bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dance Interventions for Individuals Post-Stroke - A Scoping Review Protocol
Authors: Kipnis Danielle , Kruusamäe Helena , King Miriam , Schreier Abigail , Quinn Lori , Shih Hai-Jung Steffi 
Published: May 2021

AbstractThe purpose of this scoping review will be to explore the current literature on dance interventions for individuals post-stroke. Specifically, we will conduct a systematic search of published studies to map the state of the literature on feasibility, intervention procedures, and efficacy of dance to improve health-related outcomes for individuals post-stroke. Stroke is the leading cause of long-term disability frequently causing motor and cognitive impairments that impact functional abilities. Dance inherently encompasses key principles of motor learning including cognitive-motor specific task practice, sensory feedback, and social engagement. Dance and music create an enriched environment, engaging emotion and promoting positive affect.Electronic databases were searched in February 2021. Original, peer-reviewed studies will be included if they broadly describe the use of a dance intervention for individuals post-stroke. Studies including other neurological populations will be considered only if stroke results can be isolated. We will categorize studies based on dance style, study type, population characteristics, and study setting. We will narratively synthesize results, assessing feasibility, intervention procedures, and efficacy of dance to improve health-related outcomes in stroke survivors, including potential motor, cognitive, psychological, and social benefits.This scoping review will be the first to broadly describe the existing literature on dance interventions for individuals post-stroke. We hope to identify trends in outcomes measures as well as reveal successes, limitations, and gaps in the literature to inform potential directions for future research in the field.
Impairment in acquisition of conditioned fear in schizophrenia: a pooled analysis of four studies
Authors: Tuominen Lauri , Romaniuk Liana , Milad Mohammed R. , Goff Donald C. , Hall Jeremy , Holt Daphne J. 
Published: May 2021

AbstractBackgroundIndividuals with schizophrenia show impairments in associative learning. One well-studied, quantifiable form of associative learning is Pavlovian fear conditioning. However, to date, studies of fear conditioning in schizophrenia have been inconclusive, possibly because they lacked sufficient power.MethodsTo address this issue, data were pooled from 4 independent fear conditioning studies that included a total of 77 individuals with schizophrenia and 74 control subjects. Skin conductance responses (SCRs) during fear conditioning to stimuli that were paired (the CS+) and not paired (CS-) with an aversive, unconditioned stimulus were measured, and the success of acquisition of differential conditioning (the magnitude of CS+ vs. CS-SCRs) and responses to CS+ and CS-separately were assessed.ResultsAcquisition of differential conditioned fear responses was significantly lower in individuals with schizophrenia than in healthy controls (Cohen’s d = 0.53). This effect was primarily related to a significantly higher response to the CS-stimulus in the schizophrenia compared to the control group. The magnitude of this response to the CS- in the schizophrenia group was correlated with the severity of delusional ideation. Other symptoms or antipsychotic dose were not associated with fear conditioning measures.ConclusionsIndividuals with schizophrenia who endorse delusional beliefs are over-responsive to neutral stimuli during fear conditioning. This finding is consistent with prior models of aberrant learning in psychosis.
Assessing multiplex tiling PCR sequencing approaches for detecting genomic variants of SARS-CoV-2 in municipal wastewater
Authors: Lin Xuan , Glier Melissa , Kuchinski Kevin , Mierlo Tenysha Ross-Van , McVea David , Tyson John R. , Prystajecky Natalie , Ziels Ryan M. 
Published: May 2021

AbstractWastewater-based genomic surveillance of the SARS-CoV-2 virus shows promise to complement genomic epidemiology efforts. Multiplex tiled PCR is a desirable approach for targeted genome sequencing of SARS-CoV-2 in wastewater due to its low cost and rapid turnaround time. However, it is not clear how different multiplex tiled PCR primer schemes or wastewater sample matrices impact the resulting SARS-CoV-2 genome coverage. The objective of this work was to assess the performance of three different multiplex primer schemes, consisting of 150bp, 400bp, and 1200bp amplicons, as well as two wastewater sample matrices, influent wastewater and primary sludge, for targeted genome sequencing of SARS-CoV-2. Wastewater samples were collected weekly from five municipal wastewater treatment plants (WWTPs) in the Metro Vancouver region of British Columbia, Canada during a period of increased COVID-19 case counts from February to April, 2021. RNA extracted from clarified influent wastewater provided significantly higher genome coverage (breadth and median depth) than primary sludge samples across all primer schemes. Shorter amplicons appeared more resilient to sample RNA degradation, but were hindered by greater primer pool complexity in the 150bp scheme. The identified optimal primer scheme (400bp) and sample matrix (influent) was capable of detecting the emergence of mutations associated with genomic variants of concern, of which the daily wastewater load significantly correlated with clinical case counts. Taken together, these results provide guidance on best practices for implementing wastewater-based genomic surveillance, and demonstrate its ability to inform epidemiology efforts by detecting genomic variants of concern circulating within a geographic region.ImportanceMonitoring the genomic characteristics of the SARS-CoV-2 virus circulating in a population can shed important insights into epidemiological aspects of the COVID-19 outbreak. Sequencing every clinical patient sample in a highly populous area is a difficult feat, and thus sequencing SARS-CoV-2 RNA in municipal wastewater offers great promise to augment genomic surveillance by characterizing a pooled population sample matrix, particularly during an escalating outbreak. Here, we assess different approaches and sample matrices for rapid targeted genome sequencing of SARS-CoV-2 in municipal wastewater. We demonstrate that the optimal approach is capable of detecting the emergence of SARS-CoV-2 genomic variants of concern, with strong correlations to clinical case data in the province of British Columbia. These results provide guidance on best practices on, as well as further support for, the application of wastewater genomic surveillance as a tool to augment current genomic epidemiology efforts.
Simultaneous selection of nanobodies for accessible epitopes on immune cells in the tumor microenvironment
Authors: Sekar Thillai V. , Elghonaimy Eslam A. , Swancutt Katy L. , Diegeler Sebastian , Gonzalez Isaac , Hamilton Cassandra , Leung Peter Q. , Meiler Jens , Martina Cristina E. , Whitney Michael , Aguilera Todd A. 
Published: May 2021

AbstractIn the rapidly advancing field of synthetic biology, there is a critical need for technology to discover targeting moieties for therapeutic biologics. We developed INSPIRE-seq, an approach that utilizes a nanobody library and next-generation sequencing to identify nanobodies selected for complex environments. INSPIRE-seq enables the parallel enrichment of immune cell-binding nanobodies that penetrate the tumor microenvironment. Clone enrichment and specificity varies across immune cell subtypes in the tumor, lymph node, and spleen. INSPIRE-seq identified a dendritic cell binding clone that binds PHB2. Single-cell RNA sequencing revealed a connection with cDC1s, and immunofluorescence confirmed nanobody-PHB2 colocalization along cell membranes. Structural modeling and docking studies assisted binding predictions and will guide nanobody selection. In this work, we demonstrate that INSPIRE-seq offers an unbiased approach to examine complex microenvironments and assist in the development of nanobodies, which could serve as active drugs, modified to become drugs, or used as targeting moieties.
The Evolutionary History of Small RNAs in the Solanaceae
Authors: Baldrich Patricia , Bélanger Sébastien , Kong Shuyao , Pokhrel Suresh , Tamim Saleh , Teng Chong , Schiebout Courtney , Gurazada Sai Guna Ranjan , Gupta Pallavi , Patel Parth , Razifard Hamid , Nakano Mayumi , Dusia Ayush , Meyers Blake C. , Frank Margaret H. 
Published: May 2021

ABSTRACTThe Solanaceae or “nightshade” family is an economically important group that harbors a remarkable amount of diversity. To gain a better understanding of how the unique biology of the Solanaceae relates to the family’s small RNA genomic landscape, we downloaded over 255 publicly available small RNA datasets that comprise over 2.6 billion reads of sequence data. We applied a suite of computational tools to predict and annotate two major small RNA classes: (1) microRNAs (miRNAs), typically 20-22 nt RNAs generated from a hairpin precursor and functioning in gene silencing, and (2) short interfering RNAs (siRNAs), including 24-nt heterochromatic siRNAs (hc-siRNAs) typically functioning to repress repetitive regions of the genome via RNA-directed DNA methylation, as well as secondary phased siRNAs (phasiRNAs) and trans-acting siRNAs (tasiRNAs) generated via miRNA-directed cleavage of a Pol II-derived RNA precursor. Our analyses described thousands of small RNA loci, including poorly-understood clusters of 22-nt siRNAs that accumulate during viral infection. The birth, death, expansion, and contraction of these small RNA loci are dynamic evolutionary processes that characterize the Solanaceae family. These analyses indicate that individuals within the same genus share similar small RNA landscapes, whereas comparisons between distinct genera within the Solanaceae reveal relatively few commonalities.ONE-SENTENCE SUMMARYWe use over 255 publicly-available small RNA datasets to characterize the small RNA landscape for the Solanaceae family.
Reflex single-gene non-invasive prenatal testing significantly increases the cost-effectiveness of carrier screening
Authors: Riku Shan , Hedriana Herman , Carozza Jacqueline A. , Hoskovec Jennifer 
Published: May 2021

AbstractObjectiveTo evaluate the clinical and cost savings benefits of adoption of a carrier screen with reflex single-gene non-invasive prenatal test (sgNIPT) in prenatal care.MethodA decision-analytic model was developed to compare carrier screen with reflex sgNIPT (maternal carrier status and fetal risk reported together) as first-line carrier screening to the traditional carrier screening workflow (positive maternal carrier screen followed by paternal screening to evaluate fetal risk). The model compared the clinical outcomes and cost effectiveness between the two screening methods. These results were used to simulate appropriate pricing for reflex sgNIPT.ResultsReflex sgNIPT carrier screening detected 108 of 110 affected pregnancies per 100,000 births (98.5% sensitivity), whereas traditional carrier screening detected 46 of 110 affected pregnancies (41.5% sensitivity). The cost to identify one affected pregnancy was reduced by 62% in the reflex sgNIPT scenario compared to the traditional scenario. Adding together the testing cost savings and the savings from earlier clinical intervention made possible by reflex sgNIPT, the total cost savings was $37.6 million per 100,000 pregnancies. Based on these cost savings, we simulated appropriate reflex sgNIPT pricing range: if the cost to identify one affected pregnancy is the unit cost, carrier screening with reflex sgNIPT can be priced up to $1,859 per test (or $7,233 if sgNIPT is billed separately); if the cost per 100,000 pregnancies is the unit cost, carrier screening with sgNIPT can be priced up to $1,070 per test (or $2,336 if sgNIPT is billed separately).ConclusionUsing the carrier screen with reflex sgNIPT as first-line screening improves the detection of affected fetuses by 2.4-fold and can save costs for the healthcare system. A real-life experience will be needed to assess the clinical utility and exact cost savings of carrier screen with reflex sgNIPT.
A systematic review and meta-analysis of non-workplace interventions to reduce time spent sedentary in adults
Authors: Hall Jessica Faye , Corepal Rekesh , Crocker Thomas F , Lam Natalie , Burton Louisa-Jane , Birch Karen , Carter Gill , Clarke David J , English Coralie , Farrin Amanda J , Fitzsimons Claire , Hall Jennifer , Holloway Ivana , Ozer Seline , Lawton Rebecca , Mead Gillian , Morton Sarah , Patel Anita , Forster Anne 
Published: May 2021

AbstractBackgroundSedentary behaviour has been the focus of considerable clinical, policy and research interest due to its detrimental effects on health and wellbeing. This systematic review aims to (1) develop a more precise description of different categories of interventions that aim to reduce sedentary time in adults by identifying specific components that form an intervention; (2) explore the effect of different categories of interventions in reducing time spent sedentary in adults.MethodsTen electronic databases, websites of relevant organisations (e.g. the Sedentary Behaviour Research Network), and relevant reviews were searched. Inclusion criteria: Randomised controlled trials (RCTs), including cluster and randomised cross-over trials, in the adult population (clinical and non-clinical). Any study including a measure of sedentary behaviour was included even if reducing sedentary behaviour was not the primary aim. Exclusion criteria: Interventions delivered in schools, colleges, or workplaces; studies investigating the immediate effects of breaking up sitting time as part of a supervised (usually laboratory-based) intervention. Two review authors conducted data extraction and quality assessment (GRADE approach).ResultsSearches identified 39,223 records, of which 85 studies met the inclusion criteria and were included in the review. Interventions shown to significantly reduce time spent sedentary were those which incorporated the provision of information, education, or support (advice/recommendations), in conjunction with either counselling (mean difference: -52.24 minutes/day; 95% CI: -85.37 to -19.10) or a form of structured/prescribed physical activity (standardised mean difference: -0.15; 95% CI: -0.23 to -0.07). However, this positive effect was not maintained at follow-up. No interventions were shown to break up prolonged sitting.ConclusionsThis review presents a novel way of categorising interventions according to the types of components they comprised. There is evidence that interventions might be effective in reducing time spent sedentary immediately post-intervention. There were limited studies measuring sustained behaviour change.
Assessment of mesalamine in the alterations of metabolic parameters in comorbid ulcerative colitis and metabolic syndrome patients: A retrospective study
Authors: Paniz Graziella R. , Arroyo-Mercado Fray M. , Ling Christina L. , Choi E. Eunice , Snow Harry E. , Rakov Neal E. , Castillo Eliseo F. 
Published: May 2021

BACKGROUND & AIMSIt is unclear how the gut targeting medication mesalamine alters metabolic parameters associated with Metabolic Syndrome (MetS). We completed a retrospective analysis on ulcerative colitis (UC) and MetS comorbid patients receiving mesalamine to examine the effects of mesalamine on the metabolic risk factors associated with MetS.METHODSWe performed a retrospective chart review using Cerner’s Health Facts (from July 2007 to July 2017). We identified UC patients with a MetS comorbidity and who were prescribed mesalamine within +/- 7 days of an encounter in which they were diagnosed with UC. We then collected the patient’s blood pressure, labs, and body measurement index (BMI) for each of these patient at the index date and the closest values to 12 months after the index date. We used analysis of covariance (ANCOVA) to determine the effect of mesalamine therapy in patients with both UC and MetS on the metabolic parameters after 12 months of treatment compared to baseline.RESULTSOur search of Cerner Health Facts identified 6,197 UC patients with concomitant MetS who were prescribed mesalamine. Of these individuals, 48% were female and 52% were male and within this cohort 88.3% received oral mesalamine and 11.7% received mesalamine via the rectal route. Oral mesalamine reduced fasting glucose levels and increased HDL cholesterol in these patients. C-reactive protein levels and erythrocyte sedimentation rate were also significantly reduced. Rectal mesalamine only reduced BMI. Further analysis revealed several MetS conditions risk factors were further improved when mesalamine was taken in the absence of medication for hypertension, hyperglycemia or dyslipidemia.CONCLUSIONIn a retrospective chart study of UC-MetS patients, we found oral mesalamine improved several metabolic parameters associated with MetS. Our findings suggest the PPAR agonist mesalamine that targets the gastrointestinal tract could prove beneficial in improving hypertension, hyperglycemia and dyslipidemia.
Emergency department admissions during COVID-19: explainable machine learning to characterise data drift and detect emergent health risks
Authors: Duckworth Christopher , Chmiel Francis P. , Burns Dan K. , Zlatev Zlatko D. , White Neil M. , Daniels Thomas W. V. , Kiuber Michael , Boniface Michael J. 
Published: May 2021

ABSTRACTSupervised machine learning algorithms deployed in acute healthcare settings use data describing historical episodes to predict clinical outcomes. Clinical settings are dynamic environments and the underlying data distributions characterising episodes can change with time (a phenomenon known as data drift), and so can the relationship between episode characteristics and associated clinical outcomes (so-called, concept drift). We demonstrate how explainable machine learning can be used to monitor data drift in a predictive model deployed within a hospital emergency department. We use the COVID-19 pandemic as an exemplar cause of data drift, which has brought a severe change in operational circumstances. We present a machine learning classifier trained using (pre-COVID-19) data, to identify patients at high risk of admission to hospital during an emergency department attendance. We evaluate our model’s performance on attendances occurring pre-pandemic (AUROC 0.856 95%CI [0.852, 0.859]) and during the COVID-19 pandemic (AUROC 0.826 95%CI [0.814, 0.837]). We demonstrate two benefits of explainable machine learning (SHAP) for models deployed in healthcare settings: (1) By tracking the variation in a feature’s SHAP value relative to its global importance, a complimentary measure of data drift is found which highlights the need to retrain a predictive model. (2) By observing the relative changes in feature importance emergent health risks can be identified.
Increased prevalence and clinical impact of hypocalcaemia in severe COVID-19 distinguishes it from other forms of infective pneumonia
Authors: Mehta Meera R , Ghani Hakim , Chua Felix , Draper Adrian , Calmonson Sam , Prabhakar Meghna , Shah Rijul , Navarra Alessio , Vaghela Tejal , Barlow Andrew , Vancheeswaran Rama 
Published: May 2021

AbstractBackgroundHypocalcaemia has been reported in the context of acute COVID-19, where it has been associated with an increased risk of hospitalisation and disease severity. Calcium is an important intracellular messenger that controls diverse cellular processes. Two other clinically important coronaviruses, SARS-CoV-1 and Middle East respiratory syndrome (MERS)-CoV, can use calcium ions to enter and replicate within host cells. Calcium may therefore be important in the pathophysiology of COVID-19 infection. We sought to investigate whether calcium derangement was a specific feature of COVID-19 that distinguishes it from other infective pneumonias, and its association with disease severity.MethodsWe conducted a single centre retrospective study of albumin-corrected serum calcium on adult patients with COVID-19 who presented between March 1stand May 16th2020. The primary outcome was maximal level of care based on the World Health Organization Clinical Progression Scale for COVID-19. Cases with community acquired pneumonia (CAP) and viral pneumonia (VP) were identified through a clinical database over three intervals (January to February 2018, January to February 2019 and September to December 2019).ResultsWe analysed data from 506 patients with COVID-19, 95 patients with CAP and 152 patients with VP. Hypocalcaemia (serum calcium <2.2mmol/L) was a specific and common clinical finding in patients with COVID-19 that was not present in other respiratory infections. Calcium levels were significantly lower in those with severe disease. Ordinal regression of risk estimates for categorised care levels showed that baseline hypocalcaemia was incrementally associated with odds ratio of 2.33 for higher level of care, superior to other variables that have previously been shown to predict worse COVID-19 outcome. Serial calcium levels showed improvement by day 7-9 of admission, only in in survivors of COVID-19.ConclusionHypocalcaemia may independently predict not only more severe but more progressive disease and warrants detailed prognostic investigation. The fact that decreased serum calcium is observed at the time of clinical presentation in COVID-19, but not other infective pneumonias, suggests that its early derangement is pathophysiological and may influence the deleterious evolution of this disease. If calcium is ultimately shown to be critical to the entry and replication of SARS-CoV-2 in host cells, unravelling how this mechanism could be therapeutically targeted deserves more intensive examination.Trial registration HRA20/HRA/2344.
The indirect effect of mRNA-based Covid-19 vaccination on unvaccinated household members
Authors: Salo Jussipekka , Hägg Milla , Kortelainen Mika , Leino Tuija , Saxell Tanja , Siikanen Markku , Sääksvuori Lauri 
Published: May 2021

AbstractMass vaccination is effective in reducing SARS-CoV-2 infections among vaccinated individuals. However, it remains unclear how effectively Covid-19 vaccines prevent people from spreading the virus to their close contacts in real-world circumstances. Here, using nationwide administrative datasets on SARS-CoV-2 infections, vaccination records, demographics, and unique household IDs, we provide evidence about the direct and indirect effectiveness of Covid-19 vaccines in reducing infections among vaccinated individuals and their unvaccinated household members. Our estimates for adults imply indirect effectiveness of 8.7% (95% CI: -28.9 to 35.4) two weeks and 42.9% (95% CI: 22.3 to 58.1) 10 weeks after the first dose. We find that the indirect effect of Covid-19 vaccines is smaller and less precise for unvaccinated children aged between 3 to 18 years than for adults. These results provide household-level evidence that vaccines do not only protect vaccinated individuals but provide indirect protection to unvaccinated individuals in a real-world setting.