bluuebunny/crossref_metadata_2025_split huggingface dataset:
Emotional Reactivity, Emotion Regulation, and Regulatory Choice in Somatic Symptom Disorder
Authors: Schnabel Katharina , Schulz Stefan M. , Witthöft Michael 
Published: August 2022

ABSTRACT

Objective
Despite the transdiagnostic importance of emotional dysregulation in psychopathology, the exact nature of emotional dysregulation in somatic symptom disorders (SSDs) is still unclear. The present study compared measures of emotional reactivity, emotion regulation (ER), and regulatory choice between n = 62 individuals with SSD (Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition) and n = 61 healthy participants.

Methods
Participants underwent two ER tasks, assessing a) efficacy of reappraisal and suppression, and 2) regulatory choice, while electrodermal activity and heart rate variability were recorded. In addition, self-reports (Emotion Reactivity Scale, Emotion Regulation Questionnaire, Difficulties in Emotion Regulation Scale) regarding habitual emotional reactions and regulation strategies were assessed.

Results
Individuals with SSD reported significantly higher trait emotional reactivity (Emotion Reactivity Scale; p < .001, d = 1.61), significantly more trait ER difficulties (Difficulties in Emotion Regulation Scale; p < .001, d = 1.62), and significantly lower reappraisal use in daily life (Emotion Regulation Questionnaire; p < .001, d = −0.75). On a behavioral and physiological levels, no significant group differences were found regarding emotional reactivity (subjective ratings of emotional stimuli in task 1, p values = .653–.667; electrodermal activity: p values = .224–.837), ER (task 1: p values = .077–.731; heart rate variability: p values = .522–.832), or regulatory choice (task 2: p = .380). Although individuals with SSD were equally effective in state ER (task 1), they perceived ER during the task as significantly more effortful (p = .038, d = −0.38).

Conclusions
Results suggest that dysregulated emotions might not result from lacking abilities in implementing ER effectively, but rather could arise from less frequent ER initiation because ER is perceived as more effortful.
Pain Is Associated With Depressive Symptoms, Inflammation, and Poorer Physical Function in Older Adults With HIV
Authors: Derry-Vick Heather M. , Johnston Carrie D. , Brennan-Ing Mark , Burchett Chelsie O. , Glesby Nina , Zhu Yuan-Shan , Siegler Eugenia L. , Glesby Marshall J. 
Published: August 2022

ABSTRACT

Objective
People living with HIV (PLWH) frequently experience pain, which often co-occurs with psychological symptoms and may impact functional outcomes. We investigated cross-sectional associations between pain, depressive symptoms, and inflammation, and then explored whether pain was related to poorer physical function among older PLWH.

Methods
We examined data from PLWH aged 54 to 78 years (n = 162) recruited from a single outpatient program for a larger study on HIV and aging. Participants reported depressive symptoms (10-item Center for Epidemiological Studies Depression Scale) and then attended a biomedical visit in which they reported past-month pain (Medical Outcomes Study-HIV pain subscale), completed physical function assessments, and provided blood samples (assayed for interleukin 6, interferon-γ, tumor necrosis factor α, and C-reactive protein). Links between pain, depressive symptoms, inflammation, and physical function were tested using linear regression models.

Results
PLWH with greater depressive symptoms experienced more pain than did those with fewer depressive symptoms (B = 1.31, SE = 0.28, p < .001), adjusting for age, sex, race, body mass index, smoking, disease burden, time since HIV diagnosis, and medication use. Higher composite cytokine levels were associated with worse pain (B = 5.70, SE = 2.54, p = .027 in adjusted model). Poorer physical function indicators, including slower gait speed, weaker grip strength, recent falls, and prefrail or frail status, were observed among those with worse pain. Exploratory mediation analyses suggested that pain may partially explain links between depressive symptoms and several physical function outcomes.

Conclusions
Pain is a potential pathway linking depressive symptoms and inflammation to age-related health vulnerabilities among older PLWH; longitudinal investigation of this pattern is warranted. PLWH presenting with pain may benefit from multidisciplinary resources, including behavioral health and geriatric medicine approaches.
Soluble CD14-associated DNA methylation sites predict mortality among men with HIV infection
Authors: Titanji Boghuma K. , Wang Zeyuan , Chen Junyu , Hui Qin , So-Armah Kaku , Freiberg Matthew , Justice Amy C. , Ke Xu , Marconi Vincent C. , Sun Yan V. 
Published: August 2022

Objectives:
Elevated plasma levels of sCD14 predict all-cause mortality in people with HIV (PWH). Epigenetic regulation plays a key role in infection and inflammation. To reveal the epigenetic relationships between sCD14, immune function and disease progression among PWH, we conducted an epigenome-wide association study (EWAS) of sCD14 and investigated the relationship with mortality.

Design and methods:
DNA methylation (DNAm) levels of peripheral blood samples from PWH in the Veterans Aging Cohort Study (VACS) were measured using the Illumina Infinium Methylation 450K (n = 549) and EPIC (850K) BeadChip (n = 526). Adjusted for covariates and multiple testing, we conducted an epigenome-wide discovery, replication, and meta-analysis to identify significant associations with sCD14. We then examined and replicated the relationship between the principal epigenetic sites and survival using Cox regression models.

Findings:
We identified 118 DNAm sites significantly associated with sCD14 in the meta-analysis of 1075 PWH. The principal associated DNAm sites mapped to genes (e.g. STAT1, PARP9, IFITM1, MX1, and IFIT1) related to inflammation and antiviral response. Adjusting for multiple testing, 10 of 118 sCD14-associated DNAm sites significantly predicted survival time conditional on sCD14 levels.

Conclusion:
The identification of DNAm sites independently predicting survival may improve our understanding of prognosis and potential therapeutic targets among PWH.
Brief Report: Virologic Impact of the Dolutegravir Transition: Prospective Results From the Multinational African Cohort Study
Authors: Allahna Esber , Nicole Dear , Neha Shah , Hannah Kibuuka , Jonah Maswai , John Owuoth , Valentine Singoei , Emmanuel Bahemana , Michael Iroezindu , Trevor A. Crowell , Christina S. Polyak , Joseph S. Cavanaugh , Julie A. Ake ,   on behalf of the AFRICOS Study Group
Published: August 2022

Background:
The real-world impact on viral suppression of switching from non–dolutegravir-based therapy to tenofovir/lamivudine/dolutegravir (TLD) is not thoroughly characterized in Africa. We described the virologic consequences of switching regimens in the African Cohort Study (AFRICOS), an observational cohort in Nigeria, Kenya, Uganda, and Tanzania.

Methods:
Among antiretroviral-experienced people living with HIV (PLWH) in AFRICOS, we compared viral load (VL) nonsuppression (VL ≥ 1000 copies/mL) among those who switched with those who never switched to TLD, restricting to participants who had at least 1 visit with a recorded VL after the countrywide rollout of TLD. We calculated Kaplan–Meier curves and conducted Cox proportional hazards modeling to estimate adjusted hazard ratios and 95% confidence intervals for factors potentially associated with nonsuppression.

Results:
As of September 1, 2021, there were 3108 PLWH enrolled. Among 1576 participants who switched to TLD, 1486 (94.3%) remained suppressed after transition, 12 (0.8%) remained unsuppressed, and 38 (2.4%) lost suppression, compared with 652 (82.1%), 75 (9.4%), and 46 (5.8%), respectively, of 797 participants who did not switch (P < 0.001). After adjustment for sex, age, study site, and self-reported antiretroviral therapy adherence, virally suppressed participants who did not switch to TLD had significantly higher rates of losing viral suppression compared with those who switched (adjusted hazard ratio: 4.26; 95% confidence interval: 2.72 to 6.68).

Conclusions:
PLWH transitioning to TLD had higher rates of viral suppression compared with those who remained on other regimens. Even within a highly suppressed population, TLD transition provided significant benefits for achieving or maintaining viral suppression.
Childhood trauma in patients with epileptic versus non-epileptic seizures
Authors: Yang Tianren , Roberts Caitlin , Winton-Brown Toby , Lloyd Michael , Kwan Patrick , O’Brien Terence J , Velakoulis Dennis , Rayner Genevieve , Malpas Charles B 
Published: August 2022

ABSTRACTObjectiveChildhood trauma has been implicated as a risk factor for the aetiology of psychogenic non-epileptic seizures (PNES). Relatively little attention has been paid to whether profiles of specific trauma types differ between patients with epilepsy and PNES. Investigating childhood trauma profiles in these patient groups may identify psychological vulnerabilities the predispose to developing PNES, and aid early diagnoses, prevention, and treatment.MethodsData were collected from two cohorts (nRetrospective=203;nProspective=209) admitted to video-EEG monitoring units in Melbourne Australia. The Childhood Trauma Questionnaire domain score differences between patient groups were investigated using standardised effect sizes and general linear mixed-effects models (GLMMs). Receiver operating characteristic curves were used to investigate classification accuracy.ResultsIn the retrospective cohort, patients diagnosed with PNES reported greater childhood emotional abuse, emotional neglect, physical abuse, sexual abuse, and physical neglect relative to epilepsy patients. These differences were replicated in the prospective cohort, except for physical abuse. GLMMs revealed significant main effects for group in both cohorts, but no evidence for any group by domain interactions. Reported sexual abuse showed the best screening performance of PNES, although no psychometric scores were adequate as isolated measures.SignificancePatients with PNES report greater frequency of childhood trauma than patients with epilepsy. This effect appears to hold across all trauma types, with no strong evidence emerging for a particular trauma type that is more prevalent in PNES. From a practical perspective, inquiring regarding a history of sexual abuse shows the most promise as a screening measure.SummaryRelatively little attention has been paid to whether profiles of specific trauma types differ between patients with epilepsy and PNES.We collected self-reported childhood trauma information from two independent cohorts of patients undergoing VEMPatients with PNES report greater frequency of childhood trauma than patients with epilepsy.This effect appears to hold across all trauma types, with no strong evidence emerging for a particular trauma type that is more prevalent in PNES.Inquiring regarding a history of sexual abuse shows the most promise as a screening measure.
COADREADx: A comprehensive algorithmic dissection unravels salient biomarkers and actionable insights into the discrete progression of colorectal cancer
Authors: Palaniappan Ashok , Muthamilselvan Sangeetha , Sarathi Arjun 
Published: August 2022

AbstractColorectal cancer is a common condition with an uncommon burden of disease, heterogeneity in manifestation, and no definitive treatment in the advanced stages. Against this backdrop, renewed efforts to unravel the genetic drivers of colorectal cancer progression are paramount. Early-stage detection contributes to the success of cancer therapy and increases the likelihood of a favorable prognosis. Here, we have executed a comprehensive computational workflow aimed at uncovering the discrete stagewise genomic drivers of colorectal cancer progression. Using the TCGA COADREAD expression data and clinical metadata, we constructed stage-specific linear models as well as contrast models to identify stage-salient differentially expressed genes. Stage-salient differentially expressed genes with a significant monotone trend of expression across the stages were identified as progression-significant biomarkers. Among the biomarkers identified are: CRLF1, CALB2, STAC2, UCHL1, KCNG1 (stage-I salient), KLHL34, LPHN3, GREM2, ADCY5, PLAC2, DMRT3 (stage-II salient), PIGR, HABP2, SLC26A9 (stage-III salient), GABRD, DKK1, DLX3, CST6, HOTAIR (stage-IV salient), and CDH3, KRT80, AADACL2, OTOP2, FAM135B, HSP90AB1 (top linear model genes). In particular the study yielded 31 genes that are progression-significant such as ESM1, DKK1, SPDYC, IGFBP1, BIRC7, NKD1, CXCL13, VGLL1, PLAC1, SPERT, UPK2, and interestingly three members of the LY6G6 family. Significant monotonic linear model genes included HIGD1A, ACADS, PEX26, and SPIB. The stage-salient genes were benchmarked using normals-augmented dataset, and cross-referenced with existing knowledge. In addition, the signature of a multicellular immuno-cyte community specific to colorectal cancer relative to normal tissue was identified. The candidate biomarkers were used to construct the feature space for learning an optimal model for the digital screening of early-stage colorectal cancers. A feature space of just seven biomarkers, namely ESM1, DHRS7C, OTOP3, AADACL2, LPHN3, GABRD, and LPAR1, was sufficient to optimize a RandomForest model that achieved >98% balanced accuracy (and performant recall) on blind validation with external datasets. Survival analysis yielded a panel of three stage-IV salient genes, namely HOTAIR, GABRD, and DKK1, for the design of an optimal multivariate model for patient risk stratification. Integrating the above results, we have developed COADREADx, a web-server for assisting the screening and prognosis of colorectal cancers. COADREADx has been deployed at:https://apalanialab.shinyapps.io/coadreadx/for academic research and further refinement.
Plant conservation assessment at scale: rapid triage of extinction risks
Authors: AuBuchon-Elder Taylor , Minx Patrick , Bookout Bess , Kellogg Elizabeth A. 
Published: August 2022

SummaryThe IUCN Red List criteria are widely used to determine extinction risks of plant and animal life. Here, we use The Red List’s criterion B, Geographic Range Size, to provide preliminary conservation assessments of the members of a large tribe of grasses, the Andropogoneae, with ∼1100 species, including maize, sorghum, and sugarcane and their wild relatives.We use georeferenced occurrence data from the Botanical Information and Ecology Network (BIEN) and automated individual species assessments using ConR to demonstrate efficacy and accuracy in using time-saving tools for conservation research. We validate our results with those from the IUCN-authorized assessment tool, GeoCAT.We discovered a remarkably large gap in digitized information, with slightly more than 50% of the Andropogoneae lacking sufficient information for assessment. ConR and GeoCAT largely agree on which taxa are of least concern (>90%) or possibly threatened (<10%), highlighting that automating assessments with ConR is a viable strategy for preliminary conservation assessments of large plant groups. Results for crop wild relatives are similar to those for the entire data set.Increasing digitization and collection needs to be a high priority. Available rapid assessment tools can then be used to identify species that warrant more comprehensive investigation.Societal Impact StatementThe current rate of global biodiversity loss creates a pressing need to increase efficiency and throughput of extinction risk assessments in plants. We must assess as many plant species as possible, working with imperfect knowledge, to address the habitat loss and seemingly countless extinction threats of the Anthropocene. Large-scale, preliminary conservation assessments can play a fundamental role in setting priorities for more in-depth investigation.
Combined BRCA2 and MAGEC3 expression predict outcome in Advanced Ovarian Cancers
Authors: Omole Emmanuel B. , Aijaz Iqbal , Ellegate James , Isenhart Emily , Desouki Mohamed M. , Mastri Michalis , Humphrey Kristen , Dougherty Emily M. , Rosario Spencer R. , Nastiuk Kent L. , Ohm Joyce E. , Eng Kevin H. 
Published: August 2022

AbstractLike BRCA2, MAGEC3 is an ovarian cancer predisposition gene that has been shown to have prognostic significance in ovarian cancer patients. Despite the clinical significance of each individual gene, no studies have been done to assess the clinical significance of their combined expression. We therefore sought to determine the relationship between MAGEC3 and BRCA2 expression in ovarian cancer and their association with patient characteristics and outcomes. Immuno-histochemical staining was quantitated on tumor microarrays of human tumor samples obtained from 357 patients with epithelial ovarian cancer to ascertain BRCA2 expression levels. In conjunction with our previously published MAGEC3 expression data, we observed a weak inverse correlation of MAGEC3 with BRCA2 expression (r= -0.15; p<0.05) in cases with full-length BRCA2. Patients with optimal cytoreduction, loss of MAGEC3, and detectable BRCA2 expression had better overall (median OS: 127.9 vs 65.3 months, p=0.035) and progression-free (median PFS: 85.3 vs 18.8 months, p=0.002) survival compared to patients that were BRCA2 expressors with MAGEC3 normal levels. Our results suggest that combined expression of MAGEC3 and BRCA2 serves as a better predictor of prognosis than each marker alone.Simple SummaryEarly detection of ovarian cancer is a significant clinical challenge, with most women presenting with advanced stages of disease at initial diagnosis. The aim of this study was to evaluate the role of MAGEC3 and BRCA2 in epithelial ovarian cancer progression. We evaluated the effect of MAGEC3 and BRCA2 on the other’s expression. We tested this in humans using immunohistochemical staining of human tumor samples obtained from patients with epithelial ovarian cancer (n = 357). We found a weak inverse correlation between MAGEC3 and BRCA2 expression in epithelial ovarian cancers. Further, our data suggests that the combined expression of MAGEC3 and BRCA2 may be a better predictor of outcomes in patients than the individual markers alone.
A Pair Formation Model with Recovery: Application to Monkeypox
Authors: Betti Matthew I , Farrell Lauren , Heffernan Jane 
Published: August 2022

The current global outbreaks of Monkeypox is a unique infectious disease in the way it seems to be transmitting: it has been observed to be highly concentrated in communities of men who have sex with men (MSM) through pair formation, and also provides immunity. This framework of mostly close, prolonged contact spreading a disease that admits immunity after infection is unlike similar infections which either offer little to no immunity post-infection or are lifelong infections. This creates the need for a new model framework that incorporates pair formation structure with recovery. While seemingly a straight forward model, we show how new dynamics arise from the combination of pair formation and recovery that are not present in a standard model with recovery and also not present in a pair formation model without recovery. We see that the combination of these two properties allows for waves of infection that are not seen in a standard SIR model. These dynamics suggest that outbreaks of monkeypox around the world may require special attention from public health. We also derive a reproduction number for this model and estimate the reproduction number of human monkeypox to be ≈ 2.3 using global and Canadian data. The expression derived for R0 can help estimate key parameters for diseases transmission and public health interventions and compare to equivalent models without pair formation.Significance StatementWith outbreaks of Monkeypox being observed around the world, a modeling framework which takes into account the unique properties of this emerging disease is necessary for understanding the disease and public health mitigation. Monkeypox seems to be unique in that it requires close, prolonged contact with an infected individual in order to spread, but also provides immunity after infection. We develop a model for this situation and show how this differs from simpler models which are currently being used for disease dynamics.
promor: a comprehensive R package for label-free proteomics data analysis and predictive modeling
Authors: Ranathunge Chathurani , Patel Sagar S. , Pinky Lubna , Correll Vanessa L. , Chen Shimin , Semmes O. John , Armstrong Robert K. , Combs C. Donald , Nyalwidhe Julius O. 
Published: August 2022

AbstractSummaryWe present promor, a comprehensive, user-friendly R package that streamlines label-free (LFQ) proteomics data analysis and building machine learning-based predictive models with top protein candidates.Availability and implementationpromor is freely available as an open source R package on the Comprehensive R Archive Network (CRAN)(https://CRAN.R-project.org/package=promor) and distributed under the Lesser General Public License (version 2.1 or later). Development version of promor is maintained on GitHub (https://github.com/caranathunge/promor) and additional documentation and tutorials are provided on the package website (https://caranathunge.github.io/promor/).Contactcaranathunge86@gmail.com
Cancer tissue of origin constrains the growth and metabolism of metastases
Authors: Sivanand Sharanya , Gultekin Yetis , Winter Peter S. , Vermeulen Sidney Y. , Tchourine Konstantine , Abbott Keene L. , Danai Laura V. , Gourgue Florian , Do Brian T. , Crowder Kayla , Kunchok Tenzin , Lau Allison N. , Darnell Alicia M. , Jefferson Alexandria , Morita Satoru , Duda Dan G. , Aguirre Andrew , Wolpin Brian M. , Henning Nicole , Spanoudaki Virginia , Maiorino Laura , Irvine Darrell J. , Yilmaz Omer H. , Lewis Caroline A. , Vitkup Dennis , Shalek Alex K. , Vander Heiden Matthew G. 
Published: August 2022

AbstractMetastases arise from a subset of cancer cells that disseminate from the primary tumor; however, the factors that contribute to proliferation of cancer cells in a secondary site are incompletely understood. The ability of cancer cells to thrive in a new tissue site is influenced by genetic and epigenetic changes that are important for disease initiation and progression, but these factors alone do not predict if and where cancers metastasize. Specific cancer types metastasize to consistent subsets of tissues, suggesting that factors associated with the primary tumor influence the tissue environments where cancers can grow. Using pancreatic cancer as a model, we find that primary and metastatic tumors share many metabolic similarities and that the tumor initiating capacity and proliferation of both primary- and metastasis-derived cells is favored in the primary site relative to the metastatic site. Moreover, propagating lung or liver metastatic cells in vivo to enrich for tumor cells adapted to grow in the lung or the liver does not enhance their relative ability to form large tumors in those sites, change their preference to grow in the primary site, nor stably alter some aspects of their metabolism relative to primary tumors. We also analyzed primary liver and lung cancer cells and find that these cells also exhibit a preference to grow in their primary site relative to metastatic sites. Together, these data suggest that the cancer tissue-of-origin influences the metabolism of both primary and metastatic tumors and may impact whether cancer cells can thrive in a metastatic site.