bluuebunny/crossref_metadata_2025_split huggingface dataset:
NeTOIF: A Network-based Approach for Time-Series Omics Data Imputation and Forecasting
Authors: Shi Min , Mollah Shamim 
Published: June 2021

AbstractMotivationHigh-throughput studies of biological systems are rapidly generating a wealth of ‘omics’-scale data. Many of these studies are time-series collecting proteomics and genomics data capturing dynamic observations. While time-series omics data are essential to unravel the mechanisms of various diseases, they often include missing (or incomplete) values resulting in data shortage. Data missing and shortage are especially problematic for downstream applications such as omics data integration and computational analyses that need complete and sufficient data representations. Data imputation and forecasting methods have been widely used to mitigate these issues. However, existing imputation and forecasting techniques typically address static omics data representing a single time point and perform forecasting on data with complete values. As a result, these techniques lack the ability to capture the time-ordered nature of data and cannot handle omics data containing missing values at multiple time points.ResultsWe propose a network-based method for time-series omics data imputation and forecasting (NeTOIF) that handle omics data containing missing values at multiple time points. NeTOIF takes advantage of topological relationships (e.g., protein-protein and gene-gene interactions) among omics data samples and incorporates a graph convolutional network to first infer the missing values at different time points. Then, we combine these inferred values with the original omics data to perform time-series imputation and forecasting using a long short-term memory network. Evaluating NeTOIF with a proteomic and a genomic dataset demonstrated a distinct advantage of NeTOIF over existing data imputation and forecasting methods. The average mean square error of NeTOIF improved 11.3% for imputation and 6.4% for forcasting compared to the baseline methods.Contactsmollah@wustl.edu
Behavioral effects of ethanol in the Red Swamp Crayfish (Procambarus clarkii)
Authors: Gutierrez Arnold , Creehan Kevin M. , de Guglielmo Giordano , Roberts Amanda J. , Taffe Michael A. 
Published: June 2021

AbstractAlcohol abuse and dependence remains one of the primary preventable sources of human mortality in the United States. Model laboratory species can be used to evaluate behavioral, neuropharmacological and other biological changes associated with alcohol exposure and to identify novel treatment modalities. This report describes methods for evaluating the behavioral effects of ethyl alcohol (ethanol; EtOH) in a crayfish model. Crayfish (Procambarus clarkii) were immersed in ethanol baths with concentrations ranging from 0.1 to 1.0 molar, and for durations of 10-30 minutes. Studies evaluated hemolymph alcohol concentration, locomotor behavior in an open field and anxiety-like behavior using a Light/Darktransfer approach. EtOH immersion produced dose dependent increases in hemolymph EtOH concentration (up to 249 mg/dL) and reductions in open field locomotor behavior that depended on EtOH concentration or exposure duration. Under baseline conditions, crayfish exhibit avoidance of the open parts of the locomotor arena and a preference for the covered portion, when available. Acute EtOH immersion decreased time spent in the covered portion of the Light/Dark arena, consistent with a decrease in anxiety-like behavior. EtOH immersion once per day for 5 days did not alter the acute locomotor behavioral response, however increased activity was observed 3 days after the repeated EtOH regimen. Overall, this study shows that this inexpensive, easily maintained species can be used for behavioral pharmacological experiments designed to assess the acute and repeated effects of EtOH.
Spatial prediction of air pollution levels using a hierarchical Bayesian spatiotemporal model in Catalonia, Spain
Authors: Saez Marc , Barceló Maria A. 
Published: June 2021

AbstractOur objective in this work was to present a hierarchical Bayesian spatiotemporal model that allowed us to make spatial predictions of air pollution levels in an effective way and with very few computational costs.We specified a hierarchical spatiotemporal model, using the Stochastic Partial Differential Equations of the integrated nested Laplace approximations approximation. This approach allowed us to spatially predict, in the territory of Catalonia (Spain), the levels of the four pollutants for which there is the most evidence of an adverse health effect.Our model allowed us to make fairly accurate spatial predictions of both long- term and short-term exposure to air pollutants, with a low computational cost. The only requirements of the method we propose are the minimum number of stations distributed throughout the territory where the predictions are to be made, and that the spatial and temporal dimensions are either independent or separable.HighlightsWe show a hierarchical Bayesian spatiotemporal model.Our model provides predictions of both long-term and short-term exposure.The computational cost is low.The model only needs a minimum number of stations being distributed throughout the territory.The other requirement of our model is that the spatial and temporal dimensions are either independent or separable.Graphical abstractSoftware and Data availabilityWe used open data with free access using these sources. Air pollutantsDepartament de Territori i Sostenibilitat, Generalitat de Catalunya [Available at: https://analisi.transparenciacatalunya.cat/en/Medi-Ambient/Qualitat-de-l-aire-als-punts-de-mesurament-autom-t/tasf-thgu, last accessed on March 14, 2021].Meteorological variablesMETEOCAT, Generalitat de Catalunya. Meteorological data from XEMA [Available at: https://analisi.transparenciacatalunya.cat/en/Medi-Ambient/Dades-meteorol-giques-de-la-XEMA/nzvn-apee, last accessed on March 14, 2021].AEMET. AEMET Open Data [in Spanish] [Available at: http://www.aemet.es/es/datos_abiertos/AEMET_OpenData, last accessed on March 14, 2021].Digitized cartography of the ABSDepartament de Salut. Cartography [Available at: https://salutweb.gencat.cat/ca/el_departament/estadistiques_sanitaries/cartografia/, accessed on March 14, 2021].Code will be available at www.researchprojects.es
Movement Decoding using Spatio-Spectral Features of Cortical and Subcortical Local Field Potentials
Authors: Peterson Victoria , Merk Timon , Bush Alan , Nikulin Vadim , Kühn Andrea A , Neumann Wolf-Julian , Richardson Mark 
Published: June 2021

AbstractThe application of machine learning to intracranial signal analysis has the potential to revolutionize deep brain stimulation (DBS) by personalizing therapy to dynamic brain states, specific to symptoms and behaviors. Most decoding pipelines for movement decoding in the context of adaptive DBS are based on single channel frequency domain features, neglecting spatial information available in multichannel recordings. Such features are extracted either from DBS lead recordings in the subcortical target and/or from electrocorticography (ECoG). To optimize the simultaneous use of both types of signals, we developed a supervised online-compatible movement decoding pipeline based on multichannel and multiple site recordings. We found that adding spatial information to the model has the potential to improve decoding. In addition, we demonstrate movement decoding from spatio-spectral features derived from cortical and subcortical oscillations. We demonstrate between-patients variability of the spatial neural maps and its relationship to feature decoding performance. This application of spatial filters to decode movement from combined cortical and subcortical recordings is an important step in developing machine learning approaches for intelligent DBS systems.
Cryo-EM structure of native human thyroglobulin
Authors: Adaixo Ricardo , Steiner Eva M. , Righetto Ricardo D. , Schmidt Alexander , Stahlberg Henning , Taylor Nicholas M. I. 
Published: June 2021

AbstractThe thyroglobulin (Tg) protein is essential to thyroid hormone synthesis, playing a vital role in the regulation of metabolism, development and growth. Its structure is conserved among vertebrates. Tg is delivered through the secretory pathway of the thyroid follicular unit to the central colloid depository, where it is iodinated at specific tyrosine sites to form mono- or diiodotyrosine, which combine to produce triiodothyronine (T3) and thyroxine (T4), respectively. Synthesis of these hormones depends on the precise 3D structure of Tg, which has remained unknown despite decades of research. Here, we present the cryo-electron microscopy structure of human thyroglobulin (hTg) to a global resolution of 3.2 Å. The structure provides detailed information on the location of the hTg hormonogenic sites and reveals the position as well as the role of many of its glycosylation sites. Our results offer structural insight into thyroid hormonogenesis and provide a fundamental understanding of clinically relevant hTg mutations, which can improve treatment of thyroid diseases.
Telomouse – a mouse model with human-length telomeres generated by a single amino acid change in RTEL1
Authors: Smoom Riham , May Catherine Lee , Ortiz Vivian , Tigue Mark , Kolev Hannah M. , Rowe Melissa , Reizel Yitzhak , Morgan Ashleigh , Egyes Nachshon , Lichtental Dan , Skordalakes Emmanuel , Kaestner Klaus H. , Tzfati Yehuda 
Published: June 2021

ABSTRACTTelomeres, the ends of eukaryotic chromosomes, protect genome integrity and enable cell proliferation. Maintaining optimal telomere length in the germline and throughout life limits the risk of cancer and enables healthy aging. Telomeres in the house mouse,Mus musculus, are about five times longer than human telomeres, limiting the use of this common laboratory animal for studying the contribution of telomere biology to aging and cancer. We identified a key amino acid variation in the helicase RTEL1, naturally occurring in the short-telomere mouse speciesM. spretus.Introducing this variation intoM. musculusis sufficient to reduce the telomere length set point in the germline and generate mice with human-length telomeres. While these mice are fertile and appear healthy, the regenerative capacity of their colonic epithelium is compromised. The engineered Telomouse reported here demonstrates a dominant role of RTEL1 in telomere length regulation and provides a unique model for aging and cancer.
CD36: Hemin interaction axis to control immune responses and cytokine secretion from macrophages involving Lyn kinase
Authors: Banesh Sooram , Layek Sourav , Trivedi Vishal 
Published: June 2021

AbstractThe intensity and duration of TNF-α production are mutually correlated with the level of CD36 expression level. The macrophages exposed to hemin exhibits modulation of non-opsonic phagocytosis of aged RBCs and ability to kill bacteria. Immuno-fluorescence study indicates translocation and sequestration of CD36 within the intracellular storage in the hemin treated macrophages. It in-tern dysregulate the global cytokine secretion from macrophages. CD36 has suitable hemin biophoric environment involving R292, D372 and Q382 to bind and the mutation in biophore residues (R292A, D372A or Q382A) significantly reduced the affinity. Ectopic expression of CD36 in MG63 cells showed several folds increment in cytokines TNF-α, MCP-1, RANTES and CCL1 in response to hemin stimulation but no significant amount of cytokines released with mutants (R292A, D372A or Q382A), highlights the relevance of CD36-hemin interaction for immune-dysfunction. Hemin is driving down-stream signalling involving CD36 and subsequent recruitment of adaptor proteins to the cytosolic domain of CD36. Immuno-precipitation of membrane bound CD36 and detection of adaptor proteins indicate change in level of Lyn proteins with CD36 fractions after hemin stimulation to macrophages. The Lyn targeted siRNA restored the phagocytic activity, reduced the secretion of pro-inflammatory cytokine levels clearly suggests the Src family protein Lyn is crucial for CD36-hemin mediated immune dysregulation and cytokine secretion. In summary, hemin-CD36-Lyn cytokine signalling axis could be a contribution factor to severe malaria pathology and prognosis.
A severe form of maternal separation in rat consisting of nineteen-day 6-hour daily separation at unpredictable times minimally affects behavior across the lifespan
Authors: Behring Tatyana B. , Kyle Margaret H. , Hussain Maha , Zhang Jack Y. , Manganaro Alessia , Kaidbey Jasmine H. , Ludwig Robert J. , Myers Michael M. , Welch Martha G. , Dumitriu Dani 
Published: June 2021

Maternal separation (MS), a type of early life stress, has been associated with adverse socioemotional and behavioral outcomes throughout the lifespan across multiple species. Comprehensive longitudinal biobehavioral characterization of MS in rats is sparse and conflicting, warranting more studies. We conducted an MS paradigm involving 6-hour daily separation at unpredictable start times from P2 to P21. We hypothesized this severe form of MS would lead to developmentally emerging maladaptive biobehavioral consequences from juvenile through adult periods compared to Controls (C), especially in social behaviors. We tested: (1) own dam odor preference shortly after weaning; (2) juvenile and adult anxiety-like, sociability, and play behaviors using the light-dark test, three-chambered social interaction test, and video-coded juvenile play behavior; and (3) adult coping behaviors and neuroendocrine response using the forced swim test and blood corticosterone responses. Our results show minimal effects on biobehavioral outcomes across the lifespan. Recently weaned MS male rats had a stronger preference for their dam’s odor. Juvenile MS females spent more time in rough-and-tumble play than C female rats. No differences in sociability were found in the juvenile or adult periods. MS promoted a decrease in anxiety-like behavior that persisted from juvenile to adult periods. Finally, MS led to deficits in coping behavior in male adults, but basal and reactive corticosterone levels were unaltered by MS. More studies are needed to validate our surprising findings and probe the neural mechanisms underlying some of the observed protective effects.Significance StatementMaternal separation (MS), a type of early life stress, has been shown to lead to short and long-term adverse socioemotional consequences in humans and biobehavioral outcomes in rodents. Available data on MS exposed rats are sparse, conflicting, and often lack longitudinal outcomes. We designed a 6-hour unpredictable daily MS paradigm from postnatal day (P2) to P21 to severely disrupt normal dam-pup interactions. Our results show MS leads to increased preference for own dam odor, persisting reductions in anxiety-like behaviors from juvenile to adulthood, and no effects on sociability. Adverse effects on coping behaviors were uniquely identified in males. The present study warrants reevaluation of the central dogma that MS leads to maladaptive biobehavioral outcomes.
Mutualistic interactions between B. subtilis and seeds dictate plant development
Authors: Berlanga-Clavero M.V. , Molina-Santiago C. , Caraballo-Rodríguez A.M. , Petras D. , Díaz-Martínez L. , Pérez-García A. , de Vicente A. , Dorrestein P. C. , Romero D. 
Published: June 2021

AbstractA tightly coordinated developmental program controls precise genetic and metabolic reprogramming that dictates efficient transition of the seeds from dormancy to metabolically active seedlings. Beneficial microbes are known to stimulate the germination of the seeds or adaptation of the seedlings; however, investigations of exact mechanisms mediating these interactions and the resulting physiological responses of the plants are only beginning. Bacillus subtilis is commonly detected in the plant holobiont and belongs to the group of microbes that provide multifaceted contribution to the health of the plants. The present study demonstrated that B. subtilis triggered genetic and physiological responses in the seeds that determined subsequent metabolic and developmental status of adult plants. Chemically diverse extracellular matrix of Bacillus was demonstrated to structurally cooperate in bacterial colonization of the seed storage tissues. Additionally, an amyloid protein and fengycin, which are two components of the extracellular matrix, targeted the oil bodies of the seed endosperm, provoking changes in lipid metabolism or accumulation of glutathione-related molecules that stimulated two different plant growth programs: the development of seed radicles or overgrowth and immunization of adult plants. We propose this mutualistic interaction is conserved in Bacilli and plant seeds containing storage oil bodies.
In vitro evaluation of the effect of mutations in primer binding sites on detection of SARS-CoV-2 by RT-qPCR
Authors: Zimmermann Fee , Urban Maria , Krüger Christian , Walter Mathias , Wölfel Roman , Zwirglmaier Katrin 
Published: June 2021

AbstractA number of RT-qPCR assays for the detection of SARS-CoV-2 have been published and are listed by the WHO as recommended assays. Furthermore, numerous commercial assays with undisclosed primer and probe sequences are on the market. As the SARS-CoV-2 pandemic progresses, the virus accrues mutations, which in some cases – as seen with the B.1.1.7 variant – can outperform and push back other strains of SARS-CoV-2. If mutations occur in primer or probe binding sites, this can impact RT-qPCR results and impede SARS-CoV-2 diagnostics. Here we tested the effect of primer mismatches on RT-qPCR performance in vitro using synthetic mismatch in vitro transcripts. The effects of the mismatches ranged from a shift in ct values from −0.13 to +7.61. Crucially, we found that a mismatch in the forward primer has a more detrimental effect for PCR performance than a mismatch in the reverse primer. Furthermore, we compared the performance of the original Charité RdRP primer set, which has several ambiguities, with a primer version without ambiguities and found that without ambiguities the ct values are ca. 3 ct lower. Finally, we investigated the shift in ct values observed with the Seegene Allplex kit with the B.1.1.7 SARS-CoV-2 variant and found a three-nucleotide mismatch in the forward primer of the N target.
The role of rash-impulsivity, emotional dysregulation and reward drive in comorbid disordered eating and substance use disorders
Authors: Merinuk Natalie , Varcoe Stephanie C. , Kelly Peter J. , Robinson Laura D. 
Published: June 2021

Purpose
Substance use disorder (SUD) frequently co-occurs with other psychological conditions, such as eating disorders (EDs). Psychological factors such as emotional dysregulation, rash impulsivity (RI) and reward sensitivity (RS) play a role in the etiology of each disorder, yet little is known about the combined effects of these on comorbid SUDs and EDs or disordered eating behaviours (DEBs). This study aims to examine the role of these psychological factors in comorbid DEBs and SUDs among individuals in treatment for SUDs. The role of gender is tested as a moderator.

Design/methodology/approach
A cross-sectional self-report survey was completed by 131 participants attending Australian residential substance use treatment centres. A binomial logistic regression analysis was performed to examine the effects of emotional dysregulation, RI and RS on comorbid DEB and SUD. Further, moderation analyses were used to examine the moderating effect for gender on the relationship between these three personality variables and comorbidity.

Findings
The most commonly reported primary substance of use was alcohol (43.5%), followed by amphetamines (38.6%). Findings showed that emotional dysregulation and RI were significantly related to an increase in comorbidity likelihood; however, RS was not. Gender moderated the relationship between comorbidity and RI only.

Originality/value
The significant positive relationship found between RI and comorbidity for females only was a novel finding for the current study. Further research is needed to develop an understanding of the etiology of comorbidity.
Effects of workplace rumors and organizational formalization during the COVID-19 pandemic: a case study of universities in the Philippines
Authors: Puyod Jenette Villegas , Charoensukmongkol Peerayuth 
Published: June 2021

PurposeThis study examines the effects of workplace rumors and organizational formalization on the degree of role ambiguity and emotional exhaustion that university employees in the Philippines are experiencing during the coronavirus disease 2019 (COVID-19) pandemic. The interaction between the two variables is also analyzed.Design/methodology/approachOnline survey data were obtained from 522 faculty members and staff at three public universities in the Philippines. The data were analyzed using partial least squares structural equation modeling.FindingsThe results show that both workplace rumors and organizational formalization are associated positively with role ambiguity and emotional exhaustion, and role ambiguity mediates workplace rumors' effect on emotional exhaustion. Moreover, the moderating effect analysis shows that workplace rumors and organizational formalization interact and intensify the degree of role ambiguity and emotional exhaustion that employees experience.Originality/valueThis study extends previous research by showing that employees who work in a highly formal structure can be extremely sensitive to workplace rumors during a period of uncertainty.
How do former smokers perceive information about nicotine products? Evidence from Sweden
Authors: Sohlberg Tove , Karlsson Patrik 
Published: June 2021

PurposeHealth promotion strategies often attempt to change people’s behavior through targeting their risk perceptions. These perceptions may, however, be moderated by other factors. This study therefore aimed at investigating the trustworthiness and consistency of risk information, as well as respondent perceptions of the adequacy of amount received among a representative sample of former smokers, and how this information is related to gender, age, education level and whether using nicotine or not.Design/methodology/approachThe respondents are part of a seven-year follow-up of former smokers in Sweden. Initially, 1400 respondents were contacted, whereof 705 (response rate 50%) answered a Web-survey. The majority (85 %) was still nicotine-free but some made use of nicotine in different forms. The data analysis includes descriptive statistics and logistic regressions.FindingsMost respondents trusted risk information whether offered by the public authorities or came from other sources such as media, and generally perceived that there was an adequate amount. However, there were some differences between the products, where quite a few distrusted information on Nicotine Replacement Therapies (NRTs) and some perceived the information on snus and NRTs as contradictory and too little.Originality/valueKnowledge about how former smokers perceive information regarding negative aspects of cigarette use may facilitate more effective risk communication with current smokers, and it may also be important for communicating information about other nicotine products to those who are trying to or who already have quit smoking.