bluuebunny/crossref_metadata_2025_split huggingface dataset:
Smoking and Vaping Among a National Sample of U.S. Adults During the COVID-19 Pandemic
Authors: Kalkhoran Sara , Levy Douglas E. , Rigotti Nancy A. 
Published: March 2021

AbstractIntroductionWith concerns about cigarette smoking being a risk factor for severe disease from COVID-19, understanding nicotine and tobacco use patterns is important for preventive efforts. We aimed to understand changes in product use behaviors among U.S. adult combustible cigarette smokers and electronic cigarette (e-cigarette) users.MethodsIn August 2020, we conducted a cross-sectional survey of a nationally-representative sample of adults age >18 in NORC’s AmeriSpeak Panel who reported past 6-month use of combustible cigarettes or e-cigarettes. Multivariable logistic regression assessed factors associated with increased product use and quit attempts since hearing about COVID-19.Results1024 past 6-month cigarette smokers and/or e-cigarette users were surveyed. Among cigarette smokers, 45% reported no change in cigarette smoking and 33% increased cigarette smoking since hearing about COVID-19. Higher stress was associated with increased cigarette smoking. Among e-cigarette users, 41% reported no change in and 23% reported increasing e-cigarette use. 26% of cigarette smokers and 41% of e-cigarette users tried to quit because of COVID-19. Higher perceived risk of COVID-19 was associated with attempts to quit combustible cigarettes (AOR 2.37, 95% CI 1.59-3.55) and e-cigarettes (AOR 3.14, 1.73-5.70).ConclusionsCigarette and e-cigarette use patterns varied in response to the COVID-19 pandemic. Most cigarette smokers and e-cigarette users perceived product use as increasing COVID-19-related health risks, and this was associated with attempts to quit. Others, especially those reporting higher stress, increased product use. Proactive provision of cessation support to smokers and e-cigarette users may help mitigate stress-related increases in product use during the COVID-19 pandemic.
Transdiagnostic Neural Signatures in common Pediatric Psychiatric Disorders: a data-driven meta-analysis of functional neuroimaging studies
Authors: Dugré Jules R. , Eickhoff Simon B. , Potvin Stéphane 
Published: March 2021

ABSTRACTBACKGROUNDIn the last decades, neuroimaging studies have attempted to unveil the neurobiological markers underlying pediatric psychiatric disorders. However, children diagnosed with such disorders are likely to receive an additional diagnosis in the following years. Yet, the vast majority of neuroimaging studies focus on a single nosological category, which limit our understanding of the shared/specific neural correlates between these disorders. Therefore, we aimed to investigate the transdiagnostic neural signatures through a novel meta-analytical method.METHODA data-driven meta-analysis was carried out which grouped similar experiments topographic map together, irrespectively of nosological categories and task-characteristics. Then, activation likelihood estimation meta-analysis was performed on each group of experiments to extract spatially convergent brain regions.RESULTSOne hundred forty-seven experiments were retrieved (3199 subjects): 79 attention-deficit/hyperactivity disorder, 32 conduct/oppositional defiant disorder, 14 anxiety disorders, 22 major depressive disorders. Four significant groups of experiments were observed. Functional characterization suggested that these groups of aberrant brain regions may be implicated internally/externally directed processes, attentional control of affect, somato-motor and visual processes. Furthermore, despite that some differences in rates of studies involving major depressive disorders were noticed, nosological categories were evenly distributed between these four sets of regions. Additionally, main effects of task characteristics were observed.CONCLUSIONSBy using a data-driven meta-analytic method, we observed four significant groups of aberrant brain regions that may reflect transdiagnostic neural signature of pediatric psychiatric disorders. Overall, results of this study underscore the importance of studying pediatric psychiatric disorders simultaneously rather than independently.
Implementation of a multi-modal training program for the management of comorbid mental disorders in drug and alcohol settings: Pathways to Comorbidity Care (PCC)
Authors: Louie Eva , Morley Kirsten C. , Giannopoulos Vicki , Uribe Gabriela , Wood Katie , Marel Christina , Mills Katherine L , Teesson Maree , Edwards Michael , Childs Steven , Rogers David , Dunlop Adrian , Baillie Andrew , Haber Paul S. 
Published: March 2021

AbstractBackgroundClinical guidelines recommend evidence-based treatments for comorbid mental and substance use disorders but these are not reliably translated into practice. We aimed to evaluate the impact of the Pathways to Comorbidity Care (PCC) training program for alcohol and other drug (AOD) clinicians to improve the management of comorbidity and to identify barriers and facilitators of implementation according to the Consolidated Framework for Implementation Research (CFIR).MethodsA controlled before-and-after study using PCC training was conducted across 6 matched sites in Australia including 35 clinicians. Controls received standard workplace training. PCC training included seminar presentations, workshops conducted by local ‘clinical champions’, individual clinical supervision, and access to an online information portal. A mixed methods approach examined i) identification (screening, assessment) and treatment (treatment, referral) of comorbidity in practice (N = 10 clinical files per clinician), ii) self-efficacy, knowledge and attitudes of clinicians, iii) barriers and facilitators of implementation.ResultsSignificant improvements were observed in the PCC group but not the control sites with regards to the rate of clinical files showing identification of comorbidity (+50% v −12% change from baseline respectively; X2 (1, N = 340) = 35.29, p = .01) with only a trend for improvements in the rate of files demonstrating treatment of comorbidity (X2 (1, N = 340) = 10.45, p = .06). There were significant improvements in the PCC relative to the control group for clinician self-efficacy (F (1,33) = 6.40, p = .02) and knowledge and attitudes of comorbidity monitoring (F (1,33) = 8.745, p = .01). Barriers included inner setting (e.g. allocated time for learning) and characteristics of individuals (e.g. resistance). Facilitators included intervention characteristics (e.g. credible sources), inner setting (e.g. leadership) and outer setting domains (e.g. patient needs). Clinical champions were identified as an important component of the implementation process.ConclusionsThe PCC training package effectively improved identification of comorbidity, self-efficacy and attitudes towards screening and monitoring of comorbidity. Specific barriers included provision of allocated time for learning. Specific facilitators included provision of a credible clinical supervisor, strong leadership engagement and an active clinical champion.
The responsiveness of gait and balance outcomes to disease progression in Friedreich ataxia
Authors: Milne Sarah C , Kim Seok Hun , Murphy Anna , Larkindale Jane , Farmer Jennifer , Malapira Ritchie , Danoudis Mary , Shaw Jessica , Ramakrishnan Tyagi , Rasouli Fatemeh , Yiu Eppie M , Georgiou-Karistianis Nellie , Tai Geneieve , Zesiewicz Theresa , Delatycki Martin B , Corben Louise A 
Published: March 2021

AbstractObjectiveTo identify gait and balance measures that are responsive to change during the timeline of a clinical trial in Friedreich ataxia (FRDA) we administered a battery of potential measures three times over a 12-month period.MethodsSixty-one ambulant individuals with FRDA underwent assessment of gait and balance at baseline, six months and 12 months. Outcomes included: GAITRite® spatiotemporal gait parameters; Biodex Balance System Postural Stability Test (PST) and Limits of Stability; Berg Balance Scale (BBS); Timed 25 Foot Walk Test; Dynamic Gait Index (DGI); SenseWear MF Armband step and energy activity; and the Friedreich Ataxia Rating Scale Upright Stability Subscale (FARS USS). The standardised response mean (SRM) or correlation coefficients were reported as effect size indices for comparison of internal responsiveness. Internal responsiveness was also analysed in subgroups.ResultsSenseWear Armband daily step count had the largest effect size of all the variables over six months (SRM=-0.615), while the PST medial-lateral index had the largest effect size (SRM=0.829) over 12 months. The FARS USS (SRM=0.824) and BBS (SRM=-0.720) were the only outcomes able to detect change over 12 months in all subgroups. The DGI was the most responsive outcome in children, detecting a mean change of −2.59 (95% CI −3.52 to −1.66,p<0.001, SRM=-1.429).ConclusionsThe FARS USS and BBS are highly responsive and can detect change in a wide range of ambulant individuals with FRDA. However, therapeutic effects in children may be best measured by the DGI.
Direct induction of hemogenic endothelial progenitors from hPSCs by defined factors revealed by single-cell transcriptome analysis
Authors: Randolph Lauren N. , Jiang Yuqian , Chang Yun , Bao Xiaoping , Lian Xiaojun Lance 
Published: March 2021

AbstractTranscription factors (TFs) play critical roles in stem cell maintenance and differentiation. Using single cell RNA sequencing, we investigated TFs expressed in hemogenic endothelial (HE) progenitors differentiated from human pluripotent stem cells (hPSCs) and identified upregulated expression of SOXF factorsSOX7, SOX17, andSOX18in the HE population. To test whether overexpression of these factors increases HE differentiation efficiency, we established inducible hPSC lines and found onlySOX17improved differentiation. Temporal expression analysis further revealedSOX17was turned on immediately before VE-Cadherin, indicating SOX17 may be a causative factor for HE differentiation. UponSOX17knockdown via CRISPR-Cas13d, HE differentiation was significantly abrogated. Strikingly, we discoveredSOX17overexpression alone is sufficient to generate more than 50% CD34+VE-cadherin+CD73-cells that could be directed to hematopoietic progenitors, which emerged via an endothelial-to-hematopoietic transition and significantly upregulated definitive hematopoietic transcriptional programs. Functional assays showed that these progenitors can differentiate into blood cells from multiple lineages. Our analyses reveal an uncharacterized function ofSOX17in directing hPSCs differentiation towards HE cells.Significance StatementHemogenic endothelial (HE) cells have been generated from human pluripotent stem cells (hPSCs) to study blood development. However, their full transcriptomic characterization and key genes involving in directing HE differentiation is unclear. Utilizing single cell RNA-seq analysis, we find that SOX17 is solely expressed in HE cells and is also required for HE differentiation. Strikingly, we find that overexpression of SOX17 alone is sufficient to program hPSCs into CD34+VE-cadherin+CD73-HE cells, which could further differentiate into blood progenitors. Our research reveals that SOX17 is sufficient to direct hPSCs differentiation to HE cells.ClassificationPhysical Sciences/Engineering; Biological Sciences/Cell Biology.
Correlation analysis of target selectivity and side effects of FDA-approved kinase inhibitors
Authors: Bayazeid Omer , Rahman Taufiq 
Published: March 2021

ABSTRACTKinase inhibitors (KIs) represent a popular class of therapeutic agents and chemical probes but most of them tend to be polypharmacological. Receptor and non-receptor Tyrosine KIs can target more than 100 kinases simultaneously compare to other KIs. We here analyze the molecular targets of 41 U.S. Food and Drug Administration (FDA)-approved KIs. We chose 18 drugs (Tyrosine KIs) and sought out to evaluate their selectivity profile and engagement with a number of targets in vivo at clinically relevant doses. We also wanted to see whether there prevails any correlation between the target engagement profile and the reported side effects for specific KIs chosen as test cases. To explore all clinical targets of the 18 KIs, we considered the free (unbound) maximum serum concentration (Cmax) of each KI and only chose targets for which the cognate affinities lie within the reported free Cmaxvalues, thereby allowing plausible interaction in clinical doses. We retrieved the side effects of those KIs that is reported in the FDA adverse event reporting system. We illustrate how correlation analysis of target−side effect can give a new insight into the off target of KIs and their effect on increasing the toxicity of KIs. These analyses could aid our understanding of the structural-activity relationship of KIs.
Understanding and predicting socioeconomic determinants of deforestation in Vietnam’s Central Annamites Landscape (CAL): Pilot study implementing a spatial econometric approach
Authors: Bernhard Katie P. , Zenobi Stefano , Shapiro Aurélie C. 
Published: March 2021

AbstractThe forests of the Greater Mekong Subregion, consisting of Myanmar, Thailand, Cambodia, Laos and Vietnam, are under high pressure from economic development and exploitation of natural resources, including but not limited to land concession, smallholder plantations and commercial agriculture, agroforestry development, mining, and road infrastructure development. While these threats are well-known, the magnitude and dynamics of their individual and interacting effects on forest cover are not fully understood. This pilot study aims to apply existing, publicly available macro, micro, and socioeconomic data in addition to remote sensing forest cover data to explore economic determinants of deforestation in the Greater Mekong, using the case of the Central Annamites Landscape (CAL) ecoregion of Vietnam. A longitudinal panel was constructed for 2000-2017, containing 1,658 observations for 144 variables across 95 Tier 2 (district) administrative units in CAL from 2000-2017 for modeling macroeconomic and socioeconomic conditions against annual tree cover loss aggregated to the Tier 2 administrative unit. The first phase of the study used tiered spatial regression analysis to correlatively identify which commodities, economic development activities, and social conditions have historically had the greatest effect on forest cover by magnitude in CAL. Based on first phase results, we selected a subset of these determinants for scenario modelling to predict possible deforestation outcomes given certain economic scenarios. The results, among others, indicate that, when spatially collocated, high poverty rates and smaller scale agricultural land conversion are key immediate determinants of deforestation. This therefore provides evidence to support programs targeting rubber, acacia harvesting, artisanal mining, and land conversion for cash crop plantations. Education is also key immediate socioeconomic factor, as poverty rate is consistently associated with tree cover loss and increased educational attainment is consistently associated with reduced tree cover loss, at approximately 12 ha per percentage increase in secondary school graduation. On the macro level, economic growth in China and Vietnam are correlatively associated with tree cover loss, as are rising trade in Myanmar and Laos. This study provides a methodological contribution to the current academic literature identifying socioeconomic dimensions of deforestation through spatial econometric analysis and scenario modelling at the landscape level. For practitioner work, this pilot provides a model or tool for strategic planning of conservation interventions in light of economic conditions and factors.
Deficiency of MicroRNA-181a Results in Transcriptome-Wide Cell Specific Changes in the Kidney that Lead to Elevated Blood Pressure and Salt Sensitivity
Authors: Paterson Madeleine R. , Jackson Kristy L. , Dona Malathi I. , Farrugia Gabriella E. , Visniauskas Bruna , Watson Anna M. D. , Johnson Chad , Prieto Minolfa C. , Evans Roger G. , Charchar Fadi , Pinto Alexander R. , Marques Francine Z. , Head Geoffrey A. 
Published: March 2021

AbstractMicroRNA miR-181a is down-regulated in the kidneys of hypertensive patients and hypertensive mice.In vitro, miR-181a is a posttranslational inhibitor of renin expression, but pleiotropic mechanisms by which miR-181a may influence blood pressure (BP) are unknown. Here we determined whether deletion of miR-181a/b-1in vivochanges BP and the molecular mechanisms involved at the single-cell level. We developed a knockout mouse model lacking miR-181a/b-1 genes using CRISPR/Cas9 technology. Radio-telemetry probes were implanted in twelve-week-old C57BL/6J wild-type and miR-181a/b-1 knockout mice. Systolic and diastolic BP were 4-5mmHg higher in knockout compared with wild-type mice over 24-hours (P<0.01). Compared with wild-type mice, renal renin was higher in the juxtaglomerular cells of knockout mice. BP was similar in wild-type mice on a high (3.1%) versus low (0.3%) sodium diet (+0.4±0.8mmHg) but knockout mice showed salt sensitivity (+3.3±0.8mmHg,P<0.001). Since microRNAs can target several mRNAs simultaneously, we performed single-nuclei RNA-sequencing in 6,699 renal cells. We identified 12 distinct types of renal cells, all of which had genes that were dysregulated. This included genes involved in renal fibrosis and inflammation such asStat4, Col4a1, Cd81, Flt3l, Cxcl16, Smad4. We observed up-regulation of pathways related to the immune system, inflammatory response, reactive oxygen species and nerve development, consistent with higher tyrosine hydroxylase. In conclusion, downregulation of the miR-181a gene led to increased BP and salt sensitivity in mice. This is likely due to an increase in renin expression in juxtaglomerular cells, as well as microRNA-driven pleiotropic effects impacting renal pathways associated with hypertension.
Phycobilisome breakdown effector NblD is required to maintain the cellular amino acid composition during nitrogen starvation
Authors: Krauspe Vanessa , Timm Stefan , Hagemann Martin , Hess Wolfgang R. 
Published: March 2021

AbstractSmall proteins are critically involved in the acclimation response of photosynthetic cyanobacteria to nitrogen starvation. NblD is the 66-amino-acid effector of nitrogen-limitation-induced phycobilisome breakdown, which is believed to replenish the cellular amino acid pools. To address the physiological functions of NblD, the concentrations of amino acids, intermediates of the arginine catabolism pathway and several organic acids were measured during the response to nitrogen starvation in the cyanobacteriumSynechocystissp. PCC 6803 wild type and in annblDdeletion strain. A characteristic signature of metabolite pool composition was identified, which shows that NblD-mediated phycobilisome degradation is required to maintain the cellular amino acid and organic acid pools during nitrogen starvation. Specific deviations from the wild type suggest wider-reaching effects that also affect such processes as redox homeostasis via glutathione and tetrapyrrole biosynthesis, both of which are linked to the strongly decreased glutamate pool, and transcriptional reprogramming via an enhanced concentration of 2-oxoglutarate, the metabolite co-regulator of the NtcA transcription factor. The essential role played by NblD in metabolic homeostasis is consistent with the widespread occurrence of NblD throughout the cyanobacterial radiation and the previously observed strong positive selection for thenblDgene under fluctuating nitrogen supply.ImportanceCyanobacteria play important roles in the global carbon and nitrogen cycles. In their natural environment, these organisms are exposed to fluctuating nutrient conditions. Nitrogen starvation induces a coordinated nitrogen-saving program that includes the breakdown of nitrogen-rich photosynthetic pigments, particularly phycobiliproteins. The small protein NblD was recently identified as an effector of phycobilisome breakdown in cyanobacteria. In this study, we demonstrate that the NblD-mediated degradation of phycobiliproteins is needed to sustain cellular pools of soluble amino acids and other crucial metabolites. The essential role played by NblD in metabolic homeostasis explains why genes encoding this small protein are conserved in almost all members of cyanobacterial radiation.
Genomic Evidence of Environmental and ResidentSalmonellaSenftenberg and Montevideo Contamination in the Pistachio Supply-chain
Authors: Haendiges Julie , Davidson Gordon R. , Pettengill James B. , Reed Elizabeth , Blessington Tyann , Miller Jesse D. , Anderson Nathan , Myoda Sam , Brown Eric W. , Zheng Jie , Tikekar Rohan , Hoffmann Maria 
Published: March 2021

AbstractPistachios have been implicated in two salmonellosis outbreaks and multiple recalls in the U.S. This study performed a retrospective data analysis ofSalmonellaassociated with pistachios and a storage study to evaluate the survivability ofSalmonellaon inoculated inshell pistachios to further understand the genetics and microbiological dynamics of this commodity-pathogen pair. The retrospective data analysis on isolates associated with pistachios was performed from both short-read and long-read sequencing technologies. The sequence data were analyzed using the FDA’s Center for Food Safety and Applied Nutrition Single Nucleotide Polymorphism (SNP) analysis and Whole Genome Multi-locus Sequence Typing (wgMLST) pipeline. The storage study evaluated the survival of five strains ofSalmonellaon pistachios, both in a cocktail as well as individually. Our results demonstrate: i) evidence of persistentSalmonellaSenftenberg andSalmonellaMontevideo strains in pistachio environments, some of which may be due to clonal resident strains and some of which may be due to preharvest contamination; ii) presence of the Copper Homeostasis and Silver Resistance Island (CHASRI) inSalmonellaSenftenberg and Montevideo strains in the pistachio supply chain; and iii) different serovars ofSalmonella enterica,includingSalmonellaSenftenberg andSalmonellaMontevideo, are able to survive in pistachios over an extended period of time.ImportancePistachios have been linked to multistate outbreaks caused bySalmonellaserovar Senftenberg (2013, 2016) and serovar Montevideo (2016). This comprehensive study of whole-genome-sequence (WGS) data from Senftenberg and Montevideo isolates associated with pistachio outbreaks, recalls, and investigations over a nine-year period (2009-2018) was conducted to provide insights into evolutionary relationships and persistence. Multiple analytical approaches were applied including MLST, wgMLST and phylogenetic SNP analysis. The CHASRI was identified in all isolates associated with the sequence type 14 (ST14) and ST316, suggesting an adaptation in response to extrinsic pressures, such as in the farm environment. There is evidence of persistentSalmonellaSenftenberg and Montevideo strains in pistachio pre-harvest and post-harvest environments. Utilizing metagenomic sequencing during an inoculated storage study of pistachios allowed for determination of surviving serovars over an extended period of time. Defining the mechanisms of persistence of these strains is of high importance to public health.