bluuebunny/crossref_metadata_2025_split huggingface dataset:
COLI-NET: Fully Automated COVID-19 Lung and Infection Pneumonia Lesion Detection and Segmentation from Chest CT Images
Authors: Shiri Isaac , Arabi Hossein , Salimi Yazdan , Sanaat Amir Hossein , Akhavanalaf Azadeh , Hajianfar Ghasem , Askari Dariush , Moradi Shakiba , Mansouri Zahra , Pakbin Masoumeh , Sandoughdaran Saleh , Abdollahi Hamid , Radmard Amir Reza , Rezaei-Kalantari Kiara , Oghli Mostafa Ghelich , Zaidi Habib 
Published: April 2021

AbstractBackgroundWe present a deep learning (DL)-based automated whole lung and COVID-19 pneumonia infectious lesions (COLI-Net) detection and segmentation from chest CT images.MethodsWe prepared 2358 (347’259, 2D slices) and 180 (17341, 2D slices) volumetric CT images along with their corresponding manual segmentation of lungs and lesions, respectively, in the framework of a multi-center/multi-scanner study. All images were cropped, resized and the intensity values clipped and normalized. A residual network (ResNet) with non-square Dice loss function built upon TensorFlow was employed. The accuracy of lung and COVID-19 lesions segmentation was evaluated on an external RT-PCR positive COVID-19 dataset (7’333, 2D slices) collected at five different centers. To evaluate the segmentation performance, we calculated different quantitative metrics, including radiomic features.ResultsThe mean Dice coefficients were 0.98±0.011 (95% CI, 0.98-0.99) and 0.91±0.038 (95% CI, 0.90-0.91) for lung and lesions segmentation, respectively. The mean relative Hounsfield unit differences were 0.03±0.84% (95% CI, −0.12 – 0.18) and −0.18±3.4% (95% CI, −0.8 - 0.44) for the lung and lesions, respectively. The relative volume difference for lung and lesions were 0.38±1.2% (95% CI, 0.16-0.59) and 0.81±6.6% (95% CI, −0.39-2), respectively. Most radiomic features had a mean relative error less than 5% with the highest mean relative error achieved for the lung for theRangefirst-order feature (- 6.95%) andleast axis lengthshape feature (8.68%) for lesions.ConclusionWe set out to develop an automated deep learning-guided three-dimensional whole lung and infected regions segmentation in COVID-19 patients in order to develop fast, consistent, robust and human error immune framework for lung and pneumonia lesion detection and quantification.
The association between blast exposure and transdiagnostic health symptoms on systemic inflammation
Authors: Hayes Jasmeet P. , Pierce Meghan E. , Valerio Kate E. , Miller Mark , Russell Huber Bertrand , Fortier Catherine B. , Fonda Jennifer R. , Milberg William , McGlinchey Regina 
Published: April 2021

ABSTRACTChronic elevation of systemic inflammation is observed in a wide range of disorders including PTSD, depression, and traumatic brain injury, all of which are relatively common in United States Veterans. Although previous work has demonstrated a link between inflammation and various diagnoses separately, few studies have examined transdiagnostic symptoms and inflammation within the same model. The objective of this study was to examine relationships between psychiatric and health variables and systemic inflammation, and to determine whether mild traumatic brain injury (mTBI) and/or exposure to blast munitions moderate these relationships. Confirmatory factor analysis in a large sample (N = 357) of post-9/11 Veterans demonstrated good fit to a four-factor model reflecting traumatic stress, affective, somatic, and metabolic latent variables. Hierarchical regression models revealed that each of the latent variables were associated with higher levels of systemic inflammation. However, the strongest relationship with inflammation emerged among those who had both war-zone blast exposures and metabolic dysregulation, even after adjusting for mental health latent variables. Exploratory analyses showed that blast exposure was associated with metabolic dysregulation in a dose-response manner, with self-reported closer blast proximity associated with the greatest metabolic dysregulation. Together, these results provide greater understanding of the types of symptoms most strongly associated with inflammation, and underscore the importance of maintaining a healthy lifestyle to reduce the impact of obesity and other metabolic symptoms on future chronic disease in younger to middle-aged Veterans.
Improving SARS-CoV-2 cumulative incidence estimation through mixture modelling of antibody levels
Authors: Bottomley C. , Otiende M. , Uyoga S. , Gallagher K. , Kagucia E.W. , Etyang A.O. , Mugo D. , Gitonga J. , Karanja H. , Nyagwange J. , Adetifa I.M.O. , Agweyu A. , Nokes D.J. , Warimwe G.M. , Scott J.A.G. 
Published: April 2021

AbstractAs countries decide on vaccination strategies and how to ease movement restrictions, estimates of cumulative incidence of SARS-CoV-2 infection are essential in quantifying the extent to which populations remain susceptible to COVID-19. Cumulative incidence is usually estimated from seroprevalence data, where seropositives are defined by an arbitrary threshold antibody level, and adjusted for sensitivity and specificity at that threshold. This does not account for antibody waning nor for lower antibody levels in asymptomatic or mildly symptomatic cases. Mixture modelling can estimate cumulative incidence from antibody-level distributions without requiring adjustment for sensitivity and specificity. To illustrate the bias in standard threshold-based seroprevalence estimates, we compared both approaches using data from several Kenyan serosurveys. Compared to the mixture model estimate, threshold analysis underestimated cumulative incidence by 31% (IQR: 11 to 41) on average. Until more discriminating assays are available, mixture modelling offers an approach to reduce bias in estimates of cumulative incidence.One-Sentence SummaryMixture models reduce biases inherent in the standard threshold-based analysis of SARS-CoV-2 serological data.
Addressing child health inequity through case management of under-five malaria in Nigeria: A model-based extended cost-effectiveness analysis
Authors: Dasgupta Rishav Raj , Mao Wenhui , Ogbuoji Osondu 
Published: April 2021

AbstractBackgroundUnder-five malaria in Nigeria remains one of the biggest threats to global child health, accounting for 95,000 annual child deaths. Despite having the highest GDP in Africa, Nigeria’s current health financing system has not succeeded in reducing high out-of-pocket medical expenditure, which discourages care-seeking and use of effective antimalarials in the poorest households. Resultingly, Nigeria has some of the worst indicators of child health equity among low and middle-income countries, stressing the need to evaluate how the benefits of health interventions are distributed across socioeconomic lines.MethodsWe developed a decision tree model for case management of under-five malaria in Nigeria and conducted an extended cost-effectiveness analysis of subsidies covering the direct and indirect costs of treatment. We estimated the number of under-five malaria deaths averted, out-of-pocket (OOP) expenditure averted, cases of catastrophic health expenditure (CHE) averted, and cost of implementation.FindingFully subsidizing direct medical costs plus a voucher system to cover non-medical and indirect costs with pro-poor increase in treatment coverage would annually avert over 19,000 under-five deaths, US$205.2 million in OOP spending, and 8,600 cases of CHE. Per US$1 million invested, this corresponds to 76 under-five deaths averted, 34 cases of CHE averted, and over US$800,000 in OOP expenditure averted. Due to low current treatment coverage and high disease burden, the health and financial-risk protection benefits would be pro-poor, with the poorest 40% of Nigerians accounting for 72% of all deaths averted, 55% of all OOP expenditure averted, and 74% of all cases of CHE averted. Targeted subsidies to the poor would see significantly greater health and economic benefits per US$1 million invested than broad, non-targeted interventions.ConclusionSubsidizing case management of under-five malaria for the poorest and most vulnerable children would significantly reduce illness-related impoverishment and child mortality in Nigeria while preserving limited financial resources.
Constructing germline research cohorts from the discarded reads of clinical tumor sequences
Authors: Gusev Alexander , Groha Stefan , Taraszka Kodi , Semenov Yevgeniy R. , Zaitlen Noah 
Published: April 2021

ABSTRACTBackgroundHundreds of thousands of cancer patients have had targeted (panel) tumor sequencing to identify clinically meaningful mutations. In addition to improving patient outcomes, this activity has led to significant discoveries in basic and translational domains. However, the targeted nature of clinical tumor sequencing has a limited scope, especially for germline genetics. In this work, we assess the utility of discarded, off-target reads from tumor-only panel sequencing for recovery of genome-wide germline genotypes through imputation.MethodsWe develop a framework for inference of germline variants from tumor panel sequencing, including imputation, quality control, inference of genetic ancestry, germline polygenic risk scores, and HLA alleles. We benchmark our framework on 833 individuals with tumor sequencing and matched germline SNP array data. We then apply our approach to a prospectively collected panel sequencing cohort of 25,889 tumors.ResultsWe demonstrate high to moderate accuracy of each inferred feature relative to direct germline SNP array genotyping: individual common variants were imputed with a mean accuracy (correlation) of 0.86; genetic ancestry was inferred with a correlation of >0.98; polygenic risk scores were inferred with a correlation of >0.90; and individual HLA alleles were inferred with correlation of >0.89. We demonstrate a minimal influence on accuracy of somatic copy number alterations and other tumor features. We showcase the feasibility and utility of our framework by analyzing 25,889 tumors and identifying relationships between genetic ancestry, polygenic risk, and tumor characteristics that could not be studied with conventional data.ConclusionsWe conclude that targeted tumor sequencing can be leveraged to build rich germline research cohorts from existing data, and make our analysis pipeline publicly available to facilitate this effort.
New Insight into the Neural Mechanisms of Migraine in Adolescents: Relationships with Sleep
Authors: Nahman-Averbuch Hadas , Schneider Victor J , Lee Gregory R. , Peugh James L. , Hershey Andrew D. , Powers Scott W. , de Zambotti Massimiliano , Coghill Robert C. , King Christopher D. 
Published: April 2021

AbstractAdolescents with migraine have different functional connectivity of the amygdala compared to individuals without migraine. Considering that sleep is often disturbed in those adolescents with migrane, this study examined if measures of subjective and objective (actigraphic) sleep difficulties mediate alterations in amygdalar connectivity in adolescents with migraine compared to healthy adolescents. Twenty adolescents with migraine and 20 healthy controls completed surveys about their headaches and overall sleep quality, sleep hygiene and perceived sleep difficulties, wore a wrist-worn actigraphy, and underwent an MRI scan.Adolescents with migraine differed from healthy controls only in perceived sleep difficulties related to sleep initiation and maintenance (p<0.01) and had greater functional connectivity between the amygdala and the posterior cingulate cortex, precuneus, dorsolateral prefrontal, sensorimotor, and the occipital cortexes. While the mediation model showed group differences in subjective and actigraphic sleep difficulties, these did not mediate the differences in amygdalar connectivity found between the groups. Adolescents with migraine have greater connectivity between the amygdala and areas involved in sensory, affective, and cognitive aspects of pain. These alterations may not be due to higher levels of sleep difficulties in adolescents with migraine, suggesting that both amygdala and sleep alterations may play an independent role in migraine pathophysiologyPerspectiveThis article evaluates the role plays by sleep on neural alterations in adolescents with migraine. It indicates that neural alterations due to migraine are not related to alterations in subjective and actigraphic sleep difficulties. This advances the understanding of the mechanisms underlying pediatric migraine and can potentially advance migraine management.
COVID-19 vaccine perceptions: An observational study on Reddit
Authors: Kumar Navin , Corpus Isabel , Hans Meher , Harle Nikhil , Yang Nan , McDonald Curtis , Sakai Shinpei Nakamura , Janmohamed Kamila , Tang Weiming , Schwartz Jason L. , Jones-Jang S. Mo , Saha Koustuv , Memon Shahan Ali , Bauch Chris T. , De Choudhury Munmun , Papakyriakopoulos Orestis , Tucker Joseph D. , Goyal Abhay , Tyagi Aman , Khoshnood Kaveh , Omer Saad 
Published: April 2021

AbstractObjectivesAs COVID-19 vaccinations accelerate in many countries, narratives skeptical of vaccination have also spread through social media. Open online forums like Reddit provide an opportunity to quantitatively examine COVID-19 vaccine perceptions over time. We examine COVID-19 misinformation on Reddit following vaccine scientific announcements.MethodsWe collected all posts on Reddit from January 1 2020 - December 14 2020 (n=266,840) that contained both COVID-19 and vaccine-related keywords. We used topic modeling to understand changes in word prevalence within topics after the release of vaccine trial data. Social network analysis was also conducted to determine the relationship between Reddit communities (subreddits) that shared COVID-19 vaccine posts, and the movement of posts between subreddits.ResultsThere was an association between a Pfizer press release reporting 90% efficacy and increased discussion on vaccine misinformation. We observed an association between Johnson and Johnson temporarily halting its vaccine trials and reduced misinformation. We found that information skeptical of vaccination was first posted in a subreddit (r/Coronavirus) which favored accurate information and then reposted in subreddits associated with antivaccine beliefs and conspiracy theories (e.g. conspiracy, LockdownSkepticism).ConclusionsOur findings can inform the development of interventions where individuals determine the accuracy of vaccine information, and communications campaigns to improve COVID-19 vaccine perceptions. Such efforts can increase individual- and population-level awareness of accurate and scientifically sound information regarding vaccines and thereby improve attitudes about vaccines. Further research is needed to understand how social media can contribute to COVID-19 vaccination services.FundingStudy was funded by the Yale Institute for Global Health and the Whitney and Betty MacMillan Center for International and Area Studies at Yale University. The funding bodies had no role in the design, analysis or interpretation of the data in the study.
Inpatient outcomes for hospitalized older adults with rhinovirus
Authors: Del Corpo Olivier , McDonald Emily G. , Smyth Luisa , Smyth Elizabeth , Walji Moneeza , Cheng Matthew P. , Frenette Charles , Saleh Ramy R. , Lee Todd C. 
Published: April 2021

ABSTRACTBackgroundRhinoviruses account for many cases of the “common cold” and infection is often self-limiting. As such, there is a lack of data regarding the inpatient outcomes of individuals hospitalized with rhinovirus infection. Given the generalized poorer prognosis of elderly admitted with respiratory viral infections, we assessed the mortality rate of general medical patients admitted with rhinovirus infection along with the major risk factors associated to mortality.MethodsWe performed a retrospective chart review of patients admitted to our clinical teaching ward from December 2013 to June 2017.ResultsOverall, 12.5% of patients admitted with rhinovirus infection died within 90 days of admission. The median age of admitted patients was 70 years-old. In univariable analysis, age (OR 1.05; 95% confidence interval (CI) 1.01-1.09) and the need for oxygen at presentation (OR 3.23; 95% CI 1.06-9.86) were associated with death while obstructive pulmonary disease or asthma (OR 0.10; 95% CI 0.01-0.81) was associated with survival. In the multivariable model, age (aOR 1.04; 95% CI 1.00-1.09) and obstructive lung disease (aOR 0.09 95%CI 0.01-0.73) remained significant whereas the requirement for oxygen at presentation did not (aOR 2.78; 95% CI 0.84-9.23).ConclusionOur study reveals that rhinovirus is an important cause of both morbidity and mortality in the elderly and further highlights the need for studies of potentially effective treatment options. In the meantime, we suggest that rigorous respiratory hygiene measures and quality older adult care should be practiced when caring for at-risk adults.
Prevalence, awareness, treatment, and control of hypertension in Bangladesh: Findings from National Demographic and Health Survey, 2017-18
Authors: Khan Md. Nuruzzaman , Oldroyd John C. , Chowdhury Enayet K. , Hossain Mohammad Bellal , Rana Juwel , Renzetti Stefano , Islam Rakibul M. 
Published: April 2021

AbstractObjectiveTo estimate the age-standardised prevalence, awareness, treatment, and control of hypertension and to identify their risk factors in Bangladeshi adults using the Bangladesh Demographic and Health Survey (BDHS) 2017-18 data.MethodsData from 12, 904 adults aged 18-95 years old, median (IQR) = 36 years (26-50), available from the most recent nationally representative BDHS 2017-18 were used. Hypertension was defined as having systolic blood pressure ≥140 mmHg and/or a diastolic blood pressure ≥90 mmHg, and/or taking anti-hypertensive drugs to control blood pressure. Age-standardised prevalence of hypertension and management were estimated with direct standardisation. A multilevel mixed-effects Poisson regression model with a robust variance was used to identify risk factors associated with hypertension and its awareness, treatment, and control.ResultsThe overall age-standardised prevalence of hypertension was 26.2% (95% CI, 25.5-26.9); (men: 23.5%, women: 28.9%). Among those with hypertension (n=3531), 36.7% were aware that they had the condition, and only 31.1% received anti-hypertensive medication. Among those treated for hypertension (n=1306), 43.6% had controlled hypertension. Factors independently associated with hypertension were increasing age, higher body mass index, being women, having diabetes, and residing in selected administrative divisions. A declining trend of hypertension control was observed with increasing age and low education.ConclusionsHypertension is highly prevalent (1 in 4) in Bangladeshi adults, while awareness, treatment, and control are low. Irrespective of the risks associated with hypertension and its management, awareness, treatment, and control programmes should be given high priority in reducing hypertension and improving hypertension control in Bangladesh.
Detection of conspicuous and cryptic food by marmosets (Callithrix jacchus): An evaluation of the importance of color and shape cues
Authors: Barros Priscilla Kelly Silva , Castro Felipe Nalon , Pessoa Daniel Marques Almeida 
Published: April 2021

AbstractSince 19th century, the adaptive function of color vision for object identification has fascinated science. Countless articles uncovered the advantages of trichromacy (i.e., color vision expressed by most humans) in detecting yellowish/reddish targets against a background of mature green leaves. Unfortunately, the same attention was not offered to achromatic visual information, that had their physiological foundations much more explored than their possible adaptive function. So far, mostly because of studies conducted in humans, we know that achromatic cues might also play an important role in object identification, particularly when camouflage is involved. For instance, dichromacy (i.e., color vision expressed by many colorblind humans), favors the detection of camouflaged targets by exploitation of shape cues. The present study sought to evaluate the relative importance of color and shape cues on the detection of food targets by female and male marmosets (Callithrix jacchus). Animals were observed with respect to their foraging behavior and the number of food targets captured. We confirmed that females are advantageous in detecting conspicuous food against a green background and revealed that females and males rely on shape cues to segregate cryptic food. Unexpectedly, males outperformed females in cryptic food foraging. Camouflage improved males’ (but not females’) performance.HighlightsShape cues alone improve capture of cryptic targets by female and male marmosets.The sole use of color cues leads to clear-cut foraging performances between sex.Females outperform males when searching for orange food against a green background.Males outperform females when searching for green food against a green background.Males match females’ performance when searching for orange camouflaged food.
ALS and FTD-associated missense mutations in TBK1 differentially disrupt mitophagy
Authors: Harding Olivia , Evans Chantell S. , Ye Junqiang , Cheung Jonah , Maniatis Tom , Holzbaur Erika L.F. 
Published: April 2021

ABSTRACTTANK-binding kinase 1 (TBK1) is a multi-functional kinase with an essential role in mitophagy, the selective clearance of damaged mitochondria. More than 90 distinct mutations in TBK1 are linked to amyotrophic lateral sclerosis (ALS) and fronto-temporal dementia (FTD), including missense mutations that disrupt the ability of TBK1 to dimerize, associate with the mitophagy receptor optineurin (OPTN), auto-activate, or catalyze phosphorylation. We investigated how ALS-associated mutations in TBK1 affect Parkin-dependent mitophagy using imaging to dissect the molecular mechanisms involved in clearing damaged mitochondria. Some mutations cause severe dysregulation of the pathway, while others induce limited disruption. Mutations that abolish either TBK1 dimerization or kinase activity were insufficient to fully inhibit mitophagy, while mutations that reduced both dimerization and kinase activity were more disruptive. Ultimately, both TBK1 recruitment and OPTN phosphorylation at S177 are necessary for engulfment of damaged mitochondra by autophagosomal membranes. Surprisingly, we find that ULK1 activity contributes to the phosphorylation of OPTN in the presense of either WT- or kinase inactive TBK1. In primary neurons, TBK1 mutants induce mitochondrial stress under basal conditions; network stress is exacerbated with further mitochondrial insult. Our study further refines the model for TBK1 function in mitophagy, demonstrating that some ALS-linked mutations likely contribute to disease pathogenesis by inducing mitochondrial stress or inhibiting mitophagic flux. Other TBK1 mutations exhibited much less impact on mitophagy in our assays, suggesting that cell-type specific effects, cumulative damage, or alternative TBK1-dependent pathways such as innate immunity and inflammation also factor into the development of ALS in affected individuals.SIGNIFICANCE STATEMENTMissense mutations in TANK-binding kinase 1 (TBK1) have various biophysical and biochemical effects on the molecule, and are associated with the neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and fronto-temporal dementia (FTD). TBK1 plays an essential role in clearing damaged mitochondria. Here, we investigate the impact of 10 ALS-linked TBK1 mutations on the critical early stage of mitophagy. We find that both TBK1 recruitment and kinase activity contribute to the clearance of the damaged mitochondria. Furthermore, in neurons, expression of TBK1 mutants alone affects mitochondrial network health. Our investigation utilizes disease-linked mutations to further refine the current model of mitophagy, identifying crosstalk between the regulatory kinases TBK1 and ULK1, and providing new insights into the roles of TBK1 in neurodegenerative pathogenesis.