bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trends and determinants of Acute Respiratory Infection symptoms among Under-five children in Cambodia: Analysis of 2000 to 2014 Cambodia Demographic and Health Surveys
Authors: Um Samnang , Pin Punleak , Vang Daraden , Chau Darapheak 
Published: November 2022

AbstractINTRODUCTIONAcute Respiratory Infections (ARI) is public health concern. According to the World Health Organization (WHO), ARI is responsible for 3.5% of all diseases in the world and more than 808,000 (15%) of all under-five deaths worldwide in 2017. ARI continues to be one of the leading causes of childhood morbidity and mortality in Cambodia, particularly among children under five of age. We aimed to assess the trends over time of ARI symptoms and examine the socio-demographic, behavioral, and environmental factors associated with ARI symptoms among Cambodian children aged 0-59 months across 2000, 2005, 2010, and 2014.METHODSWe used existing children’s data from the Cambodia Demographic and Health Survey (CDHS) with a total of children ages 0-59 months included 7,828 in 2000, 7,621 in 2005, 7,727 in 2010, and 6,864 in 2014, respectively. All statistical estimations were carried out using STATA V16, within the survey-specific command “svy” using the standard sampling weight (v005/1,000,000), clustering, and stratification. We used simple and multiple logistic regression to determine the main predictors of ARI symptoms.RESULTSARI symptoms in the previous two weeks in children aged 0-59 months in Cambodia decreased from 19.9% in 2000 to 8.6% in 2005 to 6.4% in 2010, then fewer at 5.5% in 2014. The main factors that increased the likelihood of ARI symptoms were children ages 6-11 months [AOR=1.91; 95% CI: 1.53-2.38], 12-23 months [AOR=1.79; 95% CI: 1.46-2.20], and 24-35 months [AOR=1.41; 95% CI: 1.13-1.76], mothers who smoke cigarette [AOR=1.61; 95% CI: 1.27-2.05], and children born into households had non-improved toilets [AOR=1.20; 95% CI: 0.99-1.46]. However, the following factors were found to be associated with decreased odds of having ARI symptoms: Mothers with higher education [AOR=0.45; 95% CI: 0.21-0.94], breastfeeding children [AOR=0.87; 95% CI: 0.77-0.98], and children born into richest wealth quantile [AOR=0.73; 95% CI: 0.56-0.95], respectively. Survey years in 2005 [AOR=0.36; 95% CI: 0.31-0.42], 2010 [AOR=0.27; 95% CI: 0.22-0.33], 2014 [AOR=0.24; 95% CI: 0.19-0.30].CONCLUSIONThe trends of ARI symptoms among children under five in Cambodia significantly decreased from 2000-2014. Mothers who smoke cigarettes, young children ages (6-35 months), and household unimproved toilet facilities are factors that independently increased the likelihood that children would develop ARI symptoms. Inversely, factors were found to be associated with decreased odds of having ARI symptoms: Mothers with higher education, breastfeeding children, and children born into the richest wealth quantile and Survey years. Therefore, government and child family programs must promote maternal education, particularly infant breastfeeding. The government ought to support maternal education and infant breastfeeding in the interest of early childhood care.
Modeling analysis of COVID 19-related delays in colorectal cancer screening on simulated clinical outcomes
Authors: Wilson Lesley-Ann Miller , Vahdat Vahab , Brooks Durado , Limburg Paul 
Published: November 2022

ABSTRACTObjectiveColorectal cancer (CRC) screening disruptions observed during the COVID-19 pandemic put patients at risk for more advanced-stage disease when diagnosed. This budget impact simulation model assessed increased use of multi-target stool DNA [mt-sDNA] or fecal immunochemical [FIT] tests to offset disruption in colonoscopy screening due to COVID-19 in adults at average-risk for CRC, from a United States payer perspectiveMain outcomes and measuresCompared to the base case (S0; 85% colonoscopy and 15% non-invasive tests), the estimated number of missed CRCs and advanced adenomas (AAs) were determined for four COVID-19-affected screening scenarios: S1, 9 months of CRC screening at 50% capacity, followed by 21 months at 75% capacity; S2, S1 followed by increasing stool-based testing by an average of 10% over 3-years; S3, 18 months of CRC screening at 50% capacity, followed by 12 months of 75% capacity; and S4, S3 followed by increasing stool-based testing by an average of 13% over 3-years.ResultsIncreasing the proportional use of mt-sDNA improved AA detection by 6.0% (Scenario 2 versus 1) to 8.4% (Scenario 4 versus 3) and decreased the number of missed CRCs by 15.1% to 17.3%, respectively. Increasing FIT utilization improved the detection of AAs by 3.3% (Scenario 2 versus 1) to 4.6% (Scenario 4 versus 3) and decreased the number of missed CRCs by 12.9% to 14.9%, respectively. Across all scenarios, the number of AAs detected was higher for mt-sDNA than for FIT, and the number of missed CRCs was lower for mt-sDNA than for FIT.Conclusions and relevanceUsing home-based stool tests for average-risk CRC screening can mitigate the consequences of reduced colonoscopy screening resulting from the COVID-19 pandemic. Use of mt-sDNA led to fewer missed CRCs and more AAs detected, compared to FIT.Key PointsQuestionWhat is the impact of increasing the use of stool-based screening tests for colorectal cancer (CRC) during the COVID-19 pandemic in the United States?FindingsIn this simulation model, increasing the use of stool-based screening tests increased the number of advanced adenomas detected and decreased the number of missed CRC cases. Use of multi-target stool DNA (mt-sDNA) resulted in a higher number of advanced adenomas detected and a lower number of missed CRC cases compared to fecal immunochemical testing (FIT).MeaningIncreased use of mt-sDNA led to fewer missed CRC cases and more advanced adenomas detected, compared to FIT, when simulating reduced colonoscopy screening resulting from the COVID-19 pandemic.
Research Letter: Association between long COVID symptoms and employment status
Authors: Perlis Roy H. , Trujillo Kristin Lunz , Safarpour Alauna , Santillana Mauricio , Ognyanova Katherine , Druckman James , Lazer David 
Published: November 2022

ABSTRACTBackgroundSymptoms of Coronavirus-19 (COVID-19) infection persist beyond 2 months in a subset of individuals, a phenomenon referred to as long COVID, but little is known about its functional correlates and in particular the relevance of neurocognitive symptoms.MethodWe analyzed a previously-reported cohort derived from 8 waves of a nonprobability-sample internet survey called the COVID States Project, conducted every 4-8 weeks between February 2021 and July 2022. Primary analyses examined associations between long COVID and lack of full employment or unemployment, adjusted for age, sex, race and ethnicity, education, urbanicity, and region, using multiple logistic regression with interlocking survey weights.ResultsThe cohort included 15,307 survey respondents ages 18-69 with test-confirmed COVID-19 at least 2 months prior, of whom 2,236 (14.6%) reported long COVID symptoms, including 1,027/2,236 (45.9%) reporting either ‘brain fog’ or impaired memory. Overall, 1,418/15,307 (9.3%) reported being unemployed, including 276/2,236 (12.3%) of those with long COVID and 1,142/13,071 (8.7%) of those without; 8,228 (53.8%) worked full-time, including 1,017 (45.5%) of those with long COVID and 7,211 (55.2%) without. In survey-weighted regression models, presence of long COVID was associated with being unemployed (crude OR 1.44, 95% CI 1.20-1.72; adjusted OR 1.23, 95% CI 1.02-1.48), and with lower likelihood of working full-time (crude OR 0.73, 95% CI 0.64-0.82; adjusted OR 0.79, 95% CI 0.70 -0.90). Among individuals with long COVID, the presence of cognitive symptoms – either brain fog or impaired memory – was associated with lower likelihood of working full time (crude OR 0.71, 95% CI 0.57-0.89, adjusted OR 0.77, 95% CI 0.61-0.97).ConclusionLong COVID was associated with a greater likelihood of unemployment and lesser likelihood of working full time in adjusted models. Presence of cognitive symptoms was associated with diminished likelihood of working full time. These results underscore the importance of developing strategies to respond to long COVID, and particularly the associated neurocognitive symptoms.
Prevalence, risk factors, and consequences of hypothyroidism among pregnant women in the health region of Lleida: a cohort study
Authors: Siscart Júlia , Perejón Dani , Serna M. Catalina , Orós Míriam , Godoy Pere , Solé Eduard 
Published: November 2022

AbstractBackgroundPrimary maternal hypothyroidism is defined as the increase of TSH levels in serum during pregnancy. Hypothyroidism in pregnancy is the second most common endocrine disease, after diabetes mellitus, with a prevalence ranging between 3.2 and 5.5%. Its variability depends on ethnical differences. Hypothyroidism in pregnancy is associated with other chronic diseases and fetal and maternal outcomes.ObjectiveTo analyze the prevalence of hypothyroidism among multiethnic pregnant women, and to evaluate the comorbidity with chronic diseases and outcomes leaded during pregnancy and newborn.MethodsRetrospective observational cohort study in pregnant women during the years 2012-2018 in the health region of Lleida. The relationship of hypothyroidism with different variables was analyzed by calculating the adjusted odds ratio (aOR) and the 95% confidence intervals (CI) with multivariate logistic regression models.ResultsWe analyzed a sample of 17177 pregnant women, which represents more than 92% of the total of pregnant women in the health region of Lleida. The annual prevalence of hypothyroidism was 5.7-7.1%. According to the region of origin, the lowest prevalence was found in the population from Sub Saharian Africa (2.1%), while the highest was from Asia and the Middle East (8.6%). Other factors associated with hypothyroidism were age, hypertension, diabetes mellitus, and dyslipidemia. In addition, we did not observe an effect of hypothyroidism on the course of pregnancy, childbirth, and on the newborn. Finally, there was a good control of the disease during pregnancy.ConclusionsThe prevalence of hypothyroidism in pregnancy was 6,5% in this study which depends on the country of origin, lower values were found in Sub Saharian African women and higher in those from Asia and the Middle East. Hypothyroidism was associated with age, diabetes mellitus, arterial hypertension, or dyslipidemia, and was not related to the Apgar score or the weight of the newborn.
Psychosocial adversity experienced in utero and early life is associated with variation in gut microbiota: a prospective case-control study
Authors: Warner Barbara B. , Rosa Bruce A. , Ndao I. Malick , Tarr Phillip I. , Miller J. Phillip , England Sara K. , Luby Joan L. , Rogers Cynthia E. , Hall-Moore Carla , Bryant Renay E. , Wang Jacqueline D. , Linneman Laura , Smyser Tara A. , Smyser Christopher D. , Barch Deanna M. , Miller Gregory E. , Chen Edith , Martin John , Mitreva Makedonka 
Published: November 2022

AbstractSocial disadvantage (SD) and psychological stressors (PS) trap some populations in poverty, resulting in health inequities. How these two factors become biologically embedded and the pathways leading to adverse health outcomes is unclear, especially in infants exposed to psychosocial adversity in utero and during early life. Variation in gut microbiome structure and functions, and systemic elevations in circulating cytokines levels as indices of inflammation, offer two possible causative pathways. Here, we interrogate the gut microbiome of mother-child dyads and maternal inflammatory markers, and compare high-SD/high-PS dyads to pairs with low-SD/Low-PS, and demonstrate that the GM of high-SD and high-PS mothers may already be compromised, resulting in the lowest observed inter-individual similarity in that group. The strong predictors of maternal high-SD and high-PS based on mothers and children microbiomes were phylogenetically very distinct bacteria indicating different GM pathways associated with SD versus PS. We identified sets of SD- and PS-discriminatory metabolic pathways in the mothers and in the children, however their predictive power was lower compared to the discriminatory bacterial species. Prediction accuracy was consistently greater for IL-6 than for the other inflammatory markers, supporting an association between systemic inflammation and psychosocial adversity. The gut microbiome of the infants can be used to predict the psychosocial adversity of mothers, and are embedded in the gut microbiota of 4-month-old infants.
Rapid structural remodeling of peripheral taste fibers is independent of taste cell turnover
Authors: Whiddon Zachary D. , Marshall Jaleia , Alston David , McGee Aaron W. , Krimm Robin F. 
Published: November 2022

ABSTRACTTaste bud cells are constantly replaced in taste buds as old cells die and new cells migrate into the bud. The perception of taste relies on new taste bud cells integrating with existing neural circuitry, yet how these new cells connect with a taste ganglion neuron is unknown. Do taste ganglion neurons remodel to accommodate taste bud cell renewal? If so, how much of the taste axon structure is fixed and how much remodels? Here we measured the motility and branching of individual taste arbors (the portion of the axon innervating taste buds) over time with two-photonin vivomicroscopy. Terminal branches of taste arbors continuously and rapidly remodel within the taste bud. This remodeling is faster than predicted by taste bud cell renewal, with terminal branches added and lost concurrently. Surprisingly, ablating new taste cells with chemotherapeutic agents revealed that remodeling of the terminal branches of taste arbors does not rely of the renewal of taste bud cells. Although the arbor structure remodeling was fast and intrinsically controlled, no new arbors were added, and few were lost over 100 days. Taste ganglion neurons maintain a stable number of nerve arbors that are each capable of high-speed remodeling. Arbor structural plasticity would permit arbors to locate new taste bud cells, while stability of arbor number could support constancy in the degree of connectivity and function for each neuron over time.
Identification of genomic alterations with clinical impact in canine splenic hemangiosarcoma
Authors: Estabrooks Timothy , Gurinovich Anastasia , Pietruska Jodie , Lewis Benjamin , Harvey Garrett , Post Gerald , Lambert Lindsay , Rodrigues Lucas , White Michelle E. , Lopes Christina , London Cheryl A. , Megquier Kate 
Published: November 2022

ABSTRACTBackgroundCanine hemangiosarcoma (HSA) is an aggressive cancer of endothelial cells associated with short survival times. Understanding the genomic landscape of HSA is critical to developing more effective therapeutic strategies.ObjectivesTo determine the relationships between genomic and clinical features including treatment and outcome in canine splenic HSA.Animals109 dogs with primary splenic HSA treated by splenectomy that had tumor sequencing via the FidoCure® Precision Medicine Platform targeted sequencing panel.MethodsPatient signalment, weight, metastasis at diagnosis, treatment, and survival time were retrospectively evaluated. The incidence of genomic alterations in individual genes and their relationship to patient variables and outcome were assessed.ResultsSomatic mutations inTP53(n = 45),NRAS(n = 20), andPIK3CA(n = 19) were most common. Survival was associated with metastases at diagnosis, germline variants inSETD2andNOTCH1, and nominally with breed. Age at diagnosis was associated withNRASmutations and breed.TP53andPIK3CAmutations were found in larger dogs, germlineSETD2variants in smaller dogs. Doxorubicin (DOX) treatment did not significantly improve survival time, while targeted therapies had a significant early survival benefit.Conclusions and clinical importanceDOX treatment may provide limited clinical benefit for dogs with splenic HSA, while targeted therapy may provide early survival benefit. Genetic signatures associated with splenic HSA may be useful in guiding targeted therapy to improve outcomes. Germline variants, age, size, and breed may be useful prognostic factors and provide insight into the genomic landscape of the tumor.
Hypothalamic vasopressin sex differentiation is established during embryonic neurogenesis
Authors: Zheng Jing , Moazen Parisa , Baimoukhametova Dinara , Lebel Catherine , Bains Jaideep , Kurrasch Deborah 
Published: November 2022

AbstractArginine vasopressin (AVP) is a conserved sexually dimorphic system regulating behaviors and physiologies. Decades of research concludes that AVP sex differentiation in mice occurs around birth when a gonadal surge of testosterone is converted to estrogen in male sexual dimorphic brain regions. We discovered that AVP neurons in the murine hypothalamus are sexually dimorphic much earlier than this surge, with male mice displaying more AVP neurons than females during neurogenesis at E11.In uteroexposure to a pan-ER antagonist blocked AVP masculinization in males, whereas embryonic exogenous 17β-estradiol or xenoestrogen bisphenol A (BPA) masculinized female AVP neurons, causing permanent masculinization effects on adult female AVP cell numbers, projections and intrinsic neuronal properties. Our data reveal that sexual dimorphism of hypothalamic AVP neurons is present from the earliest stages of their differentiation and challenges current dogma that masculinization of the male brain occurs around birth.One-Sentence SummarySexual dimorphism of hypothalamic vasopressin is established during neurogenesis and exposure to the xenoestrogen bisphenol A during pregnancy induces masculinization of female brains
Common molecular features of H3K27M DMGs and PFA ependymomas map to hindbrain developmental pathways
Authors: Pun Matthew , Pratt Drew , Nano Patricia R. , Joshi Piyush K. , Jiang Li , Englinger Bernhard , Rao Arvind , Cieslik Marcin , Chinnaiyan Arul M. , Aldape Kenneth , Pfister Stefan , Filbin Mariella G. , Bhaduri Aparna , Venneti Sriram 
Published: November 2022

AbstractGlobally decreased histone 3, lysine 27 tri-methylation (H3K27me3) is a hallmark of H3K27-altered diffuse midline gliomas (DMGs) and group-A posterior fossa ependymomas (PFAs). H3K27-altered DMGs are largely characterized by lysine-to- methionine mutations in histone 3 at position 27 (H3K27M). Most PFAs overexpress EZH inhibitory protein (EZHIP), which possesses a region of similarity to the mutant H3K27M. Both H3K27M and EZHIP inhibit function of the polycomb repressive complex 2 (PRC2) responsible for H3K27me3 deposition. These tumors often arise in neighboring regions of the brainstem and posterior fossa. In rare cases PFAs harbor H3K27M mutations, and DMGs overexpress EZHIP. These findings together raise the possibility that certain cell populations in the developing hindbrain/posterior fossa are especially sensitive to modulation of H3K27me3 states. We identified shared molecular features by comparing genomic, bulk transcriptomic, chromatin-based profiles, and single-cell RNA-sequencing (scRNA-seq) data from the two tumor classes. Our approach demonstrated that 1q gain, a key biomarker in PFAs, is prognostic in H3.1K27M, but not H3.3K27M gliomas. Conversely, Activin A Receptor Type 1 (ACVR1), which is associated with mutations in H3.1K27M gliomas, is overexpressed in a subset of PFAs with poor outcome. Despite diffuse H3K27me3 reduction, previous work shows that both tumors maintain genomic H3K27me3 deposition at select sites. We demonstrate heterogeneity in shared patterns of residual H3K27me3 for both tumors that largely segregated with inferred anatomic tumor origins and progenitor populations of tumor cells. In contrast, analysis of genes linked to H3K27 acetylation (H3K27ac)-marked enhancers showed higher expression in astrocytic-like tumor cells. Finally, common H3K27me3-marked genes mapped closely to expression patterns in the human developing hindbrain. Overall, our data demonstrate developmentally relevant molecular similarities between PFAs and H3K27M DMGs and support the overall hypothesis that deregulated mechanisms of hindbrain development are central to the biology of both tumors.
Evaluating the analytical validity of mutation calling pipeline for tumor whole exome sequencing
Authors: Cheng Chinyi , Huang Jia-Hsin , Hsu Jacob Shujui 
Published: November 2022

AbstractDetecting somatic mutations from the patients’ tumor tissues has the clinical impacts in medical decision making. Library preparation methods, sequencing platforms, read alignment tools and variant calling algorithms are the major factors to influence the data analysis results. Understanding the performance of the tool combinations of the somatic variant calling pipelines has become an important issue in the use of the whole exome sequences (WES) analysis in clinical actions. In this study, we selected four state-of-the-art sequence aligners including BWA, Bowtie2, DRAGMAP, DRAGEN aligner (DragenA) and HISAT2. For the variant callers, we chose GATK Mutect2, Sentieon TNscope, DRAGEN caller (DragenC) and DeepVariant. The benchmarking tumor whole exome sequencing data released from the FDA-led Sequencing and Quality Control Phase 2 (SEQC2) consortium was applied as the true positive variants to evaluate the overall performance.Multiple combinations of the aligners and variant callers were used to assess the variation detection capability. We measured the recall, precision and F1-score for each combination in both single nucleotide variants (SNVs) and short insertions and deletions (InDels) variant detections. We also evaluated their performances in different variant allele frequencies (VAFs) and the base pair length. The results showed that the top recall, precision and F1-score in the SNVs detection were generated by the combinations of BWA+DragenC(0.9629), Bowtie2+TNscope(0.9957) and DRAGMAP+DragenC(0.9646), respectively. In the InDels detection, BWA+DragenC(0.9546), Hisat2+TNscope(0.7519) and DragenA+DragenC(0.8081) outperformed the other combinations in the recall, precision and F1-Score, respectively. In addition, we found that the variant callers could bias the variant calling results. Finally, although some combinations yielded high accuracies of variant detection, but some variants still could not be detected by these outperformed combinations. The results of this study provided the vital information that no single combination could achieve superior results in detecting all the variants of the benchmarking dataset. In conclusion, applying both merged-based and ensemble-based variants detection approaches is encouraged to further detect variants comprehensively.