bluuebunny/crossref_metadata_2025_split huggingface dataset:
Network meta-analysis and random walks
Authors: Davies Annabel L. , Papakonstantinou Theodoros , Nikolakopoulou Adriani , Rücker Gerta , Galla Tobias 
Published: June 2021

AbstractNetwork meta-analysis (NMA) is a central tool for evidence synthesis in clinical research. The results of an NMA depend critically on the quality of evidence being pooled. In assessing the validity of an NMA, it is therefore important to know the proportion contributions of each direct treatment comparison to each network treatment effect. The construction of proportion contributions is based on the observation that each row of the hat matrix represents a so-called ‘evidence flow network’ for each treatment comparison. However, the existing algorithm used to calculate these values is associated with ambiguity according to the selection of paths. In this work we present a novel analogy between NMA and random walks. We use this analogy to derive closed-form expressions for the proportion contributions. A random walk on a graph is a stochastic process that describes a succession of random ‘hops’ between vertices which are connected by an edge. The weight of an edge relates to the probability that the walker moves along that edge. We use the graph representation of NMA to construct the transition matrix for a random walk on the network of evidence. We show that the net number of times a walker crosses each edge of the network is related to the evidence flow network. By then defining a random walk on the directed evidence flow network, we derive analytically the matrix of proportion contributions. The random-walk approach, in addition to being computationally more efficient, has none of the associated ambiguity of the existing algorithm.
Coverage and Effectiveness of mRNA COVID-19 Vaccines among Veterans
Authors: Young-Xu Yinong , Korves Caroline , Roberts Jeff , Powell Ethan I. , Zwain Gabrielle M. , Smith Jeremy , Izurieta Hector S. 
Published: June 2021

AbstractImportanceThe effectiveness of mRNA vaccination in a large and diverse American population, with older age and higher co-morbidity has not been assessed.ObjectiveTo describe the scope of the mRNA vaccination rollout among the diverse U.S. Veterans population, and to study the mRNA COVID-19 vaccine effectiveness (VE) against infection, symptomatic disease, hospitalization, and death.MethodsVaccination histories were obtained from medical records to determine if patients tested for SARS-CoV-2 were unvaccinated, partially vaccinated (first dose of mRNA COVID-19 vaccine), or fully vaccinated (two doses) at time of testing. First, coverage with any COVID-19 vaccination was described for all Veterans enrolled in Veterans Health Administration (VHA). Second, to evaluate VE, a matched test-negative case-control evaluation was conducted utilizing SARS-CoV-2 positive (cases [n=16,690]) and SARS-CoV-2 negative (controls [n=61,610]) tests from Veterans aged ≥18 years old who routinely sought care at a VHA facility and were tested from December 14, 2020, through March 14, 2021. VE was calculated from odds ratios (ORs) with 95% confidence intervals (CI).ResultsBy March 7, 2021, among 6,170,750 Veterans, 1,547,045 (23%) received at least one COVID-19 vaccination. mRNA COVID-19 VE against infection, regardless of symptoms, was 94% (95% CI 92-95) and 58% (95%CI 54-62) for full and partial vaccination (vs. no vaccination), respectively. VE against infection was similar across subpopulations, and it was not significantly different from VE against symptomatic disease. VE against COVID-19-related hospitalization and death for full vs. no vaccination was 89% (95%CI 81-93) and 99% (95%CI 87-100), respectively.Conclusions and RelevanceThe VHA’s efficient and equitable distribution of effective vaccines decreased COVID-19 infections, hospitalization, and mortality similarly for all Veterans, including Veterans with low income, homeless Veterans, immunocompromised, the elderly, minorities, and rural Veterans thus reducing health inequalities.
The valuation of outcomes for the temporary and chronic health states associated with Chlamydia trachomatis infection
Authors: Ogwulu Chidubem B.Okeke , Jackson Louise J. , Kinghorn Philip , Roberts Tracy E. 
Published: June 2021

ABSTRACTBackgroundEliciting health-state utility values (HSUVs) for some diseases is complicated by the mix of associated temporary (THSs) and chronic health states (CHSs). This study uses one such disease, chlamydia infection, to explore the challenges. The objectives were to:Define a set of health-state descriptions related to chlamydia andDerive HSUVs for these health states (both temporary and chronic).MethodsHSUVs were elicited for seven health states (five THSs and two CHSs) depicting the symptoms of chlamydia, developed using evidence from the literature and clinical experts. The chained time trade-off (TTO) and visual analogue scale (VAS) were applied to THSs while conventional TTO was applied to the CHSs. Ectopic pregnancy was used as the anchor for the chained TTO approach. The study sampled from three different population groups and the survey was administered face-to-face.ResultsOne hundred participants were assessed with an interview completion rate of 100%. Mean TTO utilities were consistently higher than VAS scores. The aggregated mean chained TTO results for the THS ranged from 0.46 (SD, 0.24) for ectopic pregnancy, to 0.77 (SD 0.21) for cervicitis.ConclusionsChained TTO was shown to be feasible in this population and the resulting HSUVs could have implications for economic evaluations for chlamydia prevention and control. Methodological challenges included the development of health-state descriptions, the selection, and the duration of appropriate anchor state.
Prognostication for prelabor rupture of membranes and the time of delivery in nationwide insured women: development, validation, and deployment
Authors: Sufriyana Herdiantri , Wu Yu-Wei , Su Emily Chia-Yu 
Published: June 2021

AbstractImportancePrognostic predictions of prelabor rupture of membranes lack proper sample sizes and external validation.ObjectiveTo develop, validate, and deploy statistical and/or machine learning prediction models using medical histories for prelabor rupture of membranes and the time of delivery.DesignA retrospective cohort design within 2-year period (2015 to 2016) of a single-payer, government-owned health insurance database covering 75.8% individuals in a countrySettingNationwide healthcare providers (n=22,024) at primary, secondary, and tertiary levelsParticipants12-to-55-year-old women that visit healthcare providers using the insurance from ∼1% random sample of insurance holders stratified by healthcare provider and category of family: (1) never visit; (2) visit only primary care; and (3) visit all levels of carePredictorsMedical histories of diagnosis and procedure (International Classification of Disease version 10) before the latest visit of outcome within the database periodMain Outcomes and MeasuresPrelabor rupture of membranes prognostication (area under curve, with sensitivity, specificity, and likelihood ratio), the time of delivery estimation (root mean square error), and inference time (minutes), with 95% confidence intervalResultsWe selected 219,272 women aged 33 ± 12 years. The best prognostication achieved area under curve 0.73 (0.72 to 0.75), sensitivity 0.494 (0.489 to 0.500), specificity 0.816 (0.814 to 0.818), and likelihood ratio being positive 2.68 (2.63 to 2.75) and negative 0.62 (0.61 to 0.63). This outperformed models from previous studies according to area under curve of an external validation set, including one using a biomarker (area under curve 0.641; sensitivity 0.419; sensitivity 0.863; positive likelihood ratio 3.06; negative likelihood ratio 0.67;n=1177). Meanwhile, the best estimation achieved ± 2.2 and 2.6 weeks respectively for predicted events and non-events. Our web application only took 5.14 minutes (5.11 to 5.18) per prediction.Conclusions and RelevancePrelabor rupture of membranes and the time of delivery were predicted by medical histories; but, an impact study is required before clinical application.Key PointsQuestionCan we use medical histories of diagnosis and procedure in electronic health records to predict prelabor rupture of membranes and the time of delivery before the day in nationwide insured women?FindingsIn this prognostic study applying retrospective cohort paradigm, a significant predictive performance was achieved and validated. The area under receiver operating characteristics curve was 0.73 with the estimation errors of ± 2.2 and 2.6 weeks for the time of delivery.MeaningPreliminary prediction can be conducted in a wide population of insured women to predict prelabor rupture of membranes and estimate the time of delivery.
The evolution of knowledge on genes associated with human diseases
Authors: Lüscher-Dias Thomaz , Dalmolin Rodrigo Juliani Siqueira , de Paiva Amaral Paulo , Alves Tiago Lubiana , Schuch Viviane , Franco Glória Regina , Nakaya Helder I 
Published: June 2021

AbstractThousands of scientific articles describing genes associated with human diseases are published every week. Computational methods such as text mining and machine learning algorithms are now able to automatically detect these associations. In this study, we used a cognitive computing text-mining application to construct a knowledge network comprised of 3,723 genes and 99 diseases. We then tracked the yearly changes on these networks to analyze how our knowledge has evolved in the past 30 years. Our approach helped to unravel the molecular bases of diseases over time, and to detect shared mechanisms between clinically distinct diseases. It also revealed that multi-purpose therapeutic drugs target genes which are commonly associated with several psychiatric, inflammatory, or infectious disorders. By navigating in this knowledge tsunami, we were able to extract relevant biological information and insights about human diseases.
ADESSO: a rapid, adaptable and sensitive Cas13-based COVID-19 diagnostic platform
Authors: Casati Beatrice , Verdi Joseph Peter , Hempelmann Alexander , Kittel Maximilian , Klaebisch Andrea Gutierrez , Meister Bianca , Welker Sybille , Asthana Sonal , Boskovic Pavle , Man Ka Hou , Schopp Meike , Ginno Paul , Radlwimmer Bernhard , Stebbins Charles Erec , Miethke Thomas , Papavasiliou Fotini Nina , Pecori Riccardo 
Published: June 2021

ABSTRACTSARS-CoV-2 is the causative agent for a pandemic that has had immense consequences for the health and economic sectors worldwide. While PCR testing and later antigen tests have proven critical for helping to stem the spread of the virus, these methods suffer from general applicability and sensitivity, respectively. Moreover, the emergence of variant strains creates the need for flexibility to correctly and efficiently diagnose the presence of substrains in the population. To address these needs we have developed the diagnostic test ADESSO (Accurate Detection of Evolving SARS-CoV-2 through SHERLOCK Optimization) which employs the Cas13 system to diagnose patients in as little as 1 hour without sophisticated equipment. Using an extensive panel of clinical samples, we demonstrate that ADESSO correctly identifies COVID-19 positive samples at a sensitivity and specificity comparable to RT-qPCR on extracted RNA and higher than antigen tests for unextracted samples. Taken together, ADESSO is a fast, sensitive and cheap method that can be applied in a point of care (POC) setting to diagnose COVID-19 and can be quickly adjusted to detect new variants.
Mucosal-Associated Invariant T (MAIT) Cells are Highly Activated in Duodenal Tissue of Humans with Vibrio cholerae O1 Infection
Authors: Bhuiyan Taufiqur R. , Rahman M. Arifur , Trivedi Shubhanshi , Afroz Taliman , Banna Hasan Al , Hoq Mohammad Rubel , Pop Ioana , Jensen Owen , Rashu Rasheduzzaman , Uddin Muhammad Ikhtear , Hossain Motaher , Khan Ashraful I. , Chowdhury Fahima , Harris Jason B. , Calderwood Stephen B. , Ryan Edward T. , Qadri Firdausi , Leung Daniel T. 
Published: June 2021

AbstractMucosal-associated invariant T (MAIT) cells are unconventional T lymphocytes with a semi-conserved TCRα, activated by the presentation of vitamin B metabolites by the MHC-I related protein, MR1, and with diverse innate and adaptive effector functions. The role of MAIT cells in acute intestinal infections, especially at the mucosal level, is not well known. Here, we analyzed the presence and phenotype of MAIT cells in duodenal biopsies and paired peripheral blood samples, in patients during and after culture-confirmed Vibrio cholerae O1 infection. Immunohistochemical staining of duodenal biopsies from cholera patients identified MAIT cells in the lamina propria, but not in the lining of villous and crypt epithelia. We observed significantly higher frequencies of duodenal MAIT cells at the acute stage (day 2) of V. cholerae infection as compared to late convalescence (day 30, p = 0.0049). By flow cytometry, we showed that duodenal MAIT cells are more activated than peripheral MAIT cells (p < 0.01 across time points), although there were no significant differences between duodenal MAITs at day 2 and day 30. We found fecal markers of intestinal permeability and inflammation to be correlated with the loss of duodenal (but not peripheral) MAIT cells, and single-cell sequencing revealed differing T cell receptor usage between the duodenal and peripheral blood MAIT cells. In summary, we show that MAIT cells are present and highly activated in the lamina propria of the duodenum during V. cholerae infection. Future work into the trafficking and tissue-resident function of MAIT cells is warranted.
Continuous Positive Airway Pressure (CPAP) for Moderate to Severe Covid19 Acute Respiratory Distress Syndrome (CARDS) in a Resource limited setting
Authors: Hoole Anbesan , Qamar Sahar , Khan Ayesha , Ejaz Mariam 
Published: June 2021

AbstractIntroductionCovid19 Acute Respiratory Distress Syndrome (CARDS) poses a challenge in management particularly due to limited capacity of ventilated intensive care beds and staffing, and this is exacerbated in resource poor settings with poor patient outcomes. Within this context CPAP has been trialled for CARDS although mainly in resource rich settings.MethodsThis study retrospectively analyses the survival outcomes and characteristics of a cohort of patients with moderate to severe CARDS were treated exclusively with CPAP in a rural secondary level hospital in Pakistan with limited previous critical care expertise.Results32 out of the 41 patients (78%) who were treated with CPAP survived overall (30/37 (81%) who were treated according to protocol).DiscussionResults suggest non inferiority to CARDS outcomes of critical care units employing Intubation and Mechanical Ventilation (IMV) in resource rich settings. CPAP should be promoted as an efficacious and cost-effective method for treating CARDS within the context of the pandemic surge of Covid19 in resource poor settings.Key MessagesWhat is the key question?Is Continuous Positive Airway Pressure (CPAP) an effective treatment for Covid19 Acute Respiratory Distress Syndrome (CARDS) in a resource poor setting in a pandemic surge context?What is the bottom line?Survival rate for CARDS on CPAP in our single centre retrospective cohort study is 78% which is similar to outcomes from critical care centres in resource rich settings employing Intubation and Mechanical Ventilation (IMV) and better than outcomes in many critical care centres in resource poor settings. This suggests CPAP should be promoted as an efficacious and cost-effective method for managing the pandemic surge of CARDS in resource poor settings.Why read on?The current surge of Covid19 CARDS in resource poor settings poses a significant challenge in terms of effective management given cost and resource restraints, reflected by poor outcomes in overwhelmed critical care centres employing IMV. This is the largest study so far documenting the survival outcomes and characteristics of patients with CARDS treated exclusively with CPAP within a resource poor setting.
The development and usability testing of two arts-based knowledge translation tools for pediatric procedural pain
Authors: Le Anne , Hartling Lisa , Scott Shannon D. 
Published: June 2021

AbstractProcedures carried out in acute care settings, such as emergency departments (EDs), are among the most common sources of acute pain experienced by children. Such procedures may include intravenous insertions (IVs), venipuncture, and wound irrigation and repair. Inadequately managed procedural pain can cause negative short-term and long-term implications for children, ranging from anxiety to aversion to healthcare. Parents have repeatedly expressed that they do not have the necessary tools to comfort or distract their child during uncomfortable medical procedures. As such, the purpose of this study was to work with parents to develop and evaluate two digital tools for pediatric procedural pain.A whiteboard animation video and interactive infographic were developed following a systematic review and interview with parents. Prototypes were tested in five ED waiting rooms in two Canadian provinces. Sites included those in urban, rural, and remote settings. Overall, parents rated the tools highly, suggesting that engaging with parents to develop arts-based digital tools is a highly effective method in ensuring that parents can understand and utilize complex health information.Author ContributionsThis study was conducted under the supervision of Drs. Shannon D. Scott (SDS) and Lisa Hartling (LH), PIs for translation Evidence in Child Health to enhance Outcomes (ECHO) Research and the Alberta Research Centre for Health Evidence (ARCHE), respectively. Both PIs designed the research study and obtained research funding through Translating Emergency Knowledge for Kids (TREKK) Networks of Centres of Excellence of Canada (NCE).SDS designed and supervised all aspects of tool development and evaluation.LH co-designed and supervised the qualitative study involving interviews with parents and systematic review of parent experiences and information needs.Tony An developed the infographic.Kassi Shave conducted and analyzed qualitative interviews with parents.Anne Le (AL) conducted usability testing.AL analyzed usability data.All authors contributed to the writing of this technical report and provided substantial feedback.This work was funded by:Networks of Centres of ExcellenceKlassen, T., Hartling, L., Jabbour, M., Johnson, D., & Scott, S.D. (2015). Translating emergency knowledge for kids (TREKK). Networks of Centres of Excellence of Canada Knowledge Mobilization Renewal ($1,200,000). January 2016 – December 2019.Women and Children’s Health Research Institute (WCHRI)Scott, S.D & Hartling L. (2016). Translating Emergency Knowledge for Kids renewal. Women and Children’s Health Research Institute (matched dollars, $150,000). April 2016 – December 2019.This report should be cited asLe, A., Hartling, L., Scott, S.D. (2021). The development and usability testing of two arts-based knowledge translation tools for pediatric procedural pain. Technical Report. ECHO Research, University of Alberta.Available at: http://www.echokt.ca/research/technical-reports/
The polarity and specificity of SARS-CoV2-specific T lymphocyte responses determine disease susceptibility
Authors: Fahrner Jean-Eudes , Carrier Agathe ,   Lyon COVID study group, De Sousa Eric , Drubay Damien , Dubuisson Agathe , Geraud Arthur , Goubet Anne-Gaëlle , Ferrere Gladys , Haddad Yacine , Lahmar Imran , Mazzenga Marine , Melenotte Cléa , Picard Marion , Thelemaque Cassandra , Cerbone Luigi , Lérias Joana R. , Laparra Ariane , Bernard Alice , Kloeckner Benoît , Gazzano Marianne , Danlos François-Xavier , Terrisse Safae , Alves Costa Silva Carolina , Pizzato Eugenie , Flament Caroline , Ly Pierre , Tartour Eric , Meziani Lydia , Ahmed-Belkacem Abdelhakim , Miyara Makoto , Gorochov Guy , Barlesi Fabrice , Pradon Caroline , Gallois Emmanuelle , Pommeret Fanny , Colomba Emeline , Lavaud Pernelle , Deutsch Eric , Gachot Bertrand , Spano Jean-Philippe , Merad Mansouria , Scotte Florian , Marabelle Aurélien , Griscelli Frank , Blay Jean-Yves , Soria Jean-Charles , Andre Fabrice , Chevalier Mathieu , Caillat-Zucman Sophie , Fenollar Florence , La Scola Bernard , Kroemer Guido , Maeurer Markus , Derosa Lisa , Zitvogel Laurence 
Published: June 2021

AbstractOptimal vaccination and immunotherapy against coronavirus disease COVID-19 relies on the in-depth comprehension of immune responses determining the individual susceptibility to be infected by SARS-CoV-2 and to develop severe disease. We characterized the polarity and specificity of circulating SARS-CoV-2-specific T cell responses against whole virus lysates or 186 unique peptides derived from the SARS-CoV-2 or SARS-CoV-1 ORFeome on 296 cancer-bearing and 86 cancer-free individuals who were either from the pre-COVID-19 era (67 individuals) or contemporary COVID-19-free (237 individuals) or who developed COVID-19 (78 individuals) in 2020/21. The ratio between the prototypic T helper 1 (TH1) cytokine, interleukin-2, and the prototypic T helper 2 (TH2) cytokine, interleukin-5 (IL-5), released from SARS-CoV-2-specific memory T cells measured in early 2020, among SARS-CoV-2-negative persons, was associated with the susceptibility of these individuals to develop PCR-detectable SARS-CoV-2 infection in late 2020 or 2021. Of note, T cells from individuals who recovered after SARS-CoV-2 re-infection spontaneously produced elevated levels of IL-5 and secreted the immunosuppressive TH2 cytokine interleukin-10 in response to SARS-CoV-2 lysate, suggesting that TH2 responses to SARS-CoV-2 are inadequate. Moreover, individuals susceptible to SARS-CoV-2 infection exhibited a deficit in the TH1 peptide repertoire affecting the highly mutated receptor binding domain (RBD) amino acids (331-525) of the spike protein. Finally, current vaccines successfully triggered anti-RBD specific TH1 responses in 88% healthy subjects that were negative prior to immunization. These findings indicate that COVID-19 protection relies on TH1 cell immunity against SARS-CoV-2 S1-RBD which in turn likely drives the phylogenetic escape of the virus. The next generation of COVID-19 vaccines should elicit high-avidity TH1 (rather than TH2)-like T cell responses against the RBD domain of current and emerging viral variants.
Recovery of deleted deep sequencing data sheds more light on the early Wuhan SARS-CoV-2 epidemic
Authors: Bloom Jesse D. 
Published: June 2021

ABSTRACTThe origin and early spread of SARS-CoV-2 remains shrouded in mystery. Here I identify a data set containing SARS-CoV-2 sequences from early in the Wuhan epidemic that has been deleted from the NIH’s Sequence Read Archive. I recover the deleted files from the Google Cloud, and reconstruct partial sequences of 13 early epidemic viruses. Phylogenetic analysis of these sequences in the context of carefully annotated existing data further supports the idea that the Huanan Seafood Market sequences are not fully representative of the viruses in Wuhan early in the epidemic. Instead, the progenitor of currently known SARS-CoV-2 sequences likely contained three mutations relative to the market viruses that made it more similar to SARS-CoV-2’s bat coronavirus relatives.