bluuebunny/crossref_metadata_2025_split huggingface dataset:
COVID-19 Outcomes Among Solid Organ Transplant Recipients: A Case-control Study
Authors: Sharma Pratima , Chen Vincent , Fung Christopher M. , Troost Jonathan P. , Patel Vaiibhav N. , Combs Michael , Norman Silas , Garg Puneet , Colvin Monica , Aaronson Keith , Sonnenday Christopher J. , Golob Jonathan L. , Somers Emily C. , Doshi Mona M. 
Published: September 2020

Background.
Solid organ transplant (SOT) recipients are considered to be “vulnerable” to COVID-19 infection due to immunosuppression. To date, there are no studies that compared the disease severity of COVID-19 in SOT recipients with nontransplant patients.

Methods.
In this case-control study, we compared the outcomes of COVID-19 between SOT recipients and their matched nontransplant controls. The cases were all adult SOT recipients (N = 41) from our academic health center who were diagnosed with COVID-19 between March 10, 2020 and May 15, 2020 using positive reverse transcriptase polymerase chain reaction for SARS-CoV2. The controls (N = 121) were matched on age (±5 y), race, and admission status (hospital or outpatient). The primary outcome was death and secondary outcomes were severe disease, intubation and renal replacement therapy (RRT).

Results.
Median age of SOT recipients (9 heart, 3 lung, 16 kidney, 8 liver, and 5 dual organ) was 60 y, 80% were male and 67% were Black. Severe disease adjusted risk of death was similar in both the groups (hazard ratio = 0.84 [0.32–2.20]). Severity of COVID-19 and intubation were similar, but the RRT use was higher in SOT (odds ratio = 5.32 [1.26, 22.42]) compared to non-SOT COVID-19 patients. Among SOT recipients, COVID-19-related treatment with hydroxychloroquine (HCQ) was associated with 10-fold higher hazard of death compared to without HCQ (hazard ratio = 10.62 [1.24–91.09]).

Conclusions.
Although African Americans constituted one-tenth of all SOT in our center, they represented two-thirds of COVID-19 cases. Despite high RRT use in SOT recipients, the severe disease and short-term death were similar in both groups. HCQ for the treatment of COVID-19 among SOT recipients was associated with high mortality and therefore, its role as a treatment modality requires further scrutiny.
SARS-CoV-2 phylogeny during the early outbreak in the Basel area, Switzerland: import and spread dominated by a single B.1 lineage variant (C15324T)
Authors: Stange Madlen , Mari Alfredo , Roloff Tim , Seth-Smith Helena MB , Schweitzer Michael , Brunner Myrta , Leuzinger Karoline , Søgaard Kirstine K. , Gensch Alexander , Tschudin-Sutter Sarah , Fuchs Simon , Bielicki Julia , Pargger Hans , Siegemund Martin , Nickel Christian H , Bingisser Roland , Osthoff Michael , Bassetti Stefano , Schneider-Sliwa Rita , Battegay Manuel , Hirsch Hans H , Egli Adrian 
Published: September 2020

AbstractBackgroundThe first case of SARS-CoV-2 in Basel, Switzerland, was detected on February 26th2020. We present a phylogenetic longitudinal study and explore viral introduction and evolution during the exponential early phase of the local COVID-19 outbreak from February 26thuntil March 23rd.MethodsWe sequenced SARS-CoV-2 from naso-oropharyngeal swabs, generated 468 high quality genomes, and called variants with our COVID-19 Pipeline (COVGAP). We analysed viral genetic diversity using PANGOLIN taxonomic lineages. To identify introduction and dissemination events we incorporated global SARS-CoV-2 genomes and inferred a time-calibrated phylogeny.FindingsThe early outbreak in Basel was dominated by lineage B.1 (83·6%), detected from March 2nd, although the first lineage identified was B.1.1. Within B.1, a clade containing 68·2% of our samples, defined by the SNP C15324T, suggests local spreading events. We infer the geographic origin of this mutation to our tri-national region. The remaining genomes map broadly over the global phylogenetic tree, evidencing several events of introduction from and/or dissemination to other regions of the world. We also observe family transmission events.InterpretationA single lineage dominated the outbreak in the City of Basel while other lineages such as the first (B1.1) did not propagate. Thus spreading events seem to have contributed most to viral spread, while travel returners and family transmissions were better controlled by the recommended measures. This phylogenetic analysis enriches epidemiological and contact tracing data, allowing connection of seemingly unconnected events, and can inform public health interventions.FundingNo dedicated funding was used for this work.
Personalized Prediction of Disease Activity in Patients with Rheumatoid Arthritis Using an Adaptive Deep Neural Network
Authors: Hügle Maria , Walker Ulrich A. , Finckh Axel , Müller Rüdiger , Kalweit Gabriel , Scherer Almut , Boedecker Joschka , Hügle Thomas 
Published: September 2020

ABSTRACTBackgroundRheumatoid arthritis (RA) lacks reliable biomarkers that predict disease evolution on an individual basis, potentially leading to over- and undertreatment. Deep neural networks learn from former experiences on a large scale and can be used to predict future events as a potential tool for personalized clinical assistance.ObjectiveTo investigate deep learning for the prediction of individual disease activity in RA.MethodsDemographic and disease characteristics from over 9500 patients and 65.000 visits from the Swiss Quality Management (SCQM) database were used to train and evaluate an adaptive recurrent neural network (AdaptiveNet). Patient and disease characteristics along with clinical and patient reported outcomes, laboratory values and medication were used as input features. DAS28-BSR was used to predict active disease and future numeric individual disease activity by classification and regression, respectively.ResultsAdaptiveNet predicted active disease defined as DAS28-BSR>2.6 at the next visit with an overall accuracy of 75.6% and a sensitivity and specificity of 84.2% and 61.5%, respectively. Regression allowed forecasting individual DAS28-BSR values with a mean squared error of 0.9, corresponding to a variation between predicted and true values at next visit of 8%. Apart from DAS28-BSR, the most influential characteristics to predict disease activity were joint pain, disease duration, age and duration of treatment. Longer disease duration, age >50 years or antibody positivity marginally improved prediction performance.ConclusionDeep neural networks have the capacity to predict individual numeric disease activity in RA. Low specificity remains challenging and might benefit from alternative input data or outcome targets.
Prospective evaluation of genome sequencing versus standard-of-care as a first molecular diagnostic test
Authors: Brockman Deanna G. , Austin-Tse Christina A. , Pelletier Renée C. , Harley Caroline , Patterson Candace , Head Holly , Leonard Courtney Elizabeth , O’Brien Kimberly , Mahanta Lisa M. , Lebo Matthew S. , Lu Christine Y. , Natarajan Pradeep , Khera Amit V. , Aragam Krishna G. , Kathiresan Sekar , Rehm Heidi L. , Udler Miriam 
Published: September 2020

AbstractPurposeTo evaluate the diagnostic yield and clinical utility of clinical genome sequencing (cWGS) as a first genetic test for patients with suspected monogenic disorders.MethodsWe conducted a prospective randomized study with pediatric and adult patients recruited from genetics clinics at Massachusetts General Hospital who were undergoing planned genetic testing. Participants were randomized into two groups: standard-of-care genetic testing (SOC) only or SOC and cWGS.Results204 participants were enrolled and 99 received cWGS. cWGS returned 23 molecular diagnoses in 20 individuals: A diagnostic yield of 20% (20/99, 95%CI 12.3-28.1%)), which was not significantly different from SOC (17%, 95%CI 9.7%-24.6%, P=0.584). 19/23 cWGS diagnoses provided an explanation for clinical features or were considered worthy of additional workup by referring providers. While cWGS detected all variants reported by SOC, SOC failed to capture 9/23 cWGS diagnoses; primarily due to genes not included in SOC tests. Turnaround time was significantly shorter for SOC compared to cWGS (33.9 days vs 87.2 days, P<0.05).ConclusionscWGS is technically suitable as a first genetic test and identified clinically relevant variants not captured by SOC. However, further studies addressing other variant types and implementation challenges are needed to support feasibility of its broad-scale adoption.
SARS-CoV-2-specific IgA and limited inflammatory cytokines are present in the stool of select patients with acute COVID-19
Authors: Britton Graham J. , Chen-Liaw Alice , Cossarini Francesca , Livanos Alexandra E. , Spindler Matthew P. , Plitt Tamar , Eggers Joseph , Mogno Ilaria , Gonzalez-Reiche Ana S. , Siu Sophia , Tankelevich Michael , Grinspan Lauren Tal , Dixon Rebekah E. , Jha Divya , Martinez-Delgado Gustavo , Amanat Fatima , Hoagland Daisy A. , tenOever Benjamin R. , Dubinsky Marla C. , Merad Miriam , Bakel Harm van , Krammer Florian , Bongers Gerold , Mehandru Saurabh , Faith Jeremiah J. 
Published: September 2020

AbstractBackground and aimsImmune dysregulation caused by SARS-CoV-2 infection is thought to play a pathogenic role in COVID-19. SARS-CoV-2 can infect a variety of host cells, including intestinal epithelial cells. We sought to characterize the role of the gastrointestinal immune system in the pathogenesis of the inflammatory response associated with COVID-19.MethodsWe measured cytokines, inflammatory markers, viral RNA, microbiome composition and antibody responses in stool and serum samples from a prospectively enrolled cohort of 44 hospitalized COVID-19 patients.ResultsSARS-CoV-2 RNA was detected in stool of 41% of patients and was found more frequently in patients with diarrhea than those without (16[44%] vs 5[19%], p=0.06). Patients who survived had lower median viral genome copies than those who did not (p=0.021). Compared to uninfected controls, COVID-19 patients had higher median fecal levels of IL-8 (166.5 vs 286.5 pg/mg; p=0.05) and lower levels of fecal IL-10 (678 vs 194 pg/mg; p<0.001) compared to uninfected controls. Stool IL-23 was higher in patients with more severe COVID-19 disease (223.8 vs 86.6 pg/mg; p=0.03) and we find evidence of intestinal virus-specific IgA responses, which was associated with more severe disease. Fecal cytokines and calprotectin levels were not correlated with gastrointestinal symptoms or with the level of virus detected.ConclusionsAlthough SARS-CoV-2 RNA was detectable in the stools of COVID-19 patients and select individuals had evidence for a specific mucosal IgA response, intestinal inflammation was limited, even in patients presenting with gastrointestinal symptoms.
Computational Modeling Identifies Embolic Stroke of Undetermined Source Patients with Potential Arrhythmic Substrate
Authors: Bifulco Savannah F. , Scott Griffin D. , Sarairah Sakher , Birjandian Zeinab , Roney Caroline H. , Niederer Steven A. , Mahnkopf Christian , Kuhnlein Peter , Mitlacher Marcel , Tirschwell David , Longstreth W. T. , Akoum Nazem , Boyle Patrick M. 
Published: September 2020

AbstractCardiac magnetic resonance imaging (MRI) has revealed fibrosis in embolic stroke of undetermined source (ESUS) patients comparable to levels seen in atrial fibrillation (AFib). We used computational modeling to understand the absence of arrhythmia in ESUS despite the presence of putatively pro-arrhythmic fibrosis. MRI-based atrial models were reconstructed for 45 ESUS and 45 AFib patients. The fibrotic substrate’s arrhythmogenic capacity in each patient was assessed computationally. Reentrant drivers were induced in 24/45 (53%) ESUS and 22/45 (49%) AFib models. Inducible models had more fibrosis (16.7±5.45%) than non-inducible models (11.07±3.61%; P<0.0001); however, inducible subsets of ESUS and AFib models had similar fibrosis levels (P=0.90), meaning theintrinsic pro-arrhythmic substrate propertiesof fibrosis in ESUS and AFib are indistinguishable. This suggests some ESUS patients have latent pre-clinical fibrotic substrate that could be a future source of arrhythmogenicity. Thus, our work prompts the hypothesis that ESUS patients with fibrotic atria are spared from AFib due to an absence of arrhythmia triggers.
Nutritional efficacy of Chlorella supplementation depends on the individual gut environment: randomized control study
Authors: Nishimoto Yuichiro , Nomaguchi Tatsuhiro , Mori Yuka , Ito Masaki , Nakamura Yuya , Fujishima Masaki , Murakami Shinnosuke , Yamada Takuji , Fukuda Shinji 
Published: September 2020

AbstractRecent studies have accumulated evidence that the intestinal environment is strongly correlated with host diet, which influences host health. A number of dietary products whose mechanisms of influence operate via the gut microbiota have been revealed, but they are still limited. Here, we investigated the dietary influence of Chlorella, a green alga commercially available as a dietary supplement. A randomized, double-blind, placebo-controlled crossover trial including 40 Japanese participants with constipation was performed and followed by integrated analysis of the gut microbiome, gut metabolome and blood parameters based on a metabologenomics approach. We revealed that the consumption of Chlorella increased the level of several dicarboxylic acids in faeces. Furthermore, the analysis showed that individuals with low concentrations of faecal propionate increased its concentration by Chlorella intake. In addition, increasing of blood folate levels were negatively correlated with defecation frequency at baseline. Our study suggested that the effect of Chlorella consumption varies by individuals depending on their intestinal environment, which illustrates the importance of stratified dietary management based on the intestinal environment in individuals.
Perception of game-based rehabilitation in upper-limb prosthetic training: a survey of users and researchers
Authors: Garske Christian , Dyson Matthew , Dupan Sigrid , Nazarpour Kianoush 
Published: September 2020

AbstractBackgroundSerious games have been investigated for their use in multiple forms of rehabilitation for decades. The rising trend to use games for physical fitness in more recent years has also provided more options and garnered more interest for their use in physical rehabilitation and motor learning. In this paper, we report the results of an opinion survey of serious games in upper limb prosthetic training.ObjectiveThis study investigates and contrasts the expectations and preferences for game based prosthetic rehabilitation of people with limb difference and researchers.MethodsBoth participant groups answered open and closed questions as well as a questionnaire to assess their user types. The distribution of the user types was compared with a Pearson’s χ2 test against a sample population. The data was analysed with the thematic framework method; answers fell within the themes of usability, training, and game design. Researchers shared their views on current challenges and what could be done to tackle these.ResultsA total of 14 people with limb difference and 12 researchers took part in this survey. The open questions resulted in an overview of the different views on prosthetic training games between the groups. The user types of people with limb difference and researchers were both significantly different from the sample population with χ2=12.31 and χ2=26.50, respectively.ConclusionsWe found that the respondents show a general willingness and tentative optimism towards the topic, but also acknowledge hurdles limiting the adoption of these games by both clinics and users. Results indicate a noteworthy difference between researchers and limb different people in their game preferences, which could lead to design choices that do not represent the target audience. Furthermore, focus on long-term in-home experiments is expected to shed more light onto the validity of games in upper limb prosthetic rehabilitation.
Evaluating the Influence of Mood and Stress on Glycemic Variability in T1DM Patients using Glucose Monitoring Sensors and Pools
Authors: Contador Sergio , Botella Marta , Aramendi Aranzazu , Martínez Remedios , Maqueda Esther , Garnica Oscar , Velasco J. Manuel , Lanchares Juan , Hidalgo J. Ignacio 
Published: September 2020

ObjectiveAssess in a sample of patients with type 1 diabetes mellitus whether mood and stress influence blood glucose levels and variability.Material and MethodsContinuous glucose monitoring was performed on 10 patients with type 1 diabetes, where interstitial glucose values were recorded every 15 minutes. A daily survey was conducted through Google Forms, collecting information on mood and stress. The day was divided into 6 slots of 4-hour each, asking the patient to assess each slot in relation to mood (sad, normal or happy) and stress (calm, normal or nervous). Different measures of glycemic control (arithmetic mean and percentage of time below/above the target range) and variability (standard deviation, percentage coefficient of variation, mean amplitude of glycemic excursions and mean of daily differences) were calculated to relate the mood and stress perceived by patients with blood glucose levels and glycemic variability. A hypothesis test was carried out to quantitatively compare the data groups of the different measures using the Student’s t-test.ResultsStatistically significant differences (p-value < 0.05) were found between different levels of stress. In general, average glucose and variability decrease when the patient is calm. There are statistically significant differences (p-value < 0.05) between different levels of mood. Variability increases when the mood changes from sad to happy. However, the patient’s average glucose decreases as the mood improves.ConclusionsVariations in mood and stress significantly influence blood glucose levels, and glycemic variability in the patients analyzed with type 1 diabetes mellitus. Therefore, they are factors to consider for improving glycemic control. The mean of daily differences does not seem to be a good indicator for variability.
Adjusted Dynamics of COVID-19 Pandemic due to Herd Immunity in Bangladesh
Authors: Hoque Md. Enamul , Islam Md. Shariful , Amin Mohammad Ruhul , Das Susanta Kumar , Mitra Dipak Kumar 
Published: September 2020

AbstractAmid growing debate between scientists and policymakers on the trade-off between public safety and reviving economy during the COVID-19 pandemic, the government of Bangladesh decided to relax the countrywide lockdown restrictions from the beginning of June 2020. Instead, the Ministry of Public Affairs officials have declared some parts of the capital city and a few other districts as red zones or high-risk areas based on the number of people infected in the late June 2020. Nonetheless, the COVID-19 infection rate had been increasing in almost every other part of the country. Ironically, rather than ensuring rapid tests and isolation of COVID-19 patients, from the beginning of July 2020, the Directorate General of Health Services restrained the maximum number of tests per laboratory. Thus, the health experts have raised the question of whether the government is heading toward achieving herd immunity instead of containing the COVID-19 pandemic. In this article, the dynamics of the pandemic due to SARS-CoV-2 in Bangladesh are analyzed with the SIRD model. We demonstrate that the herd immunity threshold can be reduced to 31% than that of 60% by considering age group cluster analysis resulting in a total of 53.0 million susceptible populations. With the data of Covid-19 cases till July 22, 2020, the time-varying reproduction numbers are used to explain the nature of the pandemic. Based on the estimations of active, severe, and critical cases, we discuss a set of policy recommendations to improve the current pandemic control methods in Bangladesh.
College campuses and COVID-19 mitigation: clinical and economic value
Authors: Losina Elena , Leifer Valia , Millham Lucia , Panella Christopher , Hyle Emily P. , Mohareb Amir M. , Neilan Anne M. , Ciaranello Andrea L. , Kazemian Pooyan , Freedberg Kenneth A. 
Published: September 2020

AbstractBackgroundDecisions around US college and university operations will affect millions of students and faculty amidst the COVID-19 pandemic. We examined the clinical and economic value of different COVID-19 mitigation strategies on college campuses.MethodsWe used the Clinical and Economic Analysis of COVID-19 interventions (CEACOV) model, a dynamic microsimulation that tracks infections accrued by students and faculty, accounting for community transmissions. Outcomes include infections, $/infection-prevented, and $/quality-adjusted-life-year ($/QALY). Strategies included extensive social distancing (ESD), masks, and routine laboratory tests (RLT). We report results per 5,000 students (1,000 faculty) over one semester (105 days).ResultsMitigation strategies reduced COVID-19 cases among students (faculty) from 3,746 (164) with no mitigation to 493 (28) with ESD and masks, and further to 151 (25) adding RLTq3 among asymptomatic students and faculty. ESD with masks cost $168/infection-prevented ($49,200/QALY) compared to masks alone. Adding RLTq3 ($10/test) cost $8,300/infection-prevented ($2,804,600/QALY). If tests cost $1, RLTq3 led to a favorable cost of $275/infection-prevented ($52,200/QALY). No strategies without masks were cost-effective.ConclusionExtensive social distancing with mandatory mask-wearing could prevent 87% of COVID-19 cases on college campuses and be very cost-effective. Routine laboratory testing would prevent 96% of infections and require low cost tests to be economically attractive.
Severe COVID-19 infection is associated with increased antibody-mediated platelet apoptosis
Authors: Althaus Karina , Marini Irene , Zlamal Jan , Pelzl Lisann , Häberle Helene , Mehrländer Martin , Hammer Stefanie , Schulze Harald , Bitzer Michael , Malek Nisar , Rath Dominik , Bösmüller Hans , Nieswandt Bernard , Gawaz Meinrad , Bakchoul Tamam , Rosenberger Peter 
Published: September 2020

AbstractThe pathophysiology of COVID-19 associated thrombosis seems to be multifactorial, involving interplay between cellular and plasmatic elements of the hemostasis. We hypothesized that COVID-19 is accompanied by platelet apoptosis with subsequent alteration of the coagulation system. We investigated depolarization of mitochondrial inner transmembrane potential (ΔΨm), cytosolic calcium (Ca2+) concentration, and phosphatidylserine (PS) externalization by flow cytometry. Platelets from intensive care unit (ICU) COVID-19 patients (n=21) showed higher ΔΨm depolarization, cytosolic Ca2+concentration and PS externalization, compared to healthy controls (n=18) and COVID-19 non-ICU patients (n=4). Moreover significant higher cytosolic Ca2+concentration and PS was observed compared to septic ICU control group (ICU control). In ICU control group (n=5; ICU non-COVID-19) cytosolic Ca2+concentration and PS externalization was comparable to healthy control, with an increase ΔΨm depolarization. Sera from ICU COVID-19 13 patients induced significant increase in apoptosis markers (ΔΨm depolarization, cytosolic Ca2+concentration and PS externalization). compared to healthy volunteer and septic ICU control. Interestingly, immunoglobulin G (IgG) fractions from COVID-19 patients induced an Fc gamma receptor IIA dependent platelet apoptosis (ΔΨm depolarization, cytosolic Ca2+concentration and PS externalization). Enhanced PS externalization in platelets from ICU COVID-19 patients was associated with increased sequential organ failure assessment (SOFA) score (r=0.5635) and DDimer (r=0.4473). Most importantly, patients with thrombosis had significantly higher PS externalization compared to those without. The strong correlations between apoptosis markers and increased D-Dimer levels as well as the incidence of thrombosis may indicate that antibody-mediated platelet apoptosis potentially contributes to sustained increased thromboembolic risk in ICU COVID-19 patients.Key pointsSevere COVID-19 is associated with increased antibody-mediated platelet apoptosis.Platelet apoptosis in severe COVID-19 is correlated with D-Dimer and higher incidence of thromboembolisms.