bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparing the predictive value of suicide risk screening to the detection of suicide risk using electronic health records in an urban pediatric emergency department
Authors: Haroz E.E. , Kitchen C. , Nestadt P.S. , Wilcox H.C. , DeVylder J.E. , Kharrazi H. 
Published: January 2021

AbstractObjectiveTo compare the accuracy, sensitivity and utility of brief screening to predictive modeling for identifying suicide-related outcomes in a pediatric emergency department. Our hypothesis was that predictive modeling would be more accurate and useful compared to brief screening.MethodsThis was a retrospective cohort study at an urban pediatric Emergency Department (PED) in the United States. Patients were aged 8 to 18 years old who presented from January 1, 2017 to June 30, 2019. Predictors included positive suicide risk screen and/or demographic, medical and mental health diagnostic Electronic Health Record (EHR) data at the time of visit. The main outcome was subsequent PED visit with suicide-related presenting problem (i.e. ideation or attempt) within a 3-month follow-up period.ResultsOf theN=13420 individuals,n=141 had a subsequent suicide-related ED visit. Approximately 63% identified as Black Non-Hispanic. Results showed that a model based only on EHR data performed only slightly worse than the ASQ alone. Combining ASQ screening and EHR data resulted in a 17.4% improvement in sensitivity and 13.4% increase in AUC compared to the ASQ alone. The LASSO models indicated a diagnosis of major depressive disorder in addition to the ASQ improved the AUC by 9%.Conclusions, Implications, Future DirectionsOur findings show that EHR data is helpful either in the absence or as an addition to brief suicide screening. To our knowledge, this is the first study to compare brief screening to EHR based predictive modeling and adds to our understanding of how best to identify youth at risk of suicidal behaviors in clinical care settings.
Maternity waiting home Utilization and associated factors among women who gave birth in the Digelu and Tijo district of the Arsi Zone, Oromia, Ethiopia
Authors: Teshome Derese , Abera Muluemebet , Nigatu Mamo 
Published: January 2021

AbstractBackgroundMaternity Waiting Homes (MWHs) is an intervention designed to reduce maternal and perinatal mortality. Ethiopia has introduced the intervention before three decades however; its utilization is very low. Therefore, this study is aimed to assess MWH utilization and associated factors among women who gave birth in the last 12 months in Digelu and Tijo district Arsi Zone Oromia Region, Ethiopia.MethodsCommunity-based cross-sectional study was conducted in April 2019 on 530 randomly selected women. Data were collected by face-to-face interview using structured questionnaire. Descriptive statistics and logistics regressions were used to analyze the results. Adjusted odds ratio and 95% confidence interval were respectively calculated to measure strength of association and its statistical significance.The confidence interval was used to declare statistical significance in the final model.ResultsOne hundred twenty-five (23.6%) of the respondents used maternity waiting home. Traveling time less than and equals to 60 minutes from a nearby health facility (AOR=0.16, 95% CI: 0.09, 0.27), women’s decision power (AOR=1.81, 95% CI: 1.10, 2.96), not utilizing antenatal care (AOR=0.6, 95% CI: 0.37, 0.97) and delivering more than three children (AOR=0.56, 95% CI: 0.34, 0.90) were independently associated with utilizing the maternity waiting home.ConclusionEven though the MWH was designed to reduce maternal and perinatal mortality, less than a quarter (23.6%) of women delivered in the last 12 months before the study in the Digelu and Tijo District had utilized the services. Increasing availability of the service, promoting antenatal care utilization, empowering women and evolving policy makers are recommended to enhance the current low utilization of the MWH.
Prevalence and clinical profile of SARS-CoV-2 infection among farmworkers in Monterey County, California: June-November, 2020
Authors: Lewnard Joseph A. , Mora Ana M. , Nkwocha Oguchi , Kogut Katherine , Rauch Stephen A. , Morga Norma , Hernandez Samantha , Wong Marcus P. , Huen Karen , Andrejko Kristin , Jewell Nicholas P. , Parra Kimberly L. , Holland Nina , Harris Eva , Cuevas Maximiliano , Eskenazi Brenda 
Published: January 2021

ABSTRACTAs essential personnel, United States farmworkers have continued working in-person throughout the COVID-19 pandemic. We undertook prospective surveillance of SARS-CoV-2 infection and antibody prevalence among farmworkers in California’s Salinas Valley from 15 June to 30 November, 2020. Over this period, we observed 22.1% (1514/6864) positivity for current SARS-CoV-2 by nucleic acid detection among farmworkers tested at federally-qualified migrant and community health clinics, as compared to 17.2% (1255/7305) among other adults from the same communities (risk ratio, 1.29; 95% confidence interval, 1.20-1.37). In a nested study enrolling 1,115 farmworkers, prevalence of current infection was 27.7% among farmworkers reporting ≥1 potential COVID-19 symptom, and 7.2% among farmworkers without symptoms (adjusted odds ratio 4.17; 2.86-6.09). Prevalence of anti-SARS-CoV-2 IgG antibodies increased from 10.5% (6.0-18.4%) between 16 July-31 August to 21.2% (16.6-27.4%) between 1-30 November. The high observed prevalence of infection among farmworkers underscores the need for vaccination and other preventive interventions.
Probability that an infection like Covid-19 stops without reaching herd immunity, calculated with a stochastic agent-based model
Authors: Eissler Manfred 
Published: January 2021

AbstractThe spread of an infection is simulated with a stochastic agent-based model. In a certain range of R0 values, the infection either rapidly comes to halt or a large proportion of the population is infected until herd immunity is achieved. Which of these two possibilities actually occurs is random. The probability of each case is determined ‘quasi-empirically’. This stochastic phenomenon may explain unexpected infection trajectories.
Tumor Suppressor Immune Gene Therapy to Reverse Immunotherapy Resistance
Authors: Chada Sunil , Wiederhold Dora , Menander Kerstin B. , Sellman Beatha , Talbott Max , Nemunaitis John J. , Ahn Hyo Min , Jung Bo-Kyeong , Yun Chae-Ok , Sobol Robert E. 
Published: January 2021

AbstractBackgroundWhile immune checkpoint inhibitors are becoming a standard of care for multiple types of cancer, the majority of patients do not respond to this form of immunotherapy. New approaches are required overcome resistance to immunotherapies.MethodsWe investigated the effects of adenoviral p53 (Ad-p53) gene therapy in combination with immune checkpoint inhibitors and selective IL2 or IL15 CD122/132 agonists in the aggressive B16F10 tumor model resistant to immunotherapies. To assess potential mechanisms action, pre and post Ad-p53 treatment biopsies were evaluated for changes in gene expression profiles by Nanostring IO 360 assays.ResultsSubstantial synergy of “triplet” Ad-p53 + CD122/132 + anti-PD-1 therapy resulted in potential curative effects associated with complete tumor remissions of both primary and contralateral tumors. Interestingly, contralateral tumors which were not injected with Ad-p53 showed robust abscopal effects resulting in statistically significant decreases in tumor size and increased survival (p<0.001). None of the monotherapies or doublet treatments induced complete tumor regressions. Ad-p53 treatment increased Type I Interferon, CD8+ T cell, immuno-proteosome antigen presentation and tumor inflammation gene signatures. Ad-p53 treatment also decreased immune suppressive TGF-beta, beta-catenin, macrophage, and endothelium gene signatures, which may contribute to enhanced immune checkpoint inhibitor (CPI) efficacy. Unexpectedly, a number of previously unidentified, strongly p53 down regulated genes associated with stromal pathways and IL10 expression identified novel anti-cancer therapeutic applications.ConclusionsThese results imply the ability of Ad-p53 to induce efficacious local and systemic anti-tumor immune responses with the potential to reverse resistance to immune checkpoint inhibitor therapy when combined with CD122/132 agonists and immune checkpoint blockade. Our findings further imply that Ad-p53 has multiple complimentary immune mechanisms of action which support future clinical evaluation of triplet Ad-p53, CD122/132 agonist and immune checkpoint inhibitor combination treatment.
Blood-based host biomarker diagnostics in active case finding for pulmonary tuberculosis: a diagnostic case-control study
Authors: Moreira Flora Martinez Figueira , Verma Renu , dos Santos Paulo Cesar Pereira , Leite Alessandra , da Silva Santos Andrea , de Araujo Rafaele Carla Pivetta , da Silva Bruna Oliveira , de Sá Queiroz Júlio Henrique Ferreira , Persing David H. , Södersten Erik , Gnanashanmugam Devasena , Khatri Purvesh , Croda Julio , Andrews Jason R. 
Published: January 2021

AbstractBackgroundThere is a need to identify scalable tuberculosis screening strategies among high burden populations. The WHO has identified a non-sputum-based triage test as a development priority.MethodsWe performed a diagnostic case-control study of point-of-care C-reactive protein (CRP) and Xpert-MTB-Host-Response (Xpert-MTB-HR) assays in the context of a mass screening program for tuberculosis in two prisons in Brazil. All incarcerated individuals irrespective of symptoms were screened by sputum Xpert-MTB/RIF and sputum culture. Among consecutive, Xpert-MTB/RIF or culture-confirmed cases and Xpert-MTB/RIF and culture-negative controls, CRP was quantified in serum by a point-of-care assay (iChroma-II) and a 3-gene expression score was quantified from whole blood using the Xpert-MTB-HR cartridge. We evaluated receiver operating characteristic area under the curve (AUC) and assessed specificity at 90% sensitivity and sensitivity at 70% specificity, consistent with WHO target product profile (TPP) benchmarks.FindingsTwo hundred controls and 100 culture- or Xpert-positive tuberculosis cases were included. Half of tuberculosis cases and 11% of controls reported any tuberculosis symptoms. AUC for CRP was 0·79 (95% CI: 0·73-0·84) and for Xpert-MTB-HR was 0·84 (95% CI: 0·79-0·89). At 90% sensitivity, Xpert-MTB-HR had significantly higher specificity (53·0%, 95% CI: 45·0-69·0%) than CRP (28·1%, 95% CI: 20·2-41·8%) (p=0·003), both well below the TPP benchmark of 70%. Among individuals with medium or high sputum Xpert semi-quantitative load, sensitivity (at 70% specificity) of CRP (90·3%, 95% CI: 74·2-98·0) and Xpert-MTB-HR (96·8%, 95% CI: 83·3-99·9%) was higher.InterpretationFor active case finding in this high tuberculosis-burden setting, CRP and Xpert-MTB-HR did not meet TPP benchmarks for a triage test. However, Xpert-MTB-HR was highly sensitive in detecting individuals with medium or high sputum bacillary burden.FundingNational Institutes of Health (R01 AI130058 and R01 AI149620) and Brazilian National Council for Scientific and Technological Development (CNPq-404182/2019-4).
Impact of Discoordinated Care on Healthcare Utilization and Survival in Stage IV Non-Small Cell Lung Cancer Patients
Authors: Heilbroner Samuel P , Xanthopoulos Eric P , Hoffman Mark A , Buono Donna , Durkee Ben Y , Corradetti Michael , Wang Tony JC , Wright Jason D , Neugut Alfred I , Hershman Dawn L , Rohs Nicholas C , Cheng Simon K 
Published: January 2021

AbstractBackgroundCancer patients’ treatment is often dispersed across multiple physician communities that may not exchange information. We measured the association between this type of discoordinated care and healthcare utilization, cost, and mortality in stage IV non-small cell lung cancer (NSCLC).MethodsStage IV NSCLC patients ≥65 years were identified from the Surveillance, Epidemiology, and End Results database attached to Medicare claims. A discoordinated care subgroup was selected using a novel index that approximated how many physician communities each patient encountered. Communities were defined by (1) using claims data to create a nationwide social network of healthcare providers and then (2) dividing that network into communities using cluster label propagation. Associations between discoordinated care and overall survival (OS), cancer-specific survival (CSS), hospitalizations, the burden of diagnostic imaging, and cost were assessed.ResultsOf the 11,417 patients in our cohort, 5,855 received discoordinated care. Discoordination was associated with younger age, higher socioeconomic status, higher physician density, and lack of a home health aide. Discoordinated care was associated with improved OS and CSS (HR = 0.92, 95% CI 0.88 - 0.95 for OS). However, discoordinated patients also received 32% more MRIs (p = 0.007) and paid $494.02 more for imaging (p = 0.004). There was no association with other kinds of imaging, rates of hospitalization, or other healthcare costs, including total cost.ConclusionsDiscoordinated care was associated with additional MRIs, but also improved survival. The reason is unclear, but discoordinated patients may be seeking the best care at the expense of continuity.Key PointsQuestionHow does dispersing healthcare across multiple physician communities impact healthcare utilization and survival in patients with advanced stage non-small cell lung cancer?FindingsIn this retrospective cohort study, we found that discoordinated care was associated with increased utilization of MRIs and total cost of imaging. Surprisingly, it was also associated with improved survival.MeaningCancer patients with dispersed healthcare may be seeking care through a tertiary care center or clinical trial. This may lead to increased healthcare utilization but also improved survival.
Secretome of senescent hepatoma cells modulate macrophage polarization and neutrophil extracellular traps formation
Authors: Sen Bijoya , Aggarwal Savera , Nath Rhisita , Sehgal Rashi , Rastogi Archana , Trehanpati Nirupma , Ramakrishna Gayatri 
Published: January 2021

AbstractPresence of dysfunctional senescent hepatocyte is a hallmark feature of cirrhosis. We now report the presence of senescent hepatocytes (p21 and p53 positive) in vicinity of infiltrated immune cells in hepatocellular carcinoma. Hence, we checked if senescent cells can alter fate of macrophage polarization and neutrophil extracellular trap (NETs) formation. Using an in vitro assay, senescence was induced in hepatoma cells (HepG2 and Huh7 cells) by doxorubicin treatment and senescent cell showed secretory phenotype with strong expression of cytokines (IL1β, IL6, IL8 and IL13) as evaluated by Flow cytometry. The senescent secretome from hepatoma cells induced macrophage differentiation predominantly with M2 markers (CD80, CD86) while that of non-senescent cell induced M1 phenotype (CD163, CD206) as analysed by flow cytometry. Human hepatocellular carcinoma harbouring senescent hepatocytes showed presence of M2 macrophages, while M1 macrophages were predominant in non-tumorous region. Additionally, the senescent secretome from Huh7 cells (p53mut) enhanced the NETs formation, while HepG2 (p53+/+) secretome had an inhibitory affect In conclusion, the “pro-inflammatory” senescent secretome drives non-inflammatory type M2 macrophage polarization and modulate neutrophil traps thereby modulating the microenvironment towards tumor promotion. Targeting senescent hepatocyte secretome appears a promising therapeutic target in liver cancer in future.Abstract FigureWork Highlight (Diagrammatic Representation).
Variability of the Surface Area of the V1, V2, and V3 Maps in a Large Sample of Human Observers
Authors: Benson Noah C. , Yoon Jennifer M. D. , Forenzo Dylan , Engel Stephen A. , Kay Kendrick N. , Winawer Jonathan 
Published: January 2021

AbstractHow variable is the functionally-defined structure of early visual areas in human cortex and how much variability is shared between twins? Here we quantify individual differences in the best understood functionally-defined regions of cortex: V1, V2, V3. The Human Connectome Project 7T Retinotopy Dataset includes retinotopic measurements from 181 subjects, including many twins. We trained four “anatomists” to manually define V1-V3 using retinotopic features. These definitions were more accurate than automated anatomical templates and showed that surface areas for these maps varied more than three-fold across individuals. This three-fold variation was little changed when normalizing visual area size by the surface area of the entire cerebral cortex. In addition to varying in size, we find that visual areas vary in how they sample the visual field. Specifically, the cortical magnification function differed substantially among individuals, with the relative amount of cortex devoted to central vision varying by more than a factor of 2. To complement the variability analysis, we examined the similarity of visual area size and structure across twins. Whereas the twin sample sizes are too small to make precise heritability estimates (50 monozygotic pairs, 34 dizygotic pairs), they nonetheless reveal high correlations, consistent with strong effects of the combination of shared genes and environment on visual area size. Collectively, these results provide the most comprehensive account of individual variability in visual area structure to date, and provide a robust population benchmark against which new individuals and developmental and clinical populations can be compared.Significance StatementAreas V1, V2, and V3 are among the best studied functionally-defined regions in human cortex. Using the largest retinotopy dataset to date, we characterized the variability of these regions across individuals and the similarity between twin pairs. We find that the size of visual areas varies dramatically (up to 3.5x) across healthy young adults, far more than the variability of the cerebral cortex size as a whole. Much of this variability appears to arise from inherited factors, as we find very high correlations in visual area size between monozygotic twin-pairs, and lower but still substantial correlations between dizygotic twin pairs. These results provide the most comprehensive assessment of how functionally defined visual cortex varies across the population to date.
Multivariate analysis of strawberry experiments: where are we now and where can we go?
Authors: Olivoto Tiago , Diel Maria Inês , Schmidt Denise , Lúcio Alessandro Dal’Col 
Published: January 2021

ABSTRACTThe multi-trait genotype-ideotype distance index (MGIDI) was used to select superior treatments in experiments with strawberries. Twenty-three productive, qualitative, physiological, and phenological traits with negative and positive desired gains were accessed in 16 treatments, a combination of two cultivars (Albion-neutral days, and Camarosa-short days), two transplants origins (National and Imported), and four organic substrates mixes (Crushed sugarcane bagasse, burnt rice husk, organic substrate, and Carolina commercial substrate). Our results suggest that most of the strawberry traits are influenced by the cultivar, transplant origin, cultivation substrates, as well as by the interaction between cultivar and transplant origin. The MGIDI index indicated that the Albion cultivar originated from imported transplants grown in substrates where the main component (70%) is burnt rice husk provides desired values for 20 of a total of 22 traits, which represents a success rate of ~ 91% in selecting traits with desired values. Thestrengths and weakness viewprovided by the MGIDI index revealed that the looking for an ideal treatment should direct the efforts on improving the water efficiency use and reducing total acidy of fruits. On the other hand, the strengths of selected treatments are mainly related to productive precocity, total soluble solids, and flesh firmness. The MGIDI index provides a unique, robust, and easy-to-handle process, standing out as a powerful tool to develop better treatment recommendations for experiments with strawberries when multiple traits are assessed.
Detecting and Reversing Myocardial Ischemia Using an Artificially Intelligent Bioelectronic Medicine
Authors: Ganzer PD , Loeian MS , Roof SR , Teng B , Lin L , Friedenberg DA , Baumgart IW , Meyers EC , Chun KS , Rich A , Muir WW , Weber DJ , Hamlin RL 
Published: January 2021

SummaryMyocardial ischemia is spontaneous, usually asymptomatic, and contributes to fatal cardiovascular consequences. Importantly, biological neural networks cannot reliably detect and correct myocardial ischemia on their own. In this study, we demonstrate an artificially intelligent and responsive bioelectronic medicine, where an artificial neural network (ANN) supplements biological neural networks enabling reliable detection and correction of myocardial ischemia. ANNs were first trained to decode spontaneous cardiovascular stress and myocardial ischemia with an overall accuracy of ∼92%. ANN-controlled vagus nerve stimulation (VNS) reversed the major biomarkers of myocardial ischemia with no side effects. In contrast, open-loop VNS or ANN-controlled VNS following a caudal vagotomy essentially failed to reverse correlates of myocardial ischemia. Lastly, variants of ANNs were used to meet clinically relevant needs, including interpretable visualizations and unsupervised detection of emerging cardiovascular stress states. Overall, these results demonstrate that ANNs can supplement deficient biological neural networks via an artificially intelligent bioelectronic medicine system.
Packpred: Predicting the functional effect of missense mutations
Authors: Tan Kuan Pern , Kanitkar Tejashree Rajaram , Keong Kwoh Chee , Madhusudhan M.S. 
Published: January 2021

1.AbstractPredicting the functional consequences of single point mutations has relevance to protein function annotation and to clinical analysis/diagnosis. We developed and tested Packpred that makes use of a multi-body clique statistical potential in combination with a depth dependent amino acid substitution matrix (FADHM) and positional Shannon Entropy to predict the functional consequences of point mutations in proteins. Parameters were trained over a saturation mutagenesis data set of T4-lysozyme (1966 mutations). The method was tested over another saturation mutagenesis data set (CcdB; 1534 mutations) and the Missense3D data set (4099 mutations). The performance of Packpred was compared against those of six other contemporary methods. With MCC values of 0.42, 0.47 and 0.36 on the training and testing data sets respectively, Packpred outperforms all method in all data sets, with the exception of marginally underperforming to FADHM in the CcdB data set. On analyzing the results, we could build meta servers that chose best performing methods of wild type amino acids and for wild type-mutant amino acid pairs. This lead to an increase of MCC value of 0.40 and 0.51 for the two meta predictors respectively on the Missense3D data set. We conjecture that it is possible to improve accuracy with better meta predictors as among the 7 methods compared, at the least one method or another is able to correctly predict ∼99% of the data.