACT) to improve care for homeless Veterans. The aim of this study was to describe the existing peer-reviewed literature on HPACTs by systematically reviewing studies published since 2011 to date.

Methods

We conducted a systematic review of peer-reviewed studies published from 2011 to June 2019 to evaluate the literature since the inception of the VHA’s Homeless PACT program implementation. We included original research articles evaluating the Homeless PACT and excluded those that did not contain original data.

Results

Of 379 studies screened, 20 studies met our inclusion criteria and were included for analysis. Given wide variability in research designs and outcome measures, a narrative review was conducted. The 20 included studies were categorized into 3 groups: Early HPACT pilot implementations; Association of HPACT clinics with quality and utilization; and Specialized programs within HPACTs. Observational findings suggest reductions in emergency department utilization, improvements in primary care treatment utilization, engagement, and patient experience; but limited rigorous studies exist beyond single site pilots and a few large observational cohort studies.

Discussion

The HPACT model has been successfully implemented in VHA medical centers throughout the country with multiple studies showing increased primary care engagement and improved patient experience; however, further studies are needed about quality, utilization and whether the model can be implemented outside the VHA system.

Registration Number/Funding source

none
Association of Heart Failure Subtypes and Atrial fibrillation: Data from the Atherosclerosis Risk in Communities (ARIC) Study
Authors: Nji Miriam A.M. , Solomon Scott D. , Chen Lin Yee , Shah Amil M. , Soliman Elsayed Z. , Alam Aniqa , Subramanya Vinita , Alonso Alvaro
Published: March 2021

Aims

To determine the prevalence and incidence of AF among HF subtypes in a biracial community-based cohort.

Methods

We studied 6,496 participants in the Atherosclerosis Risk in Community study (mean age, 75.8±5.3, 59% women, 23% black) who attended the 2011-2013 visit. HF was identified from physician adjudicated diagnosis, hospital discharges, and self-report. HF subtypes were based on echocardiography. A left ventricular ejection fraction <40% represents HF with reduced ejection fraction (HFrEF), 40%-49% for HF with midrange ejection fraction (HFmEF), and ≥50% for HF with preserved ejection fraction (HFpEF). AF was ascertained through 2017 from study electrocardiograms, hospital discharges, and death certificates. Confounder-adjusted logistic regression and Cox models were used to estimate associations of HF subtype with prevalent and incident AF.

Results

Among eligible participants, 393 had HF (HFpEF=232, HFmEF=41, HFrEF=35 and unclassified HF =85) and 735 had AF. Compared to those without HF, all HF subtypes were more likely to have prevalent AF [odds ratio (95% confidence interval (CI)) 7.4 (5.6-9.9) for HFpEF, 8.1 (4.3-15.3) for HFmEF, 10.0 (5.0-20.2) for HFrEF, 8.8 (5.6-14.0) for unclassified HF]. Among participants without AF at baseline (n=5,761), 610 of them developed AF. Prevalent HF was associated with increased risk of AF [hazard ratio (95%CI) 2.3 (1.6-3.3) for HFpEF, 4.6 (2.4-8.6) for HFmEF, 3.8 (1.8-8.2) for HFrEF, 2.3 (0.9-5.6) for unclassified HR].

Conclusion

AF and HF frequently co-occur, with small differences by HF subtype, underscoring the importance of understanding the interplay of these two epidemics and evaluating shared preventive and therapeutic strategies.
Coping with COVID-19 Pandemic: A Population-Based Study in Bangladesh
Authors: Hossain K M Amran , Saunders Karen , Sakel Mohamed , Walton Lori Maria , Raigangar Veena , Uddin Zakir , Hossain Mohammad Anwar , Islam Asma , Ahmed Faruq , Faruqui Rafey , Tasnim Tamanna , Rana Shohag , Shafin Rubayet , Ahmed Md. Shahoriar , Haque Md. Obaidul , Kabir Md. Feroz , Hossain Mohammad Sohrab , Jahid Iqbal Kabir , Yasmin Mst. Hosneara , Chakrovorty Sonjit Kumar , Hossain Md. Shahadat , Paul Joty
Published: March 2021

This study aims to investigate coping strategies used by Bangladeshi citizens during the COVID-19 pandemic.

Design

Prospective, cross-sectional survey of adults (N=2001) living in Bangladesh.

Methods

Participants were interviewed for socio-demographic data and completed the Bengali translated Brief-COPE Inventory. Statistical data analysis was conducted using SPSS (Version 20).

Results

Participants (N=2001), aged 18 to 86 years, were recruited from eight administrative divisions within Bangladesh (mean age 31.85±14.2 years). Male to female participant ratio was 53.4% (n=1074) to 46.6% (n=927). Higher scores were reported for approach coping styles (29.83±8.9), with lower scores reported for avoidant coping styles (20.83 ± 6.05). Humor coping scores were reported at 2.68±1.3 and religion coping scores at 5.64±1.8. Both men and women showed similar coping styles. Multivariate analysis found a significant relationship between male gender and both humor and avoidant coping (p <.01). Male gender was found to be inversely related to both religion and approach coping (p <.01). Marital status and education were significantly related to all coping style domains (p<.01). Occupation was significantly related to approach coping (p <.01). Rural and urban locations differed significantly in participant coping styles (p <.01). Factor analysis revealed two cluster groups (Factor 1 and 2) comprised of unique combinations from all coping style domains.

Conclusion

Participants in this study coped with the COVID-19 pandemic by utilizing a combination of coping strategies. Factor 1 revealed both avoidant and approach coping strategies and Factor 2 revealed a combination of humor and avoidant coping strategies. Overall, a higher utilization of approach coping strategies was reported, which has previously been associated with better physical and mental health outcomes. Religion was found to be a coping strategy for all participants. Future research may focus on understanding resilience in vulnerable populations, including people with disability or with migrant or refugee status in Bangladesh.
The plastid genome characteristics of a moth orchid (Phalaenopsis wilsoniii, Orchidaceae)
Authors: Xia KeKe , Liu Ding-Kun , Wang Jie-Yu
Published: March 2021

Phalaenopsis wilsonii is a typical deciduous species in the horticulturally well-known genus,Phalaenopsis. Tshi species is belonging to the sectionAphyllaein moth orchid, and is endemic to South China. Although theAphyllaesection display the deciduous feature that is unique in this genus, their genetic information is still insufficient and limited them as breeding parent in moth orchid. Here, we reported and characterized the complete chloroplast genome forPhalaenopsis wilsonii. We found the total size of the chloroplast genome was 145,373 bp, constituting of a large single copy (LSC) region (84,996 bp), a small single-copy region (10,668 bp) and two inverted repeats (IRs) regions (24,855 bp). Based on homologous searching on database, we annotated 76 protein-coding genes, 38 tRNA, and 8 rRNA. The phylogenetic reconstruction revealed thatP. wilsoniishow the closest relationship withP. lowiiwithin subgenusParishianae.
Spermiogenesis alterations in the absence of CTCF revealed by single cell RNA sequencing
Authors: Torres-Flores Ulises , Díaz-Espinosa Fernanda , López-Santaella Tayde , Rebollar-Vega Rosa , Vázquez-Jiménez Aarón , Taylor Ian J. , Ortiz-Hernández Rosario , Echeverría Olga M. , Vázquez-Nin Gerardo H. , Gutierrez-Ruiz María Concepción , De la Rosa-Velázquez Inti Alberto , Resendis-Antonio Osbaldo , Hernández-Hernandez Abrahan
Published: March 2021

CTCF is an architectonical protein that organizes the genome inside the cell nucleus in almost all eukaryotic cells. There is evidence that CTCF plays a critical role during spermatogenesis as its depletion produces abnormal sperm and infertility. However, the defects produced by the absence of CTCF throughout spermatogenesis have not been characterized. In this work, we performed single cell RNA sequencing in spermatogenic cells without CTCF. We uncovered defects in transcriptional programs that explain the severity of the damage in the produced sperm. At early stages of spermatogenesis, transcriptional alterations are mild. As germ cells go throughout the specialization stage or spermiogenesis, transcriptional profiles become more altered. We found spermatid defects that support the alterations in the transcriptional profiles, and thus we conclude that CTCF depletion alters several transcriptional profiles mostly during spermiogenesis. Our data highlights the importance of CTCF at the different stages of spermatogenesis.
Rapid characterization of spike variants via mammalian cell surface display
Authors: Javanmardi Kamyab , Chou Chia-Wei , Terrace Cynthia I. , Annapareddy Ankur , Kaoud Tamer S. , Guo Qingqing , Lutgens Josh , Zorkic Hayley , Horton Andrew P. , Gardner Elizabeth C. , Nguyen Giaochau , Boutz Daniel R. , Goike Jule , Voss William N. , Kuo Hung-Che , Dalby Kevin N , Gollihar Jimmy D. , Finkelstein Ilya J.
Published: March 2021

The SARS-CoV-2 spike (S) protein is a critical component of subunit vaccines and a target for neutralizing antibodies. Spike is also undergoing immunogenic selection with clinical variants that increase infectivity and partially escape convalescent plasma. Here, we describe spike display, a high-throughput platform to rapidly characterize glycosylated spike ectodomains across multiple coronavirus-family proteins. We assayed ∼200 variant SARS-CoV-2 spikes for their expression, ACE2 binding, and recognition by thirteen neutralizing antibodies (nAbs). An alanine scan of all five N-terminal domain (NTD) loops highlights a public class of epitopes in the N1, N3, and N5 loops that are recognized by most of the NTD-binding nAbs. Some clinical NTD substitutions abrogate binding to these epitopes but are circulating at low frequencies around the globe. NTD mutations in variants of concern B.1.1.7 (United Kingdom), B.1.351 (South Africa), B.1.1.248 (Brazil), and B.1.427/B.1.429 (California) impact spike expression and escape most NTD-targeting nAbs. However, two classes of NTD nAbs still bind B.1.1.7 spikes and neutralize in pseudoviral assays. B.1.351 and B.1.1.248 include compensatory mutations that either increase spike expression or increase ACE2 binding affinity. Finally, B.1.351 and B.1.1.248 completely escape a potent ACE2 peptide mimic. We anticipate that spike display will accelerate antigen design, deep scanning mutagenesis, and antibody epitope mapping for SARS-CoV-2 and other emerging viral threats.
Extracellular vesicles synchronize cellular phenotypes of differentiating cells
Authors: Minakawa Tomohiro , Matoba Tetsuya , Yamashita Jun K.
Published: March 2021

During embryonic development, cells differentiate in a coordinated manner, aligning their fate decisions and differentiation stages with those of surrounding cells. However, little is known about the mechanisms that regulate this synchrony. Here we show that cells in close proximity synchronize their differentiation stages and cellular phenotypes with each other via extracellular vesicle (EV)-mediated cellular communication. We previously established a mouse embryonic stem cell (ESC) line harboring an inducible constitutively active protein kinase A (CA-PKA) gene and found that the ESCs rapidly differentiated into mesoderm after PKA activation. In the present study, we performed a co-culture of control ESCs and PKA-ESCs, finding that both ESCs rapidly differentiated in synchrony even when PKA was activated only in PKA-ESCs, a phenomenon we named “Phenotypic Synchrony of Cells (PSyC)”. We further demonstrated PSyC was mediated by EVs containing miR-132. PKA-ESC-derived EVs and miR-132-containing artificial nano-vesicles similarly enhanced mesoderm and cardiomyocyte differentiation in ESCs and ex vivo embryos, respectively. PSyC is a new form of cell-cell communication mediated by EV regulation of neighboring cells and could be broadly involved in tissue development and homeostasis.