bluuebunny/crossref_metadata_2025 huggingface dataset:
Faecal sludge treatment facility site selection using GIS-based multi-criteria analysis and AHP: Case study of Bogor Regency
Authors: Devianto L A , Dewi N N A M S U , Helmy Q , Chaerul M
Published: May 2021

Sanitary condition is one of the components that influencing public health. Bogor Regency has total area 2,663.81 km2, with total population 5,965,410 in 2019. The sanitation of Bogor Regency nearly 100% is using on-site systems. Utilization of septic tank reduces the level of contamination of surface water and groundwater. However, the sludge still containing high E. Coli that potentially caused diarrhea, vomiting disease, and others, so that the handling of the sludge needs Faecal Sludge Treatment Facilities (FSTF). Before 2016, Bogor Regency already had 10 units of faecal suction truck services, but the disposal process still was done in Kalimulya FSTF, Depok City. So, this study aims to find a feasible FSTF site location which fulfils the spatial plan, technical, and non-technical criteria. The process on the determining feasible FSTF location was employing multicriteria analysis by using Geographic Information Systems (GIS) and Analytical Hierarchy Process (AHP). Several spatial data such as the land slope, the soil type, distance from water bodies/river, the administration of Bogor Regency, as well as land use and land capability were used for FSTF site selection. Spatial analysis using GIS results in 22 locations in 15 different districts. By reconsidering the area, only 8 selected locations were surveyed and evaluated using AHP. Based on the weighting, the locations which chosen for the eastern, central, and western parts of Bogor are Cileungsi, Cibinong, and Cigudeg districts respectively.
Zinc ferrite nanoparticles: simple synthesis via lyophilisation and electrochemical application as glucose biosensor
Authors: Cao Xun
Published: May 2021

With increasing diabetes patients in the near future, development of non-enzymatic glucose biosensor is highly demanded due to their greater sensitivity and resistance to external stimuli compared to enzymatic biosensors. Zinc ferrite (ZnFe2O4, ZFO) nanoparticles (NPs) were fabricated using a simple solution combustion method together with freeze drying. The NPs have high crystallinity, large aspect ratios and narrow size distributions. Plenty of defects have been induced during lyophilisation and greatly improves the glucose biosensing performance during electrochemistry test. The freeze-dried ZFO NPs are highly crystalline and agglomeration-free, these assures the sample with high sensitivity, superior selectivity, low detection limit and outstanding stability for electrochemical glucose biosensing.
Subjective Social Status and Cardiometabolic Risk Markers by Intersectionality of Race/Ethnicity and Sex Among U.S. Young Adults
Authors: McClain Amanda C , Gallo Linda C , Mattei Josiemer
Published: May 2021

Background

Subjective social status (SSS) has shown inverse relationships with cardiometabolic risk, but intersectionalities of race/ethnicity and sex may indicate more nuanced relationships.

Purpose

To investigate associations of SSS with cardiometabolic risk markers by race/ethnicity and sex.

Methods

Data were from Wave IV (2008) of the National Longitudinal Study of Adolescent to Adult Health (n = 4,847; 24–32 years), which collected biological cardiometabolic risk markers. A 10-step ladder captured SSS; respondents indicated on which step they perceived they stood in relation to other people in the U.S. higher values indicated higher SSS (range: 1–10). We tested the relationship between SSS and individual markers using generalized least square means linear regression models, testing three-way interactions between SSS, race/ethnicity, and sex (p < .10) before stratification.

Results

SSS–race/ethnicity–sex interactions were significantly associated with waist circumference (p ≤ .0001), body mass index (BMI; p ≤ .0001), systolic blood pressure (SBP; p ≤ .0001), diastolic blood pressure (DBP; p = .0004), and high-density lipoprotein cholesterol (HDL-C; p = .07). SSS was associated with waist circumference (β [SE]: −1.2 (0.4), p < .05) and BMI (−0.6 [0.2], p < .01) for non-Hispanic White females, compared with males; with HDL-C among non-Hispanic White (0.2 [0.1]; p < .05) and Hispanic (0.3 (0.1); p < .05) females, compared with males; with SBP for non-Hispanic Asian (1.7 [0.8]; p < .05) and Multiracial (1.8 [0.8]; p < .05), versus White, females; and with DBP for non-Hispanic Black (0.8 [0.3]; p < .01), versus White, males.

Conclusions

SSS was differentially related to cardiometabolic risk markers by race/ethnicity and sex, suggesting intersectional aspects. Clinical and research applications of SSS should consider race/ethnicity- and sex-specific pathways influencing cardiometabolic risk.
Estimated Prevalence of Hypertension and Undiagnosed Hypertension in a Large Inpatient Population: A Cross-sectional Observational Study
Authors: Mahdi Adam , Armitage Laura C , Tarassenko Lionel , Watkinson Peter
Published: May 2021

Background

Hypertension is a major cause of morbidity and mortality. In community populations the prevalence of hypertension, both in diagnosed and undiagnosed states, has been widely reported. However, estimates for the prevalence of hospitalized patients with average blood pressures (BPs) that meet criteria for the diagnosis of hypertension are lacking. We aimed to estimate the prevalence of patients in a UK hospital setting, whose average BPs meet current international guidelines for hypertension diagnosis.

Methods

We performed a retrospective cross-sectional observational study of patients admitted to adult wards in 4 acute hospitals in Oxford, United Kingdom, between March 2014 and April 2018.

Results

We identified 41,455 eligible admitted patients with a total of 1.7 million BP measurements recorded during their hospital admissions. According to European ESC/ESH diagnostic criteria for hypertension, 21.4% (respectively 47% according to American ACC/AHA diagnostic criteria) of patients had a mean BP exceeding the diagnostic threshold for either Stage 1, 2, or 3 hypertension. Similarly, 5% had a mean BP exceeding the ESC/ESH (respectively 13% had a mean BP exceeding the ACC/AHA) diagnostic criteria for hypertension, but no preexisting diagnostic code for hypertension or a prescribed antihypertensive medication during their hospital stay.

Conclusions

Large numbers of hospital inpatients have mean in-hospital BPs exceeding diagnostic thresholds for hypertension, with no evidence of diagnosis or treatment in the electronic record. Whether opportunistic screening for in-hospital high BP is a useful way of detecting people with undiagnosed hypertension needs evaluation.
Treatment With Oxygen-Enriched Olive Oil Improves Healing Parameters Following Augmentation-Mastopexy
Authors: Santorelli Adriano , Bernini Marco , Orzalesi Lorenzo , Avvedimento Stefano , Palumbo Paolo , Kothari Ashutosh , Fausto Alfonso , Magalotti Cesare , Buzzi Giuseppina , Sandroni Sara , Calabrese Claudio
Published: May 2021

Background

Breast augmentation-mastopexy can yield an aesthetically attractive breast, but the 1-stage procedure is prone to unsatisfactory outcomes, including poor wound healing.

Objectives

The authors evaluated whether postsurgical application of a polyurethane bra cup coated with oxygen-enriched olive oil (NovoX Cup; Moss SpA, Lesa, Novara, Italy) would decrease pain associated with augmentation-mastopexy and improve the quality of the surgical scar.

Methods

This retrospective study was conducted at a single center from January 2016 to June 2019. All patients underwent 1-stage augmentation-mastopexy with the inverted T incision. For 2 weeks postsurgically, wounds were dressed either with the oxygen-enriched olive oil bra or with Fitostimoline (Farmaceutici Damor SpA, Naples, Italy). Patients indicated their pain intensity on postoperative days 2, 3, and 10, and patients and independent observers scored scar quality on the Patient and Observer Scar Assessment Scale (POSAS) 6 and 12 months after the procedure.

Results

A total of 240 women (120 per study arm) completed the study. All the patients had satisfactory aesthetic results, and there were no tolerability concerns with either postoperative dressing. Compared with patients in the Fitostimoline group, patients who received the oxygen-enriched olive oil bra cup had significantly lower pain levels, and their surgical scars were given better scores on the POSAS.

Conclusions

The results suggest that maintenance of the surgical wound in a film of oxygen-enriched olive oil for 2 weeks is a safe, effective modality for suppressing pain and promoting healing following augmentation-mastopexy.

Level of Evidence: 2
Visual obstruction, but not moderate traffic noise, increases reliance on heterospecific alarm calls
Authors: Ratnayake Chaminda P , Zhou You , Dawson Pell Francesca S E , Potvin Dominique A , Radford Andrew N , Magrath Robert D
Published: May 2021

Animals rely on both personal and social information about danger to minimize risk, yet environmental conditions constrain information. Both visual obstructions and background noise can reduce detectability of predators, which may increase reliance on social information, such as from alarm calls. Furthermore, a combination of visual and auditory constraints might greatly increase reliance on social information, because the loss of information from one source cannot be compensated by the other. Testing these possibilities requires manipulating personal information while broadcasting alarm calls. We therefore experimentally tested the effects of a visual barrier, traffic noise, and their combination on the response of Australian magpies, Cracticus tibicen, to heterospecific alarm calls. The barrier blocked only visual cues, while playback of moderate traffic noise could mask subtle acoustic cues of danger, such as of a predator’s movement, but not the alarm-call playback. We predicted that response to alarm calls would increase with either visual or acoustic constraint, and that there would be a disproportionate response when both were present. As predicted, individuals responded more strongly to alarm calls when there was a visual barrier. However, moderate traffic noise did not affect responses, and the effect of the visual barrier was not greater during traffic-noise playback. We conclude that a reduction of personal, visual information led to a greater reliance on social information from alarm calls, confirming indirect evidence from other species. The absence of a traffic-noise effect could be because in Australian magpies hearing subtle cues is less important than vision in detecting predators.
Smart mating: the cognitive ability of females influences their preference for male cognitive ability
Authors: Álvarez-Quintero Náyade , Velando Alberto , Kim Sin-Yeon
Published: May 2021

Cognitive abilities may be crucial for individuals to respond appropriately to their social and natural environment, thereby increasing fitness. However, the role of cognitive traits in sexual selection has received relatively little attention. Here, we studied 1) whether male secondary sexual traits (colour, courtship, and nest) reflect their cognitive ability, 2) whether females choose mates based on males' and their own cognitive abilities, and 3) how the interplay between secondary sexual traits and cognitive ability determines male attractiveness in the three-spined stickleback (Gasterosteus aculetaus). For this, we first evaluated the cognitive ability of sexually mature males and females in a detour-reaching task. Then, female preference was repeatedly assessed in a dichotomous-choice test, where the female was exposed to two males with contrasting performances (relatively good and bad) in the detour-reaching task. Female preference for better performing males was affected by the female's own cognitive ability. Females with relatively medium-low cognitive ability preferred males with high ability, whereas females with high ability showed no preference. We also found that males with higher cognitive abilities built more elaborated nests, but showed weaker red nuptial colouration. To our knowledge, this is among the first results that illustrate how cognitive traits of both sexes influence female mate preference, which has implications for the strength and direction of sexual selection.
Methods of privacy-preserving genomic sequencing data alignments
Authors: Lu Dandan , Zhang Yue , Zhang Ling , Wang Haiyan , Weng Wanlin , Li Li , Cai Hongmin
Published: May 2021

Genomic data alignment, a fundamental operation in sequencing, can be utilized to map reads into a reference sequence, query on a genomic database and perform genetic tests. However, with the reduction of sequencing cost and the accumulation of genome data, privacy-preserving genomic sequencing data alignment is becoming unprecedentedly important. In this paper, we present a comprehensive review of secure genomic data comparison schemes. We discuss the privacy threats, including adversaries and privacy attacks. The attacks can be categorized into inference, membership, identity tracing and completion attacks and have been applied to obtaining the genomic privacy information. We classify the state-of-the-art genomic privacy-preserving alignment methods into three different scenarios: large-scale reads mapping, encrypted genomic datasets querying and genetic testing to ease privacy threats. A comprehensive analysis of these approaches has been carried out to evaluate the computation and communication complexity as well as the privacy requirements. The survey provides the researchers with the current trends and the insights on the significance and challenges of privacy issues in genomic data alignment.
A new approach to decode DNA methylome and genomic variants simultaneously from double strand bisulfite sequencing
Authors: Liang Jialong , Zhang Kun , Yang Jie , Li Xianfeng , Li Qinglan , Wang Yan , Cai Wanshi , Teng Huajing , Sun Zhongsheng
Published: May 2021

Genetic and epigenetic contributions to various diseases and biological processes have been well-recognized. However, simultaneous identification of single-nucleotide variants (SNVs) and DNA methylation levels from traditional bisulfite sequencing data is still challenging. Here, we develop double strand bisulfite sequencing (DSBS) for genome-wide accurate identification of SNVs and DNA methylation simultaneously at a single-base resolution by using one dataset. Locking Watson and Crick strand together by hairpin adapter followed by bisulfite treatment and massive parallel sequencing, DSBS simultaneously sequences the bisulfite-converted Watson and Crick strand in one paired-end read, eliminating the strand bias of bisulfite sequencing data. Mutual correction of read1 and read2 can estimate the amplification and sequencing errors, and enables our developed computational pipeline, DSBS Analyzer (https://github.com/tianguolangzi/DSBS), to accurately identify SNV and DNA methylation. Additionally, using DSBS, we provide a genome-wide hemimethylation landscape in the human cells, and reveal that the density of DNA hemimethylation sites in promoter region and CpG island is lower than that in other genomic regions. The cost-effective new approach, which decodes DNA methylome and genomic variants simultaneously, will facilitate more comprehensive studies on numerous diseases and biological processes driven by both genetic and epigenetic variations.
Improved inference of tandem domain duplications
Authors: Aluru Chaitanya , Singh Mona
Published: May 2021

Motivation

Protein domain duplications are a major contributor to the functional diversification of protein families. These duplications can occur one at a time through single domain duplications, or as tandem duplications where several consecutive domains are duplicated together as part of a single evolutionary event. Existing methods for inferring domain-level evolutionary events are based on reconciling domain trees with gene trees. While some formulations consider multiple domain duplications, they do not explicitly model tandem duplications; this leads to inaccurate inference of which domains duplicated together over the course of evolution.

Results

Here, we introduce a reconciliation-based framework that considers the relative positions of domains within extant sequences. We use this information to uncover tandem domain duplications within the evolutionary history of these genes. We devise an integer linear programming approach that solves our problem exactly, and a heuristic approach that works well in practice. We perform extensive simulation studies to demonstrate that our approaches can accurately uncover single and tandem domain duplications, and additionally test our approach on a well-studied orthogroup where lineage-specific domain expansions exhibit varying and complex domain duplication patterns.

Availability and implementation

Code is available on github at https://github.com/Singh-Lab/TandemDuplications.

Supplementary information

Supplementary data are available at Bioinformatics online.
Population Receptive Field Characteristics in the between- and Within-Digit Dimensions of the Undominant Hand in the Primary Somatosensory Cortex
Authors: Wang Luyao , Zhang Zhilin , Okada Tomohisa , Li Chunlin , Chen Duanduan , Funahashi Shintaro , Wu Jinglong , Yan Tianyi
Published: May 2021

Somatotopy is an important guiding principle for sensory fiber organization in the primary somatosensory cortex (S1), which reflects tactile information processing and is associated with disease-related reorganization. However, it is difficult to measure the neuronal encoding scheme in S1 in vivo in normal participants. Here, we investigated the somatotopic map of the undominant hand using a Bayesian population receptive field (pRF) model. The model was established in hand space with between- and within-digit dimensions. In the between-digit dimension, orderly representation was found, which had low variability across participants. The pRF shape tended to be elliptical for digits with high spatial acuity, for which the long axis was along the within-digit dimension. In addition, the pRF width showed different change trends in the 2 dimensions across digits. These results provide new insights into the neural mechanisms in S1, allowing for in-depth investigation of somatosensory information processing and disease-related reorganization.
Population-Based Estimates of Post-acute Sequelae of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection (PASC) Prevalence and Characteristics
Authors: Hirschtick Jana L , Titus Andrea R , Slocum Elizabeth , Power Laura E , Hirschtick Robert E , Elliott Michael R , McKane Patricia , Fleischer Nancy L
Published: May 2021

Background

Emerging evidence suggests many people have persistent symptoms after acute coronavirus disease 2019 (COVID-19) illness. Our objective was to estimate the prevalence and correlates of post-acute sequelae of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (PASC).

Methods

We used a population-based probability survey of adults with COVID-19 in Michigan. Living noninstitutionalized adults aged ≥18 in the Michigan Disease Surveillance System with COVID-19 onset through mid-April 2020 were eligible for selection (N = 28 000). Among 2000 selected, 629 completed the survey between June–December 2020. We estimated PASC prevalence, defined as persistent symptoms ≥30 (30-day COVID-19) or ≥60 (60-day COVID-19) days post–COVID-19 onset, overall and by sociodemographic and clinical factors. We used modified Poisson regression to produce adjusted prevalence ratios (aPRs) for potential risk factors.

Results

The analytic sample (n = 593) was predominantly female (56.1%), aged ≥45 years (68.2%), and non-Hispanic White (46.3%) or Black (34.8%). Thirty- and 60-day COVID-19 were highly prevalent (52.5% and 35.0%), even among nonhospitalized respondents (43.7% and 26.9%) and respondents reporting mild symptoms (29.2% and 24.5%). Respondents reporting very severe (vs mild) symptoms had 2.25 times higher prevalence of 30-day COVID-19 (aPR, 2.25; 95% CI, 1.46–3.46) and 1.71 times higher prevalence of 60-day COVID-19 (aPR, 1.71; 95% CI: 1.02–2.88). Hospitalized (vs nonhospitalized) respondents had ~40% higher prevalence of both 30-day (aPR, 1.37; 95% CI: 1.12–1.69) and 60-day (aPR, 1.40; 95% CI: 1.02–1.93) COVID-19.

Conclusions

PASC is highly prevalent among cases reporting severe initial symptoms and, to a lesser extent, cases reporting mild and moderate symptoms.
Combination Therapy With Tocilizumab and Dexamethasone Cost-Effectively Reduces Coronavirus Disease 2019 Mortality
Authors: Sinha Pranay , Linas Benjamin P
Published: May 2021

Recent randomized trials suggest that interleukin-6 inhibitors reduce mortality due to severe coronavirus disease 2019. Using a decision tree model, we found that tocilizumab is cost-effective with an estimated incremental cost-effectiveness ratio of $16 520 per quality-adjusted life year gained (95% credible interval, 10 760–51 530).
mRNA modifications in cardiovascular biology and disease: with a focus on m6A modification
Authors: Kumari Rajesh , Ranjan Prabhat , Suleiman Zainab Gbongbo , Goswami Sumanta Kumar , Li Jing , Prasad Ram , Verma Suresh Kumar
Published: May 2021

Among several known RNA modifications, N6-methyladenosine (m6A) is the most studied RNA epitranscriptomic modification and controls multiple cellular functions during development, differentiation, and disease. Current research advancements have made it possible to examine the regulatory mechanisms associated with RNA methylation and reveal its functional consequences in the pathobiology of many diseases, including heart failure. m6A methylation has been described both on coding (mRNA) and non-coding RNA species including rRNA, tRNA, small nuclear RNA and circular RNAs. The protein components which catalyze the m6A methylation are termed methyltransferase or ‘m6A writers’. The family of proteins that recognize this methylation are termed ‘m6A readers’ and finally the enzymes involved in the removal of a methyl group from RNA are known as demethylases or ‘m6A erasers’. At the cellular level, different components of methylation machinery are tightly regulated by many factors to maintain the m6A methylation dynamics. The m6A methylation process impacts different stages of mRNA metabolism and the biogenesis of long non-coding RNA and miRNA. Although, mRNA methylation was initially described in the 1970s, its regulatory roles in various diseases, including cardiovascular diseases are broadly unexplored. Recent investigations suggest the important role of m6A mRNA methylation in both hypertrophic and ischaemic heart diseases. In the present review, we evaluate the significance of m6A methylation in the cardiovascular system, in cardiac homeostasis and disease, all of which may help to improve therapeutic intervention for the treatment of heart failure. RNA methylation in cardiovascular diseases: altered m6A RNA (coding and non-coding RNA) methylation is identified during different cardiovascular diseases. Increased cardiac hypertrophy is observed following METTL3 overexpression. In contrast, reduced FTO level was seen in mice following myocardial infarction. Increased cardiac fibroblasts activation or increased atherosclerotic plaques were also co-related with m6A RNA methylation.
Secondary School-based Interventions and Social Engagement of Deaf Young Adults
Authors: Ryan Claire , Shaver Debra , Garberoglio Carrie Lou , Newman Lynn A
Published: May 2021

Successful social engagement is one of many important outcomes for deaf youth as they transition from high school to adult life. This study examined the effect of self-advocacy and social/life skill trainings in secondary school settings on social engagement after high school using propensity score modeling and data from the large-scale and nationally representative National Longitudinal Transition Study-2. Analyses focused on three types of post-high school social engagement: frequency of seeing friends, involvement in group activities, and participation in community service. A fourth outcome variable was created to indicate whether the individual was at least minimally engaged. Results found that deaf youth who received self-advocacy training in secondary school were significantly more likely to be at least minimally engaged than those who had not. These findings suggest that self-advocacy training in high school can help protect deaf youth against social isolation in young adulthood.
Spatial characterization of the tachycardia circuit of atrioventricular nodal re-entrant tachycardia
Authors: Katritsis Demosthenes G , Marine Joseph E , Katritsis George , Latchamsetty Rakesh , Zografos Theodoros , Zimetbaum Peter , Buxton Alfred E , Calkins Hugh , Morady Fred , Sánchez-Quintana Damián , Anderson Robert H
Published: May 2021

Aims

The exact circuit of atrioventricular nodal re-entrant tachycardia (AVNRT) remains elusive. To assess the location and dimensions of the AVNRT circuit.

Methods and results

Both typical and atypical AVNRT were induced at electrophysiology study of 14 patients. We calculated the activation time of the fast and slow pathways, and consequently, the length of the slow pathway, by assuming an average conduction velocity of 0.04 mm/ms in the nodal area. The distance between the compact atrioventricular node and the slow pathway ablating electrode was measured on three-dimensionally reconstructed fluoroscopic images obtained in diastole and systole. We also measured the length of the histologically discrete right inferior nodal extension in 31 human hearts. The length of the slow pathway was calculated to be 10.8 ± 1.3 mm (range 8.2–12.8 mm). The distance from the node to the ablating electrode was measured in five patients 17.0 ± 1.6 mm (range 14.9–19.2 mm) and was consistently longer than the estimated length of the slow pathway (P < 0.001). The length of the right nodal inferior extension in histologic specimens was 8.1 ± 2.3 mm (range 5.3–13.7 mm). There were no statistically significant differences between these values and the calculated slow pathway lengths.

Conclusion

Successful ablation affects the tachycardia circuit without necessarily abolishing slow conduction, probably by interrupting the circuit at the septal isthmus.
SARS-CoV-2 infections in kindergartens and associated households at the start of the second wave in Berlin, Germany—a cross-sectional study
Authors: Thielecke Marlene , Theuring Stefanie , van Loon Welmoed , Hommes Franziska , Mall Marcus A , Rosen Alexander , Böhringer Falko , von Kalle Christof , Kirchberger Valerie , Kurth Tobias , Seybold Joachim , Mockenhaupt Frank P ,   the BECOSS study group, Chylla Tanja , Linzbach Elisabeth , von der Haar Annkathrin , Körner Jennifer , Gertler Maximilian , Bernhard Julian , Rössig Heike , Kurzmann Marco , Peters Frederike , Wiesmann Christoph , Horn Johanna , Steger Julia , Bethke Norma , Schmidergall Tobias , Holz Frederik , van den Berg Antje , Peña-Groth Maria Luz
Published: May 2021

Actual surveys in kindergartens on SARS-CoV-2 infections are rare. At the beginning of the second pandemic wave, we screened 12 randomly selected kindergartens in Berlin, Germany. A total of 720 participants (pre-school children, staff and connected household members) were briefly examined and interviewed, and SARS-CoV-2 infections and anti-SARS-Cov-2 IgG antibodies were assessed. About a quarter of the participants showed common cold-resembling symptoms. However, no SARS-CoV-2 infection was detected, and only one childcare worker showed IgG seroreactivity. Against a backdrop of increased pandemic activity in the community, this cross-sectional study does not suggest that kindergartens are silent transmission reservoirs.
The Transposable Elements of the Drosophila serrata Reference Panel
Authors: Tiedeman Zachery , Signor Sarah
Published: May 2021

Transposable elements (TEs) are an important component of the complex genomic ecosystem. Understanding the tempo and mode of TE proliferation, that is whether it is in maintained in transposition selection balance, or is induced periodically by environmental stress or other factors, is important for understanding the evolution of organismal genomes through time. Although TEs have been characterized in individuals or limited samples, a true understanding of the population genetics of TEs, and therefore the tempo and mode of transposition, is still lacking. Here, we characterize the TE landscape in an important model Drosophila, Drosophila serrata using the D. serrata reference panel, which is comprised of 102 sequenced inbred genotypes. We annotate the families of TEs in the D. serrata genome and investigate variation in TE copy number between genotypes. We find that many TEs have low copy number in the population, but this varies by family and includes a single TE making up to 50% of the genome content of TEs. We find that some TEs proliferate in particular genotypes compared with population levels. In addition, we characterize variation in each TE family allowing copy number to vary in each genotype and find that some TEs have diversified very little between individuals suggesting recent spread. TEs are important sources of spontaneous mutations in Drosophila, making up a large fraction of the total number of mutations in particular genotypes. Understanding the dynamics of TEs within populations will be an important step toward characterizing the origin of variation within and between species.
Inversion of electromagnetic induction data using a novel wavelet-based and scale-dependent regularization term
Authors: Deleersnyder Wouter , Maveau Benjamin , Hermans Thomas , Dudal David
Published: May 2021

The inversion of electromagnetic induction data to a conductivity profile is an ill-posed problem. Regularization improves the stability of the inversion and a smoothing constraint is typically used. However, the conductivity profiles are not always expected to be smooth. Here, we develop a new inversion scheme in which we transform the model to the wavelet space and impose a sparsity constraint. This sparsity constrained inversion scheme will minimize an objective function with a least-squares data misfit and a sparsity measure of the model in the wavelet domain. A model transform to the wavelet domain allows to investigate the temporal resolution (periodicities at different frequencies) and spatial resolution (location of the peaks) characteristics of the model, and penalizing small-scale coefficients effectively reduces the complexity of the model. The novel scale-dependent regularization term can be used to favour either blocky or smooth structures, as well as high-amplitude models in globally smooth structures in the inversion. Depending on the expected conductivity profile, a suitable wavelet basis function can be chosen. The scheme supports multiple types of regularization with the same algorithm and is thus flexible. Finally, we apply this new scheme on a frequency domain electromagnetic sounding data set, but the scheme could equally apply to any other 1-D geophysical method.
Elastic symmetry with beachball pictures
Authors: Tape Walter , Tape Carl
Published: May 2021

The elastic map, or generalized Hooke’s Law, associates stress with strain in an elastic material. A symmetry of the elastic map is a reorientation of the material that does not change the map. We treat the topic of elastic symmetry conceptually and pictorially. The elastic map is assumed to be linear, and we study it using standard notions from linear algebra—not tensor algebra. We depict strain and stress using the ‘beachballs’ familiar to seismologists. The elastic map, whose inputs and outputs are strains and stresses, is in turn depicted using beachballs. We are able to infer the symmetries for most elastic maps, sometimes just by inspection of their beachball depictions. Many of our results will be familiar, but our versions are simpler and more transparent than their counterparts in the literature.
Missing the sweet spot: one of the two N-glycans on human Gb3/CD77 synthase is expendable
Authors: Mikolajczyk Krzysztof , Bereznicka Anna , Szymczak-Kulus Katarzyna , Haczkiewicz-Lesniak Katarzyna , Szulc Bozena , Olczak Mariusz , Rossowska Joanna , Majorczyk Edyta , Kapczynska Katarzyna , Bovin Nicolai , Lisowska Marta , Kaczmarek Radoslaw , Miazek Arkadiusz , Czerwinski Marcin
Published: May 2021

N-glycosylation is a ubiquitous posttranslational modification that may influence folding, subcellular localization, secretion, solubility and oligomerization of proteins. In this study, we examined the effects of N-glycans on the activity of human Gb3/CD77 synthase, which catalyzes the synthesis of glycosphingolipids with terminal Galα1→4Gal (Gb3 and the P1 antigen) and Galα1→4GalNAc disaccharides (the NOR antigen). The human Gb3/CD77 synthase contains two occupied N-glycosylation sites at positions N121 and N203. Intriguingly, we found that while the N-glycan at N203 is essential for activity and correct subcellular localization, the N-glycan at N121 is dispensable and its absence did not reduce, but, surprisingly, even increased the activity of the enzyme. The fully N-glycosylated human Gb3/CD77 synthase and its glycoform missing the N121 glycan correctly localized in the Golgi, whereas a glycoform without the N203 site partially mislocalized in the endoplasmic reticulum. A double mutein missing both N-glycans was inactive and accumulated in the endoplasmic reticulum. Our results suggest that the decreased specific activity of human Gb3/CD77 synthase glycovariants resulted from their improper subcellular localization and, to a smaller degree, a decrease in enzyme solubility. Taken together, our findings show that the two N-glycans of human Gb3/CD77 synthase have opposing effects on its properties, revealing a dual nature of N-glycosylation and potentially a novel regulatory mechanism controlling the biological activity of proteins.
The need for adolescents’ agency in salutogenic approaches shaping physical activity in schools
Authors: Boonekamp Gwendolijn M M , Jansen Erik , O’Sullivan Tracey , Dierx John A J , Lindström Bengt , Pérez-Wilson Patricia , Álvarez-Dardet Díaz Carlos
Published: May 2021

Physical activity (PA) contributes to health throughout life. In particular, young people can benefit from this. Schools can play a key role in providing learning conditions to experience meaningful PAs aimed at inspiring students to lifelong PA. In this article, we argue the need for a salutogenic approach in schools focussing on respecting and enhancing adolescents’ agency with regard to their PA. This approach entails listening to adolescents’ perspectives and inviting them to participate in actively designing and carrying out PA as a prerequisite for their inclusive engagement. We unpack the concept of agency by drawing on insights from the Capability Approach. This provides input for the integration of agency in health promoting schools and salutogenic approaches, to enhance PA-related agency. Finally, we outline a research agenda to, eventually, create opportunities for students in schools to expand their PA-related agency.

Lay Summary Physical activity (PA) contributes to health throughout life. Schools can play a key role in fostering meaningful PA experiences to inspire students to lifelong PA. This requires schools to focus on students’ personal aspirations, providing them with the space to develop their autonomy and find opportunities to decide and act upon expanding their agency with respect to the physically active lifestyles they deem meaningful.
Impaired neuronal activity and differential gene expression in STXBP1 encephalopathy patient iPSC-derived GABAergic neurons
Authors: Ichise Eisuke , Chiyonobu Tomohiro , Ishikawa Mitsuru , Tanaka Yasuyoshi , Shibata Mami , Tozawa Takenori , Taura Yoshihiro , Yamashita Satoshi , Yoshida Michiko , Morimoto Masafumi , Higurashi Norimichi , Yamamoto Toshiyuki , Okano Hideyuki , Hirose Shinichi
Published: May 2021

Syntaxin-binding protein 1 (STXBP1; also called MUNC18–1), encoded by STXBP1, is an essential component of the molecular machinery that controls synaptic vesicle docking and fusion. De novo pathogenic variants of STXBP1 cause a complex set of neurological disturbances, namely STXBP1 encephalopathy (STXBP1-E) that includes epilepsy, neurodevelopmental disorders and neurodegeneration. Several animal studies have suggested the contribution of GABAergic dysfunction in STXBP1-E pathogenesis. However, the pathophysiological changes in GABAergic neurons of these patients are still poorly understood. Here, we exclusively generated GABAergic neurons from STXBP1-E patient-derived induced pluripotent stem cells (iPSCs) by transient expression of the transcription factors ASCL1 and DLX2. We also generated CRISPR/Cas9-edited isogenic iPSC-derived GABAergic (iPSC GABA) neurons as controls. We demonstrated that the reduction in STXBP1 protein levels in patient-derived iPSC GABA neurons was slight (approximately 20%) compared to the control neurons, despite a 50% reduction in STXBP1 mRNA levels. Using a microelectrode array–based assay, we found that patient-derived iPSC GABA neurons exhibited dysfunctional maturation with reduced numbers of spontaneous spikes and bursts. These findings reinforce the idea that GABAergic dysfunction is a crucial contributor to STXBP1-E pathogenesis. Moreover, gene expression analysis revealed specific dysregulation of genes previously implicated in epilepsy, neurodevelopment and neurodegeneration in patient-derived iPSC GABA neurons, namely KCNH1, KCNH5, CNN3, RASGRF1, SEMA3A, SIAH3 and INPP5F. Thus, our study provides new insights for understanding the biological processes underlying the widespread neuropathological features of STXBP1-E.
Metachronal Swimming with Flexible Legs: A Kinematics Analysis of the Midwater Polychaete Tomopteris
Authors: Daniels Joost , Aoki Nadège , Havassy Josh , Katija Kakani , Osborn Karen J
Published: May 2021

Synopsis

Aquatic animals have developed a wide array of adaptations specific to life underwater, many of which are related to moving in the water column. Different swimming methods have emerged, such as lift-based flapping, drag-based body undulations, and paddling. Patterns occur across scales and taxa, where animals with analogous body features use similar locomotory methods. Metachronal paddling is one such wide-spread propulsion mechanism, occurring in taxa as diverse as ctenophores, crustaceans, and polychaetes. Sequential movement of multiple, near identical appendages, allows for steady swimming through phase-offsets between adjacent propulsors. The soft-bodied, holopelagic polychaete Tomopteris has two rows of segmental appendages (parapodia) positioned on opposite sides along its flexible body that move in a metachronal pattern. The outer one-third of their elongate parapodia consist of two paddle-like pinnules that can be spread or, when contracted, fold together to change the effective width of the appendage. Along with metachronal paddling, tomopterid bodies undulate laterally, and by using high speed video and numerical modeling, we seek to understand how these two behaviors combine to generate effective swimming. We collected animals using deep-diving remotely operated vehicles, and recorded video data in shore- and ship-based imaging laboratories. Kinematics were analyzed using landmark tracking of features in the video data. We determined that parapodia are actively moved to generate thrust and pinnules are actively spread and contracted to create differences in drag between power and recovery strokes. At the same time, the body wave increases the parapodium stroke angle and extends the parapodia into undisturbed water adjacent to the body, enhancing thrust. Based on kinematics measurements used as input to a 1D numerical model of drag-based swimming, we found that spreading of the pinnules during the power stroke provides a significant contribution to propulsion, similar to the contribution provided by the body wave. We conclude that tomopterids combine two different propulsive modes, which are enabled by their flexible body plan. This makes their anatomy and kinematics of interest not only for biologists, but also for soft materials and robotics engineers.
Hormonal Prostaglandin F2α Mediates Behavioral Responsiveness to a Species-Specific Multi-component Male Hormonal Sex Pheromone in a Female Fish
Authors: Sorensen Peter W , Levesque Haude M
Published: May 2021

Synopsis

Although hormonally-derived female sex pheromones have been well described in approximately a dozen species of teleost fish, only a few male sex pheromones have been characterized and the neuroendocrine underpinnings of behavioral responsiveness to them is not understood. Herein, we describe a study that addresses this question using the goldfish, Carassius auratus, an important model species of how hormones drive behavior in egg-laying teleost fishes. Our study had four components. First, we examined behavioral responsiveness of female goldfish and found that when injected with prostaglandin F2α (PGF2α), a treatment that drives female sexual receptivity, and found that they became strongly and uniquely attracted to the odor of conspecific mature males, while non-PGF2α-treated goldfish did not discern males from females. Next, we characterized the complexity and specificity of the male pheromone by examining the responsiveness of PGF2α-treated females to the odor of either mature male conspecifics or male common carp odor, as well as their nonpolar and polar fractions. We found that the odor of male goldfish was more attractive than that of male common carp, and that its activity was attributable to both its nonpolar and polar fractions with the later conveying information on species-identity. Third, we hypothesized that androstenedione (AD), a 19-carbon sex steroid produced by all male fish might be the nonpolar fraction and tested whether PGF2α-treated goldfish were attracted to either AD alone or as part of a mixture in conspecific water. We found that while AD was inactive on its own, it became highly attractive when added to previously unattractive female conspecific water. Lastly, in a test of whether nonhormonal conspecific odor might determine species-specificity, we added AD to water of three species of fish and found that while AD made goldfish water strongly attractive, its effects on other species holding water were small. We conclude that circulating PGF2α produced at the time of ovulation induces behavioral sensitivity to a male sex pheromone in female goldfish and that this male pheromone is comprised of AD and a mixture of body metabolites. Because PGF2α commonly mediates ovulation and female sexual behavior in egg-laying fishes, and AD is universally produced by male fishes as a precursor to testosterone, we suggest that these two hormones may have similar roles mediating male–female behavior and communication in many species of fish.
Antibody status and cumulative incidence of SARS-CoV-2 infection among adults in three regions of France following the first lockdown and associated risk factors: a multicohort study
Authors: Carrat Fabrice , de Lamballerie Xavier , Rahib Delphine , Blanché Hélène , Lapidus Nathanael , Artaud Fanny , Kab Sofiane , Renuy Adeline , Szabo de Edelenyi Fabien , Meyer Laurence , Lydié Nathalie , Charles Marie-Aline , Ancel Pierre-Yves , Jusot Florence , Rouquette Alexandra , Priet Stéphane , Saba Villarroel Paola Mariela , Fourié Toscane , Lusivika-Nzinga Clovis , Nicol Jérôme , Legot Stephane , Druesne-Pecollo Nathalie , Esseddik Younes , Lai Cindy , Gagliolo Jean-Marie , Deleuze Jean-François , Bajos Nathalie , Severi Gianluca , Touvier Mathilde , Zins Marie ,   for the SAPRIS and SAPRIS-SERO study groups
Published: May 2021

Background

We aimed to estimate the seropositivity to anti-SARS-CoV-2 antibodies in May–June 2020 after the first lockdown period in adults living in three regions in France and to identify the associated risk factors.

Methods

Between 4 May 2020 and 23 June 2020, 16 000 participants in a survey on COVID-19 from an existing consortium of three general adult population cohorts living in the Ile-de-France (IDF) or Grand Est (GE) (two regions with high rate of COVID-19) or in the Nouvelle-Aquitaine (NA) (with a low rate) were randomly selected to take a dried-blood spot for anti-SARS-CoV-2 antibodies assessment with three different serological methods (ClinicalTrial Identifier #NCT04392388). The primary outcome was a positive anti-SARS-CoV-2 ELISA IgG result against the spike protein of the virus (ELISA-S). Estimates were adjusted using sampling weights and post-stratification methods. Multiple imputation was used to infer the cumulative incidence of SARS-CoV-2 infection with adjustments for imperfect tests accuracies.

Results

The analysis included 14 628 participants, 983 with a positive ELISA-S. The weighted estimates of seropositivity and cumulative incidence were 10.0% [95% confidence interval (CI): 9.1%, 10.9%] and 11.4% (95% CI: 10.1%, 12.8%) in IDF, 9.0% (95% CI: 7.7%, 10.2%) and 9.8% (95% CI: 8.1%, 11.8%) in GE and 3.1% (95% CI: 2.4%, 3.7%) and 2.9% (95% CI: 2.1%, 3.8%) in NA, respectively. Seropositivity was higher in younger participants [odds ratio (OR) = 1.84 (95% CI: 1.79, 6.09) in <40 vs 50–60 years old and OR = 0.56 (95% CI: 0.42, 0.74) in ≥70 vs 50–60 years old)] and when at least one child or adolescent lived in the same household [OR = 1.30 (95% CI: 1.11, 1.53)] and was lower in smokers compared with non-smokers [OR = 0.71 (95% CI: 0.57, 0.89)].

Conclusions

Seropositivity to anti-SARS-CoV-2 antibodies in the French adult population was ≤10% after the first wave. Modifiable and non-modifiable risk factors were identified.
Biomedical and clinical English model packages for the Stanza Python NLP library
Authors: Zhang Yuhao , Zhang Yuhui , Qi Peng , Manning Christopher D , Langlotz Curtis P
Published: May 2021

Objective

The study sought to develop and evaluate neural natural language processing (NLP) packages for the syntactic analysis and named entity recognition of biomedical and clinical English text.

Materials and Methods

We implement and train biomedical and clinical English NLP pipelines by extending the widely used Stanza library originally designed for general NLP tasks. Our models are trained with a mix of public datasets such as the CRAFT treebank as well as with a private corpus of radiology reports annotated with 5 radiology-domain entities. The resulting pipelines are fully based on neural networks, and are able to perform tokenization, part-of-speech tagging, lemmatization, dependency parsing, and named entity recognition for both biomedical and clinical text. We compare our systems against popular open-source NLP libraries such as CoreNLP and scispaCy, state-of-the-art models such as the BioBERT models, and winning systems from the BioNLP CRAFT shared task.

Results

For syntactic analysis, our systems achieve much better performance compared with the released scispaCy models and CoreNLP models retrained on the same treebanks, and are on par with the winning system from the CRAFT shared task. For NER, our systems substantially outperform scispaCy, and are better or on par with the state-of-the-art performance from BioBERT, while being much more computationally efficient.

Conclusions

We introduce biomedical and clinical NLP packages built for the Stanza library. These packages offer performance that is similar to the state of the art, and are also optimized for ease of use. To facilitate research, we make all our models publicly available. We also provide an online demonstration (http://stanza.run/bio).