bluuebunny/crossref_metadata_2025_split huggingface dataset:
Red flags useful to screen for gastrointestinal and hepatic diseases in patients with shoulder pain: a scoping review protocol
Authors: Roncone A , Fiorentino F , Pennella D , Maselli F , Brindisino F , Giagio S 
Published: March 2021

ABSTRACTShoulder pain (SP) is the third most common musculoskeletal disorder worldwide and its prevalence ranges from 5 to 47%.However, the clinical presentation of signs and symptoms may hide other serious conditions; the so-called Red Flags (RFs).For these reasons, clinicians dealing with neuro-musculoskeletal shoulder disorders should pay particular attention during the medical history and clinical examination screening and identifying signs that may cause probable referred symptoms.Considering the variety of clinical presentations of SP and the importance of the screening for referral, identifying and summarizing the possible gastrointestinal and hepatic diseases among these patients may give a comprehensive overview to the clinicians and consequently may improve the overall management.To the authors knowledge, there are no published studies on the topic and, in this context, a scoping review is strongly required and corresponded to the objectives of this project.
Point-of-care lung ultrasonography for early identification of mild COVID-19: a prospective cohort of outpatients in a Swiss screening center
Authors: Schaad Siméon , Brahier Thomas , Hartley Mary-Anne , Cordonnier Jean-Baptiste , Bosso Luca , Espejo Tanguy , Pantet Olivier , Hugli Olivier , Carron Pierre-Nicolas , Meuwly Jean-Yves , Boillat-Blanco Noémie 
Published: March 2021

AbstractBackgroundEarly identification of SARS-CoV-2 infection is important to guide quarantine and reduce transmission. This study evaluates the diagnostic performance of lung ultrasound (LUS), an affordable, consumable-free point-of-care tool, for COVID-19 screening.MethodsThis prospective observational cohort included adults presenting with cough and/or dyspnea at a SARS-CoV-2 screening center of Lausanne University Hospital between March 31st and May 8th, 2020. Investigators recorded standardized LUS images and videos in 10 lung zones per subject. Two blinded independent experts reviewed LUS recording and classified abnormal findings according to pre-specified criteria to investigate their predictive value to diagnose SARS-CoV-2 infection according to PCR on nasopharyngeal swabs (COVIDpos vs COVIDneg). We finally combined LUS and clinical findings to derive a multivariate logistic regression diagnostic score.ResultsOf 134 included patients, 23% (n=30/134) were COVIDpos and 77% (n=103/134) were COVIDneg; 85%, (n=114/134) cases were previously healthy healthcare workers presenting within 2 to 5 days of symptom onset (IQR). Abnormal LUS findings were significantly more frequent in COVIDpos compared to COVIDneg (45% versus 26%, p=0.045) and mostly consisted of focal pathologic B-lines. Combining LUS findings in a multivariate logistic regression score had an area under the receiver-operating curve of 63.9% to detect COVID-19, but improved to 84.5% with the addition of clinical featuresConclusionsCOVIDpos patients are significantly more likely to have lung pathology by LUS. Our findings have potential diagnostic value for COVID-19 at the point of care. Combination of clinical and LUS features showed promising results, which need confirmation in a larger study population.What is already known on the subjectLung ultrasonography (LUS) is a consumable-free, easy-to-use, portable, non-radiating and non-invasive screening tool that can be performed at the bedside: its diagnostic performance for pneumonia has been established.Recent studies conducted in emergency department showed a correlation between LUS findings and COVID-19 diagnosis.What the study adsThis is the first study assessing the diagnostic performance of LUS for COVID-19 in outpatients with mild acute respiratory tract infection.Mild COVID-19 patients are more likely to have lung pathology by LUS compared with COVID-19 negative.Combination of clinical and LUS features showed promising results with a potential diagnostic value for COVID-19 at the point of care.
Shielding of Viruses such as SARS-CoV-2 from Ultraviolet Radiation in Particles Generated by Sneezing or Coughing: Numerical Simulations of Survival Fractions
Authors: Hill Steven C. , Doughty David C. , Mackowski Daniel W. 
Published: March 2021

ABSTRACTSARS-CoV-2 and other microbes within aerosol particles can be partially shielded from UV radiation. The particles refract and absorb light, and thereby reduce the UV intensity at various locations within the particle. Shielding has been demonstrated in calculations of UV intensities within spherical approximations of SARS-CoV-2 virions that are within spherical particles approximating dried-to-equilibrium respiratory fluids. The purpose of this paper is to calculate the survival fractions of virions (i.e., the fractions of virions that can infect cells) within spherical particles approximating dried respiratory fluids, and to investigate the implications of these calculations for using UV light for disinfection. The particles may be on a surface or in air. In this paper the survival fraction (S) of a set of virions illuminated with a UV fluence (F, in J/m2) is approximated as S=exp(-kF), where k is the UV inactivation rate constant (m2/J). The average survival fractions (Sp) of all the simulated virions in a particle are calculated using the calculated decreases in fluence. The results show that virions in particles of dried respiratory fluids can have significantly larger Sp than do individual virions. For individual virions, and virions in 1-, 5-, and 9-µm particles illuminated (normal incidence) on a surface with 260-nm UV light, the Sp = 0.00005, 0.0155, 0.22 and 0.28, respectively, when kF=10. The Sp decrease to <10−7, <10−7, 0.077 and 0.15, respectively, for kF=100. Calculated results also show that illuminating particles with UV beams from widely separated directions can strongly reduce the Sp. These results suggest that the size distributions and optical properties of the dried particles of virion-containing respiratory fluids are likely important in effectively designing and using UV germicidal irradiation systems for microbes in particles. The results suggest the use of reflective surfaces to increase the angles of illumination and decrease the Sp. The results suggest the need for measurements of the Sp of SARS-CoV-2 in particles having compositions and sizes relevant to the modes of disease transmission.
Understanding the prevalence of psychiatric disorders in people with cerebral palsy: A systematic review protocol
Authors: Eres R. , Dutia I. , Walsh M. , Mulraney M. , Sawyer S.M , Reddihough D.S , Coghill D. 
Published: March 2021

AbstractBackgroundThere is an abundance of research investigating physical health outcomes in people with cerebral palsy, however evidence from studies investigating psychiatric disorders in this group is less well developed. Specifically, there is little research synthesising the prevalence rates of psychiatric disorders in people with cerebral palsy, and there is no summary of the instruments used to measure this. This systematic review will summarise the current body of evidence investigating psychiatric disorders in people with cerebral palsy, as well as the measurement or diagnostic instruments used to measure psychiatric disorder.FindingsTo be included in the review, articles must report on psychiatric disorders in people with cerebral palsy or use standardised tools that allow for clinical thresholds to be derived, written in English, and published after 1980. A comprehensive, electronic database search strategy will be implemented targeting relevant papers indexed in MEDLINE, PsycINFO, Cochrane Library, and PubMed. Searches will include terms that relate to psychiatric disorders (E.g., mood disorders, anxiety disorders, ADHD, autism) in people with cerebral palsy. Data will be extracted based on age, psychiatric disorder, and cerebral palsy severity. We will summarise the findings as a narrative and will provide overall prevalence estimates for psychiatric disorders.DiscussionThe systematic review will provide novel insights into the prevalence of psychiatric disorders in people with cerebral palsy. It will also provide recommendations about the types of instruments that have been used and implemented in health research related to cerebral palsy. It will guide future work on interventions and primary research in clinical sciences and allied health disciplines.
Improving COVID-19 vaccination centre operation through computer modelling and simulation
Authors: Wood RM , Moss SJ , Murch BJ , Davies C , Vasilakis C 
Published: March 2021

AbstractMass vaccination is widely considered to offer the only route out of the COVID-19 pandemic in a way that social restrictions can be eased and economic activity can safely resume without compromising healthcare services. For many countries, dedicated vaccination centres are a key part of that effort. However, with no directly comparable historical experience there is little information to guide the operational configuration and management of these sites. In addressing this gap in knowledge, the objective of this study is to demonstrate the value of computer modelling. This is achieved through providing an account of its use in supporting management considerations and decisions at two major vaccination centres, at an early stage of the UK’s mass vaccination effort. We report on how modelling insight has influenced the initial setup of one site, including quantification of daily booking numbers. For the same site, we reveal how analysis has informed a significant operational shift in combining two key activities on the vaccination pathway into one. Finally, we describe how, at a second site, modelling has been used to examine pathway stability, in terms of resilience to unforeseen ‘shocks’ such as delayed arrivals and staff unavailability. Alongside the open-source simulation software, the modelling insights reported here can support managers to better plan and improve the operation of COVID-19 vaccination centres.
Dental mitigation strategies to reduce aerosolization of SARS-CoV-2
Authors: Vernon Jon J. , Black Emma V. I. , Dennis Thomas , Devine Deirdre A. , Fletcher Louise , Wood David J , Nattress Brian R 
Published: March 2021

AbstractLimiting infection transmission is central to the safety of all in dentistry, particularly during the current SARS-CoV-2 pandemic. Aerosol-generating procedures (AGPs) are crucial to the practise of dentistry; it is imperative to understand the inherent risks of viral dispersion associated with AGPs and the efficacy of available mitigation strategies.In a dental surgery setting, crown preparation and root canal access procedures were performed with an air turbine or electric speed-controlled hand-piece, with mitigation via rubber dam or high-volume aspiration and a no mitigation control. A phantom head was used with a 1.5 mL flow of artificial saliva infected with Φ6 bacteriophage (a surrogate virus for SARS-CoV-2) at ∼108plaque forming units mL-1, reflecting the upper limits of reported salivary SARS-CoV-2 levels. Bioaerosol dispersal was measured using agar settle plates lawned with the bacteriophage’s host,Pseudomonas syringae. Viral air concentrations were assessed using MicroBio MB2 air sampling, and particle quantities using Kanomax 3889 GEOα particle counters.Compared to an air turbine, the electric hand-piece reduced settled bioaerosols by 99.72%, 100.00% and 100.00% for no mitigation, aspiration and rubber dam, respectively. Bacteriophage concentrations in the air were reduced by 99.98%, 100.00% and 100.00%, with the same mitigation strategies. Use of the electric hand-piece with high-volume aspiration, resulted in no detectable bacteriophage, both on settle plates and in air samples taken 6-10-minutes post-procedure.To our knowledge, this study is the first to report the aerosolization of active virus as a marker for risk determination in the dental setting. Whilst this model represents a worst-case scenario for possible SARS-CoV-2 dispersal, these data showed that the use of electric hand-pieces can vastly reduce the risk of viral aerosolization, and therefore remove the need for clinic fallow time. Furthermore, our findings indicate that the use of particle analysis alone cannot provide sufficient insight to understand bioaerosol infection risk.
Detecting cognitive decline using speech only: The ADReSSOChallenge
Authors: Luz Saturnino , Haider Fasih , de la Fuente Sofia , Fromm Davida , MacWhinney Brian 
Published: March 2021

AbstractBuilding on the success of the ADReSS Challenge at Inter-speech 2020, which attracted the participation of 34 teams from across the world, the ADReSSoChallenge targets three difficult automatic prediction problems of societal and medical relevance, namely: detection of Alzheimer’s Dementia, inference of cognitive testing scores, and prediction of cognitive decline. This paper presents these prediction tasks in detail, describes the datasets used, and reports the results of the baseline classification and regression models we developed for each task. A combination of acoustic and linguistic features extracted directly from audio recordings, without human intervention, yielded a baseline accuracy of 78.87% for the AD classification task, a root mean squared (RMSE) error of 5.28 for prediction of cognitive scores, and 68.75% accuracy for the cognitive decline prediction task.
COVID-19 RT-PCR diagnostic assay sensitivity and SARS-CoV-2 transmission: A missing link?
Authors: Sahahjpal Nikhil Shri , Hon Ephrem Chin Lip , Dallaire Stephanie , Williams Colin , Ananth Sudha , Mondal Ashis K , Rojiani Amyn M , Hegde Madhuri , Kolhe Ravindra 
Published: March 2021

AbstractBackgroundThe sensitivity of commercially available RT-PCR assays varies over 10,000 fold, ranging from 10 to 20,000 viral copies/ml. The reporting of high Ct value results has been under scrutiny, as the clinical significance of these values is not yet completely understood. The early detection of infected individuals (high Ct results) in the pre-symptomatic phase of the disease using highly sensitive RT-PCR methods has been argued as a strategy to prevent transmission, while on the contrary, the reporting of high Ct has been criticized as false-positive results causing unnecessary testing and having several negative implications. The purpose of this study was to verify the presence of SARS-CoV-2 genomes in samples with a wide range of RT-PCR Ct values including samples with high Ct (37 to 42) using next-generation sequencing (NGS).MethodsThe study evaluated a total of 547 previously positive samples tested with the PerkinElmer® New Coronavirus Nucleic Acid Detection RT-PCR kit. The samples included in this study ranged from Ct values of 17-42, with 44 samples having a Ct > 37. Of the 547 samples, 149 were sequenced using PerkinElmer NEXTFLEX Variant-Seq SARS-CoV2 assay on NovaSeq 6000, and 398 samples were sequenced using Illumina SARS-CoV-2 respiratory viral panel kits using the NextSeq 500/550 system.ResultsBetween the two clinical laboratories, a total of ∼1.95 million samples were tested using the FDA-EUA PerkinElmer® New Coronavirus RT-PCR assay. Of the 1.95 million samples, ∼1.72 million were negative, ∼250,000 positive, and ∼16,500 in the range of 37-42. Of the 547 samples sequenced, the percentage of sequencing reads that aligned to the SARS-CoV-2 Wuhan-hu-1 reference genome (NC_045512.2) ranged from 25.5% to 99.69%. All samples sequenced showed high sequence specificity to the SARS-CoV-2 virus. Low Ct samples showed complete uniform coverage across the entire 29kb SAR-CoV-2 genome. The average coverage in samples with high Ct (>37) was found to be 55.5% (range 16.1-99.2%). However, as sample Ct increased, a gradual decrease in coverage uniformity was observed for few samples.ConclusionThis study demonstrates for the first time that the viral RNA is present in the high Ct value range of 37-42 and the sequence is unique to SARS-CoV-2 confirmed using two separate sequencing assays. This confirms that the detected Ct values are reflective of the presence of the SARS-CoV-2 virus and they are not an artifact or contamination. In light of the recent work highlighting the majority of transmission being pre-symptomatic/ asymptomatic, and high Ct results being observed at both the early and late phases of infection warrants further investigation into the clinical utility of high Ct results to curtail the spread of the virus.
Survey data on European organic multi-species livestock farms
Authors: Ulukan Defne , Steinmetz Lucille , Moerman Marie , Bernes Gun , Blanc Mathilde , Brock Christopher , Destruel Marie , Dumont Bertrand , Lang Elise , Meischner Tabea , Moraine Marc , Oehen Bernadette , Parsons David , Primi Riccardo , Ronchi Bruno , Schanz Lisa , Vanwindekens Frédéric , Veysset Patrick , Winckler Christoph , Martin Guillaume , Benoit Marc 
Published: March 2021

AbstractWhile there is increasing evidence of the sustainability benefits of diversified systems in the organic cropping sector, this has been much less investigated with organic livestock farming. To fill this knowledge gap, we surveyed a sample of 128 European organic multi-species livestock farms located across seven countries – Austria, Belgium, France, Germany, Italy, Sweden and Switzerland – and covering a large range of livestock species combinations. We recorded 1574 variables as raw data out of which we calculated 107 indicators describing farm structure, management and several sustainability dimensions: resource use efficiency and conservation, animal, land and work productivities, animal and human welfare. After technical validation of the data, we withdrew 26 farms and the database covers 102 farms. This database is well suited to unveil relationships between various dimensions of organic multi-species livestock farm sustainability and their structure and management. It can help reveal sustainable strategies for organic multi-species livestock farming systems and understand levers or barriers to their development.
Autism_genepheno: Text mining of gene-phenotype associations reveals new phenotypic profiles of autism-associated genes
Authors: Li Sijie , Guo Ziqi , Ioffe Jacob B. , Hu Yunfei , Zhen Yi , Zhou Xin 
Published: March 2021

ABSTRACTAutism is a spectrum disorder with wide variation in type and severity of symptoms. Understanding gene–phenotype associations is vital to unravel the disease mechanisms and advance its diagnosis and treatment. To date, several databases have stored a large portion of gene–phenotype associations which are mainly obtained from genetic experiments. However, a large proportion of gene–phenotype associations are still buried in the autism-related literature and there are limited resources to investigate autism-associated gene-phenotype associations. Given the abundance of the autism-related literature, we were thus motivated to develop Autism_genepheno, a text mining pipeline to identify sentence-level mentions of autism-associated genes and phenotypes in literature through natural language processing methods. We have generated a comprehensive database of gene-phenotype associations in the last five years’ autism-related literature that can be easily updated as new literature becomes available. We have evaluated our pipeline through several different approaches, and we are able to rank and select top autism-associated genes through their unique and wide spectrum of phenotypic profiles, which could provide a unique resource for the diagnosis and treatment of autism. The data resources and the Autism_genpheno pipeline are available at:https://github.com/maiziezhoulab/Autism_genepheno.
The fish pathogenAliivibrio salmonicidaLFI1238 can degrade and metabolize chitin despite major gene loss in the chitinolytic pathway
Authors: Skåne Anna , Minniti Giusi , Loose Jennifer S.M. , Mekasha Sophanit , Bissaro Bastien , Mathiesen Geir , Arntzen Magnus Ø. , Vaaje-Kolstad Gustav 
Published: March 2021

ABSTRACTThe fish pathogenAliivibrio (Vibrio) salmonicidaLFI1238 is thought to be incapable of utilizing chitin as a nutrient source since approximately half of the genes representing the chitinolytic pathway are disrupted by insertion sequences. In the present study, we combined a broad set of analytical methods to investigate this hypothesis. Cultivation studies revealed thatAl. salmonicidagrew efficiently onN-acetylglucosamine (GlcNAc) and chitobiose ((GlcNAc)2), the primary soluble products resulting from enzymatic chitin hydrolysis. The bacterium was also able to grow on chitin particles, albeit at a lower rate compared to the soluble substrates. The genome of the bacterium contains five disrupted chitinase genes (pseudogenes) and three intact genes encoding a glycoside hydrolase family 18 (GH18) chitinase and two auxiliary activity family 10 (AA10) lytic polysaccharide monooxygenases (LPMOs). Biochemical characterization showed that the chitinase and LPMOs were able to depolymerize both α- and β-chitin to (GlcNAc)2and oxidized chitooligosaccharides, respectively. Notably, the chitinase displayed up to 50-fold lower activity compared to other well-studied chitinases. Deletion of the genes encoding the intact chitinolytic enzymes showed that the chitinase was important for growth on β-chitin, whereas the LPMO gene-deletion variants only showed minor growth defects on this substrate. Finally, proteomic analysis ofAl. salmonicidaLFI1238 growth on β-chitin showed expression of all three chitinolytic enzymes, and intriguingly also three of the disrupted chitinases. In conclusion, our results show thatAl. salmonicidaLFI1238 can utilize chitin as a nutrient source and that the GH18 chitinase and the two LPMOs are needed for this ability.IMPORTANCEThe ability to utilize chitin as a source of nutrients is important for the survival and spread of marine microbial pathogens in the environment. One such pathogen isAliivibrio (Vibrio) salmonicida, the causative agent of cold water vibriosis. Due to extensive gene decay, many key enzymes in the chitinolytic pathway have been disrupted, putatively rendering this bacterium incapable of chitin degradation and utilization. In the present study we demonstrate thatAl. salmonicidacan degrade and metabolize chitin, the most abundant biopolymer in the ocean. Our findings shed new light on the environmental adaption of this fish pathogen.
Isolation and Purification of Lipoarabinomannan from Urine of Adults with Active Tuberculosis
Authors: Cantera Jason L. , Rashid Andrew A. , Lillis Lorraine L. , Peck Roger B. , Drain Paul K. , Pinter Abraham , Kawasaki Masanori , Moreau Emmanuel , Boyle David S. 
Published: March 2021

AbstractLipoarabinomannan (LAM) is a cell wall component ofMycobacterium tuberculosisthat is excreted in the urine of persons with active tuberculosis (TB). Limited diagnostic sensitivity of LAM immunoassays has been due to selecting antibodies against LAM derived fromin vitroculturedM. tuberculosis, rather than LAM purified fromin vivoclinical urine specimens. Urinary LAM (uLAM) is critical to enable the development of and/or screening of novel uLAM-specific antibodies but is typically dilute and in heterogeneous mixtures with other urine components. We used physical, enzymatic, and chemical processes for the scaled isolation and purification of uLAM. The purified material may then be used to develop more sensitive uLAM diagnostic tests for active TB disease.