bluuebunny/crossref_metadata_2025_split huggingface dataset:
Source-level EEG and graph theory reveal widespread functional network alterations in focal epilepsy
Authors: Hatlestad-Hall Christoffer , Bruña Ricardo , Syvertsen Marte Roa , Erichsen Aksel , Andersson Vebjørn , Vecchio Fabrizio , Miraglia Francesca , Rossini Paolo M. , Renvall Hanna , Taubøll Erik , Maestú Fernando , Haraldsen Ira H. 
Published: December 2020

AbstractObjectiveThe hypersynchronous neuronal activity associated with epilepsy causes widespread functional network disruptions extending beyond the epileptogenic zone. This altered functional network topology is considered a mediator from which non-seizure symptoms arise, such as cognitive impairment. The aim of the present study was to demonstrate the presence of functional network alterations in focal epilepsy patients with good seizure control and high quality of life.MethodsWe compared twenty-two focal epilepsy patients and sixteen healthy controls on graph metrics derived from functional connectivity (phase-locking value) of source reconstructed resting-state EEG. Graph metrics were calculated over a predefined range of network densities in five frequency bands.ResultsIn terms of global network topology alterations, we observed a significantly increased small world index in epilepsy patients relative to the healthy controls. On the local level, two left-hemisphere regions displayed a shift towards greater alpha band “hubness”.ConclusionsSubtle widespread functional network alterations are evident in focal epilepsy, even in a cohort characterised by successful anti-seizure medication therapy and high quality of life. These findings suggest a possible clinical relevance of functional network analysis in epilepsy.SignificanceFocal epilepsy is accompanied by global and local functional network aberrancies which might be implied in the sustenance of non-seizure symptoms.HighlightsFocal epilepsies are associated with widespread interictal functional network alterations, extending beyond the epilepsy focus.Global and local graph theoretical analyses of source-space EEG functional connectivity networks capture these network changes, and might thus be of clinical relevance.Group-level differences in network metrics are relatively stable across network analysis parameters.
Screening and identification of key biomarkers in clear cell renal cell carcinoma based on bioinformatics analysis
Authors: Vastrad Basavaraj , Vastrad Chanabasayya , Kotturshetti Iranna 
Published: December 2020

AbstractClear cell renal cell carcinoma (ccRCC) is one of the most common types of malignancy of the urinary system. The pathogenesis and effective diagnosis of ccRCC have become popular topics for research in the previous decade. In the current study, an integrated bioinformatics analysis was performed to identify core genes associated in ccRCC. An expression dataset (GSE105261) was downloaded from the Gene Expression Omnibus database, and included 26 ccRCC and 9 normal kideny samples. Assessment of the microarray dataset led to the recognition of differentially expressed genes (DEGs), which was subsequently used for pathway and gene ontology (GO) enrichment analysis. This data was utilized in the construction of the protein-protein interaction network and module analysis was conducted using Human Integrated Protein-Protein Interaction rEference (HIPPIE) and Cytoscape software. In addation, target gene - miRNA regulatory network and target gene - TF regulatory network were constructed and analysed. Finally, hub genes were validated by survival analysis, expression analysis, stage analysis, mutation analysis, immune histochemical analysis, receiver operating characteristic (ROC) curve analysis, RT-PCR and immune infiltration analysis. The results of these analyses led to the identification of a total of 930 DEGs, including 469 up regulated and 461 down regulated genes. The pathwayes and GO found to be enriched in the DEGs (up and down regulated genes) were dTMP de novo biosynthesis, glycolysis, 4-hydroxyproline degradation, fatty acid beta-oxidation (peroxisome), cytokine, defense response, renal system development and organic acid metabolic process. Hub genes were identified from PPI network according to the node degree, betweenness centrality, stress centrality, closeness centrality and clustering coefficient. Similarly, targate genes were identified from target gene - miRNA regulatory network and target gene - TF regulatory network according to the node degree. Furthermore, survival analysis, expression analysis, stage analysis, mutation analysis, immune histochemical analysis, ROC curve analysis, RT-PCR and immune infiltration analysis revealed that CANX, SHMT2, IFI16, P4HB, CALU, CDH1, ERBB2, NEDD4L, TFAP2A and SORT1 may be associated in the tumorigenesis, advancement or prognosis of ccRCC. In conclusion, the 10 hub genes diagonised in the current study may help researchers in exemplify the molecular mechanisms linked with the tumorigenesis and advancement of ccRCC, and may be powerful and favorable candidate biomarkers for the prognosis, diagnosis and treatment of ccRCC.
Clinical characteristics of COVID-19 patients in Latvia under low incidence in Spring 2020
Authors: Viksna Ludmila , Kolesova Oksana , Kolesovs Aleksandrs , Vanaga Ieva , Arutjunana Seda , Laivacuma Sniedze , Storozenko Jelena , Tolmane Ieva , Berzina Ilze , Rozentale Baiba 
Published: December 2020

ABSTRACTBackgroundCOVID-19 is a new infectious disease with severe disease course and high mortality in some groups. Blood tests on admission to the hospital can be useful for stratification of patients and timely correction. Our study investigated the clinical features of COVID-19 patients in Latvia and differences in blood tests in groups with different disease severity.MethodsThe retrospective study included 100 patients hospitalized in Riga East Clinical University Hospital in Spring 2020. The severity of the disease course was classified by the presence of pneumonia and its combination with respiratory failure. We have assessed blood cells’ count, hemoglobin, hematocrit, erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), alanine aminotransferase, lactate dehydrogenase (LDH), troponin T, electrolytes, creatinine, glomerular filtration rate (GFR), D-dimer, prothrombin time, prothrombin index, oxygen saturation, and temperature on admission to the hospital.ResultsPatients were from 18 to 99 (57±18 years, 57% males). Comorbidities were found in 74% of patients. The mild, moderate, and severe groups included 35, 44, and 16 patients, respectively. In the severe group, the mortality rate was 50%. The progression to severe COVID-19 was associated positively with temperature, ESR, CRP, creatinine, LDH, and troponin T and negatively associated with oxygen saturation, eosinophils, and GFR on admission to the hospital.ConclusionsCOVID-19 severity associates with lower renal function and a higher level of inflammation and tissue damage. Eosinophils, CRP, ESR, LDH, troponin T, creatinine, and GFR are blood indicators for monitoring patients’ condition.
Effective design of barrier enclosure to contain aerosol emissions from COVID-19 patients
Authors: Daniel Dan , Lin Marcus , Luhung Irvan , Lui Tony , Sadovoy Anton , Koh Xueqi , Sng Anqi , Tran Tuan , Schuster Stephan C. , Loh Xian Jun , Thet Oo Schwe , Tan Chee Keat 
Published: December 2020

AbstractFacing shortages of personal protective equipment, some clinicians have advocated the use of barrier enclosures (typically mounted over the head, with and without suction) to contain aerosol emissions from coronavirus disease 2019 (COVID-19) patients. There is however little evidence for its usefulness. To test the effectiveness of such a device, we built a manikin that can expire micron-sized aerosols at flow rates close to physiological conditions. We then placed the manikin inside the enclosure and used a laser sheet to visualize the aerosol leaking out. We show that with sufficient suction, it is possible to effectively contain aerosol from the manikin even at high flow rates (up to 60 L min−1) of oxygen, reducing aerosol exposure outside the enclosure by 99%. In contrast, a passive barrier without suction only reduces aerosol exposure by 60%.
Real-world clinical performance of commercial SARS-CoV-2 rapid antigen tests in suspected COVID-19: A systematic meta-analysis of available data as per November 20, 2020
Authors: Hayer Johannes , Kasapic Dusanka , Zemmrich Claudia 
Published: December 2020

AbstractBackgroundImmunochromatographic rapid antigen tests (RATs) emerged onto the COVID-19 pandemic testing landscape to aid in the rapid diagnosis of people with suspected SARS-CoV-2 infection. RATs are particularly useful where RT-PCR is not immediately available and symptoms suggestive of a high viral load and infectiousness are assumed. Several lateral flow immunoassays have been authorized for use under EUA and/or the CE mark, presenting varying overall clinical performance data generated by the manufacturer or by independent investigators. To compare the real-world clinical performance of commercially available rapid chromatographic immunoassays intended for the qualitative detection of SARS-CoV-2, we performed a systematic meta-analysis of published data.MethodsWe searched the MEDLINE®, Embase, BIOSIS and Derwent Drug File (ProQuest)for manufacturer-independent prospective clinical performance studies comparing SARS-CoV-2 RATs and RT-PCR assays. Only studies on lateral flow assays not needing a separate reader for retrieving the result were included, if data were available on viral load, patients’ symptom status, sample type, and PCR assay used. For better data comparability, recalculation of the studies’ single performance data confidence intervals using the exact Clopper–Pearson method was applied.ResultsWe could include 19 studies (ten peer-reviewed) presenting detailed clinical performance data on 11,209 samples with 2449 RT-PCR-positives out of study prevalence rates between 1.9–100 % and between 50– 100% symptomatic samples. Four studies directly compared two to three different RATs and 15 studies compared one RAT to RT-PCR. Overall specificity ranged, with one test outlier, between 92.4% (87.4– 95.9) and 100% (99.7–100), and overall clinical sensitivity varied between 28.9% (16.4–44.3) and 98.3% (91.1–99.7), depending on assay, population characteristics, viral load, and symptom status. Sensitivity in high-viral-load samples (cycle threshold ≤25) showed a considerable heterogeneity among the assays ranging from 66.7% to 100%.ConclusionOnly two RATs offered sufficient manufacturer-independent, real-world performance data supporting use for the detection of current SARS-CoV-2 infection in symptomatic or high-viral-load patient populations. Reliable positive predictive values require testing of symptomatic patients or asymptomatic individuals only in case of a high pre-test probability. If RATs are used for screening of asymptomatic cases in low-prevalence scenarios, a lower positive predictive value of the result has to be considered.
Environmental scan of provincial and territorial planning for COVID-19 vaccination programs
Authors: MacDonald Shannon E. , Sell Hannah , Wilson Sarah , Meyer Samantha B. , Gagneur Arnaud , Assi Ali , Sadarangani Manish ,   And members of the COVImm study team
Published: December 2020

AbstractBackgroundPublic health departments in Canada are currently facing the challenging task of planning and implementing COVID-19 vaccination programs.ObjectiveTo collect and synthesize information regarding COVID-19 vaccination programs in each of the provinces and territories (P/Ts).MethodsProvincial/territorial public health leaders were interviewed via teleconference between August-October 2020 to collect information on the following topics, drawn from scientific literature and media: unique factors for COVID-19 vaccination, adoption of National Advisory Committee on Immunization (NACI) recommendations, priority groups for early vaccination, and vaccine safety and effectiveness monitoring. Data were grouped according to common responses and descriptive analysis was performed.ResultsEighteen interviews occurred with 25 participants from 11 of 13 P/Ts. Factors unique to COVID-19 vaccination included prioritizing groups for early vaccination (n=7), public perception of vaccines (n=6), and differing eligibility criteria (n=5). Almost all P/Ts (n=10) reported reliance on NACI recommendations. Long-term care residents (n=10) and health care workers (n=10) were most frequently prioritized for early vaccination, followed by people with chronic medical conditions (n=9) and seniors (n=8). Most P/Ts (n=9) are planning routine adverse event monitoring to assess vaccine safety. Evaluation of effectiveness was anticipated to occur within public health departments (n=3), by researchers (n=3), or based on national guidance (n=4).ConclusionPlans for COVID-19 vaccination programs in the P/Ts exhibit some similarities and are largely consistent with NACI guidelines, with some discrepancies. Further research is needed to evaluate the success of COVID-19 vaccination programs once implemented.
The main factors influencing COVID-19 spread and deaths in Mexico: A comparison between Phases I and II
Authors: Benita Francisco , Gasca-Sanchez Francisco 
Published: December 2020

AbstractThis article investigates the geographical spread of confirmed COVID-19 cases and deaths across municipalities in Mexico. It focuses on the spread dynamics and containment of the virus between Phase I (from March 23 to May 31, 2020) and Phase II (from June 1 to August 22, 2020) of the social distancing measures. It also examines municipal-level factors associated with cumulative COVID-19 cases and deaths to understand the spatial determinants of the pandemic. The analysis of the geographic pattern of the pandemic via spatial scan statistics revealed a fast spread among municipalities. During Phase I, clusters of infections and deaths were mainly located at the country’s center, whereas in Phase II, these clusters dispersed to the rest of the country. The regression results from the zero-inflated negative binomial regression analysis suggested that income inequality, the prevalence of obesity and diabetes, and concentration of fine particulate matter (PM 2.5) are strongly positively associated with confirmed cases and deaths regardless of lockdown.
“There’s No Place Like Home for The Holidays:” Travel and SARS-CoV-2 Test Positivity Following Thanksgiving Weekend
Authors: Mehta Shruti H. , Clipman Steven J. , Wesolowski Amy , Solomon Sunil S. 
Published: December 2020

AbstractIn the US, public health officials discouraged travel and social gatherings for Thanksgiving. Data suggests that many individuals did travel over the holidays, albeit in smaller numbers than previous years. Using an online panel survey of individuals across ten US states, we found that many individuals reported spending Thanksgiving outside of their home (25.9%) or at home with at least one non-household member (27.3%). Among those who were tested, those who had Thanksgiving outside their home were significantly more likely to self-report a positive PCR test for SARS-CoV-2 infection in the prior two weeks compared to those who had Thanksgiving at home with non-household members or with household members only (41.7% vs. 21.4% and 13.8%, respectively; p<0.001). Persons who had Thanksgiving outside their home and tested positive for SARS-CoV-2 participated in a median 35 (IQR: 21 - 53). non-essential activities compared to those who had Thanksgiving at home and tested positive (median 3 activities, IQR 0-13). Notably, planned travel over the December holidays was most common among those who tested positive for SARS-CoV-2 in the prior 2 weeks (66.5%) compared with 25.4% of those who tested negative in the prior 2 weeks and 11.0% among those who were not tested. While public health authorities should continue promoting messages to dissuade travel and social gatherings over the holidays, as supported by these data, it is equally important to promote messaging on how to get together in a “low-risk” manner for those who travel and plan gatherings. In particular, it is critical that those who do travel or visit with others outside their household do so cautiously and avoid or significantly minimize all other activities where they may potentially acquire and transmit infection in the weeks prior to and after their visit.
REAL-TIME MECHANISTIC BAYESIAN FORECASTS OF COVID-19 MORTALITY
Authors: Gibson Graham C. , Reich Nicholas G. , Sheldon Daniel 
Published: December 2020

AbstractThe COVID-19 pandemic emerged in late December 2019. In the first six months of the global outbreak, the US reported more cases and deaths than any other country in the world. Effective modeling of the course of the pandemic can help assist with public health resource planning, intervention efforts, and vaccine clinical trials. However, building applied forecasting models presents unique challenges during a pandemic. First, case data available to models in real-time represent a non-stationary fraction of the true case incidence due to changes in available diagnostic tests and test-seeking behavior. Second, interventions varied across time and geography leading to large changes in transmissibility over the course of the pandemic. We propose a mechanistic Bayesian model (MechBayes) that builds upon the classic compartmental susceptible-exposed-infected-recovered (SEIR) model to operationalize COVID-19 forecasting in real time. This framework includes non-parametric modeling of varying transmission rates, non-parametric modeling of case and death discrepancies due to testing and reporting issues, and a joint observation likelihood on new case counts and new deaths; it is implemented in a probabilistic programming language to automate the use of Bayesian reasoning for quantifying uncertainty in probabilistic forecasts. The model has been used to submit forecasts to the US Centers for Disease Control, through the COVID-19 Forecast Hub. We examine the performance relative to a baseline model as well as alternate models submitted to the Forecast Hub. Additionally, we include an ablation test of our extensions to the classic SEIR model. We demonstrate a significant gain in both point and probabilistic forecast scoring measures using MechBayes when compared to a baseline model and show that MechBayes ranks as one of the top 2 models out of 10 submitted to the COVID-19 Forecast Hub. Finally, we demonstrate that MechBayes performs significantly better than the classical SEIR model.
Improving on estimates of the potential relative harm to health from using modern ENDS (vaping) compared to tobacco smoking
Authors: Wilson Nick , Summers Jennifer A , Ait Ouakrim Driss , Hoek Janet , Edwards Richard , Blakely Tony 
Published: December 2020

ABSTRACTBackgroundAlthough the harm to health from electronic nicotine delivery systems (ENDS) compared to smoked tobacco remains highly uncertain, society and governments still need to know the likely range of the relative harm to inform regulatory policies for ENDS and smoking.MethodsWe identified biomarkers with specificity of association with different disease groupings e.g., volatile organic compound (VOCs) for chronic obstructive pulmonary disease; and tobacco-specific N’-nitrosamines (TSNAs) and polycyclic aromatic hydrocarbons (PAHs) for all cancers. We conducted a review of recent studies (post January 2017) that compared these biomarkers between people exclusively using ENDS and those exclusively smoking tobacco. The percentage differences in these biomarkers, weighted by study size and adjusted for acrolein from other sources, were used as a proxy for the assumed percentage difference in disease harm between ENDS and smoking. These relative differences were applied to previously modelled estimates of smoking-related health loss (in health-adjusted life-years; HALYs).ResultsThe respective relative biomarker levels (ENDS vs smoking) were: 28% for respiratory diseases (five results, three studies); 42% for cancers (five results, four studies); and 35% for cardiovascular (seven results, four studies). When integrated with the HALY impacts by disease, the overall harm to health from ENDS was estimated to be 33% that of smoking.ConclusionsThis analysis, suggests that the use of modern ENDS devices (vaping) could be a third as harmful to health as smoking in a high-income country setting. But this estimate is based on a limited number of biomarker studies and is best be considered a likely upper level of ENDS risk given potential biases in our method (i.e., the biomarkers used being correlated with more unaccounted for toxicants in smoking compared to with using ENDS).
Unravelling the early warning capability of wastewater surveillance for COVID-19: A temporal study on SARS-CoV-2 RNA detection and need for the escalation
Authors: Kumar Manish , Joshi Madhvi , Patel Arbind Kumar , Joshi Chaitanya G 
Published: December 2020

ABSTRACTWastewater-based Epidemiological (WBE) surveillance offers a promising approach to assess the pandemic situation covering pre-symptomatic and asymptomatic cases in highly populated area under limited clinical tests. In the present study, we analysed SARS-CoV-2 RNA in the influent wastewater samples (n = 43) from four wastewater treatment plants (WWTPs) in Gandhinagar, India, during August 7th to September 30th, 2020. A total of 40 samples out of 43 were found positive i.e. having at least two genes of SARS-CoV-2. The average Ct values for S, N, and ORF 1ab genes were 32.66, 33.03, and 33.95, respectively. Monthly variation depicted a substantial rise in the average copies of N (∼120%) and ORF 1ab (∼38%) genes in the month of September as compared to August, while S-gene copies declined by 58% in September 2020. The SARS-CoV-2 genome concentration was higher in the month of September (∼924.5 copies/ L) than August (∼897.5 copies/ L), corresponding to a ∼ 2.2-fold rise in the number of confirmed cases during the study period. Further, the percentage change in genome concentration level on a particular date was found in the lead of 1-2 weeks of time with respect to the official confirmed cases registered based on clinical tests on a temporal scale. The results profoundly unravel the potential of WBE surveillance to predict the fluctuation of COVID-19 cases to provide an early warning. Our study explicitly suggests that it is the need of hour that the wastewater surveillance must be included as an integral part of COVID-19 pandemic monitoring which can not only help the water authorities to identify the hotspots within a city but can provide up to 2 weeks of time lead for better tuning the management interventions.HIGHLIGHTS□Study unravels the early warning potential of wastewater based surveillance of COVID-19.□Adequate SARS-CoV-2 RNA were detected despite of limited reported case in the vicinity.□Up to 2 weeks of lead is possible from a regular wastewater based COVID-19 surveillance.□SARS-CoV-2 RNA was higher in September than August in response to a ∼ 2.2-fold rise in COVID-19 active cases.Graphical Abstract