bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design considerations of a wearable electronic-skin for mental health and wellness: balancing biosignals and human factors
Authors: Khan Yasser , Mauriello Matthew L. , Nowruzi Parsa , Motani Akshara , Hon Grace , Vitale Nicholas , Li Jinxing , Kim Jayoung , Foudeh Amir , Duvio Dalton , Shols Erika , Chesnut Megan , Landay James , Liphardt Jan , Williams Leanne , Sudheimer Keith D. , Murmann Boris , Bao Zhenan , Paredes Pablo E. 
Published: January 2021

AbstractChronic stress has been associated with a variety of pathophysiological risks including developing mental illness. Conversely, appropriate stress management, can be used to foster mental wellness proactively. Yet, there is no existing method that accurately and objectively monitors stress. With recent advances in electronic-skin (e-skin) and wearable technologies, it is possible to design devices that continuously measure physiological parameters linked to chronic stress and other mental health and wellness conditions. However, the design approach should be different from conventional wearables due to considerations like signal-to-noise ratio and the risk of stigmatization. Here, we present a multi-part study that combines user-centered design with engineering-centered data collection to inform future design efforts. To assess human factors, we conducted ann=24 participant design probe study that examined perceptions of an e-skin for mental health and wellness as well as preferred wear locations. We complement this with ann=10 andn=16 participant data collection study to measure physiological signals at several potential wear locations. By balancing human factors and biosignals, we conclude that the upper arm and forearm are optimal wear locations.
Effect of Adolescent Stress on Adult Morphine-Induced Behavioral Sensitization is Dependent Upon Genetic Background
Authors: Kamens Helen M. , Miller Carley N. , Caulfield Jasmine I. , Zeid Dana , Horton William J. , Silva Constanza , Sebastian Aswathy , Albert Istvan , Gould Thomas J. , Fishbein Diana , Grigson P. Sue , Cavigelli Sonia A. 
Published: January 2021

1AbstractDeaths related to opioid use have skyrocketed in the United States, leading to a public health epidemic. Research has shown that both biological (genes) and environmental (stress) precursors are linked to opioid use. In particular, stress during adolescence – a critical period of frontal lobe development – influences the likelihood of abusing drugs. However, little is known about the biological mechanisms through which adolescent stress leads to long-term risk of opioid use, or whether genetic background moderates this response. Male and female C57BL/6J and BALB/cJ mice were exposed to chronic variable social stress (CVSS) or control conditions throughout adolescence and then tested for morphine locomotor sensitization or morphine consumption in adulthood. To examine possible mechanisms that underlie stress-induced changes in morphine behaviors, we assessed physiological changes in response to acute stress exposure and prefrontal cortex miRNA gene expression. Adolescent stress did not influence morphine sensitization or consumption in BALB/cJ animals, and there was limited evidence of stress effects in female C57BL/6J mice. In contrast, male C57BL/6J mice exposed to adolescent CVSS had blunted morphine sensitization compared to control animals; no differences were observed in the acute locomotor response to morphine administration or morphine consumption. Physiologically, C57BL/6J mice exposed to CVSS had an attenuated corticosterone recovery following an acute stressor and downregulation of twelve miRNA in the prefrontal cortex compared to control mice. The specificity of the effects for C57BL/6J versus BALB/cJ mice provides evidence of a gene by environmental interaction influencing opioid behaviors. Long-term differences in stress reactivity or miRNA expression suggests two possible biological mechanisms to evaluate in future research.
A critical role of AREG for bleomycin-induced skin fibrosis
Authors: Zhang Mary Yinghua , Fang Shuyi , Gao Hongyu , Zhang Xiaoli , Gu Dongsheng , Liu Yunlong , Wan Jun , Xie Jingwu 
Published: January 2021

ABSTRACTWe report our discovery of an important player in the development of skin fibrosis, a hallmark of scleroderma. Scleroderma is a fibrotic disease, affecting 70,000 to 150,000 Americans. Fibrosis is a pathological wound healing process that produces an excessive extracellular matrix to interfere with normal organ function. Fibrosis contributes to nearly half of human mortality. Scleroderma has heterogeneous phenotypes, unpredictable outcomes, no validated biomarkers, and no effective treatment. Thus, strategies to slow down scleroderma progression represent an urgent medical need. While a pathological wound healing process like fibrosis leaves scars and weakens organ function, oral mucosa wound healing is a scarless process. After re-analyses of gene expression datasets from oral mucosa wound healing and skin fibrosis, we discovered that several pathways constitutively activated in skin fibrosis are transiently induced during oral mucosa wound healing process, particularly the amphiregulin (Areg) gene.Aregexpression is upregulated ~10 folds 24hrs after oral mucosa wound but reduced to the basal level 3 days later. During bleomycin-induced skin fibrosis, a commonly used mouse model for skin fibrosis,Aregis up-regulated throughout the fibrogenesis and is associated with elevated cell proliferation in the dermis. To demonstrate the role of Areg for skin fibrosis, we used mice withAregknockout, and found thatAregdeficiency essentially prevents bleomycin-induced skin fibrosis. We further determined that bleomycin-induced cell proliferation in the dermis was not observed in theAregnull mice. Furthermore, we found that inhibiting MEK, a downstream signaling effector of Areg, by selumetinib also effectively blocked bleomycin-based skin fibrosis model. Based on these results, we concluded that the Areg-EGFR-MEK signaling axis is critical for skin fibrosis development. Blocking this signaling axis may be effective in treating scleroderma.
Early detection of SARS-CoV-2 infection cases or outbreaks at nursing homes by targeted wastewater tracking
Authors: Davó Laura , Seguí Raimundo , Botija Pilar , Beltrán María José , Albert Eliseo , Torres Ignacio , López-Fernández Pablo Ángel , Ortí Rafael , Maestre Juan Francisco , Sánchez Gloria , Navarro David 
Published: January 2021

ABSTRACTObjectivesNear-source tracking of SARS-CoV-2 RNA in the sewage drains serving particular buildings may allow rapid identification of SARS-CoV-2 infection cases or local outbreaks. In this pilot study, we investigated whether this was the case for nursing homes (NH).MethodsThe study involved five NH (from A to E) affiliated to the Clínico-Malvarrosa Health Department, Valencia (Spain). These were nursing or mixed nursing/care homes of different sizes, altogether providing care for 472 residents attended by a staff of 309. Near-source sewage samples were screened for presence of SARS-CoV-2 RNA by RT-qPCR at least 5 days per week during the study period. SARS-CoV-2 RNA testing in nasopharyngeal swabs from residents and staff was performed with the TaqPath COVID-19 Combo Kit (Thermo Fisher Scientific, Massachusetts, USA).ResultsSARS-CoV-2 RNA was detected in wastewater samples from four of the five NH. SARS-CoV-2 infection cases were documented in three of these four NH. Of the two NH without SARS-CoV-2 infection cases, no SARS-CoV-2 RNA was detected in sewer samples from one facility, while it was repeatedly detected in samples from the other. Presence of SARS-CoV-2 RNA in sewage preceded identification of isolated cases among residents or staff or outbreak declaration in two NH, with lag times ranging from 5 to 19 days.ConclusionOur study demonstrated that intermittent or persistent detection of SARS-CoV-2 RNA in NH sewers can provide an early warning of subsequent individual cases or outbreaks in these facilities.
Associations between indicators of socioeconomic position and DNA methylation: A systematic review
Authors: Cerutti Janine K. , Lussier Alexandre A. , Zhu Yiwen , Liu Jiaxuan , Dunn Erin C. 
Published: January 2021

AbstractSocioeconomic position (SEP) is a major determinant of health across the life course. Yet, little is known about the biological mechanisms explaining this relationship. One possible explanation is through an epigenetic process called DNA methylation (DNAm), wherein the socioeconomic environment causes no alteration in the DNA sequence but modifies gene activity, gene expression, and therefore long-term health. To understand the evidence supporting a potential SEP-DNAm link, we performed a systematic review of published empirical findings on the association between SEP (from prenatal development to adulthood) and DNAm measured across the life course, with an eye toward evaluating how the timing, duration, and type of SEP exposure influenced DNAm. Across the 37 studies we identified, there was some evidence for the effect of SEP timing and duration on DNAm, with early-life SEP and persistently low SEP being particularly strong indicators of DNAm. Different indicators of SEP also had some unique associations with DNAm profiles, suggesting that SEP is not a singular concept, but rather that different aspects of the socioeconomic environment can shift DNAm patterns through distinct pathways. These differences with respect to SEP timing, duration, and type were notable because they were detected even among heterogenous study designs. Overall, findings from this review underscore the importance of analyzing SEP timing, duration, and type, given the complex relationship between SEP and DNAm across the lifespan. To guide future research, we highlight current limitations in the literature and propose recommendations for overcoming some of these challenges.
Simulating the impact of different vaccination policies on the COVID-19 pandemic in New York City
Authors: Yang Wan , Kandula Sasikiran , Shaman Jeffrey 
Published: January 2021

PurposeTo analyze potential COVID-19 epidemic outcomes in New York City under different SARS-CoV-2 virus circulation scenarios and vaccine rollout policies from early Jan 2021 to end of June 2021.Key findingsIn anticipation of the potential arrival and dominance of the more infectious SARS-CoV-2 variant:Mass-vaccination would be critical to mitigating epidemic severity (26-52% reduction in infections, hospitalizations, and deaths, compared to no vaccination, provided the new UK variant supplants currently circulating variants).Prioritizing key risk groups for earlier vaccination would lead to greater reductions in hospitalizations and deaths than infections. Thus, in general this would be a good strategy.Current vaccination prioritization policy is suboptimal. To avert more hospitalizations and deaths, mass-vaccination of all individuals 65 years or older should be done as soon as possible. For groups listed in the same phase, 65+ year-olds should be given first priority ahead of others.Available vaccine doses should be given to the next priority groups as soon as possible without awaiting hesitant up-stream groups.While efficacy of vaccination off-protocol is unknown, provided immune response following a first vaccine dose persists, delaying the 2nd vaccine dose by ∼1 month (i.e. administer the two doses 8 weeks apart) can substantially reduce infections, hospitalizations, and deaths compared to the 3-week apart regimen. Across all scenarios tested here, delaying the 2nd vaccine dose leads to the largest reduction in severe epidemic outcomes (e.g. hospitalizations and deaths). Therefore, to protect as many people as possible, this strategy should be considered if rapid increases in infections, hospitalization or deaths and/or shortages in vaccines were to occur.
Incentivizing Multiple Objectives in Active Surveillance for Urban Disease Vectors
Authors: Arevalo-Nieto Claudia , Sheen Justin , Condori-Luna Gianfranco , Condori-Pino Carlos , Shinnick Julianna , Peterson Jennifer K. , Castillo-Neyra Ricardo , Levy Michael Z. 
Published: January 2021

ABSTRACTLarge-scale vector control campaigns have successfully reduced infectious disease incidence around the world. In addition to preventing new infections, these campaigns produce a wealth of information about the distribution and density of insect vectors, which can be incorporated into risk maps. These maps can effectively communicate risk map data to technicians on the ground, although encouraging them to use the data remains a challenge. We carried out a series of rolling trials in which we evaluated risk map use under different incentive schemes. Participants in the studies were trained field technicians tasked with house-to-house surveillance for insect vectors of Chagas disease in Arequipa, Peru. A novel incentive scheme based on poker best achieved a dual objective: to encourage technicians to preferentially visit higher-risk houses while surveilling evenly across the search zone. The poker incentive structure may be well-suited to improve entomological surveillance activities and other complex multi-objective tasks.
Comparative Effects of E-cigarette Aerosol on Periodontium
Authors: Xu Fangxi , Aboseria Eman , Janal Malvin N , Pushalkar Smruti , Bederoff Maria V , Vasconcelos Rebeca , Sapru Sakshi , Paul Bidisha , Queiroz Erica , Makwana Shreya , Solarewicz Julia , Guo Yuqi , Aguallo Deanna , Gomez Claudia , Shelly Donna , Aphinyanaphongs Yindalon , Gordon Terry , Corby Patricia , Kamer Angela R. , Li Xin , Saxena Deepak 
Published: January 2021

AbstractIntroductionTobacco use is one of the main causes of periodontitis. E-cigarettes are gaining in popularity, and studies are needed to better understand the impact of e-cigarettes on oral health. Objective: To perform a longitudinal study to evaluate the adverse effects of e-cigarettes on periodontal health.MethodsNaïve e-cigarette users, cigarette smokers, and non-smokers were recruited using newspaper and social media. Demographics, age, gender, and ethnicity, were recorded. Participants were scheduled for two visits 6 months apart. At each visit, we collected data on the daily frequency puffs of an e-cigarette, the number of cigarettes smokes, and other parameters, such as alcohol consumption. Carbon monoxide levels, cotinine levels, salivary flow rate, probing depth, and bleeding on probing were determined at both baseline and follow-up visits. P-values less than 0.05 were considered statistically significant.ResultsWe screened 159 subjects and recruited 140 subjects. One-hundred-one subjects (31 cigarette smokers, 32 e-cigarette smokers, and 38 non-smokers) completed every assessment in both visits. The retention and compliance rate of subjects was 84.1%. The use of social media and craigslist was significant in recruiting e-cigarette subjects. Ethnicity and race differed between cohorts, as did average age in the male subjects. Carbon monoxide and salivary cotinine levels were highest among cigarette smokers. Bleeding on probing and average probing depths similarly increased over time in all three cohorts. Increase in the rates of severe periodontal disease were significantly higher in cigarette smokers and e-cigarette users than non-smokers. Confounding factors were subjects’ age as most of the e-cigarette group were much younger than cigarette smokers.ConclusionAmong the recruited participants, periodontal severity status after 6 month was significantly worse in cigarette smokers and e-cigarette smokers than non-smokers. This study design and protocol will assist in future larger studies on e-cigarette and oral health.
ORFLine: a bioinformatic pipeline to prioritise small open reading frames identifies candidate secreted small proteins from lymphocytes
Authors: Hu Fengyuan , Lu Jia , Munoz Manuel D. , Saveliev Alexander , Turner Martin 
Published: January 2021

AbstractThe annotation of small open reading frames (smORFs) of less than 100 codons (<300 nucleotides) is challenging due to the large number of such sequences in the genome. The recent development of next generation sequence and ribosome profiling enables identification of actively translated smORFs. In this study, we developed a computational pipeline, which we have named ORFLine, that stringently identifies smORFs and classifies them according to their position within transcripts. We identified a total of 5744 unique smORFs in datasets from mouse B and T lymphocytes and systematically characterized them using ORFLine. We further searched smORFs for the presence of a signal peptide, which predicted known secreted chemokines as well as novel micropeptides. Five novel micropeptides show evidence of secretion and are therefore candidate mediators of immunoregulatory functions.
A combined computational fluid dynamics and MRI Arterial Spin Labeling modeling strategy to quantify patient-specific cerebral hemodynamics in cerebrovascular occlusive disease
Authors: Schollenberger Jonas , Osborne Nicholas Harold , Hernandez-Garcia Luis , Figueroa C. Alberto 
Published: January 2021

AbstractCerebral hemodynamics in the presence of cerebrovascular occlusive disease (CVOD) are influenced by the anatomy of the intracranial arteries, the degree of stenosis, the patency of collateral pathways, and the condition of the cerebral microvasculature. Accurate characterization of cerebral hemodynamics is a challenging problem. In this work, we present a strategy to quantify cerebral hemodynamics using computational fluid dynamics (CFD) in combination with arterial spin labeling MRI (ASL). First, we calibrated patient-specific CFD outflow boundary conditions using ASL-derived flow splits in the Circle of Willis. Following, we validated the calibrated CFD model by evaluating the fractional blood supply from the main neck arteries to the vascular territories using Lagrangian particle tracking and comparing the results against vessel-selective ASL (VS-ASL). Finally, cerebral hemodynamics were assessed in two patients with CVOD and a healthy control subject. We demonstrated that the calibrated CFD model accurately reproduced the fractional blood supply to the vascular territories, as obtained from VS-ASL. The two patients revealed significant differences in pressure drop over the stenosis, collateral flow, and resistance of the distal vasculature, despite similar degrees of clinical stenosis severity. Our results demonstrated the advantages of a patient-specific CFD analysis for assessing the hemodynamic impact of stenosis.
Spiking recurrent neural networks represent task-relevant neural sequences in rule-dependent computation
Authors: Xue Xiaohe , Halassa Michael M. , Chen Zhe S. 
Published: January 2021

AbstractPrefrontal cortical neurons play in important roles in performing rule-dependent tasks and working memory-based decision making. Motivated by experimental data, we develop an excitatory-inhibitory spiking recurrent neural network (SRNN) to perform a rule-dependent two-alternative forced choice (2AFC) task. We imposed several important biological constraints onto the SRNN, and adapted the spike frequency adaptation (SFA) and SuperSpike gradient methods to update the network parameters. These proposed strategies enabled us to train the SRNN efficiently and overcome the vanishing gradient problem during error back propagation through time. The trained SRNN produced rule-specific tuning in single-unit representations, showing rule-dependent population dynamics that strongly resemble experimentally observed data in rodent and monkey. Under varying test conditions, we further manipulated the parameters or configuration in computer simulation setups and investigated the impacts of rule-coding error, delay duration, weight connectivity and sparsity, and excitation/inhibition (E/I) balance on both task performance and neural representations. Overall, our modeling study provides a computational framework to understand neuronal representations at a fine timescale during working memory and cognitive control.Author SummaryWorking memory and decision making are fundamental cognitive functions of the brain, but the circuit mechanisms of these brain functions remain incompletely understood. Neuroscientists have trained animals (rodents or monkeys) to perform various cognitive tasks while simultaneously recording the neural activity from specific neural circuits. To complement the experimental investigations, computational modeling may provide an alternative way to examine the neural representations of neuronal assemblies during task behaviors. Here we develop and train a spiking recurrent neural network (SRNN) consisting of balanced excitatory and inhibitory neurons to perform the rule-dependent working memory tasks Our computer simulations produce qualitatively similar results as the experimental findings. Moreover, the imposed biological constraints on the trained network provide additional channel to investigate cell type-specific population responses, cortical connectivity and robustness. Our work provides a computational platform to investigate neural representations and dynamics of cortical circuits a fine timescale during complex cognitive tasks.
A computational and structural analysis of germline and somatic variants affecting the DDR mechanism, and their impact on human diseases and prostate cancer progression
Authors: Magraner-Pardo Lorena , Laskowski Roman A. , Pons Tirso , Thornton Janet M. 
Published: January 2021

AbstractDNA-Damage Response (DDR) proteins are crucial for maintaining the integrity of the genome by identifying and repairing errors in DNA. Variants affecting their function can have dire consequences as damaged DNA can result in cells turning cancerous. Here we compare germline and somatic variants in DDR genes, specifically looking at their locations in the corresponding three-dimensional (3D) structures, Pfam domains, and protein-protein interaction interfaces. We show that somatic variants are more likely to be found in Pfam domains and protein interaction interfaces than are pathogenic germline variants or variants of unknown significance (VUS). We also show that there are hotspots in the structures of ATM and BRCA2 proteins where pathogenic germline, and recurrent somatic variants from primary and metastatic tumours, cluster together in 3D. Moreover, in theATM, BRCA1andBRCA2genes from prostate cancer patients, the distributions of germline benign, pathogenic, VUS, and recurrent somatic variants differ across Pfam domains. Together, these results provide a better characterisation of the most recurrent affected regions in DDRs and could help in the understanding of individual susceptibility to tumour development.