bluuebunny/crossref_metadata_2025_split huggingface dataset:
The diagnostic certainty levels of junior clinicians: A retrospective cohort study
Authors: Chen Yang , Nagendran Myura , Kilic Yakup , Cavlan Dominic , Feather Adam , Westwood Mark , Rowland Edward , Gutteridge Charles , Lambiase Pier D 
Published: July 2020

ABSTRACTPurpose of the StudyTo characterise the documentation of working diagnoses and their associated level of certainty by clinicians assessing patients referred to the medical team from the emergency department.DesignThis was a single centre retrospective cohort study of non-consultant grade clinicians at the Royal London Hospital, Barts Health NHS Trust between 01/03/19 to 31/03/19. De-identified electronic health record data was collected to include the type of diagnosis documented (clinical, laboratory result or symptom/sign defined) and the certainty adjective used for single diagnoses. Presence or absence of diagnostic uncertainty was collected for multiple diagnoses.Results865 medical assessments were recorded during the study period. 850 were available for further analysis. 420 presented a single diagnosis while 430 presented multiple diagnoses. Of the 420 single diagnoses, 67 (16%) were documented as either a symptom or physical sign, and 16 (4%) were laboratory-result defined diagnoses. No uncertainty was expressed in 309 (74%) of the diagnoses. Of 430 multiple diagnoses, uncertainty was expressed in 346 (80%) compared to 84 (20%) in which no uncertainty was expressed.ConclusionThe documentation of working diagnoses is highly variable amongst non-consultant grade clinicians assessing patients admitted via the emergency department. In nearly three quarters of assessments with single diagnoses, no element of uncertainty was implied or quantified. More uncertainty was expressed in multiple diagnoses than single diagnoses however documentation style was heterogenous. These data have implications for prospective studies examining the quantification of diagnostic certainty and its association with important process or outcome measures.What is already known on this subject-The factors which influence medical decision-making is almost exclusively assessed by vignettes, simulations or retrospective questionnaires. The certainty or confidence level of a clinician in making a decision can be a source of bias which can lead to patient harm if their confidence is miscalibrated with their accuracy.-A recent review assessing real world studies of decision-making found only nine, all of which used a Likert or visual analogue scaleMain messages-The documentation of working diagnoses is highly variable amongst non-consultant grade clinicians-In nearly three quarters of assessments with single diagnoses, no element of uncertainty was implied or quantified-Existing documentation is too heterogeneous to meaningfully analyse in a quantitative manner – increased standardisation will allow leveraging of electronic health record platforms to become better educational and research tools for clinicians and educators.
Non-communicable disease and the risk of infection death: a UK Biobank prospective cohort study
Authors: Drozd Michael , Lillie Patrick J , Pujades-Rodriguez Mar , Straw Sam , Morgan Ann W , Kearney Mark T , Witte Klaus K , Cubbon Richard M 
Published: July 2020

AbstractObjectivesNon-communicable diseases (NCDs) have recently been highlighted as important risk factors for COVID-19 fatality. We set out to investigate the association between NCDs and the risk of death from any infection in the pre-COVID-19 era.DesignProspective population-based studySettingUK BiobankParticipants493,295 participantsMain outcome measuresInfection death prior to December 31st2019.ResultsDuring 5,277,344 participant-years of follow-up, 1,385 infection deaths occurred, accounting for 5% of all deaths. Competing risks regression revealed that advancing age, male sex, smoking, socio-economic deprivation and all studied NCDs were independently associated with both the risk of infection death and non-infection death; ethnicity was associated with neither. Only smoking, socio-economic deprivation, hypertension, respiratory disease, chronic kidney disease, psychiatric disease and rheumatological disease were associated with greater hazard ratios for infection than non-infection death. Accrual of multimorbidity was also associated with a greater increases in the risk of infection death (HR 9.03 [95% confidence interval 6.61 to 12.34] for 5+ comorbidities versus none; p<0.001), than non-infection death (HR 5.68 [95% confidence interval 5.22 to 6.17] for 5+ comorbidities versus none; p<0.001).ConclusionsDiverse NCDs are associated with increased risk of infection death, suggesting that recently reported associations with COVID-19 death may be non-specific. Moreover, only a subset of NCDs, together with the accrual of multimorbidity, smoking and socio-economic deprivation, are associated with greater relative risks of infection death than other causes of death. Further research is needed to define why these risk factors are biased toward infection death so that more effective preventative strategies can be targeted to high-risk groups.What is already known on this topicInfection contributes to approximately one in five deaths globally and this often occurs in people with non-communicable diseases (NCDs).Many NCDs have recently been highlighted as risk factors for fatal COVID-19 infection.What this study addsWhilst diverse NCDs are associated with greater risk of infection death, only some pose greater hazards of infection than non-infection death.The association of many NCDs with fatal COVID-19 infection is unlikely to be specific to this pathogen.
Mathematical Modelling the Impact Evaluation of Lockdown on Infection Dynamics of COVID-19 in Italy
Authors: Kadyrov S. , Orynbassar A. , Saydaliyev H.B , Yergesh D. 
Published: July 2020

AbstractThe Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the cause of the coronavirus disease-2019 (COVID-19), within months of emergence from Wuhan, China, has rapidly spread, exacting a devastating human toll across around the world reaching the pandemic stage at the the beginning of March 2020. Thus, COVID-19’s daily increasing cases and deaths have led to worldwide lockdown, quarantine and some restrictions. Covid-19 epidemic in Italy started as a small wave of 2 infected cases on January 31. It was followed by a bigger wave mainly from local transmissions reported in 6387 cases on March 8. It caused the government to impose a lockdown on 8 March to the whole country as a way to suppress the pandemic. This study aims to evaluate the impact of the lockdown and awareness dynamics on infection in Italy over the period of January 31 to July 17 and how the impact varies across different lockdown scenarios in both periods before and after implementation of the lockdown policy. The findings SEIR reveal that implementation lockdown has minimised the social distancing flattening the curve. The infections associated with COVID-19 decreases with quarantine initially then easing lockdown will not cause further increasing transmission until a certain period which is explained by public high awareness. Completely removing lockdown may lead to sharp transmission second wave. Policy implementation and limitation of the study were evaluated at the end of the paper.
Prevalence of hypertension and controlled hypertension among United States adults: Evidence from NHANES 2017-18 survey
Authors: Rana Juwel , Oldroyd John , Islam Md. Momin , Tarazona-Meza Carla E , Islam Rakibul M. 
Published: July 2020

AbstractBackgroundThis study aims to compare the prevalence of hypertension (HTN) and controlled hypertension (CHTN) in US adults and determine the absolute difference in the prevalence of HTN and CHTN between the JNC7 and ACC/AHA 2017 guidelines.MethodsData for this study were derived from the most recent cycle of the National Health and Nutrition Examination Survey (NHANES) 2017-2018. After excluding participants with missing systolic blood pressure (BP) or diastolic BP and aged <18 years, 4730 participants were included in the final analyses. BP was defined as the average of the first three measurements. The prevalence of HTN and CHTN, including absolute differences of these prevalences, were estimated using both JNC7 and ACC/AHA 2017 guidelines.ResultsThe overall weighted prevalence of HTN was 31.7% (95% CI: 28.7, 34.8) based on JNC7, while the corresponding prevalence was 45.6% (95% CI: 43.0, 48.3) when new guideline of ACC/AHA was used. Of the people who had HTN according to the JNC7 and ACC/AHA 2017 guidelines, 48.2% (95% CI: 44.4-52.0) and 21.0% (95% CI: 18.1-24.2) had a controlled blood pressure level, respectively. When blood pressure was assessed using both guidelines, the greatest absolute increase in rates of HTN and CHTN was 17.4% and 30.0% in people aged 40-59 years, respectively.ConclusionGiven the high burden of disease due to complications arising from untreated HTN, as well as the higher costs of untreated disease, new guidelines have important public health implications to early detection of patients at risk and prevent complications across different populations.
The German Corona Consensus Dataset (GECCO): A standardized dataset for COVID-19 research
Authors: Sass Julian , Bartschke Alexander , Lehne Moritz , Essenwanger Andrea , Rinaldi Eugenia , Rudolph Stefanie , Heitmann Kai U. , Vehreschild Jörg J. , von Kalle Christof , Thun Sylvia 
Published: July 2020

ABSTRACTBackgroundThe current COVID-19 pandemic has led to a surge of research activity. While this research provides important insights, the multitude of studies results in an increasing segmentation of information. To ensure comparability across projects and institutions, standard datasets are needed. Here, we introduce the “German Corona Consensus Dataset” (GECCO), a uniform dataset that uses international terminologies and health IT standards to improve interoperability of COVID-19 data.MethodsBased on previous work (e.g., the ISARIC-WHO COVID-19 case report form) and in coordination with experts from university hospitals, professional associations and research initiatives, data elements relevant for COVID-19 research were collected, prioritized and consolidated into a compact core dataset. The dataset was mapped to international terminologies, and the Fast Healthcare Interoperability Resources (FHIR) standard was used to define interoperable, machine-readable data formats.ResultsA core dataset consisting of 81 data elements with 281 response options was defined, including information about, for example, demography, anamnesis, symptoms, therapy, medications or laboratory values of COVID-19 patients. Data elements and response options were mapped to SNOMED CT, LOINC, UCUM, ICD-10-GM and ATC, and FHIR profiles for interoperable data exchange were defined.ConclusionGECCO provides a compact, interoperable dataset that can help to make COVID-19 research data more comparable across studies and institutions. The dataset will be further refined in the future by adding domain-specific extension modules for more specialized use cases.
How much reserve capacity is justifiable for hospital pandemic preparedness? A cost-effectiveness analysis for COVID-19 in Germany
Authors: Gandjour Afschin 
Published: July 2020

AbstractIntroductionIn preparation for a possible second COVID-19 pandemic wave, expanding intensive care unit (ICU) bed capacity is an important consideration. The purpose of this study was to determine the costs and benefits of this strategy in Germany.MethodsThis study compared the provision of additional capacity to no intervention from a societal perspective. A decision model was developed using, e.g., information on age-specific fatality rates, ICU costs and outcomes, and the herd protection threshold. The net monetary benefit (NMB) was calculated based upon the willingness to pay for new medicines for the treatment of cancer, a condition with a similar disease burden in the near term.ResultsThe marginal cost-effectiveness ratio (MCER) of supplying one additional ICU bed is €24,815 per life year gained and increases with the number of additional beds. The NMB remains positive for utilization rates as low as 1.5% and, assuming full capacity utilization, for multiples of the currently available bed capacity. Expanding the ICU bed capacity by 10,000 beds is projected to result in societal costs of €41 billion and to reduce mortality of ICU candidates by 20% compared with no intervention (assuming full capacity utilization). In a sensitivity analysis, the variables with the highest impact on the MCER were the mortality rates in the ICU and after discharge.ConclusionsIn Germany, the provision of additional ICU bed capacity appears to be cost-effective over a large increase in the number of beds. Nevertheless, bed utilization is constrained by labor supply and possibly other input factors.
The optimal level of serum vitamin D in apparently healthy Bangladeshi adult volunteer
Authors: Yadav Anil , Selim Shahjada , Haq Tahniyah , Shah Anil Kumar , Morshed Md. Shahed , Ghani Md. Habibul , Faisal Ibrahim , khan Murshed Ahamed , Mustari Marufa , Rajiv Mostafa Hasan , Hasanat M A , Uddin Farid 
Published: July 2020

AbstractIntroductionVitamin D level has profound clinical implications but there is dilemma of optimal vitamin D cut off level among Bangladeshi population as well in many parts of the world. This study aimed to determine the optimal level of vitamin D in relation to intact parathyroid hormone (iPTH) and serum calcium in apparently healthy adult volunteer.MethodsThis observational cross-sectional study was carried out in 130 apparently healthy adult participants of BSMMU. All the subjects were taken their demographic profile and investigated for vitamin D level, iPTH, corrected calcium and phosphate. Serum 25(OH)D was measured by high performance liquid chromatography (HPLC) whereas iPTH, corrected serum calcium and serum phosphate were measured by chemiluminescent method.ResultsThe mean 25(OH)D level was found to be 16.78(SD8.47) ng/ml and extensively distinct by age distribution and adequacy of sun exposure. There was substantially inverse correlation between serum iPTH and serum 25(OH)D (r = - 0.22, p = 0.01). Serum 25(OH)D levels < 27.5ng/ml were associated with a steep increase in serum iPTH levels. Serum iPTH was stabilized at level 54.5pg/ml by using the quadratic fit with plateau model.ConclusionsFrom this study the optimal level of 25(OH)D for apparently healthy adult in Bangladesh is 27.5 ng/ml.
Genotype and defects in microtubule-based motility correlate with clinical severity in KIF1A Associated Neurological Disorder
Authors: Boyle Lia , Rao Lu , Kaur Simranpreet , Fan Xiao , Mebane Caroline , Hamm Laura , Thornton Andrew , Ahrendsen Jared T , Anderson Matthew P , Christodoulou John , Gennerich Arne , Shen Yufeng , Chung Wendy K 
Published: July 2020

AbstractKIF1A Associated Neurological Disorder (KAND) encompasses a recently identified group of rare neurodegenerative conditions caused by variants in KIF1A, a member of the kinesin-3 family of microtubule (MT) motor proteins. Here we characterize the natural history of KAND in 117 individuals using a combination of caregiver or self-reported medical history, a standardized measure of adaptive behavior, clinical records, and neuropathology. We developed a heuristic severity score using a weighted sum of common symptoms to assess disease severity. Focusing on 100 individuals, we compared the average clinical severity score for each variant with in silico predictions of deleteriousness and location in the protein. We found increased severity is strongly associated with variants occurring in regions involved with ATP and MT-binding: the P-loop, switch I, and switch II. For a subset of identified variants, we generated recombinant mutant proteins which we used to assess transport in vivo by assessing neurite tip accumulation, and to assess MT binding, motor velocity, and processivity using total internal reflection fluorescence microscopy. We find all patient variants result in defects in transport, and describe three classes of protein dysfunction: reduced MT binding, reduced velocity and processivity, and increased non-motile rigor MT binding. The molecular rigor phenotype is consistently associated with the most severe clinical phenotype, while reduced binding is associated with milder clinical phenotypes. Our findings suggest the clinical phenotypic heterogeneity in KAND likely reflects and parallels diverse molecular phenotypes. We propose a new way to describe KAND subtypes to better capture the breadth of disease severity.
Impact Assessment of Full and Partial Stay-at-Home Orders, Face Mask Usage, and Contact Tracing: An Agent-Based Simulation Study of COVID-19 for an Urban Region
Authors: Tatapudi Hanisha , Das Rachita , Das Tapas K. 
Published: July 2020

AbstractPurposeVarious social intervention strategies to mitigate COVID-19 are examined using a comprehensive agent-based simulation model. A case study is conducted using a large urban region, Miami-Dade County, Florida, USA. Results are intended to serve as a planning guide for public health decision makers.MethodsThe simulation model mimics daily social mixing behavior of the susceptible and infected generating the spread. Data representing demographics of the region, virus epidemiology, and social interventions shapes model behavior. Results include daily values of infected, reported, hospitalized, and dead.ResultsStudy results show that stay-at-home order is quite effective in flattening and then reversing the case growth curve subsiding the pandemic with only 5.8% of the population infected. Whereas, following Florida’s current Phase II reopening plan could end the pandemic via herd immunity with 75% people infected. Use of surgical variety face masks reduced infected by 20%. A further reduction of 66% was achieved through contact tracing.ConclusionsFor Miami-Dade County, a strategy comprising mandatory use of face masks and aggressive contact tracing to identify 50% of the asymptomatic and pre-symptomatic, if adopted now, can potentially steer the COVID-19 pandemic to subside within next 3 months with approximately one fifth of the population infected.
High-throughput SARS-CoV-2 and host genome sequencing from single nasopharyngeal swabs
Authors: Gorzynski J. E. , De Jong H. N. , Amar D. , Hughes C. , Ioannidis A. , Bierman R. , Liu D. , Tanigawa Y. , Kistler A. L. , Kamm J. , Kim J. , Cappello L. , Neff N. F. , Rubinacci S. , Delaneau O. , Shoura M. J. , Seo K. , Kirillova A. , Raja A. , Sutton S. , Huang C. , Sahoo M. K. , Mallempati K. C. , Montero-Martin G. , Osoegawa K. , Watson N. , Hammond N. , Joshi R. , Fernández-Viña M. A. , Christle J. W. , Wheeler M.T. , Febbo P. , Farh K. , Schroth G. P. , DeSouza F. , Palacios J. , Salzman J. , Pinsky B. A. , Rivas M. A. , Bustamante C.D. , Ashley E. A. , Parikh V. N. 
Published: July 2020

AbstractDuring COVID19 and other viral pandemics, rapid generation of host and pathogen genomic data is critical to tracking infection and informing therapies. There is an urgent need for efficient approaches to this data generation at scale. We have developed a scalable, high throughput approach to generate high fidelity low pass whole genome and HLA sequencing, viral genomes, and representation of human transcriptome from single nasopharyngeal swabs of COVID19 patients.
Combining structured and unstructured data in eMRs to create clinically-defined eMR-derived cohorts
Authors: Tam Charmaine S , Gullick Janice , Saavedra Aldo , Vernon Stephen T , Figtree Gemma A , Chow Clara K , Cretikos Michelle , Morris Richard W , William Maged , Morris Jonathan , Brieger David 
Published: July 2020

ABSTRACTBackgroundThere have been few studies describing how eMR systems can be systematically queried to identify clinically-defined populations and limited studies utilising free-text in this process. The aim of this study is to provide a generalisable methodology for constructing clinically-defined eMR-derived patient cohorts using structured and unstructured data in eMRs.MethodsPatients with possible acute coronary syndrome (ACS) were used as an exemplar. Cardiologists defined clinical criteria for patients presenting with possible ACS. These were mapped to data tables within the eMR system creating seven inclusion criteria comprised of structured data fields (orders and investigations, procedures, scanned electrocardiogram (ECG) images, and diagnostic codes) and unstructured clinical documentation. Data were extracted from two local health districts (LHD) in Sydney, Australia. Outcome measures included examination of the relative contribution of individual inclusion criteria to the identification of eligible encounters, comparisons between inclusion criterion and evaluation of consistency of data extracts across years and LHDs.ResultsAmong 802,742 encounters in a 5 year dataset (1/1/13 to 30/12/17), the presence of an ECG image (54.8% of encounters) and symptoms and keywords in clinical documentation (41.4-64.0%) were used most often to identify presentations of possible ACS. Orders and investigations (27.3%) and procedures (1.4%), were less often present for identified presentations. Relevant ICD-10/SNOMED codes were present for 3.7% of identified encounters. Similar trends were seen when the two LHDs were examined separately, and across years.ConclusionsClinically-defined eMR-derived cohorts combining structured and unstructured data during cohort identification is prerequisite for critical validation work required for secondary use of eMR data.
Haloargentinum marplatensisgen. nov., sp. nov., a novel extremely halophilic bacterium isolated from salted-ripened anchovy (Engraulis anchoita)
Authors: Perez Silvina , Gomila Margarita , Murialdo Silvia Elena , Ameztoy Irene Mabel , Gonzalez-Escalona Narjol , Ramírez Elida Elvia , Yeannes María Isabel 
Published: July 2020

ABSTRACTA facultative aerobic, Gram-negative, motile, non-endospore forming and extremely halophilic bacterium, strain 11aii⊺, isolated from salted-ripened anchovy, was examined using a polyphasic approach to characterize and clarify its phylogenetic and taxonomic position. Sequences of the 16S rRNA gene revealed close relationships to species of the generaLentibacillusandVirgibacillus(94.2% similarity). The organism grew optimally in the presence of 20-35 % NaCl. The major fatty acids of strain 11aii⊺were C16:0(42.1%) and anteiso-C15:0(31.2%) and also presented iso-C16:0(11.0%), anteiso-C17:0(10.4%) and C18:0(5.2%). Based on data presented here, strain 11aii⊺is considered to represent a novel genus and species, for which the nameHaloargentinum marplatensis gen. nov. sp. nov. is proposed with the strain 11aii⊺as type strain.