bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis on Action Tracking Reports of COVID-19 Informs Control Strategies and Vaccine Delivery in Post-Pandemic Era
Authors: Sun Xiaofei , Guan Tianjia , Xue Tao , Fan Chun , Yang Meng , Meng Yuxian , Zhang Tianwei , Jiangtulu Bahabaike , Wu Fei , Li Jiwei
Published: April 2021

Understanding the spread of SARS-CoV-2 provides important insights for control policies such as social-distancing interventions and vaccine delivery in the post-pandemic era. In this work, we take the advantage of action tracking reports of confirmed COVID-19 patients, which contain the mobility trajectory of patients. We analyzed reports of patients from April 2020 to January 2021 in China, a country where the residents are well-prepared for the “new normal” world following COVID-19 spread. We developed natural language processing (NLP) tools to transform the unstructured text of action-tracking reports to a structured network of social contacts. An epidemiology model was built on top of the network. Our analysis provides important insights for the development of control policies. Under the “new normal” conditions, we find that restaurants, locations less protected by mask-wearing, have a greater risk than any other location categories, including locations where people are present at higher densities (e.g., flight). We find that discouraging railway transports is crucial to avoid another wave of breakout during the Chunyun season (a period of travel in China with extremely high traffic load around the Chinese New Year). By formalizing the challenge of finding the optimal vaccine delivery among various different population groups as an optimization problem, our analysis helps to maximize the efficiency of vaccine delivery under the general situation of vaccine supply shortage. We are able to reduce the numbers of infections and deaths by 7.4% and 10.5% respectively with vaccine supply for only 1% of the population. Furthermore, with 10% vaccination rate, the numbers of infections and deaths further decrease by 52.6% and 78.1% respectively. Our work will be helpful in the design of effective policies regarding interventions, reopening, contact tracing and vaccine delivery in the “new normal” world following COVID-19 spread.
Two Distinct Dynamic Process Models of COVID-19 Spread with Divergent Vaccination Outcomes
Authors: Chang Ernie , Moselle Kenneth A.
Published: April 2021

Kinematic models of contagion-based viral transmission describe patterns of events over time (e.g., new infections), relying typically on systems of differential equations to reproduce those patterns. By contrast, agent-based models of viral transmission seek to relate those events or patterns of events to causes, expressed in terms of factors (parameters) that determine the dynamics that give rise to those events.

This paper is concerned with the dynamics of contagion-based spread of infection. Dynamics that reflect time homogeneous vs inhomogeneous transmission rates are generated via an agent-based infectious disease modeling tool (CovidSIMVL - github.com/ecsendmail/MultiverseContagion). These different dynamics are treated as causal factors and are related to differences in vaccine efficacy in an array of simulated vaccination trials. Visualizations of simulated trials and associated metrics illustrate graphically some cogent reasons for not effectively hard-coding assumptions of dynamic temporal homogeneity, which come ‘pre-packaged’ with the mass action incidence assumption that underpins typical equation-based models of infection spread.
Impacts of COVID-19 on sick leave
Authors: Skyrud Katrine , Telle Kjetil , Hernæs Kjersti , Magnusson Karin
Published: April 2021

Aim

To explore sick leave after COVID-19, by comparing doctor-certified sick leave for up to 6 months after testing for SARS-CoV-2 across employees who tested positive and negative.

Methods

In all persons (20-70 year of age) with an employment contract, who were tested for the SARS-CoV-2 in Norway from March 1st to November 1st 2020 (N=740 182 with mean [SD] age 39 [13] years, 44% men), we used a difference-in-difference design to contrast doctor-certified sick leave before and after testing, across employees with negative test and positive test by age and sex groups.

Results

Sick leave for those testing positive (N=11 414) remained elevated for up to 2 months after testing when compared to those testing negative (N= 728 768), for men and women aged 20-44 and for men aged 45-70 years (relative increase in sick-leave ∼344-415%, (Ball strata=0.079, 95% CI=0.076, 0.082). The increase in sick leave was prolonged for women aged 45-70 years only, persisting for up to 4 months after testing positive (relative increase = 35%, B=0.010, 95% CI=0.004-0.035).

Conclusion

Sick leave following COVID-19 is elevated for up to two to four months after initial infection, thereafter not elevated compared with employees who tested negative for COVID-19. Women aged 45-70 years tend to have a larger impact of COVID-19 on their work ability than men and younger women.
Analysis across Taiwan Biobank, Biobank Japan and UK Biobank identifies hundreds of novel loci for 36 quantitative traits
Authors: Chen Chia-Yen , Chen Tzu-Ting , Feng Yen-Chen Anne , Longchamps Ryan J. , Lin Shu-Chin , Wang Shi-Heng , Hsu Yi-Hsiang , Yang Hwai-I , Kuo Po-Hsiu , Daly Mark J. , Chen Wei J. , Huang Hailiang , Ge Tian , Lin Yen-Feng
Published: April 2021

Genome-wide association studies (GWAS) have identified tens of thousands of genetic loci associated with human complex traits and diseases1,2. However, the majority of GWAS were conducted in individuals of European ancestry3. Failure to capture global genetic diversity has limited biological discovery and impeded equitable delivery of genomic knowledge to diverse populations4. Here we report findings from 102,900 individuals across 36 human quantitative traits in the Taiwan Biobank (TWB), a major biobank effort that broadens the population diversity of genetic studies in East Asia (EAS). We identified 979 novel genetic loci, pinpointed novel causal variants through fine-mapping, compared the genetic architecture across TWB, Biobank Japan (BBJ)5–7 and UK Biobank (UKBB)8,9, and evaluated the utility of cross-phenotype, cross-population polygenic risk scores (PRS) in disease risk prediction. These results demonstrated the potential to advance genomic discovery through increasing and diversifying GWAS populations, and provided insights into the common genetic background for human complex traits in East Asian populations.
Breakpoint modelling of temporal associations between non-pharmaceutical interventions and the incidence of symptomatic COVID-19 in the Republic of Ireland
Authors: Boudou M , ÓhAiseadha C , Garvey P , O’Dwyer J , Hynds P
Published: April 2021

Background

To constrain propagation and mitigate the burden of COVID-19, most countries initiated and continue to implement several non-pharmaceutical interventions (NPIs), including national and regional lockdowns. In the Republic of Ireland, the first national lockdown was decreed on 23rdof March 2020, followed by a succession of restriction increases and decreases (phases) over the the following year. To date, the effects of these interventions remain unclear, and particularly within differing population subsets. The current study sought to assess the impact of individual NPI phases on COVID-19 transmission patterns within delineated population subgroups in the Republic of Ireland.

Methods and Findings

Confirmed, anonymised COVID-19 cases occurring between the 29thof February 2020 and 30thNovember 2020 (n= 72,654) were obtained. Segmented modelling via breakpoint regression with multiple turning points was employed to identify structural breaks across sub-populations, including primary/secondary infections, age deciles, urban/commuter/rural areas, patients with underlying health conditions, and socio-demographic profiles. These were subsequently compared with initiation dates of eight overarching NPI phases.

Five distinct breakpoints were identified. The first breakpoint, associated with a decrease in the daily COVID-19 incidence, was reported within 14 days of the first set of restrictions in mid-March 2020 for most population sub-groups. Results suggest that moderately strict NCIs were more effective than the strictest Phase 5 (National Lockdown). Divergences were observed across population sub-groups; lagged response times were observed among populations >80 years, residents of rural/ commuter regions, and cases associated with a below-median deprivation score.

Conclusions

Study findings suggest that many NPIs have been successful in decreasing COVID-19 incidence rates, however the strictest Phase 5 NPI was not. Moreover, NPIs were not equally successful across all sub-populations, with differing response times noted. Mitigation strategies and interventions may need to be increasingly bespoke, based on sub-population profiles and required responses.
Seroepidemiology among Employees of New York City Health and Hospitals during the First Wave of the SARS-CoV-2 Epidemic
Authors: Bryan Alexander D. , Tatem Kathleen , Diuguid-Gerber Jillian , Cooke Caroline , Romanoff Anya , Choudhury Nandini , Scanlon Michael , Kishore Preeti , Sydney Elana , Masci Joseph , Bakshi Parampreet , Pemmasani Sahithi , Davis Nichola J. , Maru Duncan
Published: April 2021

Objective

Estimate the seroprevalence of SARS-CoV-2 antibodies among New York City Health + Hospitals healthcare workers, and identify demographic and occupational factors associated with SARS-CoV-2 antibodies among healthcare workers.

Methods

This was an observational, cross-sectional study using data from SARS-CoV-2 serological tests accompanied by a demographic and occupational survey administered to healthcare workers. Participants were employed by New York City Health + Hospitals (NYC H+H) and either completed serologic testing at NYC H+H between April 30 and June 30, 2020, or completed SARS-CoV-2 antibody testing outside of NYC H+H and were able to self-report results.

Results

Seven hundred twenty-seven survey respondents were included in analysis. Participants had a mean age of 46 years (SD= 12.19) and 543 (75%) were women. Two hundred fourteen (29%) participants tested positive or reported testing positive for the presence of SARS-CoV-2 antibodies (IgG+). Characteristics associated with positive SARS-CoV-2 serostatus were Black race (25% IgG+ vs. 15% IgG-, p=0.001), having someone in the household with COVID symptoms (49% IgG+ vs. 21% IgG-, p<0.001), or having a confirmed COVID-19 case in the household (25% IgG+ vs 5% IgG-, p<0.001). Characteristics associated with negative SARS-CoV-2 serostatus included working on a COVID patient floor (27% IgG+ vs. 36% IgG-, p=0.02), working in the ICU (20% IgG+ vs. 28% IgG-, p=0.03), or having close contact with a patient with COVID-19 (51% IgG+ vs. 62% IgG-, p=0.03).

Conclusions

Results underscore the significance of community factors and inequities might have on SARS-CoV-2 exposure for healthcare workers.

What is already known about this subject?

Healthcare workers are at risk of occupational transmission of SARS-CoV-2, and the risk of infection varies by demographic characteristics and work location.

What are the new findings?

Healthcare worker race and household contacts were significantly associated with SARS-CoV-2 seropositivity, while working on a COVID patient floor or ICU was associated with seronegativity.

How might this impact on policy or clinical practice in the foreseeable future?

Results underscore the significance of community factors and inequities on healthcare worker exposure to SARS-CoV-2, and the need to address these inequities at the community level where healthcare workers live.
Stress related network activity in the intact adrenal medulla
Authors: Ruiz Jose R. Lopez , Ernst Stephen A. , Holz Ronald W. , Stuenkel Edward L.
Published: April 2021

The adrenal medulla has long been recognized as playing a critical role in mammalian homeostasis and the stress response. The adrenal medulla is populated by clustered chromaffin cells that secrete epinephrine or norepinephrine along with other peptides into the general bloodstream affecting multiple distant target organs. Although the sympatho-adrenal pathway has been heavily studied, detailed knowledge on the central control and in-situ spatiotemporal responsiveness remains poorly understood. For this work we implemented electrophysiological techniques originally developed to elucidate CNS circuitry to characterize the functional micro-architecture of the adrenal medulla. To achieve this, we continuously monitored the electrical activity inside the adrenal medulla in the living anesthetized rat under basal conditions and under physiological stress. Under basal conditions, chromaffin cells fired action potentials with frequencies between ∼0.2 and 4 Hz. Activity was exclusively driven by sympathetic inputs coming through the splanchnic nerve. Furthermore, chromaffin cells were organized into arrays of independent local networks in which cells fire in a specific order, with latencies from hundreds of microseconds to few milliseconds. Electrical stimulation of the splanchnic nerve evoked the exact same spatiotemporal firing patterns that occurred spontaneously. Induction of hypoglycemic stress by administration of insulin resulted in an increase in the activity of a subset of the chromaffin cell networks. In contrast, respiratory arrest induced by anesthesia overdose resulted in an increase in the activity of the entire adrenal medulla before cessation of all activity when the animal died. The results suggest the differential activation of specific networks inside the adrenal gland depending on the stressor. These results revealed a surprisingly complex electrical organization and circuitry of the adrenal medulla that likely reflects the dynamic nature of its neuroendocrine output during basal conditions and during different types of physiological stress. To our knowledge, these experiments are the first to use multi-electrode arraysin vivoto examine the electrical and functional architecture of any endocrine gland.

Significance Statement

Stress from extrinsic (environmental, psychological) and intrinsic (biological) challenges plays a critical role in disturbing the homeostatic balance. While the body’s responses to stress are designed to ameliorate these imbalances, prolonged and dysregulated stress often drives adverse health consequences in many chronic illnesses. The better understanding of the sympatho-adrenal stress response, will potentially impact and improve the treatment of several stress related illnesses. This work focusses on the study of the functional architecture of the adrenal medulla, a key component in neuronal stress response.
Laminar perfusion imaging with zoomed arterial spin labeling at 7 Tesla
Authors: Shao Xingfeng , Guo Fanhua , Shou Qinyang , Wang Kai , Jann Kay , Yan Lirong , Toga Arthur W. , Zhang Peng , Wang Danny JJ
Published: April 2021

Laminar fMRI based on BOLD and CBV contrast at ultrahigh magnetic fields has been applied for studying the dynamics of mesoscopic brain networks. However, the quantitative interpretations of BOLD/CBV fMRI results are confounded by different baseline physiology across cortical layers. Here we introduce a novel 3D zoomed pseudo-continuous arterial spin labeling technique at 7T that offers the unique capability for quantitative measurements of laminar cerebral blood flow (CBF) both at rest and during task activation with high spatial specificity and sensitivity. We found arterial transit time in superficial layers is ∼100 msec shorter than in middle/deep layers revealing the dynamics of labeled blood flowing from pial arteries to downstream microvasculature. Resting state CBF peaked in the middle layers which is highly consistent with microvascular density measured from human cortex specimens. Finger tapping induced a robust two-peak laminar profile of CBF increases in the superficial (somatosensory and premotor input) and deep (spinal output) layers of M1, while finger brushing task induced a weaker CBF increase in superficial layers (somatosensory input). We further demonstrated that top-down attention induced a predominant CBF increase in deep layers and a smaller CBF increase on top of the lower baseline CBF in superficial layers of V1 (feedback cortical input), while bottom-up stimulus driven activity peaked in the middle layers (feedforward thalamic input). These quantitative laminar profiles of perfusion activity suggest an important role of M1 superficial layers for the computation of finger movements, and that visual attention may amplify deep layer output to the subcortex.

Significance Statement

CBF or microvascular perfusion measured by arterial spin labeling (ASL) is a key parameter forin vivoassessment of neurovascular function. Compared to BOLD or VASO fMRI, ASL perfusion contrast offers the unique capability for quantitative CBF measurements both at baseline and during task activation, which is critical for quantitative estimation of metabolic activities tightly related to neuronal activation. We proposed a zoomed 3D ASL technique at 7T for laminar perfusion imaging with high spatial specificity and sensitivity. This technique is able to differentiate and quantify the input/output and feedforward/feedback activities of human motor and visual cortex, thereby providing an important tool for quantitative assessment of neurovascular function and metabolic activities of neural circuits across cortical layers.
Disparities in SARS-CoV-2 Vaccination-to-Infection Risk, Massachusetts 2020-2021
Authors: Dryden-Peterson Scott , Velásquez Gustavo E. , Stopka Thomas J. , Davey Sonya , Gandhi Rajesh T. , Lockman Shahin , Ojikutu Bisola O.
Published: April 2021

Background

Effective vaccine-based containment strategies for SARS-CoV-2 require equitable coverage of communities at greatest risk of infection. We sought to examine the alignment of vaccination and SARS-CoV-2 risk in Massachusetts to inform public health response.

Methods

We aggregated cumulative SARS-CoV-2 testing and vaccination data from the Massachusetts Department of Public Health and the Boston Public Health Commission from January 29, 2020 to April 9, 2021. We used two approaches to assess vaccination equity: vaccination-to-infection risk (VIR) ratio and Lorenz curves. The VIR ratio was calculated for each community as the quotient of the number of fully vaccinated individuals divided by the cumulative number of confirmed SARS-CoV-2 infections. Lorenz curves were used to describe vaccination relative to COVID-19 burden. A multivariable Poisson model was used to assess predictors of VIR ratio.

Results

A total of 607,120 (8.9%) SARS-CoV-2 infections were confirmed in Massachusetts residents and 1,485,266 (21.8%) residents were fully vaccinated. Communities with increased socioeconomic vulnerability had lower VIR ratios indicating less equitable vaccination relative to infection risk. In multivariable analysis, decreased vaccination relative to infection risk was independently associated with increasing socioeconomic vulnerability (aRR 0.82 per quartile increase, 95% CI 0.77 to 0.87) and with greater than 20% of the community identified as Black and/or Latinx (aRR 0.67, 95% CI 0.56 to 0.81). Improved community vaccine delivery was associated with higher community proportion of residents aged 65 or older (aRR 1.23 per 5% increase in proportion, 95% CI 1.15 to 1.31). Lorenz curves indicated considerable inequity (Gini 0.46 between communities). An estimated 330,000 full vaccination courses would need to be diverted to under-vaccinated communities to achieve equity.

Conclusion

In conclusion, disparities in vaccine delivery highlight ongoing inequities in our approach to COVID-19 and imperil efforts to control the pandemic.
Cryo-electron tomography of large biological specimens vitrified by plunge freezing
Authors: Bäuerlein Felix J.B. , Renner Max , Chami Dana El , Lehnart Stephan E. , Pastor-Pareja José C. , Fernández-Busnadiego Rubén
Published: April 2021

Cryo-focused ion beam (cryo-FIB) milling allows thinning vitrified cells for high resolution imaging by cryo-electron tomography (cryo-ET). However, it remains challenging to apply this workflow to voluminous biological specimens such as tissues or particularly large mammalian cells, which usually require high-pressure freezing for vitrification. Here we show that adult mouse cardiomyocytes and dissectedDrosophilatissues can be directly vitrified by plunge freezing upon a short incubation in 10% glycerol. This expedites subsequent cryo-FIB/ET, enabling systematic analyses of the molecular architecture of complex native specimens. Our data provides unanticipated insights into the molecular architecture of samples hitherto unexplored by cryo-ET.
Prolonged Lifespan, Ameliorated Cognition, and Improved Host Defense ofCaenorhabditis elegansbyLactococcus lactissubsp.cremoris
Authors: Komura Tomomi , Takemoto Asami , Kosaka Hideki , Suzuki Toshio , Nishikawa Yoshikazu
Published: April 2021

This study evaluated whether the lactic acid bacteriaLactococcus lactissubsp.cremorisstrain FC (FC) could ameliorate host defenses and cognitive ability and extend the lifespan ofCaenorhabditis elegans, a model of senescence. The lifespan and resistance to physical, chemical, and biological stressors were compared betweenC. elegansfed FC and those fedEscherichia coliOP50 (OP), an international standard food forC. elegans. Living FC successfully extended the health span, enhanced host defense, and ameliorated the cognitive ability of the nematodes; even the exopolysaccharides (EPSes) of FC could extend the lifespan ofC. elegans. The chemotaxis index, which was used to evaluate the senescence of sensory neurons, tended to decrease with aging; however, it was more stable in worms fed FC and was significantly higher than that of the control worms at 7 days of age. The worms fed FC were tolerant toSalmonella entericaserovar Enteritidis orStaphylococcus aureusinfection and had better survival than the control worms fed OP. FC showed beneficial effects inC. elegans daf-16andpmk-1mutants, but not inskn-1mutants. Since SKN-1 is theC. elegansortholog of Nrf2, we measured the transcription of heme oxygenase-1 (HO-1), which is regulated by Nrf2, in murine macrophages and found that HO-1 mRNA expression was increased >5 times by inoculation with either FC cells or heat-killed bacteria with EPSes. Thus, both FC and the EPSes can affect longevityviathe SKN-1/Nrf2 pathway in both nematodes and mammalian cells.

IMPORTANCE

Ageing is one of our greatest challenges. The World Health Organization proposed the concept of “Active Ageing” might encourage people to continue to work according to their capacities and preferences as they grow old and would prevent or delay disabilities and chronic diseases that are costly to both individuals and the society, considering that disease prevention is more economical than treatment. Probiotic bacteria such as lactobacilli are living microorganisms that exert beneficial effects on human health when ingested in sufficient amounts and can promote longevity. The significance of this study is that it revealed the anti-senescence and various beneficial effects of the probiotic representative bacteriumLactococcus lactissubsp.cremorisstrain FC and its exopolysaccharides in the nematodeCaenorhabditis elegans.
MicroRNA-202 safeguards meiotic progression by preventing premature degradation of REC8 mediated by separase
Authors: Chen Jian , Gao Chenxu , Zheng Chunwei , Lin Xiwen , Ning Yan , Ma Longfei , He Wei , Xie Dan , Liu Kui , Han Chunsheng
Published: April 2021

MicroRNAs (miRNAs) are believed to play important roles in mammalian spermatogenesis but thein vivofunctions of single miRNAs in this highly complex developmental process remain unclear. Here, we reported thatmiR-202, a member of thelet-7family, played an important role in mouse spermatogenesis by phenotypic evaluation ofmiR-202knockout (KO) mice. InmiR-202KO mice, germ cells underwent apoptosis. Multiple processes in meiosis I including synapsis and crossover formation were disrupted, and inter-sister chromatid synapses were detected. More importantly, we found that uponmiR-202KO, meiotic-specific cohesin protein REC8 was prematurely cleaved by precociously activated separase, whose mRNA was a direct target ofmiR-202-3p. Our findings identifymiR-202as a novel regulator of meiosis and contribute to the list of miRNAs that play specific and important roles in developmental processes.
Latent functional diversity may accelerate microbial community responses to temperature fluctuations
Authors: Smith Thomas P. , Mombrikotb Shorok , Ransome Emma , Kontopoulos Dimitrios-Georgios , Pawar Samraat , Bell Thomas
Published: April 2021

How complex microbial communities respond to climatic fluctuations remains an open question. Due to their relatively short generation times and high functional diversity, microbial populations harbor great potential to respond as a community through a combination of strain-level phenotypic plasticity, adaptation, and species sorting. However, the relative importance of these mechanisms remains unclear. We conducted a laboratory experiment to investigate the degree to which bacterial communities can respond to changes in environmental temperature through a combination of phenotypic plasticity and species sorting alone. We grew replicate soil communities from a single location at six temperatures between 4°C and 50°C. We found that phylogenetically- and functionally-distinct communities emerge at each of these temperatures, with K-strategist taxa favoured under cooler conditions, and r-strategist taxa under warmer conditions. We show that this dynamic emergence of distinct communities across a wide range of temperatures (in essence, community-level adaptation), is driven by the resuscitation of latent functional diversity: the parent community harbors multiple strains pre-adapted to different temperatures that are able to “switch on” at their preferred temperature without immigration or adaptation. Our findings suggest that microbial community function in nature is likely to respond rapidly to climatic temperature fluctuations through shifts in species composition by resuscitation of latent functional diversity.
Automated Analysis of Bacterial Flow Cytometry Data with FlowGateNIST
Authors: Ross David
Published: April 2021

Flow cytometry is commonly used to evaluate the performance of engineered bacteria. With increasing use of high-throughput experimental methods, there is a need for automated analysis methods for flow cytometry data. Here, we describe FlowGateNIST, a Python package for automated analysis of bacterial flow cytometry data. The main components of FlowGateNIST perform automatic gating to differentiate between cells and background events and then between singlet and multiplet events. FlowGateNIST also includes a method for automatic calibration of fluorescence signals using fluorescence calibration beads. FlowGateNIST is open source and freely available with tutorials and example data to facilitate adoption by users with minimal programming experience.
Simple amplicon sequencing library preparation for plant root microbial community profiling
Authors: Kumaishi Kie , Usui Erika , Suzuki Kenta , Kobori Shungo , Sato Takumi , Toda Yusuke , Takanashi Hideki , Shinozaki Satoshi , Noda Munehiro , Takakura Akiko , Matsumoto Kayoko , Yamasaki Yuji , Tsujimoto Hisashi , Iwata Hiroyoshi , Ichihashi Yasunori
Published: April 2021

Microbiota are a major component of agroecosystems. Root microbiota, which inhabit the inside and surface of plant roots, play a significant role in plant growth and health. As next-generation sequencing technology allows the capture of microbial profiles without culturing the microbes, profiling of plant microbiota has become a staple tool in plant science and agriculture. Here, we have developed a novel high-throughput method based on a two-step PCR amplification protocol, involving DNA extraction using magnetic beads and PCR purification using exonuclease, for 16S rRNA gene amplicon sequencing of plant root microbiota. This method reduces sample handling and captures microbial diversity comparable to that obtained by the standard method. We found that using a buffer with magnetic beads enabled efficient extraction of microbial DNA directly from plant roots. In addition, we demonstrated that purification using exonuclease before the second PCR step enabled the capture of higher degrees of microbial diversity, thus allowing for the detection of minor bacteria compared with the purification using magnetic beads in this step. Our method offers a simple and high-throughput solution for maintaining the quality of plant root microbial community profiling.
Measuring Transcription Factor Binding and Gene Expression using Barcoded Self-Reporting Transposon Calling Cards and Transcriptomes
Authors: Lalli Matthew , Yen Allen , Thopte Urvashi , Dong Fengping , Moudgil Arnav , Chen Xuhua , Milbrandt Jeffrey , Dougherty Joseph D. , Mitra Robi D.
Published: April 2021

Calling cards technology using self-reporting transposons enables the identification of DNA-protein interactions through RNA sequencing. Although immensely powerful, current implementations of calling cards in bulk experiments on populations of cells are technically cumbersome and require many replicates to identify independent insertions into the same genomic locus. Here, we have drastically reduced the cost and labor requirements of calling card experiments in bulk populations of cells by introducing a DNA barcode into the calling card itself. An additional barcode incorporated during reverse transcription enables simultaneous transcriptome measurement in a facile and affordable protocol. We demonstrate that barcoded self-reporting transposons recoverin vitrobinding sites for four basic helix-loop-helix transcription factors with important roles in cell fate specification: ASCL1, MYOD1, NEUROD2, and NGN1. Further, simultaneous calling cards and transcriptional profiling during transcription factor overexpression identified both binding sites and gene expression changes for two of these factors. Lastly, we demonstrated barcoded calling cards can record bindingin vivoin the mouse brain. In sum, RNA-based identification of transcription factor binding sites and gene expression through barcoded self-reporting transposon calling cards and transcriptomes is an efficient and powerful method to infer gene regulatory networks in a population of cells.
Tissue-specific reprogramming of host tRNA transcriptome by the microbiome
Authors: Huang Jia , Chen Wenjun , Zhou Fan , Pang Zhichang , Wang Luoluo , Pan Tao , Wang Xiaoyun
Published: April 2021

Transfer RNAs (tRNAs) are essential for translation, and tRNA expression and modifications are regulated by many factors. However, the interplay between the microbiome and host tRNA profiles through host-microbiome interactions has not been explored. In this study, we investigated host-microbiome interactions via the tRNA profiling of four tissue types from germ-free and specific pathogen-free mice. Our analyses reveal that cytosolic and mitochondrial tRNA expression and tRNA modifications in the host are reprogrammed in a tissue-specific and microbiome-dependent manner. In terms of tRNA expression, the intestines and brains are more sensitive to the influence of the microbiome than the livers and kidneys. In terms of tRNA modifications, cytosolic tRNAs show more obvious changes in the livers and kidneys in the presence of the microbiome. Our findings reveal a previously unexplored relationship among the microbiome, tRNA abundance, and epitranscriptome in a mammalian host.
Appraisal overvaluation: Evidence of price adjustment bias in sales Comparisons
Authors: Mayer Yanling G. , Nothaft Frank E.
Published: April 2021

Home appraisal came under scrutiny for contributing to the home‐price bubble and enabling the origination of risky mortgages that led to the post‐2006 foreclosure crisis. Subsequent regulations tried to minimize or eliminate conflicts of interest and improve valuations. Nonetheless, our study of appraisals completed in 2015 and 2016 find that appraisal bias still occurred. Our analysis delves into the underlying appraisal development to identify causes of appraisal bias. Contributing factors are that comps are generally higher valued than the subject property, and appraisers are more likely to comparatively adjust upward lower priced comps but less likely to adjust downward higher priced comps.
Refugee employment support: The HRM–CSR nexus and stakeholder co‐dependency
Authors: Lee Eun Su , Szkudlarek Betina
Published: April 2021

Recent research suggests that human resource management (HRM) can play a crucial role in corporate social responsibility (CSR) and in addressing grand challenges, such as refugee workforce integration. This paper investigates how employers carry out their CSR goals through HRM practices, while working closely with non‐profit organisations (NPOs) that facilitate refugee employment support programmes. Using qualitative semi‐structured interviews with employers and NPOs in Australia, we highlight their co‐dependent relationship in addressing the challenge of refugee workforce integration. We demonstrate how the achievement of both CSR goals and social impact is enhanced in this co‐dependent relationship, where each stakeholder's unique expertise and access to resources are shared and leveraged. Our research findings advance the current understanding of the HRM–CSR literature on external stakeholder engagement by suggesting that a co‐dependent, rather than just a collaborative, relationship can underpin the effective execution of HRM practices with CSR goals.
Proxy Variable Estimation of Multiproduct Production Functions
Authors: Malikov Emir , Lien Gudbrand
Published: April 2021

Productivity studies that use proxy variable estimators routinely specify single‐output production functions despite most firms producing multiple outputs. This is usually accomplished by aggregating the firm's outputs using total revenue. Such a formulation rarely provides an adequate representation of the multiproduct firm's production: (a) it cannot identify technological cross‐output trade‐offs along the production possibilities frontier, and (b) it unrealistically assumes perfect output substitutability that, if misspecified, produces biased estimates. We develop a new methodology for estimating multiproduct production functions that addresses these limitations without requiring information beyond that which is available in most datasets and showcase it on Norwegian dairy‐and‐beef farming.
TYK2 is a prognostic biomarker and associated with immune infiltration in the lung adenocarcinoma microenvironment
Authors: He Aoxiao , Zhang Rongguiyi , Wang Jiakun , Huang Zhihao , Liao Wenjun , Li Yong , Wang Cong , Yang Jun , Feng Qian , Wu Linquan
Published: April 2021

Background

Lung adenocarcinoma (LUAD) remains a major disease with high morbidity and mortality. The Janus kinases (JAKs) play a significant part in cellular biological process, inflammation and immunity. The role of JAK family in LUAD is still ambiguous.

Methods

Various bioinformatics web portals were applied to explore the prognostic value of JAK family and their correlation with immune infiltration in LUAD.

Results

JAK1/2 was downregulated, whereas JAK3/TYK2 was upregulated in patients with LUAD compared with the healthy controls in subgroup analyses based on gender, age, smoking habits, cancer stage, TP53 mutation status, and nodal metastasis status. Drug sensitivity indicated that low expression of JAK3 and TYK2 were resistant to most of the small molecules or drugs. High TYK2 expression was associated with favorable overall survival and relapse free survival in LUAD. Moreover, univariate and multivariate analysis revealed that clinical stage, lymphatic node metastasis and TYK2 expression were the independent factors affecting the prognosis of LUAD patients. TYK2 expression in LUAD patients was positively associated with the abundance of immune cells (B cells, CD8+ T cells, CD4+ T cells, neutrophils, and dendritic cells) and immune biomarker sets. Moreover, TYK2 was mainly involved in RNA binding, transcriptional mis‐regulation in cancer and cell cycles. We also identified several TYK2‐associated miRNA or transcription factor targets in LUAD.

Conclusion

Our results indicated that TYK2 was a biomarker and associated with prognosis and immune infiltration in LUAD, laying a foundation for further study about the role of TYK2 in the carcinogenesis and progression of LUAD.
It won't happen to me! Psychosocial factors influencing risk perception for respiratory infectious diseases: A scoping review
Authors: Tagini Sofia , Brugnera Agostino , Ferrucci Roberta , Mazzocco Ketti , Compare Angelo , Silani Vincenzo , Pravettoni Gabriella , Poletti Barbara
Published: April 2021

Understanding the determinants of risk perception for COVID‐19 might help to promote self‐preventive behaviours. This scoping review aimed to map the extent, variety and characteristics of the evidence on the possible determinants of risk perception for COVID‐like diseases. PubMed, Scopus and Web of Science were searched for original, peer‐reviewed English‐written articles published up to March 2020 and investigating risk perception determinants for respiratory infectious diseases in adults. Titles and abstracts were screened, and full texts were analysed by the first author; when unsure, eligibility was discussed with the last author. Data were collected according to an extraction sheet developed by the first and last authors. The cross‐sectional evidence covers a variety of diseases, countries and timings of testing. Mostly, questionnaires recorded socio‐demographics, media exposure, trust in institutions, disease proximity and knowledge; psychological variables, including personality traits, distress and self‐efficacy, were less investigated. A miscellaneous operationalization of risk perception emerged, including the likelihood of getting sick, perceived dangerousness, concerns or a combination of them. A comprehensive understanding of the substantial amount of evidence may be challenging due to methodological heterogeneity. Referring to uniform theoretical frameworks is recommended; also, longitudinal research may be implemented to probe causal relationships.
Global Value Chains and Intermediaries in Multi‐stakeholder Initiatives in Pakistan and India
Authors: Lund‐Thomsen Peter , Riisgaard Lone , Singh Sukhpal , Ghori Shakil , Coe Neil M.
Published: April 2021

In this article, we analyse the role of regulatory intermediaries of the Better Cotton Initiative, a multi‐stakeholder initiative (MSI) in the global cotton value chain, with a regional focus on India and Pakistan. We conceptualize how the key roles of regulatory intermediaries — translating and verifying compliance with abstract rules in ways that make these rules practical and intelligible for target audiences (in this case, cotton farmers) — may be compromised by global value chain pressures and contradictory MSI requirements, thereby undermining the aim of mainstreaming sustainability standard systems. In other words, we theorize how MSIs can become subject to regulatory capture, serving the needs of global brands (for rapid upscaling, price minimization and verification) and sustainability standard bodies (contradictory demands for capacity building and compliance) at the expense of the intended beneficiaries — farmers at the base of global value chains. Based on an empirical analysis of the Better Cotton Initiative's implementing partners in Pakistan and India, we conclude that such weaknesses in standard implementation are likely to translate into poorer field‐level results in terms of ensuring the large‐scale, global mainstreaming of more sustainable commodity production sought by MSI practitioners.
Interfacial fracture toughness measurement of welded Babbitt alloy SnSb11Cu6/20Steel
Authors: Gao Yuepeng , Wang Jianmei , Liu Yuyang
Published: April 2021

The interface fracture toughness of SnSb11Cu6/20steel was measured by calculating the critical energy release rate and stress phase angle of the interface crack. A three‐point bending test was used to introduce cracks into the bonding interface, and the cohesion model of the bonding interface was established through experimental data. Through finite element analysis of load‐deflection curves with and without interface crack propagation, the crack initiation point is found. Then the energy calculation model of crack propagation is established, and the critical energy release rate is obtained using the virtual crack growth criterion. The calculation results of the stress phase angle show that the crack propagation is greatly affected by the normal stress after the babbitt alloy layer fractures. If the strength of the substrate material is weaker, the crack will continue to expand in the tangent perpendicular to the crack tip.
Self‐study in language learning: Relationships among time, activities, and learning outcomes
Authors: Bonilla Carrie , Hughes Meredith M. , Tare Medha , Vatz Karen
Published: April 2021

While much second language acquisition research has focused on characteristics of in‐class language study, little is known about the characteristics and effectiveness of out‐of‐class language study. This exploratory study addresses this gap by analyzing questionnaire data from 707 adult students enrolled in intensive (6–16 months) language study regarding preferred out‐of‐class activities and time spent on these activities in relation to language outcome scores (e.g., Defense Language Proficiency Test [DLPT] and Oral Proficiency Interview [OPI] scores), while also controlling for background variables such as language aptitude. Regarding time spent on out‐of‐class activities, mixed‐effects linear regression modeling (approximately 400 students) showed that more time spent on assigned and unassigned course study was associated with lower end‐of‐course language outcomes, and less time spent was associated with higher language outcomes. Engagement in some target‐language activities, however, such as using social media to interact in the target language (e.g., chat) showed positive relationships with achieving overall language proficiency. The findings offer important insight into the complex relationships between time spent on out‐of‐class study, target language activities, background variables, and course outcomes.
Maximizing the effectiveness of national commitments to protected area expansion for conserving biodiversity and ecosystem carbon under climate change
Authors: Carroll Carlos , Ray Justina C.
Published: April 2021

Global commitments to protected area expansion should prioritize opportunities to protect climate refugia and ecosystems which store high levels of irrecoverable carbon, as key components of an effective response to biodiversity loss and climate change. The United States and Canada are responsible for one‐sixth of global greenhouse gas emissions but hold extensive natural ecosystems that store globally significant above‐ and below‐ground carbon. Canada has initiated a process of protected area network expansion in concert with efforts at reconciliation with Indigenous Peoples, and acknowledged nature‐based solutions as a key aspect of climate change mitigation. The US, although not a party to global biodiversity conventions, has recently committed to protecting 30% of its extent by 2030 and achieving the UNFCCC Paris Agreement's mitigation targets. The opportunities afforded by these dual biodiversity conservation and climate commitments require coordinated national and regional policies to ensure that new protected areas maximize biodiversity‐focused adaptation and nature‐based mitigation opportunities. We address how global commitments can best inform national policy initiatives which build on existing agency mandates for regional planning and species conservation. Previous analyses of global conservation priorities under climate change have been tenuously linked to policy contexts of individual nations and have lacked information on refugia due to limitations of globally available datasets. Comparison and synthesis of predictions from a range of recently developed refugia metrics allow such data to inform planning despite substantial uncertainty arising from contrasting model assumptions and inputs. A case study for endangered species planning for old‐forest‐associated species in the US Pacific Northwest demonstrates how regional planning can be nested hierarchically within national biodiversity‐focused adaptation and nature‐based mitigation strategies which integrate refugia, connectivity, and ecosystem carbon metrics to holistically evaluate the role of different land designations and where carbon mitigation and protection of biodiversity's resilience to climate change can be aligned.
Prison is power: Federal correctional officers, gender, and professional identity work
Authors: Compton Cristin A. , Brandhorst Jaclyn K.
Published: April 2021

Federal correctional officers (COs) face a compelling amount of professional stress and rigid professional expectations. The Bureau of Prisons (BOP), in an effort to improve employee wellness, has instituted a number of policies and programs addressing gender, sexual harassment, the treatment of inmates, and the role of the BOP in rehabilitation efforts. As a result, COs are navigating how they see themselves and their role within the BOP. Using interviews with 26 federal COs, we use the communication theory of identity (CTI) to explore how correctional workers are communicatively managing their professional identities as the BOP's policies shift. Officers described idealized professional identities in oppositional gendered terms (e.g., masculinity is privileged; femininity derided). Female‐identifying officers described being unable to meet professional ideals, and some male‐identifying officers struggled enacting their masculinity. However, COs described managing gaps between their personal and professional identities in ways that elucidated connections, rather than separation, between officers. We provide theoretical and practical implications from participant voices, including the use of CTI to better understand identity work processes in workplace contexts.
Onychomycosis in patients with multiple sclerosis: prevalence, clinical description, mycological, and dermoscopic study in a Mexican population
Authors: Sánchez‐Cárdenas Carlos D. , Vega‐Sánchez Diana , Vargas‐Santana Sarah B. , Flores‐Rivera José , Arenas Roberto , Corona Teresa
Published: April 2021

Background

Multiple sclerosis (MS) is a chronic demyelinating disease related to HLA‐DR8. Susceptibility to onychomycosis has been found in Mexican mestizos with HLA‐DR8. The frequency of onychomycosis in this neurological disease is unknown.

Objectives

To determine the frequency of onychomycosis and its clinical, mycological, and dermoscopic characteristics in patients with MS in comparison with the general population.

Methods

Observational, cross‐sectional, case–control study in patients with MS from October 2017 to February 2018. Age, gender, MS type, and time of progression from diagnosis to date and baseline treatment were collected after signed informed consent. A neurological exploration and clinical examination of fingernails and toenails for onychomycosis was conducted. Mycological and dermoscopic studies of the infected nails were performed on patients with clinical diagnosis of onychomycosis. A healthy control group was taken for each case (1:1), paired by age and gender.

Results

The frequency of onychomycosis in patients with MS was higher than the healthy population (32% vs. 26%, P = 0.509). A higher frequency of non‐dermatophyte fungi was found, although it was not statistically significant. The clinical manifestations and dermoscopic findings in patients with MS and onychomycosis were similar to those of the general population.

Conclusion

The frequency of onychomycosis in patients with MS is slightly higher than that of the general population. A possible association of HLA‐DR8 as a susceptibility factor for onychomycosis is proposed. The etiology of opportunistic fungi in MS patients with onychomycosis may be related to immunosuppressive treatment.