bluuebunny/crossref_metadata_2025_split huggingface dataset:
The psychological distress of parents is associated with reduced linear growth of children: evidence from a nationwide population survey
Authors: Susiloretni Kun A , Smith Emily R , Suparmi  , Marsum  , Agustina Rina , Shankar Anuraj H 
Published: November 2020

AbstractBackgroundStunting, an indicator of restricted linear growth, has become a primary measure of childhood undernutrition due to its persistent high prevalence globally, and importance for health and development. Although the etiology is recognized to be complex, most analyses have focused on biomedical determinants, with limited attention to social factors affecting care and nurturing in the home.ObjectivesTo identify the association between parental distress and linear growth and stunting and to examine z score loss due to any parental distress and socioeconomic, behavioral, and physiologic risk factors on for linear growthDesignCross sectional studyParticipants54,261 households from the Indonesia National Health Survey 2013. Main outcome measures. Multivariate linear, logistic, and multilevel multinomial logistic regression, using survey weights, were used to assess the relationship between parental distress, as assessed by the WHO Self Reporting Questionnaire, with height-for-age z score (HAZ), stunting, and behavioral risk factors for stunting.ResultsMaternal, paternal and parental distress (i.e. both maternal and paternal distress) were associated with reduced linear growth of the children by 0.091, 0.13 and 0.21 z-scores, respectively. Maternal and paternal distress increased the risk of mild stunting (HAZ < -1) by 38% and 39%, and the risk of moderate stunting (HAZ < -2) by 41% and 23%, respectively. Parental stress increased the risk of moderate and severe stunting by 67% and 41%. Any parental distress accounted for 5.6% of the modeled overall loss of HAZ-score due to interactions with socioeconomic status (low maternal occupational status, low wealth, low maternal occupation) and behavioral (poor garbage sanitation) factors, rendering it amongst the more influential factors on linear growth. The modeled overall loss of HAZ-score incorporating any parental distress was associated with socioeconomic factors (26.1%) including, in descending order, low maternal occupational status, low wealth, low maternal education, low paternal occupational status, rural residence; behavioral factors (15.3%) including open garbage disposal, unimproved water disposal, paternal smoking, not using iodized salt; physiological factors (13.5%) including low maternal height, female child, paternal height, maternal mid-upper arm circumference.ConclusionsThese findings highlight the complex etiology of stunting, and suggest nutritional and other biomedical interventions are insufficient, and that promotion of mental and behavioral health programs for parents are essential to achieve child growth and development, and would likely foster taller, healthier, smarter, and thriving populations.
One year cross-sectional study in adult and neonatal intensive care units reveals the bacterial and antimicrobial resistance genes profiles in patients and hospital surfaces
Authors: Christoff Ana Paula , Rodrigues Sereia Aline Fernanda , Flores Cruz Giuliano Netto , de Bastiani Daniela Carolina , Silva Vanessa Leitner , Hernandes Camila , Metran Nascente Ana Paula , dos Reis Ana Andrea , Gonçalves Viessi Renata , Pereira Marques Andrea dos Santos , Braga Bianca Silva , Lovizio Raduan Telma Priscila , Valle Martino Marines Dalla , de Menezes Fernando Gatti , de Oliveira Luiz Felipe Valter 
Published: November 2020

AbstractSeveral studies have shown the ubiquitous presence of bacteria in the hospital environmental surfaces, staff, and patients. Frequently, these bacteria are related to HAI (healthcare-associated infections) and carry antimicrobial resistance (AMR). These HAI-related bacteria contributes to a major public health issue by increasing patient morbidity and mortality during or after hospital stay. Bacterial high-throughput amplicon gene sequencing along with AMR genes identification and whole genome sequencing (WGS) are new biotechnological tools that allow multiple-sample screening for a diversity of bacteria. In this paper, we used these methods to perform an one-year cross sectional profiling of bacteria and AMR genes in adult and neonatal intensive care units (ICU and NICU) in a Brazilian public hospital. Our results showed high abundances of HAI-related bacteria as S. epidermidis, S. aureus, K. pneumoniae, A. baumannii complex, E. coli, E. faecalis and P. aeruginosa in patients and hospital surfaces. Most abundant AMR genes detected throughout ICU and NICU were mecA, blaCTX-M-1 group, blaSHV-like and blaKPC-like. We found that NICU environment and patients were more widely contaminated with pathogenic bacteria than ICU. Patient samples, despite the higher bacterial load, have lower bacterial diversity than environmental samples in both units. Finally, we also identified contamination hotspots in the hospital environment showing constant frequencies of bacterial and AMR contamination throughout the year. WGS sequencing, 16S rRNA oligotypes and AMR identification allowed a high-resolution data analysis for bacterial characterization and its distributions along the hospital microbiome profile.
Ancestral ecological regime shapes reaction to food limitation in the Least Killifish,Heterandria formosa
Authors: Felmy Anja , Leips Jeff , Travis Joseph 
Published: November 2020

AbstractIn populations with contrasting densities of conspecifics, we often see genetically-based differences in life histories. The divergent life histories could be driven by several distinct agents of selection, including, amongst other factors, variation in per-capita food levels, the intensity of crowding-induced stress, rates of pathogen transmission, mate encounter rates, and the rates with which waste products accumulate. Understanding which selective agents act in a particular population is important as the type of agents can affect both population dynamics and evolutionary responses to density-dependent selection. Here we used a full-factorial laboratory experiment to examine whether two populations of a small live-bearing freshwater fish, characterised by high-density/low-predation or low-density/high-predation conditions, are adapted to different per-capita food levels. As expected, fish from the higher density regime handled food limitation better than those from the lower density regime. Although the lower food level resulted in slower growth, smaller body size, delayed maturation and reduced survival in both populations, especially survival to maturity showed a highly significant population x food-level interaction. At low food, 75% of fish from the low-density population died, compared to only 15% of fish from the high-density population. This difference was much smaller at high food (15% vs. 0% mortality), and was mediated, at least partly, through a larger size at birth of fish from the high-density regime. While we cannot preclude other agents of selection from operating differently in the study populations, we demonstrate that selection at higher density confers a greater ability to cope with low per-capita food availability.
Single-cell Multi-omics reveal heterogeneity and metastasis potential in different liver cancer cell lines
Authors: Wang Shanshan , Xie Jiarui , Zou Xuanxuan , Pan Taotao , Zhuang Zhenkun , Wang Zifei , Yuan Yue , Liu Longqi , Liu Shiping , Wu Liang 
Published: November 2020

AbstractHepatocellular carcinoma (HCC) is a malignant neo-plasm with a high recurrence and metastatic rate, accounted for poor prognosis. Commonly existed heterogeneity is concerned with neoplasia, cancer progression, therapeutic resistance and metastasis is the principal cause of cancer lethality. As development of multi-omics methods in single-cell technology provides multi-faceted insight into disease processes in the era of precision medicine. Here, we interrogated single-cell transcriptomes, proteomes and epigenetic information, revealing metastasis potential heterogeneity in 5 HCC cell lines across different metastasis capacity. We confirmed that higher mesenchymal (M) status but not proliferation rate was associated with stronger metastasis ability of cell lines. Besides, we identified a subgroup being common in several cell lines, showing a higher hypoxic signature. A gene set involving 14 genes were chosen to represent the hypoxia state, much consistent than previous reported gene set, and showed worse prognosis association in TCGA data. This hypoxic subgroup prefers glycolysis metabolism than OXPO, and showed non-cycling, quiescent state which could be resistant to many proliferation-targeting drugs. Our results provide a comprehensive understanding of characteristic associated with metastasis capacity of HCC cell line, which will guide the metastasis mechanism study of HCC.
Physical and psychiatric comorbidity among patients with severe mental illness as seen in Uganda
Authors: Mpango Richard Stephen , Ssembajjwe Wilber , Rukundo Godfrey Zari , Birungi Carol , Kalungi Allan , Gadow Kenneth D. , Patel Vikram , Nyirenda Moffat , Kinyanda Eugene 
Published: November 2020

AbstractThis study established the prevalence of physical and psychiatric comorbidity and associated risk factors among 1,201 out-patients with severe mental illness (SMI) attending Butabika and Masaka hospitals in Uganda. Participants completed an assessment battery; structured, standardized and locally translated instruments. SMIs were established using the MINI International Neuropsychiatric Interview version 7.2. We used logistic regression to determine the association between physical and psychiatric comorbidity and risk factors. Prevalence of physical and psychiatric comorbidity was 13.1 %. Childhood sexual abuse (aOR 1.06, 95% CI 1.03 -1.10, P=0.001), sexual abuse in adulthood (aOR 2.22, 95% CI 1.60 - 3.08, P<0.001), childhood physical abuse (aOR 1.07, 95% CI 1.03 - 1.10, P<0.001) and physical abuse in adulthood (aOR 1.69, 95% CI 1.30 - 2.20, P<0.001) were associated with an increased risk of having comorbid psychiatric and physical disorders. Emerging healthcare models in Uganda should optimise care for people with physical and psychiatric comorbidity.
Clinical and microbiological assessments of COVID-19 in healthcare workers: a prospective longitudinal study
Authors: Bal Antonin , Brengel-Pesce Karen , Gaymard Alexandre , Quéromès Grégory , Guibert Nicolas , Frobert Emile , Bouscambert Maude , Trabaud Mary-Anne , Allantaz-Frager Florence , Oriol Guy , Cheynet Valérie , d’Aubarede Constance , Massardier-Pilonchery Amélie , Buisson Marlyse , Lupo Julien , Pozzetto Bruno , Poignard Pascal , Lina Bruno , Fassier Jean-Baptiste , Morfin-Sherpa Florence , Trouillet-Assant Sophie 
Published: November 2020

BackgroundA comprehensive assessment of COVID-19 in healthcare workers (HCWs) including the investigation of viral shedding duration is critical.MethodsA longitudinal study including 319 HCWs was conducted. After SARS-CoV-2 screening with RT-PCR assay, other respiratory pathogens were tested with a multiplex molecular panel. For SARS-CoV-2 positive HCWs, the normalized viral load was determined weekly; viral culture and virus neutralization assays were also performed. For 190 HCWs tested negative, SARS-CoV-2 serological testing was performed one month after the inclusion.FindingsOf the 319 HCWs included, 67 (21.0%) were tested positive for SARS-CoV-2; two of them developed severe COVID-19. The proportion of smell and taste dysfunction was significantly higher in SARS-CoV-2 positive HCWs than in negative ones (38.8% vs 9.5% and 37.3% vs 10.7%, respectively, p<0.001). Of the 67 positive patients, 9.1% were tested positive for at least another respiratory pathogen (vs19.5%, p=0.07). The proportion of HCWs with a viral load > 5.0 log10cp/ml (Ct value <25) was less than 15% at 8 days after symptom onset; 12% of them were still positive after 40 days (Ct >37). More than 90% of culturable virus had a viral load > 4.5 log10cp/ml (Ct < 26) and were collected within 10 days after symptom onset. From HCWs tested negative, 6/190 (3.2%) exhibited seroconversion for IgG antibodies.InterpretationOur data suggest that the determination of normalized viral load (or its estimation through Ct values) can be useful for discontinuing isolation of HCWs and facilitating their safe return to work. HCWs presenting mild COVID-19 are unlikely infectious 10 days after symptom onset.FundingFondation des Hospices Civils de Lyon. bioMérieux provided diagnostic kits.
Nowcasting and forecasting provincial-level SARS-CoV-2 case positivity using google search data in South Africa
Authors: Nsoesie Elaine O. , Sy Karla Therese L. , Oladeji Olubusola , Sefala Raesetje , Nichols Brooke E. 
Published: November 2020

ABSTRACTData from non-traditional data sources, such as social media, search engines, and remote sensing, have previously demonstrated utility for disease surveillance. Few studies, however, have focused on countries in Africa, particularly during the SARS-CoV-2 pandemic. In this study, we use searches of COVID-19 symptoms, questions, and at-home remedies submitted to Google to model COVID-19 in South Africa, and assess how well the Google search data forecast short-term COVID-19 trends. Our findings suggest that information seeking trends on COVID-19 could guide models for anticipating COVID-19 trends and coordinating appropriate response measures.
Effectiveness of an Ozone Disinfecting and Sanitizing Cabinet to Decontaminate a Surrogate Virus for SARS-CoV-2 on N-95 Masks
Authors: Beaudry Megan S. , Frederick Julia C. , Lott Megan E. J. , Norfolk William A. , Glenn Travis C. , Lipp Erin K. 
Published: November 2020

AbstractMedical demands during the COVID-19 pandemic have triggered a grave shortage of medical-grade personal protective equipment (PPE), especially, N95 respirators. N95 respirators are critical for the personal protection of medical providers and others when being exposed to individuals with infections caused by the SARS-CoV-2 coronavirus. To address the shortage of N95 respirators, innovative methods are needed to decontaminate coronaviruses from N95 respirators, allowing them to be safely reused by healthcare workers. For this research, we use a commercial ozone disinfecting cabinet to examine the efficacy of ozone-based disinfection of a conservative surrogate virus for SARS-CoV-2, the MS2 bacteriophage. Treatment of mask materials with enhanced ozone treatment resulted in 2.38-log 10 (>99%) reduction of phage from household dust masks and a range of 1.43-log 10 (96.2%) to 4-log 10 (99.99%) reductions of phage from common N95 mask materials.
Age and diet shape the genetic architecture of body weight in Diversity Outbred mice
Authors: Wright Kevin M. , Deighan Andrew , Di Francesco Andrea , Freund Adam , Jojic Vladimir , Churchill Gary , Raj Anil 
Published: November 2020

AbstractUnderstanding how genetic variation shapes an age-dependent complex trait relies on accurate quantification of both the additive genetic effects and genotype-environment interaction effects in an age-dependent manner. We used a generalization of the linear mixed model to quantify diet-dependent genetic contributions to body weight and growth rate measured from early development through adulthood of 960 Diversity Outbred female mice subjected to five dietary interventions. We observed that heritability of body weight remained substantially high (h2≈ 0.8) throughout adulthood under the 40% calorie restriction diet, while heritability, although still appreciably high, declined with age under all other dietary regimes. We identified 14 loci significantly associated with body weight in an age-dependent manner and 19 loci that contribute to body weight in an age- and diet-dependent manner. We found the effect of body weight alleles to be dynamic with respect to genomic background, age, and diet, identifying the scope of pleiotropy and several instances of allelic heterogeneity. In many cases, we fine-mapped these loci to narrow genomic intervals containing a few genes and impute putative functional variants from the genome sequence of the DO founders. Of the loci associated with body weight in a diet-dependent manner, many have been previously linked to neurological function and behavior in mice or humans. These results enable us to more fully understand the dynamics of the genetic architecture of body weight with age and in response to different dietary interventions, and to predict the effectiveness of dietary intervention on overall health in distinct genetic backgrounds.
Vascular cognitive impairment in the mouse reshapes visual, spatial network functional connectivity
Authors: Hall Gerard R , Boehm-Sturm Philipp , Dirnagl Ulrich , Finke Carsten , Foddis Marco , Harms Christoph , Koch Stefan Paul , Kuchling Joseph , Madan Christopher R , Mueller Susanne , Sassi Celeste , Sotiropoulos Stamatios N , Trueman Rebecca C , Wallis Marcus , Yildirim Ferah , Farr Tracy D 
Published: November 2020

AbstractConnectome analysis of neuroimaging data is a rapidly expanding field to identify disease specific biomarkers. Structural diffusion MRI connectivity has been useful in individuals with radiological features of small vessel disease, such as white matter hyperintensities. Global efficiency, a network metric calculated from the structural connectome, is an excellent predictor of cognitive decline. To dissect the biological underpinning of these changes, animal models are required. We tested whether the structural connectome is altered in a mouse model of vascular cognitive impairment. White matter damage was more pronounced by 6 compared to 3 months. Global efficiency remained intact, but the visual association cortex exhibited increased structural connectivity with other brain regions. Exploratory resting state functional MRI connectivity analysis revealed diminished default mode network activity in the model compared to shams. Further perturbations were observed in a primarily cortical hub and the retrosplenial and visual cortices, and the hippocampus were the most affected nodes. Behavioural deficits were observed in the cued water maze, supporting the suggestion that the visual and spatial memory networks are affected. We demonstrate specific circuitry is rendered vulnerable to vascular stress in the mouse, and the model will be useful to examine pathophysiological mechanisms of small vessel disease.Graphical abstract
A systemic whole-plant change in redox levels accompanies the rapid systemic response of Arabidopsis to wounding
Authors: Fichman Yosef , Mittler Ron 
Published: November 2020

AbstractReactive oxygen species (ROS) play a key role in regulating plant responses to different abiotic stresses, wounding and pathogen attack. In addition to triggering responses at the tissues directly subjected to stress, ROS were recently shown to mediate a rapid whole-plant systemic signal, termed the “ROS wave”, required for inducing a state of systemic acquired acclimation, or systemic wound response. However, whether the ROS wave that spreads from the local tissues subjected to wounding to the rest of the plant triggers alterations in redox levels, is mostly unknown at present. Here, using a genetically-encoded reporter for cellular glutathione redox changes, roGFP1, we show that the wounding-induced systemic ROS wave in Arabidopsis thaliana is accompanied by a rapid systemic wave of cytosolic redox oxidation, termed a “redox wave”. The ROS wave may therefore trigger changes in redox levels in systemic leaves that in turn can trigger transcriptional, metabolic and proteomic changes resulting in acclimation and/or systemic wound responses.One sentence summaryThe wounding-induced reactive oxygen species (ROS) wave is accompanied by a systemic whole-plant redox response.
BASE: a novel workflow to integrate non-ubiquitous genes in comparative genomics analyses for selection
Authors: Forni Giobbe , Ruggeri Angelo Alberto , Piccinini Giovanni , Luchetti Andrea 
Published: November 2020

AbstractInferring the selective forces that different ortholog genes underwent across different lineages can make us understand the evolutionary processes which shaped their extant diversity. The more widespread metric to estimate coding sequences selection regimes across across their sites and species phylogeny is the ratio of nonsynonymous to synonymous substitutions (dN/dS, also known asω). Nowadays, modern sequencing technologies and the large amount of already available sequence data allow the retrieval of thousands of genes orthology groups across large numbers of species. Nonetheless, the tools available to explore selection regimes are not designed to automatically process all orthogroups and practical usage is often restricted to those consisting of single-copy genes which are ubiquitous across the species considered (i.e.the subset of genes which is shared by all the species considered). This approach limits the scale of the analysis to a fraction of single-copy genes, which can be as lower as an order of magnitude in respect to non-ubiquitous ones (i.e.those which are not present across all the species considered). Here we present a workflow named BASE that - leveraging the CodeML framework - ease the inference and interpretation of selection regimes in the context of comparative genomics. Although a number of bioinformatics tools have already been developed to facilitate this kind of analyses, BASE is the first to be specifically designed to ease the integration of non-ubiquitous genes orthogroups. The workflow - along with all the relevant documentation - is available at github.com/for-giobbe/BASE.
DNAscent v2: Detecting Replication Forks in Nanopore Sequencing Data with Deep Learning
Authors: Boemo Michael A. 
Published: November 2020

AbstractThe detection of base analogues in Oxford Nanopore Technologies (ONT) sequencing reads has become a promising new method for the high-throughput measurement of DNA replication dynamics with single-molecule resolution. This paper introduces DNAscent v2, software that uses a residual neural network to achieve fast, accurate detection of the thymidine analogue BrdU with single-base resolution. DNAscent v2 comes equipped with an autoencoder that detects replication forks, origins, and termination sites in ONT sequencing reads from both synchronous and asynchronous cell populations, outcompeting previous versions and other tools across different experimental protocols. DNAscent v2 is open-source and available athttps://github.com/MBoemo/DNAscent.
Artemin and its cognate receptor, GFRα3, play a function role in osteoarthritis pain
Authors: Minnema Laura , Mishra Santosh K. , Lascelles B Duncan X 
Published: November 2020

AbstractOsteoarthritis associated pain (OA-pain) is a significant global problem. OA-pain limits limb use and mobility, and is associated with widespread sensitivity. Therapeutic options are limited, and the ones that are available are often associated with side or adverse effects. The lack of therapeutic options is partly due to a lack of understanding of clinically relevant underlying neural mechanisms of OA-pain. In previous work in naturally occurring OA-pain in dogs, we identified potential signaling molecules (artemin/GFRα3) that were upregulated. Here, we use multiple approaches including knockout mice, immunological suppression in a mouse model of OA, and clinically relevant measures of sensitivity and limb use to explore the functional role of artemin/GFRα3 signaling in OA-pain. We found the monoiodoacetate (MIA)-induced OA model in mice is associated with decreased limb use and hypersensitivity. GFRα3 expression is increased in sensory neurons. Exogenous artemin induces heat, cold and mechanical hypersensitivity, and anti-artemin monoclonal antibody administration reverses this hypersensitivity and restores limb use in mice with MIA-induced OA pain. Our results provide a molecular basis of arthritis pain linked with artemin/GFRα3 signaling and indicate that further work is warranted to investigate the neuronal plasticity and the pathways that drive pain in OA.