bluuebunny/crossref_metadata_2025 huggingface dataset:
Soft-Attention Improves Skin Cancer Classification Performance
Authors: Datta Soumyya Kanti , Shaikh Mohammad Abuzar , Srihari Sargur N , Gao Mingchen
Published: May 2021

In clinical applications, neural networks must focus on and highlight the most important parts of an input image. Soft-Attention mechanism enables a neural network to achieve this goal. This paper investigates the effectiveness of Soft-Attention in deep neural architectures. The central aim of Soft-Attention is to boost the value of important features and suppress the noise-inducing features. We compare the performance of VGG, ResNet, Inception ResNet v2 and DenseNet architectures with and without the Soft-Attention mechanism, while classifying skin lesions. The original network when coupled with Soft-Attention outperforms the baseline[16] by 4.7% while achieving a precision of 93.7% on HAM10000 dataset [25]. Additionally, Soft-Attention coupling improves the sensitivity score by 3.8% compared to baseline[31] and achieves 91.6% on ISIC-2017 dataset [2]. The code is publicly available at github1.
Differential overlap in human and animal fecal microbiomes and resistomes in rural versus urban Bangladesh
Authors: Swarthout Jenna M. , Fuhrmeister Erica R. , Hamzah Latifah , Harris Angela R. , Ahmed Mir A. , Gurley Emily S. , Satter Syed M. , Boehm Alexandria B. , Pickering Amy J.
Published: May 2021

Background

Low- and middle-income countries (LMICs) bear the largest mortality burden due to antimicrobial-resistant infections. Small-scale animal production and free-roaming domestic animals are common in many LMICs, yet data on zoonotic exchange of gut bacteria and antimicrobial resistance genes (ARGs) in low-income communities are sparse. Differences between rural and urban communities in population density, antibiotic use, and cohabitation with animals likely influence the frequency of transmission of gut bacterial communities and ARGs between humans and animals. Here, we determined the similarity in gut microbiomes, using 16S rRNA gene amplicon sequencing, and resistomes, using long-read metagenomics, between humans, chickens, and goats in rural compared to urban Bangladesh.

Results

Gut microbiomes were more similar between humans and chickens in rural (where cohabitation is more common) compared to urban areas, but there was no difference for humans and goats. Urbanicity did not impact the similarity of human and animal resistomes; however, ARG abundance was higher in urban animals compared to rural animals. We identified substantial overlap of ARG alleles in humans and animals in both settings. Humans and chickens had more overlapping ARG alleles than humans and goats. All fecal hosts carried ARGs on contigs classified as potentially pathogenic bacteria – including Escherichia coli, Campylobacter jejuni, Clostridiodes difficile, and Klebsiella pneumoniae.

Conclusions

While the development of antimicrobial resistance in animal gut microbiomes and subsequent transmission to humans has been demonstrated in intensive farming environments and high-income countries, evidence of zoonotic exchange of antimicrobial resistance in LMIC communities is lacking. This research provides genomic evidence of overlap of antimicrobial resistance genes between humans and animals, especially in urban communities, and highlights chickens as important reservoirs of antimicrobial resistance. Chicken and human gut microbiomes were more similar in rural Bangladesh, where cohabitation is more common. Incorporation of long-read metagenomics enabled characterization of bacterial hosts of resistance genes, which has not been possible in previous culture-independent studies using only short-read sequencing. These findings highlight the importance of developing strategies for combatting antimicrobial resistance that account for chickens being reservoirs of ARGs in community environments, especially in urban areas.
Longitudinal changes in home-based arts engagement during and following the first national lockdown due to the COVID-19 pandemic in the United Kingdom
Authors: Bu Feifei , Mak Hei Wan , Bone Jessica K , Fancourt Daisy
Published: May 2021

Aims

This study aimed to examine potential heterogeneity in longitudinal changes in home-based arts engagement during the first national lockdown and following gradual easing of restrictions in the UK. Further, it sought to explore factors that were associated with patterns of longitudinal changes in home-based arts engagement.

Methods

Data were from the UCL COVID-19 Social Study. The analytical sample consisted of 29,147 adults in the UK who were followed up for 22 weeks from 21st March to 21st August 2020. Data were analysed using growth mixture models.

Results

Our analyses identified five classes of growth trajectories. There were two stable classes showing little change in arts engagement over time (64.4% in total), two classes showing initial increases in arts engagement followed by declines as restrictions were eased (29.8%), and one class showing slight declines during strict lockdown followed by an increase in arts engagement after the easing of restrictions (5.9%). A range of factors were found to be associated with class membership of these arts engagement trajectories, such as age, gender, education, income, employment status, and health.

Conclusions

There is substantial heterogeneity in longitudinal changes in home-based arts engagement. For participants whose engagement changed over time, growth trajectories of arts engagement were related to changes in lockdown measures. These findings suggest that some individuals may have drawn on the arts when they needed them the most, such as during the strict lockdown period, even if they usually had lower levels of arts engagement before the pandemic. Overall, our results indicate the importance of promoting arts engagement during pandemics and periods of lockdown as part of public health campaigns.
Controlling risk of SARS-CoV-2 infection in essential workers of enclosed food manufacturing facilities
Authors: Sobolik Julia S. , Sajewski Elizabeth T. , Jaykus Lee-Ann , Cooper D. Kane , Lopman Ben A. , Kraay Alicia NM. , Ryan P. Barry , Leon Juan S.
Published: May 2021

The SARS-CoV-2 global pandemic poses significant health risks to workers who are essential to maintaining the food supply chain. Using a quantitative risk assessment model, this study characterized the impact of risk reduction strategies for controlling SARS-CoV-2 transmission (droplet, aerosol, fomite-mediated) among front-line workers in a representative enclosed food manufacturing facility. We simulated: 1) individual and cumulative SARS-CoV-2 infection risks from close contact (droplet and aerosols at 1-3m), aerosol, and fomite-mediated exposures to a susceptible worker following exposure to an infected worker during an 8h-shift; and 2) the relative reduction in SARS-CoV-2 infection risk attributed to infection control interventions (physical distancing, mask use, ventilation, surface disinfection, hand hygiene). Without mitigation measures, the SARS-CoV-2 infection risk was largest for close contact (droplet and aerosol) at 1m (0.96, 95%CI: 0.67–1.0). In comparison, risk associated with fomite (0.26, 95%CI: 0.10–0.56) or aerosol exposure alone (0.05, 95%CI: 0.01–0.13) at 1m distance was substantially lower (73-95%). At 1m, droplet transmission predominated over aerosol and fomite-mediated transmission, however, this changed by 3m, with aerosols comprising the majority of the exposure dose. Increasing physical distancing reduced risk by 84% (1 to 2m) and 91% (1 to 3m). Universal mask use reduced infection risk by 52-88%, depending on mask type. Increasing ventilation (from 0.1 to 2-8 air changes/hour) resulted in risk reductions of 14-54% (1m) and 55-85% (2m). Combining these strategies, together with handwashing and surface disinfection, resulted in <1% infection risk. Current industry SARS-CoV-2 risk reduction strategies, particularly when bundled, provide significant protection to essential food workers.

Significance Statement

Using mathematical modeling, we find that workers in enclosed food manufacturing facilities are at higher risk of SARS-CoV-2 infection from close contact transmission (exposure to large droplets and small aerosol particles) than fomite transmission. Thus, strategies protecting workers should prioritize close contact transmission pathways, such as physical distancing, universal mask use, and room air changes, with surface disinfection (reducing fomite transmission) and handwashing of secondary importance. Our work supports current international (EU-OSHA), domestic (FDA, OSHA), and food industry-standard guidance for managing COVID-19 transmission in essential workers in the food manufacturing sector. Although our model was designed for an indoor food manufacturing setting, it can be readily adapted to other indoor environments and infectious respiratory pathogens.
Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations
Authors: Shen Lishuang , Bard Jennifer Dien , Triche Timothy J. , Judkins Alexander R. , Biegel Jaclyn A. , Gai Xiaowu
Published: May 2021

The SARS-CoV-2 B.1.1.7 lineage is highly infectious and as of April 2021 accounted for 92% of COVID-19 cases in Europe and 59% of COVID-19 cases in the U.S. It is defined by the N501Y mutation in the receptor binding domain (RBD) of the Spike (S) protein, and a few other mutations. These include two mutations in the N terminal domain (NTD) of the S protein, HV69-70del and Y144del (also known as Y145del due to the presence of tyrosine at both positions). We recently identified several emerging SARS-CoV-2 variants of concerns, characterized by Membrane (M) protein mutations, including I82T and V70L. We now identify a sub-lineage of B.1.1.7 that emerged through sequential acquisitions of M:V70L in November 2020 followed by a novel S:D178H mutation first observed in early February 2021. The percentage of B.1.1.7 isolates in the U.S. that belong to this sub-lineage increased from 0.15% in February 2021 to 1.8% in April 2021. To date this sub-lineage appears to be U.S.-specific with reported cases in 31 states, including Hawaii. As of April 2021 it constituted 36.8% of all B.1.1.7 isolates in Washington. Phylogenetic analysis and transmission inference with Nextstrain suggests this sub-lineage likely originated in either California or Washington. Structural analysis revealed that the S:D178H mutation is in the NTD of the S protein and close to two other signature mutations of B.1.1.7, HV69-70del and Y144del. It is surface exposed and may alter NTD tertiary configuration or accessibility, and thus has the potential to affect neutralization by NTD directed antibodies.
The landscape of COVID-19 vaccination among healthcare workers at the first round of COVID-19 vaccination in China: willingness, acceptance and self-reported adverse effects
Authors: Ye Xinxin , Ye Wan , Yu Jinyue , Gao Yuzhen , Ren Ziyang , Chen Lanzhen , Dong Ao , Yi Qian , Zhan Chenju , Lin Yanni , Wang Yangxin , Huang Simin , Song Peige
Published: May 2021

Background

The COVID-19 vaccines have been developed in a wide range of countries. This study aims to examine factors influencing vaccination rate and willingness to vaccinate against COVID-19 among Chinese healthcare workers (HCWs).

Methods

From 3rd February to 18th February, 2021, an online cross-sectional survey was conducted among HCWs to investigate factors associated with the acceptance and willingness of COVID-19 vaccination. Socio-demographic characteristics and the acceptance of COVID-19 vaccination among Chinese HCWs were evaluated.

Results

A total of 2156 HCWs from 21 provinces in China responded to this survey (response rate: 98.99%)), among whom 1433 (66.5%) were vaccinated at least one dose. Higher vaccination rates were associated with older age (40-50 years vs. less than 30 years, OR=1.63, 95%CI: 1.02-2.58; >50 years vs. 30 years, OR=1.90, 95%CI: 1.02-3.52), working as a clinician (OR=1.54, 95% CI: 1.05-2.27), having no personal religion (OR=1.35, 95%CI: 1.06-1.71), working in a fever clinic (OR=4.50, 95%CI:1.54-13.17) or higher hospital level (Municipal vs. County, OR=2.01, 95%CI: 1.28-3.16; Provincial vs. County, OR=2.01, 95%CI: 1.25-3.22) and having knowledge training of vaccine (OR=1.67, 95%CI:1.27-2.22), family history for influenza vaccination (OR=1.89, 95%CI:1.49-2.35) and strong familiarity with the vaccine (OR=1.43, 95%CI:1.05-1.95) (All P<0.05). Strong willingness for vaccination was related to having a working in midwestern China (OR=1.89, 95%CI:1.24-2.89), considerable knowledge of the vaccine (familiar vs. not familiar, OR=1.67, 95%CI: 1.17-2.39; strongly familiar vs. not familiar, OR=2.47, 95%CI: 1.36-4.49), knowledge training of vaccine (OR=1.61, 95%CI: 1.05-2.48) and strong confidence in the vaccine (OR=3.84, 95%CI: 2.09-7.07).

Conclusion

Personal characteristics, working environments, familiarity and confidence in the vaccine were related to vaccination rates and willingness to get vaccinated among healthcare workers. Results of this study could provide evidence for the government to improve vaccine coverage by addressing vaccine hesitancy in the COVID-19 pandemic and future public health emergencies.
Irremediable psychiatric suffering in the context of medical assistance in dying: a qualitative study
Authors: van Veen Sisco M.P. , Ruissen Andrea M. , Beekman Aartjan T.F. , Evans Natalie , Widdershoven Guy A.M.
Published: May 2021

Background

Establishing irremediability is a central challenge in determining the appropriateness of medical assistance in dying (MAID) for patients with a psychiatric disorder. The objective of this study is to learn how experienced psychiatrists define irremediable psychiatric suffering (IPS) in the context of MAID and what challenges they face while establishing IPS.

Methods

In a qualitative study, we performed 11 in-depth interviews with psychiatrists who have experience assessing IPS in the context of MAID.

Results

Although determining IPS is, essentially, a prospective assessment, psychiatrists mostly rely on retrospective dimensions, such as the history of failed treatments, when defining IPS. When establishing IPS, psychiatrists face diagnosis and treatment challenges. The main challenge regarding diagnosis is that patients requesting MAID are often diagnosed with more than one psychiatric disorder. Important treatment related challenges are: assessing the quality of past treatments, establishing the limits of approaches that aim to alter the patient’s perception, and managing ‘treatment fatigue’ and treatment refusal.

Interpretation

IPS is mostly defined in terms of failed past treatments. Challenges regarding diagnosis and treatment complicate the process of establishing IPS. The finding that most patients are diagnosed with more than one psychiatric disorder calls for a critical appraisal of the due diligence procedure for MAID. In response to the challenges related to treatment, intersubjective clinical criteria for IPS in the context of MAID should be developed. Also, further investigation of the concept of ‘treatment fatigue’ in psychiatry may provide insight into why patients requesting MAID.

Registration

this study was preregistered under osf.io/2jrnd.
Long-term symptoms after SARS-CoV-2 infection in school children: population-based cohort with 6-months follow-up
Authors: Radtke Thomas , Ulyte Agne , Puhan Milo A , Kriemler Susi
Published: May 2021

Although long COVID in children exists, it is still unclear to what extent children are affected. The Ciao Corona study is a longitudinal cohort investigating SARS-CoV-2 seroprevalence and clustering of cases among around 2500 children and adolescents (hereafter referred to as children) from 55 randomly selected primary and secondary schools in the canton of Zurich in Switzerland. Between June 2020 and April 2021, we completed three testing phases where we collected venous blood for serological analysis and asked about symptoms with online questionnaires. We compared children who tested positive for SARS-CoV-2 antibodies in October/November 2020 with those who tested negative. Children who were seronegative in October/November 2020 and seroconverted or were not retested in March/April 2021 were excluded from the analysis (n=256). In March-May 2021 we assessed the presence of symptoms occurring since October 2020, lasting for at least 4 weeks, and persisting for either >4 weeks or >12 weeks. Overall, 1355 of 2503 children with a serology result in October/November 2020 and follow up questionnaire in March-May 2021 were included. Among seropositive and seronegative 6-to 16-year-old children, 9% versus 10% reported at least one symptom beyond 4 weeks, and 4% versus 2% at least one symptom beyond 12 weeks. None of the seropositive children reported hospitalization after October 2020. This study suggests a low prevalence of symptoms compatible with long COVID in a randomly selected population-based cohort of children followed over 6 months after serological testing.
Pre-Exposure Prophylaxis with Various Doses of Hdroxychloroquine among high-risk COVID 19 Healthcare Personnel: CHEER randomized controlled trial
Authors: Syed Fibhaa , Arif Mohammad Ali , Niazi Rauf , Baqar Jaffer Bin , Hashmi Ume Laila , Batool Sadia , Ashraf Sadia , Arshad Junaid , Musarrat Saira
Published: May 2021

Background

Pre-exposure prophylaxis (PrEP) is a promising strategy to break the chain of transmission of novel coronavirus (2019-nCoV).

Aims

This trial aimed to evaluate the safety and efficacy of PrEP with various doses of HCQ against a placebo among high-risk healthcare providers (HCPs).

Methods

A phase II, randomized, placebo-controlled trial was conducted at a tertiary care hospital. A total of 228 HCPs were screened, we included 200 subjects with no active or past SARS-CoV-2 infection. Subjects of experimental groups 1-3 received HCQ in various doses and those in the control group received placebo. The study outcomes in terms of safety and efficacy were monitored. Participants exhibiting COVID-19 symptoms were tested for SARS-CoV-2 during the study and also by the end of the 12th week, with PCR or IgM and IgG serology.

Results

Overall, 146 of 200 participants reported exposure to a confirmed COVID-19 case in the first month, 189 in the 2nd month and 192 were exposed by the 12th week of the study. Moreover, the precautionary practices, i.e. use of personal protective equipment (PPE), significantly varied; initially more than 80% of the exposed HCPs weren’t ensuring the PPE used by the patients treated by them. However, it gradually developed with the increasing knowledge of the virus. As far as safety is concerned, mild treatment-related side effects were observed among the interventional and placebo arm patients. While none of the participants were critical, and a few had mild illness by the end of the 12th week, requiring only outpatient observation with no hospitalization. There was no significant clinical benefit of PrEP with HCQ as compared to placebo (p>0.05).

Conclusion

It is concluded from the study findings that the PrEP HCQ does not significantly prevent illness compatible with COVID-19 or confirmed infection among high-risk HCPs.
Application of BRACE Method to Address Treatment Selection Bias in Observational Data
Authors: Williamson Casey W. , Nelson Tyler , Thompson Caroline A. , Vitzthum Lucas K. , Zakeri Kaveh , Riviere Paul , Bryant Alex K. , Sharabi Andrew B. , Zou Jingjing , Mell Loren K.
Published: May 2021

Background

Cancer treatments can paradoxically appear to reduce the risk of non-cancer mortality in observational studies, due to residual confounding from treatment selection bias. Here we apply a novel method, Bias Reduction through Analysis of Competing Events (BRACE), to reduce bias in the presence of residual confounding.

Methods

We studied 36630 prostate cancer patients, 4069 lung cancer patients, and 7117 head/neck cancer patients, using the Veterans Affairs Informatics and Computing Infrastructure database. We estimated effects of intensive treatment (prostate: prostatectomy vs. radiotherapy; lung: lobectomy vs. sublobar resection or radiotherapy; head/neck: radiotherapy with concurrent cisplatin and/or multiagent induction vs. radiotherapy with or without alternative systemic therapy) on cancer-specific mortality, non-cancer mortality, and overall survival (OS), using both multivariable Cox (MVA) and propensity score (inverse probability treatment weighting (IPTW)) models. Next, we applied the BRACE method to adjust for residual confounding, based on the observed treatment effect on competing event and relative event hazards.

Results

For each cohort, intensive treatment was associated with significantly reduced hazards for cancer-specific mortality, non-cancer mortality, and OS. Compared to the results for MVA and IPTW models, hazard ratios (95% confidence intervals) for the effect of intensive treatment on OS were attenuated in each cohort after applying BRACE: (prostate-MVA: 0.75 (0.71, 0.80), IPTW: 0.73 (0.66, 0.75), BRACE: 0.98 (0.95, 1.00); lung-0.79 (0.68, 0.91), 0.79 (0.66, 0.89), BRACE: 0.81 (0.65, 0.94); head/neck-0.71 (0.66, 0.76), 0.70 (0.66, 0.76), BRACE: 0.81 (0.76, 0.86)). BRACE estimates were similar to findings from meta-analyses and randomized trials.

Conclusions

We found evidence of residual confounding in several observational cohorts after applying standard methods, which were mitigated after applying BRACE. Application of this method could provide more reliable estimates and inferences when residual confounding is identified and represents a novel approach to improving the validity of outcomes research.
“How do we do this at a distance?!” A descriptive study of remote undergraduate research programs during COVID-19
Authors: Erickson Olivia A. , Cole Rebecca B. , Isaacs Jared M. , Alvarez-Clare Silvia , Arnold Jonathan , Augustus-Wallace Allison , Ayoob Joseph C. , Berkowitz Alan , Branchaw Janet , Burgio Kevin R. , Cannon Charles H. , Ceballos Ruben Michael , Cohen C. Sarah , Coller Hilary , Disney Jane , Doze Van A. , Eggers Margaret J. , Farina Stacy , Ferguson Edwin L. , Gray Jeffrey J. , Greenberg Jean T. , Hoffman Alexander , Jensen-Ryan Danielle , Kao Robert M. , Keene Alex C. , Kowalko Johanna E. , Lopez Steven A. , Mathis Camille , Minkara Mona , Murren Courtney J. , Ondrechen Mary Jo , Ordoñez Patricia , Osano Anne , Padilla-Crespo Elizabeth , Palchoudhury Soubantika , Qin Hong , Ramírez-Lugo Juan , Reithel Jennifer , Shaw Colin A. , Smith Amber , Smith Rosemary , Summers Adam P. , Tsien Fern , Dolan Erin L.
Published: May 2021

The COVID-19 pandemic shut down undergraduate research programs across the U.S. Twenty-three sites offered remote undergraduate research programs in the life sciences during summer 2020. Given the unprecedented offering of remote research experiences, we carried out a study to describe and evaluate these programs. Using structured templates, we documented how programs were designed and implemented, including who participated. Through focus groups and surveys, we identified programmatic strengths and shortcomings as well as recommendations for improvements from the perspectives of participating students. Strengths included the quality of mentorship, opportunities for learning and professional development, and development of a sense of community. Weaknesses included limited cohort building, challenges with insufficient structure, and issues with technology. Although all programs had one or more activities related to diversity, equity, inclusion, and justice, these topics were largely absent from student reports even though programs coincided with a peak in national consciousness about racial inequities and structural racism. Our results provide evidence for designing remote REUs that are experienced favorably by students. Our results also indicate that remote REUs are sufficiently positive to further investigate their affordances and constraints, including the potential to scale up offerings, with minimal concern about disenfranchising students.
KmerKeys: a web resource for searching indexed genome assemblies and variants
Authors: Pavlichin Dmitri S. , Lee HoJoon , Greer Stephanie U. , Grimes Susan M. , Weissman Tsachy , Ji Hanlee P.
Published: May 2021

K-mers are short DNA sequences that are used for genome sequence analysis. Applications that use k-mers include genome assembly and alignment. Despite these current applications, the wider bioinformatic use of k-mers in has challenges related to the massive scale of genomic sequence data. A single human genome assembly has billions of these short sequences. The sheer amount of computation for effective use of k-mer information is enormous, particularly when involving multiple genome assemblies. To address these issues, we developed a new k-mer indexing data structure based on a hash table tuned for the lookup of k-mer keys. This web application, referred to as KmerKeys (https://kmerkeys.dgi-stanford.org/), provides performant, rapid query speeds for cloud computation on genome assemblies. We enable fuzzy as well as exact k-mer-based searches of assemblies. To enable robust and speedy performance, the website implements cache-friendly hash tables, memory mapping and massive parallel processing. Our method employs a scalable and efficient data structure that can be used to jointly index and search a large collection of human genome assembly information. One can include variant databases and their associated metadata such as the gnomAD population variant catalog. This feature enables the incorporation of future genomic information into sequencing analysis.
Skeletal Muscle Transcriptome Alterations Related to Physical Function Decline in Older Mice
Authors: Graber Ted G. , Maroto Rosario , Thompson Jill , Widen Steve , Man Zhaohui , Pajski Megan L. , Rasmussen Blake B.
Published: May 2021

One inevitable consequence of aging is the gradual deterioration of physical function and exercise capacity, driven in part by the adverse effect of age on muscle tissue. Our primary purpose was to determine the relationship between patterns of gene expression in skeletal muscle and this loss of physical function. We hypothesized that some genes changing expression with age would correlate with functional decline, or conversely with preservation of function. Male C57BL/6 mice (6-months old, 6m, 24-months, 24m, and 28+-months, 28m; all n=8) were tested for physical ability using acomprehensivefunctionalassessmentbattery (CFAB). CFAB is a composite scoring system comprised of five functional tests: rotarod (overall motor function), grip strength (fore-limb strength), inverted cling (4-limb strength/endurance), voluntary wheel running (activity rate/volitional exercise), and treadmill (endurance). We then extracted total RNA from the tibialis anterior muscle, analyzed with Next Generation Sequencing RNAseq to determine differential gene expression during aging, and compared these changes to physical function. Aging resulted in gene expression differences >│1.0│ log2 fold change (multiple comparison adjusted p<0.05) in219genes in the 24m and in6587genes in the 28m. Linear regression with CFAB determined253differentially expressed genes strongly associated (R>0.70) with functional status in the 28m, and22genes in the 24m. We conclude that specific age-related transcriptomic changes are associated with declines in physical function, providing mechanistic clues. Future work will establish the underlying cellular mechanisms and the physiological relevance of these genes to age-related loss of physical function.

Graphical Abstract

RNA sequencing of skeletal muscle from young and old mice were compared to physical function status obtained by performing a comprehensive functional assessment battery of tests. Between adulthood (6-months) and older age (28-months), 6707 genes were differentially expressed with 253 of these genes being significantly associated with physical function. Specific age-related changes to the skeletal muscle transcriptome are associated with a decline in physical function.
Mass Recovery following Caloric Restriction Reverses Lipolysis and Proteolysis, but not Gluconeogenesis, in Insulin Resistant OLETF Rats
Authors: Cornejo Manuel A. , Dhillon Jaapna , Nishiyama Akira , Nakano Daisuke , Ortiz Rudy M.
Published: May 2021

Caloric restriction (CR) is one of the most important behavioral interventions to reduce excessive abdominal adiposity, which is a risk factor for the development of insulin resistance. Previous metabolomics studies have characterized substrate metabolism during healthy conditions; however, the effects of CR and subsequent mass recovery on shifts in substrate metabolism during insulin resistance (IR) have not been widely investigated. To assess the effects of acute CR and the subsequent mass recovery on shifts in substrate metabolism, a cohort of 15-week old Long Evans Tokushima Otsuka (LETO) and Otsuka Long Evans Tokushima Fatty (OLETF) rats were calorie restricted (CR: 50% × 10 days) with or without partial body mass recovery (PR; 73% x 7 days), along with their respective ad libitum controls. End-of-study plasma samples were analyzed for primary carbon metabolites by gas chromatography (GC) time-of-flight (TOF) mass spectrometry (MS) data acquisition. Data analysis included PCA, Pearson correlation vs previously reported variables (adipose and body masses, and insulin resistance index, IRI), and metabolomics maps (MetaMapp) generated for the most significant group comparisons. All treatments elicited a significant group differentiation in at least one principal component. CR improved TCA cycle in OLETF, and increased lipolysis and proteolysis. These changes were reversed after PR except for gluconeogenesis. Plasma lipid concentrations were inversely correlated to IRI in LETO, but not OLETF. These shifts in substrate metabolism suggest that the CR-induced decreases in adipose may not be sufficient to more permanently alter substrate metabolism to improve IR status during metabolic syndrome.
Fluorinated oil-surfactant mixtures with the density of water: artificial cells for synthetic biology
Authors: Laos Roberto , Benner Steven
Published: May 2021

There is a rising interest in biotechnology for the compartmentalization of biochemical reactions in water droplets. Several applications, such as the widely used digital PCR, seek to encapsulate a single molecule in a droplet to be amplified. Directed evolution, another technology with growing popularity, seeks to replicate what happens in nature by encapsulating a single gene and the protein encoded by this gene, linking genotype with phenotype. Compartmentalizing reactions in droplets also allows the experimentalist to run millions of different reactions in parallel. Compartmentalization requires a fluid that is immiscible with water and a surfactant to stabilize the droplets. While there are fluids and surfactants on the market that have been used to accomplish encapsulation, there are reported concerns with these. Span® 80, for example, a commonly used surfactant, has contaminants that interfere with various biochemical reactions. Similarly, synthetic fluids distributed by the cosmetic industry allow some researchers to produce experimental results that can be published, but then other researchers fail to reproduce some of these protocols due to the unreliable nature of these products, which are not manufactured with the intent of being used in biotechnology. The most reliable fluids, immiscible with water and suitable for biochemical reactions, are fluorinated fluids. Fluorinated compounds have the peculiar characteristic of being immiscible with water while at the same time not mixing with hydrophobic molecules. This peculiar characteristic has made fluorinated fluids attractive because it seems to be the basis of their being biologically inert. However, commercially available fluorinated fluids have densities between 1.4 to 1.6 g/mL. The higher-than-water density of fluorinated oils complicates handling of the droplets since these would float on the fluid since the water droplets would be less dense. This can cause aggregation and coalescence of the droplets. Here, we report the synthesis, characterization, and use of fluorinated polysiloxane oils that have densities similar to the one of water at room temperature, and when mixed with non-ionic fluorinated surfactants, can produce droplets encapsulating biochemical reactions. We show how droplets in these emulsions can host many biological processes, including PCR, DNA origami, rolling circle amplification (RCA), and Taqman® assays. Some of these use unnatural DNA built from an Artificially Expanded Genetic Information System (AEGIS) with six nucleotide “letters”.
Genetic diversity and population structure of cowpea [Vigna unguiculata (L.) Walp.] accessions from Togo using SSR Markers
Authors: Dagnon Yao Dodzi , Palanga Koffi Kibalou , Bammite Damigou , Akabassi Ghislain Comlan , Tozo Koffi
Published: May 2021

Cowpea [Vigna unguiculata (L.) Walp.] is a crop with significant agronomic and nutritional potential. I is very appreciate by local people. It is the third food habit in Togo after maize and rice. However, several accessions of cowpea cultivated in Togo are now prone to extinction, creating a risk of genetic erosion. It is therefore urgent to assess the genetic diversity of accessions in order to set up a good conservation program. To achieve this, genetic diversity and phylogenetic relationships among 70 accessions of cowpea collected in the five (5) administrative regions of Togo were assessed using Simple Sequence Repeat (SSR) molecular markers. Twenty-eight out of the thirty-two (32) primer pairs screened for polymorphism were polymorphic, and a total of 164 alleles were detected for the 28 loci with an average of 5.82 alleles per locus. Polymorphic Information Content (PIC) values ranged from 0.18 to 0.895, with an average value of 0.67. Population structure analysis using model-based revealed that the cowpea germplasm was grouped into two subpopulations. The analysis of molecular variance (AMOVA) revealed that 85% of genetic variation existed among individuals within regions. The fixation index (Fst) value, which was 0.018, was low, indicating relatively low population differentiation. The Togolese cowpea germplasm collection was grouped into four groups independently of theirs origins. This study provides a foundation for a Togolese cowpea germplasm conservation program and can serve for the selection of parental material for further studies aimed at the genetic improvement of local germplasm.
Fusarium graminearumDICER-like-dependent sRNAs are required for the suppression of host immune genes and full virulence
Authors: Werner Bernhard , Koch Aline , Šečić Ena , Engelhardt Jonas , Jelonek Lukas , Steinbrenner Jens , Kogel Karl-Heinz
Published: May 2021

In filamentous fungi, gene silencing by RNA interference (RNAi) shapes many biological processes, including pathogenicity. Recently, fungal small RNAs (sRNAs) have been shown to act as effectors that disrupt gene activity in interacting plant hosts, thereby undermining their defence responses. We show here that the devastating mycotoxin-producing ascomyceteFusarium graminearum(Fg) utilizes DICER-like (DCL)-dependent sRNAs to target defence genes in two Poaceae hosts, barley (Hordeum vulgare Hv) andBrachypodium distachyon(Bd). We identified 104Fg-sRNAs with sequence homology to host genes that were repressed during interactions ofFgandHv, while they accumulated in plants infected by the DCL double knock-out (dKO) mutant PH1-dcl1/2. The strength of target gene expression correlated with the abundance of the correspondingFg-sRNA. Specifically, the abundance of three tRNA-derived fragments (tRFs) targeting immunity-relatedEthylene overproducer 1-like 1(HvEOL1)and three Poaceae orthologues ofArabidopsis thaliana BRI1-associated receptor kinase 1(HvBAK1, HvSERK2andBdSERK2) was dependent on fungal DCL. Additionally, RNA-ligase-mediated Rapid Amplification of cDNA Ends (RLM-RACE) identified infection-specific degradation products for the three barley gene transcripts, consistent with the possibility that tRFs contribute to fungal virulence via targeted gene silencing.

Significance Statement

Fusarium graminearumis one of the most devastating fungal pathogens in cereals, while understanding the mechanisms of fungal pathogenesis is a prerequisite for developing efficient and environmentally friendly crop protection strategies. We show exploratory data suggesting that fungal small RNAs play a critical role in Fusarium virulence by suppressing plant immunity.
Comparative genomics reveals insights into phylogenomic taxonomy and potential algae-bacteria interactions of novel versatile Mameliella alba strain LZ-28 isolated from highly-toxic marine phycosphere
Authors: Zhu Wen-zhuo , Xu Fei-fei , Ye Yun , Yang Qiao , Zhang Xiao-ling
Published: May 2021

Phycosphere harbors cross-kingdom interactions with significant ecological relevance for harmful algal blooms (HAB) and phycotoxins biosynthesis. Previously, a new red-pigmented bacterium designated as strain LZ-28 was isolated from phycosphere microbiota of typical HAB dinoflagellate Alexandrium catenella LZT09 which is a vitamin B12 auxotroph and produces high levels of paralytic shellfish poisoning toxins (PST). Strain LZ-28 exhibited obvious growth-promoting activity toward its algal host, along with the production of active bioflocculanting exopolysaccharides (EPS). But the phylogenetic affiliation and genomic potential of this versatile bacterium has not yet been elucidated. In this study, we carried out combined taxonomic and phylogenomic analysis to clarify the taxonomic classification of strain LZ-28. The obtained 16S rRNA phylogeny revealed close taxonomic relationship between strain LZ-28 and other Mameliella alba members. Additional calculations of key phylogenomic parameters, average nucleotide identity (ANI), the average amino acid identity (AAI) and the digital DNA-DNA hybridization (dDDH) values based on genomes of strain LZ-28 and type strain of Mameliella alba were all exceeded the limit of species circumscription. Collectively considering the phenotypic and biochemical characterizations, strain LZ-28 was therefore identified as a new member of Mameliella alba. Furthermore, based on the genomic evidence, potential algae-bacteria interactions of strain LZ-28 with host algae LZT09 were elucidated through the associations with photosynthetic and antioxidant carotenoids, supplying of bacterial VB12 to auxotroph host, and versatile EPS serving for bacterial colonization and nutrient exchange during their interactions, along with stress response systems to defense oxidative stress and quorum sensing (QS) signals benefited survival for bacteria in the symbiotic system. Comparative genomics shed light on similar genomic features between M. alba strains, revealed potential close associations of strain LZ-28 with its algae host, and further enriched the genomic repertoire of interactions between phycosphere microbiota and algal host LZT09.
Flexibility-aware graph-based algorithm improves antigen epitopes identification
Authors: Gao Chuang , Wang Yiqi , Luo Jie , Zhou Ziyi , Dong Zhiqiang , Zhao Liang
Published: May 2021

Epitopes of an antigen are the surface residues in the spatial proximity that can be recognized by antibodies. Identifying such residues has shown promising potentiality in vaccine design, drug development and chemotherapy, thus attracting extensive endeavors. Although great efforts have been made, the epitope prediction performance is still unsatisfactory. One possible issue accounting to this poor performance could be the ignorance of structural flexibility of antigens. Flexibility is a natural characteristic of antigens, which has been widely reported. However, this property has never been used by existing models. To this end, we propose a novel flexibility-aware graph-based computational model to identify epitopes. Unlike existing graph-based approaches that take the static structures of antigens as input, we consider all possible variations of the side chains in graph construction. These flexibility-aware graphs, of which the edges are highly enriched, are further partitioned into subgraphs by using a graph clustering algorithm. These clusters are subsequently expanded into larger graphs for detecting overlapping residues between epitopes if exist. Finally, the expanded graphs are classified as epitopes or non-epitopes via a newly designed graph convolutional network. Experimental results show that our flexibility-aware model markedly outperforms existing approaches and promotes the F1-score to 0.656. Comparing to the state-of-the-art, our approach makes an increment of F1-score by 16.3%. Further in-depth analysis demonstrates that the flexibility-aware strategy contributes the most to the improvement. The source codes of the proposed model is freely available athttps://github.com/lzhlab/epitope.

Author summary

Epitope prediction is helpful to many biomedical applications so that dozens of models have been proposed aiming at improving prediction efficiency and accuracy. However, the performances are still unsatisfactory due to its complicated nature, particularly the noteworthy flexible structures, which makes the precise prediction even more challenging. The existing approaches have overlooked the flexibility during model construction. To this end, we propose a graph model with flexibility heavily involved. Our model is mainly composed of three parts: i) flexibility-aware graph construction; ii) overlapping subgraph clustering; iii) graph convolutional network-based subgraph classification. Experimental results show that our newly proposed model markedly outperforms the existing best ones, making an increment of F1-score by 16.3%.
Compartmap enables inference of higher-order chromatin structure in individual cells from scRNA-seq and scATAC-seq
Authors: Johnson Benjamin K. , Fortin Jean-Philippe , Hansen Kasper D. , Shen Hui , Triche Timothy
Published: May 2021

Single-cell profiling of chromatin structure remains a challenge due to cost, throughput, and resolution. We introduce compartmap to reconstruct higher-order chromatin domains in individual cells from transcriptomic (RNAseq) and epigenomic (ATACseq) assays. In cell lines and primary human samples, compartmap infers higher-order chromatin structure comparable to specialized chromatin capture methods, and identifies clinically relevant structural alterations in single cells. This provides a common lens to integrate transcriptional and epigenomic results, linking higher-order chromatin architecture to gene regulation and to clinically relevant phenotypes in individual cells.
Moxidectin and ivermectin inhibit SARS-CoV-2 replication in Vero E6 cells but not in human primary airway epithelium cells
Authors: Kumar Nilima Dinesh , ter Ellen Bram M. , Bouma Ellen M. , Troost Berit , van de Pol Denise P. I. , van der Ende-Metselaar Heidi H. , van Gosliga Djoke , Apperloo Leonie , Carpaij Orestes A. , van den Berge Maarten , Nawijn Martijn C. , Stienstra Ymkje , Rodenhuis-Zybert Izabela A , Smit Jolanda M.
Published: May 2021

Antiviral therapies are urgently needed to treat and limit the development of severe COVID-19 disease. Ivermectin, a broad-spectrum anti-parasitic agent, has been shown to have anti-SARS-CoV-2 activity in Vero cells at a concentration of 5 µM. These in vitro results triggered the investigation of ivermectin as a treatment option to alleviate COVID-19 disease. In April 2021, the World Health Organization stated, however, the following: “the current evidence on the use of ivermectin to treat COVID-19 patients is inconclusive”. It is speculated that the in vivo concentration of ivermectin is too low to exert a strong antiviral effect. Here, we performed a head-to head comparison of the antiviral activity of ivermectin and a structurally related, but metabolically more stable, moxidectin in multiple in vitro models of SARS-CoV-2 infection, including physiologically relevant human respiratory epithelial cells. Both moxidectin and ivermectin exhibited antiviral activity in Vero E6 cells. Subsequent experiments revealed that the compounds predominantly act on a step after virus cell entry. Surprisingly, however, in human airway-derived cell models, moxidectin and ivermectin failed to inhibit SARS-CoV-2 infection, even at a concentration of 10 µM. These disappointing results calls for a word of caution in the interpretation of anti-SARS-CoV-2 activity of drugs solely based on Vero cells. Altogether, these findings suggest that, even by using a high-dose regimen of ivermectin or switching to another drug in the same class are unlikely to be useful for treatment against SARS-CoV-2 in humans.
CoREST has a conserved role in facilitating SPR-5/LSD1 maternal reprogramming of histone methylation
Authors: Carpenter Brandon S. , Scott Alyssa , Goldin Robert , Chavez Sindy R. , Myrick Dexter A. , Curlee Marcus , Schmeichel Karen , Katz David J.
Published: May 2021

Maternal reprogramming of histone methylation is critical for reestablishing totipotency in the zygote, but how histone modifying enzymes are regulated during maternal reprogramming is not well characterized. To address this gap, we asked whether maternal reprogramming by the H3K4me1/2 demethylase SPR-5/LSD1/KDM1A, is regulated by the co-repressor protein, SPR-1/CoREST in C. elegans and mice. In C. elegans, SPR-5 functions as part of a reprogramming switch together with the H3K9 methyltransferase MET-2. By examining germline development, fertility and gene expression in double mutants between spr-1 and met-2, we find that spr-1 mutants are partially compromised for spr-5; met-2 reprogramming. In mice, we generated a separation of function Lsd1 M448V point mutation that compromises CoREST binding, but only slightly affects LSD1 demethylase activity. When maternal LSD1 in the oocyte is derived exclusively from this allele, the progeny phenocopy the increased perinatal lethality that we previously observed when LSD1 was reduced maternally. Together, these data are consistent with CoREST having a conserved function in facilitating maternal LSD1 epigenetic reprogramming.
In mice and humans, the brain’s blood vessels mature postnatally to acquire barrier and contractile properties
Authors: Slaoui Leila , Gilbert Alice , Federici Laetitia , Rancillac Armelle , Gelot Antoinette , Favier Maryline , Robil Noémie , Letort Gaëlle , Dias Karine , Jourdren Laurent , Mailly Philippe , Auvity Sylvain , Cisternino Salvatore , Cohen-Salmon Martine , Boulay Anne-Cécile
Published: May 2021

The brain dense vascular network is essential for distributing oxygen and nutrients to neural cells. The network develops during embryogenesis and leads to the formation of the endothelial blood-brain barrier (BBB). This barrier is surrounded by mural cells (pericytes and vascular smooth muscle cells (VSMCs)) and fibroblasts. Here, we compared the molecular and functional properties of brain vascular cells on postnatal day (P)5 vs. P15, via a transcriptomic analysis of purified mouse cortical microvessels (MVs) and the identification of vascular-cell-type-specific or -preferentially expressed transcripts. We found that endothelial cells (ECs), VSMCs and fibroblasts follow specific molecular maturation programs over this time period. In particular, ECs acquire P-glycoprotein (P-gP)-mediated efflux capacities. The arterial VSMC network expands, acquires contractile proteins (such as smooth muscle actin (SMA) and myosin heavy chain 11 (Myh11)) and becomes contractile. We also analyzed samples of human brain cortex from the early prenatal stage through to adulthood: the expression of endothelial P-gP increased at birth and Myh11 in VSMCs acts as a developmental switch (as in the mouse) at birth and up to the age of 2 of 5 years. Thus, in both mice and humans, the early postnatal phase is a critical period during which the essential properties of cerebral blood vessels (i.e. the endothelial efflux of xenobiotics and other molecules, and the VSMC contractility required for vessel tone and brain perfusion) are acquired and mature.