bluuebunny/crossref_metadata_2025_split huggingface dataset:
A vulnerability analysis for the management of and response to the COVID-19 epidemic in the second most populous state in Brazil
Authors: Campos Igor Silva , Aratani Vinícius Ferreira , Cabral Karina Baltor , Limongi Jean Ezequiel , de Oliveira Stefan Vilges 
Published: July 2020

AbstractThe COVID-19 pandemic has the potential to affect all individuals, however in a heterogeneous way. In this sense, identifying specificities of each location is essential to minimize the damage caused by the disease. Therefore, the aim of this research was to assess the vulnerability of the 853 municipalities in the second most populous state in Brazil, Minas Gerais (MG), in order to direct public policies. Then, an epidemiological study was carried out based on Multi-Criteria Decision Analysis (MCDA) using indicators with some relation to the process of illness and death caused by COVID-19. The indicators were selected by a literature review and categorized into: demographic, social, economic, health infrastructure, population at risk and epidemiological. The variables were collected in Brazilian government databases at the municipal level and evaluated according to MCDA, through the Program to Support Decision Making based on indicators (PRADIN). Based on this approach, the study performed simulations by category of indicators and a general simulation that allowed to divide the municipalities into groups of 1 to 5, with 1 being the least vulnerable and 5 being the most vulnerable. The groupings of municipalities were exposed in their respective mesoregions of MG in a thematic map, using the software Tabwin 32. The results revealed that the mesoregion of Norte de Minas stands out with more than 40% of its municipalities belonging to group 5, according to economic, social and health infrastructure indicators. Similarly, the Jequitinhonha mesoregion exhibited almost 60% of the municipalities in this group for economic and health infrastructure indicators. For demographic and epidemiological criteria, the Metropolitana de Belo Horizonte mesoregion is the most vulnerable, with 42.9% and 26.7% of the municipalities in group 5, respectively. Considering the presence of a population at risk, Zona da Mata reported 42.3% of the municipalities in the most vulnerable group. In the joint analysis of data, the Jequitinhonha, Vale do Mucuri and Vale do Rio Doce mesoregions were the most vulnerable in the state of MG. Thus, through the outlined profile, the present study proved how socioeconomic diversity affects the vulnerability of the municipalities to face COVID-19 outbreak, highlighting the need for interventions directed to each reality.
Covid-19 serology in nephrology health care workers
Authors: Reiter Thomas , Pajenda Sahra , Wagner Ludwig , Gaggl Martina , Atamaniuk Johanna , Holzer Barbara , Zimpernik Irene , Gerges Daniela , Mayer Katharina , Aigner Christof , Straßl Robert , Jansen-Skoupy Sonja , Födinger Manuela , Sunder-Plassmann Gere , Schmidt Alice 
Published: July 2020

AbstractBackgroundChronic kidney disease patients show a high mortality in case of a SARS-CoV-2 infection. Thus, to be informed on Nephrology personnel’s sero-status might be crucial for patient protection. However, limited information exists about the presence of SARS-CoV-2 antibodies in asymptomatic individuals.MethodsWe examined the seroprevalence of SARS-CoV-2 IgG and IgM antibodies among health care workers of a tertiary care kidney center during the peak phase of the Covid-19 crisis in Austria using an orthogonal test strategy and a total of 12 commercial nucleocapsid protein or spike glycoprotein based assays as well as Western blotting and a neutralization assay.ResultsAt baseline 60 of 235 study participants (25.5%, 95% CI: 20.4-31.5) were judged to be borderline positive or positive for IgM or IgG using a high sensitivity/low specificity threshold in one test system. Follow-up analysis after about two weeks revealed IgG positivity in 12 (5.1%, 95% CI: 2.9-8.8) and IgM positivity in six (2.6%, 95% CI: 1.1-5.6) in at least one assay. 2.1% (95% CI: 0.8-5.0) of health care workers showed IgG nucleocapsid antibodies in at least two assays. By contrast, positive controls with proven Covid-19 showed antibody positivity among almost all test systems. Moreover, serum samples obtained from health care workers did not show SARS-CoV-2 neutralizing capacity, in contrast to positive controls.ConclusionsUsing a broad spectrum of antibody tests the present study revealed inconsistent results for SARS-CoV-2 seroprevalence among asymptomatic individuals, while this was not the case among Covid-19 patients.Trial registration numberCONEC, ClinicalTrials.gov number NCT04347694
SECOND ALLOGENEIC STEM CELL TRANSPLANTATION: A MORTALITY ANALYSIS
Authors: Alani Mustafa , Bourhis Jean Henri 
Published: July 2020

AbstractSecond allogeneic stem cell transplantation was realized in 48 patients with myeloid and lymphoid neoplasms at Gustave Roussy institute since 1987. Overall survival rate was about 30 % with better outcome in acute myeloid leukemia cases. Non-relapse related mortality is overwhelming, especially in myelodysplasia patients and despite the fact that complete remission was obtained in their majority. Graft versus Host disease is very common after second transplantation with many grade III – IV cases and one death from severe pulmonary GvHD lesions. Reduced intensity conditioning is certainly less toxic and together with optimal GvHD and infectious disease management, Second SCT may be a reasonable therapeutic option and the only curative treatment for many hematological malignancies.
Altered resting-state network dynamics in Schizophrenia
Authors: Lopes Ana R. , Letournel Anna , Cabral Joana 
Published: July 2020

AbstractSchizophrenia remains a poorly understood disease, hence the interest in assessing and indirectly characterizing brain activity and connectivity. This paper aims to search for potential biomarkers in schizophrenia with functional magnetic resonance data, between subjects in the resting state. Firstly, we used fMRI from an open database, SchizConnect, of 48 subjects, in which 27 were control subjects, with no apparent disease and the others 21 were patients with schizophrenia. With the SPM tool, we proceeded to manually pre-process the images obtained, at the risk of having influenced the final results. Then, with the AAL atlas as a reference, we divided the brain into 116 areas. Then, brain activity in these areas were analysed, using the LEiDA method, which aims to characterize brain activity at each time point t by phase locking patterns of the BOLD signal. After the application of LEiDA, brain activity was evaluated based on trajectories and bar graphs of functional connectivity states in which the probability of occurrence and their dwell time were calculated for each state. It was also found that the visual cortex was the subsystem that showed significantly more probability of occurrence in schizophrenia patients to be assessed, and may correspond to symptoms of hallucinations by the patients with schizophrenia.
Candida (Diutina) mesorugosa in Non-Albicans Candida Species Clinical Isolates in South West Nigeria
Authors: Owoicho Oloche , Oguzie Judith Uche , Ogunbiyi Tosin Segun , Adulsalam Toyin , Eromon Philomena , Folarin Onikepe , Durugbo Ernest Uzodimma , Happi Christian T. 
Published: July 2020

AbstractIntroductionThe emerging role of non-albicans Candida species (NACS) as causal agents of mild to life-threatening mycoses is increasingly being appreciated. Some NACS are known for intrinsic resistance or reduced susceptibility to some antifungal drugs. To inform on therapeutic options and management of candidiasis, we embarked on Candida species surveillance in South west Nigeria.MethodWe obtained retrospective yeast isolates from urogenital samples of patients in a tertiary hospital in South west Nigeria. Among 47 isolates identified phenotypically, we encountered a yeast which failed to produce pseudohyphae in human serum but was morphologically similar to Candida albicans. We characterized this yeast by sequencing the internal transcribed spacer (ITS1-5.8S-ITS2) region of the ribosomal DNA.ResultsA BLAST search and sequence homology identified the yeast as Candida (Diutina)mesorugosa, with a strong bootstrap.ConclusionCandida mesorugosa, a rarely isolated yeast from clinical samples worldwide, should be considered among potentially relevant NACS in Nigerian clinics. To the best our knowledge, this is the first report of Candida mesorugosa from a clinical sample in Nigeria. This finding confirms the need for more specific methods, such as DNA sequencing, for extensive surveillance of NACS.
EffiCare: Better Prognostic Models via Resource-Efficient Health Embeddings
Authors: Rethmeier Nils , Serbetci Necip Oguz , Möller Sebastian , Roller Roland 
Published: July 2020

ABSTRACTRecent medical prognostic models adapted from high data-resource fields like language processing have quickly grown in complexity and size. However, since medical data typically constitute low data-resource settings, performances on tasks like clinical prediction did not improve expectedly. Instead of following this trend of using complex neural models in combination with small, pre-selected feature sets, we proposeEffiCare, which focuses on minimizing hospital resource requirements for assistive clinical prediction models. First, by embedding medical events, we eliminate manual domain feature-engineering and increase the amount of learning data. Second, we use small, but data-efficient models, that compute faster and are easier to interpret. We evaluate our approach on four clinical prediction tasks and achieve substantial performance improvements over highly resource-demanding state-of-the-art methods. Finally, to evaluate our model beyond score improvements, we apply explainability and interpretability methods to analyze the decisions of our model and whether it uses data sources and parameters efficiently.1
A new model to prioritize and optimize access to elective surgery throughout the COVID-19 pandemic: A feasibility & pilot study
Authors: Valente Roberto , Domenico Stefano Di , Mascherini Matteo , Santori Gregorio , Papadia Francesco , Orengo Giovanni , Gratarola Angelo , Cafiero Ferdinando , De Cian Franco 
Published: July 2020

Mini abstractWe tested usability, safety, and ability to manage elective surgery flow of a multidisciplinary pathway adopting the SWALIS-2020 model in an interhospital setting during the COVID-19 pandemic. This pilot included 295 adults. The pathway prioritized, monitored and scheduled surgery in an 840.000-inhabitants area. Using the COVID-19-GOA-Sur-MDT-SWALIS-2020 model may be warranted.Structured abstractThe COVID-19 outbreak burdens non-COVID elective surgery patients with figures similar to the SARS-Cov-2, by creating an overwhelming demand, increasing waiting times and costs. New tools are urgently needed to manage elective access. The study assesses the “SWALIS-2020” model’s ability to prioritize and optimize access to surgery during the pandemic.A 2020 March - May feasibility-pilot study, tested a software-aided, inter-hospital, multidisciplinary pathway. All specialties patients in the Genoa Departments referred for urgent elective surgery were included in a multidisciplinary pathway adopting a modified Surgical Waiting List InfoSystem (SWALIS) cumulative prioritization method (PAT-2020) based on waiting time and clinical urgency, in three subcategories: A1-15 days (certain rapid disease progression), A2-21 days (probable progression), and A3-30 days (potential progression).Following the feasibility study (N=55 patients), 240 referrals were evaluated in 4 weeks without major criticalities (M/F=73/167, Age=68.7±14.0). Waiting lists were prioritized and monitored, and theatres allocated based on demand. The SWALIS-2020 score (% of waited-against-maximum time) at operation was 88.7±45.2 at week 1 and then persistently over 100% (efficiency), over a controlled variation (equity), with a difference between A3 (153.29±103.52) vs. A1 (97.24 ± 107.93) (p <0.001), and A3 vs. A2 (88.05±77.51) (p<0.001). 222 patients underwent surgery, without related complications or delayed/failed discharges.The pathway has selected the very few patients with the greatest need, optimizing access even with +30% capacity weekly modifications. We will use the pathway to manage active, backlog, and hidden waiting lists throughout the further pandemic phases, and are looking for collaboration for multi-center research.https://www.isrctn.com/ISRCTN11384058.
Time is of the essence: containment of the SARS-CoV-2 epidemic in Switzerland from February to May 2020
Authors: Althaus Christian L. , Probst Daniel , Hauser Anthony , Riou Julien 
Published: July 2020

ABSTRACTAIMIn late February and early March 2020, Switzerland experienced rapid growth of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections with 30,243 confirmed cases and 1,860 deaths as of 10 May 2020. The sequential introduction of non-pharmaceutical interventions (NPIs) resulted in successful containment of the epidemic. A better understanding of how the timing of implementing NPIs influences the dynamics and outcome of SARS-CoV-2 epidemics will be crucial for the management of a potential resurgence in Switzerland.METHODSWe developed a dynamic transmission model that describes infection, hospitalization, recovery and death due to SARS-CoV-2 in Switzerland. Using a maximum likelihood framework, we fitted the model to aggregated daily numbers of hospitalized patients, ICU occupancy and death from 25 February to 10 May 2020. We estimated critical parameters of SARS-CoV-2 transmission in Switzerland and explored counterfactual scenarios of an earlier and later implementation of NPIs.RESULTSWe estimated the basic reproduction numberR0= 2.61 (95% compatibility interval, CI: 2.51–2.71) during the early exponential phase of the SARS-CoV-2 epidemic in Switzerland. After the implementation of NPIs, the effective reproduction number approachedRe= 0.64 (95% CI: 0.61–0.66). Based on the observed doubling times of the epidemic before and after the implementation of NPIs, we estimated that one week of early exponential spread required 3.1 weeks (95% CI: 2.8–3.3 weeks) of ‘lockdown’ to reduce the number of infections to the same level. Introducing the same sequence of NPIs one week earlier or later would have resulted in substantially lower (399, 95% prediction interval, PI: 347–458) and higher (8,683, 95% PI: 8,038–9,453) numbers of deaths, respectively.CONCLUSIONSThe introduction of NPIs in March 2020 prevented thousands of SARS-CoV-2-related deaths in Switzerland. Early implementation of NPIs during SARS-CoV-2 outbreaks can reduce the number of deaths and the necessary duration of strict control measures considerably.
Development and external validation of machine learning algorithms for postnatal gestational age estimation using clinical data and metabolomic markers
Authors: Hawken Steven , Ducharme Robin , Murphy Malia S.Q. , Olibris Brieanne , Bota A. Brianne , Wilson Lindsay A. , Cheng Wei , Little Julian , Potter Beth K. , Denize Kathryn M. , Lamoureux Monica , Henderson Matthew , Rittenhouse Katelyn J. , Price Joan T. , Mwape Humphrey , Vwalika Bellington , Musonda Patrick , Pervin Jesmin , Chowdhury AK Azad , Rahman Anisur , Chakraborty Pranesh , Stringer Jeffrey S.A. , Wilson Kumanan 
Published: July 2020

AbstractAccurate estimates of gestational age at birth are important for preterm birth surveillance but can be challenging to reliably acquire in low and middle income countries. Our objective was to develop machine learning models to accurately estimate gestational age shortly after birth using clinical and metabolic data. We derived and internally validated three models using ELASTIC NET multivariable linear regression in heel prick blood samples and clinical data from a retrospective cohort of newborns from Ontario, Canada. We conducted external model validation in heel prick and cord blood sample data collected from prospective birth cohorts in Lusaka, Zambia (N=311) and Matlab, Bangladesh (N=1176). The best-performing model accurately estimated gestational age within about 6 days of early pregnancy ultrasound estimates in both cohorts when applied to heel prick data (MAE (95% CI) = 0.79 weeks (0.69, 0.90) for Zambia; 0.81 weeks (0.75, 0.86) for Bangladesh), and within about 7 days when applied to cord blood data (1.02 weeks (0.90, 1.15) for Zambia; 0.95 weeks (0.90, 0.99) for Bangladesh). Algorithms developed in Canada provided accurate estimates of gestational age when applied to external cohorts from Zambia and Bangladesh. Model performance was superior in heel prick data as compared to cord blood data.
Endemic Chikungunya Fever in Kenyan Children
Authors: Nyamwaya Doris K. , Otiende Mark , Omuoyo Donwilliams O. , Githinji George , Karanja Henry K. , Gitonga John N. , de Laurent Zaydah , Otieno James R. , Sang Rosemary , Kamau Everlyn , Cheruiyot Stanley , Otieno Edward , Agoti Charles N. , Bejon Philip , Thumbi Samuel M. , Warimwe George M. 
Published: July 2020

ABSTRACTBackgroundChikungunya virus (CHIKV) was first identified in Tanzania in 1952. Several epidemics including East Africa are described, but there are no descriptions of longitudinal surveillance of endemic disease. Here, we estimate the incidence of CHIKV and describe viral phylogeny in coastal Kenya.MethodsOver a 5-year period (2014-2018), 11,708 febrile illnesses in 5,569 children visiting two primary healthcare facilities linked to a demographic surveillance system in coastal Kenya were recorded and blood samples obtained. Reverse-transcriptase PCR was used to identify CHIKF cases in 3,500 children randomly selected from the 5,569 children.ResultsWe found CHIKF to be endemic in this setting, associated with 12.7% (95% CI 11.60, 13.80) of all febrile presentations to primary healthcare. The prevalence of CHIKV infections among asymptomatic children in a community survey was 0.7% (95% CI 0.22, 2.12). CHIKF incidence among children <1 year of age was 1703 cases/100,000-person years and 46 cases/100,000-person years among children aged ≥ 10 years. Recurrent CHIKF episodes, associated with fever and viraemia, were observed among 19 of 170 children with multiple febrile episodes during the study period and confirmed by genome sequencing. All sequenced viral genomes mapped to the ECSA genotype albeit distinct from CHIKV strains associated with the 2004 East African epidemic.ConclusionsCHIKF may be a substantial public health burden in primary healthcare on the East African coast outside epidemic years, and recurrent infections are common.
Previous and active tuberculosis in COVID-19 patients increases risk of death and prolongs recovery
Authors: Sy Karla Therese L. , Haw Nel Jason L. , Uy Jhanna 
Published: July 2020

AbstractBackgroundThere is growing literature on the association of SARS-CoV-2 and other chronic respiratory conditions, such as COPD and asthma. However, little is known about the relationship between coinfection with tuberculosis (TB) and COVID-19. We aimed to compare the risk and survival time of death and recovery among COVID-19 patients with and without TB.MethodsWe created a 4:1 propensity score matched sample of COVID-19 patients without and with TB, using SARS-CoV-2 surveillance data in the Philippines. We conducted a longitudinal cohort analysis of matched COVID-19 patients as of May 17, 2020, following them until June 15, 2020. The primary analysis estimated the risk ratios of death and recovery comparing COVID-19 patients with and without TB. Kaplan-Meier curves described time-to-death and time-to-recovery stratified by TB status, and differences in survival were assessed using the Wilcoxon test. We also conducted the same analysis on a subsample of admitted COVID-19 patients only.ResultsThe risk of death in COVID-19 patients with TB was 2.17 times greater compared to those without TB (95% CI: 1.40-3.37). The risk of recovery in TB patients was 25% less than the risk among those without TB (RR=0.75, 0.63-0.91). Similarly, time-to-death among COVID-19 patients with TB was significantly shorter (p=0.0031) and time-to-recovery in TB patients was significantly longer than patients without TB (p=0.0046).Among those admitted, COVID-19 TB patients also had a similar significant increase in risk of death (RR=2.25, 95% CI: 1.35-3.75); however, the risk of recovery was not significantly less (RR=0.84, 95% CI: 0.68-1.06). Time-to-death among those with TB was also significantly longer (p=0.0031) than those without TB, but there was no difference in time-to-recovery (p=0.17).ConclusionsOur findings show that coinfection with tuberculosis increases morbidity and mortality in COVID-19 patients. Our findings reiterate the need to prioritize routine and testing services for tuberculosis, even with increased disruptions to health systems during the SARS-CoV-2 pandemic. Additional research needs to focus on the interrelationship between TB and COVID-19 for appropriate planning and resource allocation, as SARS-CoV-2 continues to spread worldwide.
Hospital Trainees’ Worries, Perceived Sufficiency of Information and Reported Psychological Health During The COVID-19 Pandemic
Authors: Aziminia Nikoo , Khani Aria , Smith Colette , Bakhai Ameet , Lisk Clifford 
Published: July 2020

AbstractIntroductionThe COVID-19 pandemic has been unsurpassed in clinical severity or infectivity since the 1918 Spanish influenza pandemic and continues to impact the world. During the A/H1N1 influenza pandemic, healthcare workers presented frequent concerns regarding their ownand their families’ health, as well as high levels of psychological distress.ObjectivesTo assess hospital trainees ‘concerns, perceived sufficiency of information, behaviour and reported psychological health during the COVID-19 pandemic in the NHSDesignCross-sectional 39-point questionnaire study conducted in May 2020SettingA large NHS foundation trust in LondonParticipants204 hospital trainee doctorsOutcome measuresQuantitative analysis of trainees’ worries and concerns while working during the COVID-19 pandemic were assessed across 8 domains: trainee demographics; concerns and worries regarding COVID-19; perceived sufficiency of information about the COVID-19 pandemic; social distancing; use of personal protective equipment (PPE) and training in PPE; COVID-19 acquisition and risk; reported psychological health; and medical education.Results91.7% looked after COVID-19 patients. 91.6% were worried about COVID-19; the most frequent concern was that of family and friends dying from COVID-19 (74.6%). 22.2% reported being infected with COVID-19. 6.8% of trainees were so concerned about COVID-19 infection that they would avoid going to work. Perceived sufficiency of information about COVID-19 was moderately high. 25.9% reported that they were able to socially distance at work compared to 94.4% able to socially distance outside work. 98.2% reported using PPE and 24.7% were confident the provided PPE protected them against infection with COVID-19. 41.9% reported that their psychological health had been affected by their work with the commonest being anxiety (56.6%), emotional distress (50.9%) and burnout (37.7%). 95.6% felt it is important to have a service that provides psychological support during this pandemic and 62.5% reported they would consider using this at work.ConclusionsA significant proportion of hospital trainees are worried about the COVID-19 pandemic with high levels of reported psychological distress. Given that almost a third would not use psychological support services at work, hospital leaders and liaison psychiatry need to explore the reasons for not wanting to use services at work and highlight the provision of psychological services provided outside work such that provided by the London deaneries professional support unit (PSU). Seeking solutions to support trainee wellbeing in addition to this, such as larger offices, adequate rest facilities and alternative methods of teaching, with their input would enable empowerment of trainees and improve their health and morale while working in a pandemic.