bluuebunny/crossref_metadata_2025_split huggingface dataset:
miRbiom: Machine-Learning on Bayesian Causal Nets of RBP-miRNA interactions successfully predicts miRNA profiles
Authors: Pradhan Upendra Kumar , Sharma Nitesh Kumar , Kumar Prakash , Kumar Ashwani , Gupta Sagar , Shankar Ravi 
Published: June 2020

AbstractFormation of mature miRNAs and their expression is a highly controlled process. It is very much dependent upon the post-transcriptional regulatory events. Recent findings suggest that several RNA binding proteins beyond Drosha/Dicer are involved in the processing of miRNAs. Deciphering of conditional networks for these RBP-miRNA interactions may help to reason the spatio-temporal nature of miRNAs which can also be used to predict miRNA profiles. In this direction, >25TB of data from different platforms were studied (CLIP-seq/RNA-seq/miRNA-seq) to develop Bayesian causal networks capable of reasoning miRNA biogenesis. The networks ably explained the miRNA formation when tested across a large number of conditions and experimentally validated data. The networks were modeled into an XGBoost machine learning system where expression information of the network components was found capable to quantitatively explain the miRNAs formation levels and their profiles. The models were developed for 1,204 human miRNAs whose accurate expression level could be detected directly from the RNA-seq data alone without any need of doing separate miRNA profiling experiments like miRNA-seq or arrays. A first of its kind, miRbiom performed consistently well with high average accuracy (91%) when tested across a large number of experimentally established data from several conditions. It has been implemented as an interactive open access web-server where besides finding the profiles of miRNAs, their downstream functional analysis can also be done. miRbiom will help to get an accurate prediction of human miRNAs profiles in the absence of profiling experiments and will be an asset for regulatory research areas. The study also shows the importance of having RBP interaction information in better understanding the miRNAs and their functional projectiles where it also lays the foundation of such studies and software in future.
Calcitriol, the active form of vitamin D, is a promising candidate for COVID-19 prophylaxis
Authors: Mok Chee Keng , Ng Yan Ling , Ahidjo Bintou Ahmadou , Hua Lee Regina Ching , Choy Loe Marcus Wing , Liu Jing , Tan Kai Sen , Kaur Parveen , Chng Wee Joo , Wong John Eu-Li , Wang De Yun , Hao Erwei , Hou Xiaotao , Tan Yong Wah , Mak Tze Minn , Lin Cui , Lin Raymond , Tambyah Paul , Deng JiaGang , Hann Chu Justin Jang 
Published: June 2020

AbstractCOVID-19, the disease caused by SARS-CoV-2 (1), was declared a pandemic by the World Health Organization (WHO) in March 2020 (2). While awaiting a vaccine, several antivirals are being used to manage the disease with limited success (3, 4). To expand this arsenal, we screened 4 compound libraries: a United States Food and Drug Administration (FDA) approved drug library, an angiotensin converting enzyme-2 (ACE2) targeted compound library, a flavonoid compound library as well as a natural product library. Of the 121 compounds identified with activity against SARS-CoV-2, 7 were shortlisted for validation. We show for the first time that the active form of Vitamin D, calcitriol, exhibits significant potent activity against SARS-CoV-2. This finding paves the way for consideration of host-directed therapies for ring prophylaxis of contacts of SARS-CoV-2 patients.
Responsibility for vitamin D supplementation of elderly care home residents in England: falling through the gap between medicine and food
Authors: Williams Joseph , Williams Carol 
Published: June 2020

AbstractIntroductionVitamin D supplements are recommended for elderly care home residents with little sunlight exposure. However, their use in care homes is limited and vitamin D deficiency in residents is widespread. This study aimed to understand perceived responsibility for the vitamin D status of residents and the determinants of current practice around supplementation.MethodsThirteen semi-structured interviews were conducted with key informants in two areas of Southern England including care home managers, general practitioners (GPs) and public health professionals. Interviews were audio recorded and transcribed verbatim.ResultsInductive thematic analysis identified four themes – medical framing; professional and sector boundaries; awareness of national guidance; and ethical and practical issues. Vitamin D supplements were not routinely given to residents, and most participants, including the GPs, believed the vitamin D status of residents was the responsibility of the GP. Care home managers felt unable to make decisions about vitamin D and vulnerable to suggestions of wrongdoing in administering over-the-counter vitamin tablets. This results in vitamin D requiring prescription by medical professionals and few care home residents receiving vitamin D supplements.ConclusionThe medical framing of vitamin D supplements in care homes is a practical barrier to residents receiving them and is out of step with public health recommendations. Vitamin D levels in care home residents could be improved through universal supplementation. This requires a paradigm shift so that vitamin D is understood as a protective nutrient as well as a medicine, and a public health as well as a medical responsibility. The failure to ensure vitamin D adequacy of residents may emerge as a factor in the spread and severity of COVID-19 in care homes and gives increased urgency to addressing this issue.KEY MESSAGESWhat is already known about the subject?Nutrition guidelines recommend elderly care home residents take vitamin D supplements as a preventative measure. This is rarely implemented in practice and vitamin D inadequacy is widespread.What are the new findings?Medical framing of vitamin D in the care sector puts elderly residents at risk of vitamin D deficiency. Vitamin D supplements are perceived as medicines requiring an individual prescription and diagnosis by a medical professional. This is out of step with public health recommendations. The system’s failure to protect the vitamin D status of the elderly in care homes may have implications in the context of COVID-19.How might these results change the focus of research or practice?Prompt a review of current guidelines and regulations in England to establish responsibility for implementing public health recommendations on vitamin D supplementation in care homes. Further research on feasibility of implementation strategies is needed.
Artificial light at night amplifies seasonal relapse of haemosporidian parasites in a widespread songbird
Authors: Becker Daniel J. , Singh Devraj , Pan Qiuyun , Montoure Jesse D. , Talbott Katherine M. , Wanamaker Sarah , Ketterson Ellen D. 
Published: June 2020

AbstractUrban habitats can shape interactions between hosts and parasites by altering not only exposure rates but also within-host processes. Artificial light at night is common in urban environments, and chronic exposure can impair host immunity in ways that may increase infection. However, studies of causal links between this stressor, immunity, and infection dynamics are rare, particularly in migratory animals. Here, we experimentally tested how artificial light at night affects cellular immunity and haemosporidian parasite intensity across the annual cycle of migrant and resident subspecies of the dark-eyed junco (Junco hyemalis). We monitored an experimental group exposed to light at night and a control group under natural light/dark cycles as they passed through short days simulating early spring to longer days simulating the breeding season, followed by fall migration. Using generalized additive models, we show that artificial light at night increased inflammation, and leukocyte counts were greatest in early spring and fall. At the start of the experiment, few birds had active infections based on microscopy, but PCR revealed many birds had chronic infections. Artificial light at night increased parasitemia across the annual cycle, with strong peaks in spring and fall that were largely absent in control birds. As birds were kept in indoor aviaries to prevent vector exposure, this increased parasitemia indicates relapse of chronic infection during costly life history stages (i.e., reproduction). Although the immunological and parasitological time series were in phase for control birds, cross-correlation analyses also revealed artificial light at night desynchronized leukocyte profiles and parasitemia, which could suggest a general exaggerated inflammatory response. Our study shows how a common anthropogenic influence can shape within-host processes to affect infection dynamics.
Connectome spectral analysis to track EEG task dynamics on a subsecond scale
Authors: Glomb Katharina , Queralt Joan Rue , Pascucci David , Defferrard Michaël , Tourbier Sebastien , Carboni Margherita , Rubega Maria , Vulliemoz Serge , Plomp Gijs , Hagmann Patric 
Published: June 2020

AbstractWe present an approach for tracking fast spatiotemporal cortical dynamics in which we combine white matter connectivity data with source-projected electroencephalographic (EEG) data. We employ the mathematical framework ofgraph signal processingin order to derive the Fourier modes of the brain structural connectivity graph, or “network harmonics”. These network harmonics are naturally ordered by smoothness. Smoothness in this context can be understood as the amount of variation along the cortex, leading to a multi-scale representation of brain connectivity. We demonstrate that network harmonics provide a sparse representation of the EEG signal, where, at certain times, the smoothest 15 network harmonics capture 90% of the signal power. This suggests that network harmonics are functionally meaningful, which we demonstrate by using them as a basis for the functional EEG data recorded from a face detection task. There, only 13 network harmonics are sufficient to track the large-scale cortical activity during the processing of the stimuli with a 50 ms resolution, reproducing well-known activity in the fusiform face area as well as revealing co-activation patterns in somatosensory/motor and frontal cortices that an unconstrained ROI-by-ROI analysis fails to capture. The proposed approach is simple and fast, provides a means of integration of multimodal datasets, and is tied to a theoretical framework in mathematics and physics. Thus, network harmonics point towards promising research directions both theoretically - for example in exploring the relationship between structure and function in the brain - and practically - for example for network tracking in different tasks and groups of individuals, such as patients.
Feeding state functionally reconfigures a sensory circuit to drive thermosensory behavioral plasticity
Authors: Takeishi Asuka , Yeon Jihye , Harris Nathan , Yang Wenxing , Sengupta Piali 
Published: June 2020

AbstractInternal state alters sensory behaviors to optimize survival strategies. The neuronal mechanisms underlying hunger-dependent behavioral plasticity are not fully characterized. Here we show that feeding state regulatesC. elegansnegative thermotaxis behavior by engaging a modulatory circuit whose activity gates the output of the core thermotaxis network. Feeding state does not alter the activity of the core thermotaxis circuit comprised of AFD thermosensory and AIY interneurons. Instead, prolonged food deprivation potentiates temperature responses in the AWC sensory neurons, which inhibit the postsynaptic AIA interneurons to override and disrupt AFD-driven thermotaxis behavior. Acute inhibition and activation of AWC and AIA, respectively, restores negative thermotaxis in starved animals. We find that state-dependent modulation of AWC-AIA temperature responses requires INS-1 insulin-like peptide signaling from the gut and DAF-16 FOXO function in AWC. Our results describe a mechanism by which functional reconfiguration of a sensory network via gut-brain signaling drives state-dependent behavioral flexibility.
Quantifying the wave resistance of a swimmer
Authors: Dickson Thomas A. J. , Taunton Dominic , Banks Joe , Hudson Dominic , Turnock Stephen 
Published: June 2020

AbstractQuantifying the wave resistance of a swimmer as a function of depth assists in identifying the optimum depth for the glide phases of competition. Previous experiments have inferred how immersed depth influences the drag acting on a swimmer [1], but have not directly quantified the magnitude of wave resistance. This research experimentally validates the use of thin-ship theory for quantifying the wave resistance of a realistic swimmer geometry. The drag and wave pattern of a female swimmer mannequin were experimentally measured over a range of depths from 0.05m to 1.00m at a speed of 2.50 m/s. Numerical simulations agree with experiment to confirm that there were negligible reductions in wave resistance below a depth of 0.40m. Larger swimming pool dimensions are shown to be significant at reducing wave resistance at speeds above 2.0 m/s and depths below 0.40m. Truncating the swimmer’s body at the upper thigh increases the wave resistance at speeds below 2.0m/s but is not significant at higher speeds, indicating that the upper body is the main contributor to the wave system. Numerical experiments indicate that rotating the shoulders towards the surface is more influential than the feet, demonstrating the impact of the upper body on wave resistance.
Genome-wide association study of flowering time reveals complex genetic heterogeneity and epistatic interactions in rice
Authors: Liu Chang , Tu Yuan , Liao Shiyu , Fu Xiangkui , Lian Xingming , He Yuqing , Xie Weibo , Wang Gongwei 
Published: June 2020

AbstractSince domestication, rice has cultivated in a wide range of latitudes with different day lengths. Selection of diverse natural variations in heading date and photoperiod sensitivity is critical for adaptation of rice to different geographical environments. To unravel the genetic architecture underlying natural variation of rice flowering time, we conducted a genome wide association study (GWAS) using several association analysis strategies with a diverse worldwide collection of 529O. sativaaccessions. Heading date was investigated in three environments under long-day or short-day conditions, and photosensitivity was evaluated. By dividing the whole association panel into subpopulations and performing GWAS with both linear mixed models and multi-locus mixed-models, we revealed hundreds of significant loci harboring novel candidate genes as well as most of the known flowering time genes. In total, 127 hotspots were detected in at least two GWAS. Universal genetic heterogeneity was found across subpopulations. We further detected abundant interactions between GWAS loci, especially inindica. Functional gene families were revealed from enrichment analysis of the 127 hotspots. The results demonstrated a rich of genetic interactions in rice flowering time genes and such epistatic interactions contributed to the large portions of missing heritability in GWAS. It suggests the increased complexity of genetic heterogeneity might discount the power of increasing the sample sizes in GWAS.
EMC2: A versatile algorithm for robust tracking of calcium dynamics from individual neurons in behaving animals
Authors: Lagache Thibault , Hanson Alison , Pérez-Ortega Jesús E. , Fairhall Adrienne , Yuste Rafael 
Published: June 2020

AbstractMeasuring the activity of neuronal populations with calcium imaging can capture emergent functional properties of neuronal circuits with single cell resolution. However, the motion of freely behaving animals, together with the intermittent detectability of calcium sensors, can hinder automatic long-term monitoring of neuronal activity and the subsequent functional characterization of neural circuits. We report the development and open-source implementation of a multi-step cellular tracking algorithm (Elastic Motion Correction and Concatenation or EMC2) that compensates for the intermittent disappearance of moving neurons by integrating local deformation information from detectable neurons. We demonstrate the accuracy and versatility of our algorithm using calcium imaging data from two-photon volumetric microscopy in visual cortex of awake mice, and from confocal microscopy in behavingHydra, which experiences major body deformation during its contractions. We quantify the performance of our algorithm using ground truth manual tracking of neurons, along with synthetic time-lapse sequences, covering a wide range of particle motions and detectability parameters. By monitoring the calcium activity of the same neuronal populations along several days in layer 2/3 of visual cortex of mice, we report important turn-over within the active neurons across days, with only few neurons that remained active across days. Then, by combining automatic tracking of single neuron activity over long time-lapse sequences with statistical clustering, we characterize and map neuronal ensembles in behavingHydra. We document the existence three major non-overlapping ensembles of neurons (CB, RP1 and RP2) whose activity correlates with contractions and elongations. Our results prove that the EMC2algorithm can be used as a robust platform for neuronal tracking in behaving animals.
Molecular Detection of bla OXA-48 Gene Encoding Carbapenem Resistance Pseudomonas aeruginosa Clinical Isolates from Khartoum State Hospitals, Sudan
Authors: Ali Doha Omer , Nagla Mohamed M.A. 
Published: June 2020

AbatractCarbapenem resistance in Pseudomonas.aeruginosa is particularly worrisome because this class of β-lactam represents the last therapeutic resource for control of bacterial infection.So this study aimed to detect the frequency of bla OXA-48 resistance gene among Pseudomonas aeruginosa clinical isolates during the period from November 2018 to November 2019.Hundred Pseudomonas aeruginosa clinical isolates, 81 carbapenems (imipenem meropenem) resistant and 19 carbapenems sensitive were collected from Omdurman Teaching Hospital, Fedail Hospital and Soba Teaching Hospital in Khartoum State-Sudan. All isolates were re-identified using conventional bacteriological techniques, their susceptibility to carbapenems were tested using Kirby-Bauer method for confirmation and investigated for the presence of the bla OXA-48 gene using conventional PCR technique.60 (60.0%) out of 100 Pseudomonas aeruginosa clinical isolates were positive for blaOXA-48 gene. Out of 81 carbapenem resistant isolates 54(66.7%) were positive for bla OXA-48 gene, while among the (19) carbapenem sensitive isolates 6 (31.6%) were positive for blaOXA-48 gene. There was statistically significant association between carbapenem resistant isolates and the presence of blaOXA-48 gene (P-value = 0.006).Wound swabs were the predominant clinical samples detected harboring bla OXA-48 gene both among the sensitive 5 (83.3%) and carbapenem resistant isolates 29(53.7) (P.value> 0.05).Our findings revealed high frequency of bla OXA-48 among carbapenem resistant isolates so identification of bla OXA-48 producing strains and taking efforts to reduce the rate of transferring these gene between the different strains is essential for optimization of therapy and improves of patients outcomes.
Neuroscience-Informed Psychoeducation for Recovery (NIPER): A Program to Promote Metacognition in People with Substance Use Disorders
Authors: Rezapour Tara , Barzegari Mohammad , Sharifi Elham , Malmir Nastaran , Ghiasvand Hamid Reza , Salehi Mohammad , Noroozi Alireza , Ekhtiari Hamed 
Published: June 2020

BackgroundA brief neuroscience-informed psychoeducation program (neuroscience-informed psychoeducation for recovery, NIPER) was developed to promote awareness (metacognition) in the main cognitive domains affected by drug and alcohol use to increase willingness to invest time and effort in the brain and cognition recovery process. The primary aim of this study was to determine the feasibility and acceptability of the NIPER program and its potential effectiveness in terms of increasing metacognition, psychological wellbeing and willingness for the brain and cognition recovery programs among people with substance use disorders (SUDs).Methodology56 individuals with SUDs recruited from four outpatient treatment centres in Tehran, Iran and attended four 90-min sessions delivered weekly adjunct to their treatment as usual. The effectiveness was measured in terms of metacognition, and psychological wellbeing at baseline and at the end of the program. Rate of adherence and participation as well as willingness to continue with brain and cognition recovery programs were measured as feasibility outcomes.ResultsA total of 51 participants completed the study. Compared to the baseline assessments, participants reported significantly higher problems in dimensions of attention, memory, inhibitory control, decision making, motor/speech, interocpetion and insight, as well as higher level of psychological wellbeing (t=4.66. p<0.001). In terms of feasibility outcomes, the adherence and participation rates were found above 85%. The majority of participants expressed their high willingness to continue the brain and cognition recovery programs (86.2%) and introduce NIPER to their peers (98%).ConclusionTaking into account the results in terms of feasibility and preliminary effectiveness of NIPER in clinical context of addiction treatment, we consider NIPER as a potentially beneficial interventions to be offered to people with SUD to increase their awareness and engage them to the brain and cognition recovery process. The clinical efficacy of the intervention should be tested in future randomized clinical trials.
Hydroxychloroquine serum concentrations in non-critical care patients infected with SARS-CoV-2
Authors: MacGowan Alasdair , Hamilton Fergus , Bayliss Mark , Read Liam , Attwood Marie , Noel Alan , Grier Sally , Morley Anna , Arnold David , Maskell Nicholas 
Published: June 2020

AbstractHydroxychloroquine(HCQ) has been widely used to treat SARS-CoV-2 infection however HCQ pharmacokinetics in this condition have not been studied in non-critical care patient groups. Here we report the serum concentrations of HCQ in a small cohort of patients treated with HCQ as part of the RECOVERY trial.
Qualitative assessment of SARS-CoV-2-specific antibody avidity by lateral flow immunochromatographic IgG/IgM antibody assay
Authors: Valdivia Arantxa , Torres Ignacio , Huntley Dixie , Alcaraz María Jesús , Albert Eliseo , Colomina Javier , Ferrer Josep , Carratalá Arturo , Navarro David 
Published: June 2020

AbstractQualitative assessment of SARS-CoV-2-specific antibody avidity was conducted using an urea (6M) dissociation test performed on a lateral flow immunochromatographic IgG/IgM device. We included a total of 76 serum specimens collected from 57 COVID-19 patients, of which 39 tested positive for both IgG and IgM and 37 only for IgG. Sera losing IgG reactivity after urea treatment (n=28) were drawn significantly earlier (P=0.04) after onset of symptoms than those which preserved it (n=48). This assay may be helpful to estimate the time of acquisition of infection in patients with mild to severe COVID-19.