bluuebunny/crossref_metadata_2025_split huggingface dataset:
Linking brain structure, cognition, and sleep: insights from clinical data
Authors: Wei Ruoqi , Ganglberger Wolfgang , Sun Haoqi , Hadar Peter  N , Gollub Randy  L , Pieper Steve , Billot Benjamin , Au Rhoda , Eugenio Iglesias Juan , Cash Sydney S , Kim Soriul , Shin Chol , Westover M Brandon , Joseph Thomas Robert 
Published: November 2023

Abstract

Study Objectives
To use relatively noisy routinely collected clinical data (brain magnetic resonance imaging (MRI) data, clinical polysomnography (PSG) recordings, and neuropsychological testing), to investigate hypothesis-driven and data-driven relationships between brain physiology, structure, and cognition.

Methods
We analyzed data from patients with clinical PSG, brain MRI, and neuropsychological evaluations. SynthSeg, a neural network-based tool, provided high-quality segmentations despite noise. A priori hypotheses explored associations between brain function (measured by PSG) and brain structure (measured by MRI). Associations with cognitive scores and dementia status were studied. An exploratory data-driven approach investigated age-structure-physiology-cognition links.

Results
Six hundred and twenty-three patients with sleep PSG and brain MRI data were included in this study; 160 with cognitive evaluations. Three hundred and forty-two participants (55%) were female, and age interquartile range was 52 to 69 years. Thirty-six individuals were diagnosed with dementia, 71 with mild cognitive impairment, and 326 with major depression. One hundred and fifteen individuals were evaluated for insomnia and 138 participants had an apnea–hypopnea index equal to or greater than 15. Total PSG delta power correlated positively with frontal lobe/thalamic volumes, and sleep spindle density with thalamic volume. rapid eye movement (REM) duration and amygdala volume were positively associated with cognition. Patients with dementia showed significant differences in five brain structure volumes. REM duration, spindle, and slow-oscillation features had strong associations with cognition and brain structure volumes. PSG and MRI features in combination predicted chronological age (R2 = 0.67) and cognition (R2 = 0.40).

Conclusions
Routine clinical data holds extended value in understanding and even clinically using brain-sleep-cognition relationships.
Between Peripherality and Privilege: “Women Wage Peace” as a Case Study of Intersectionality Practices in Women’s Movements
Authors: Lion Veronica 
Published: November 2023

Abstract
This article analyzes Women Wage Peace (WWP), an Israeli grassroots peace movement, as a case study of intersectionality in women’s movements. Using an ethnographic model based on semi-structured interviews with previous and current movement members, I investigate the dilemmas and strategies of WWP in its pursuit of a diverse membership base, a goal considered unique in Israeli peace discourse. This study contributes to understanding intersectional theory and practice, explaining why such an approach is not (always) effective in women’s movements despite the best intentions. Examining WWP through the lens of peripherality and privilege highlights the movement’s hierarchical power structure, identifying the places where intersectional awareness does not translate into political practice. By providing examples of the challenges of intersectionality in women’s movements, these findings offer a response to the need for more nuanced analysis in current feminist and social movement research.
Activation of moderate autophagy promotes survival of fat graft
Authors: Pei Su‐Jun , Zhu Yuan‐Zheng , Yang Juan‐Min , Zhang Min‐Chen , Shi Chen‐Long , Ding Ying , Yi Yang‐Yan 
Published: November 2023

AbstractClinically unpredictable retention following fat grafting remains outstanding problems because of the unrevealed mechanism of grafted fat survival. The role of autophagy, a process to maintain cellular homeostasis through recycling cellular debris, has yet been to be reported in fat grafting. This study aims to improve the survival of fat grafting through the autophagy. First, the relationship between cell death and autophagy in the early stage of fat grafting was evaluated through immunostaining, RNA sequencing, and western blot. Next, rapamycin, an autophagic agonist, was used for the culturing of adipose‐derived stem cells and adipocytes during ischemia. Cell death, autophagy, and reactive oxygen species (ROS) were assayed. Finally, rapamycin was used to assist fat grafting in nude mice. The results demonstrated that the peak of cell death at the early stage of fat grafting was accompanied by a decrease in autophagy. In vitro, during ischemia, 25 nM was confirmed as the optimal dose of rapamycin that reduces cell death with enhanced autophagy and mitophagy, improved mitochondrial quality as well as decreased ROS accumulation. In vivo, promoted mitophagy, alleviated oxidative stress, and decreased cell apoptosis of rapamycin‐treated fat grafts were observed in the early stage. In addition, rapamycin increased the survival of fat grafts with increased neovascularization and reduced fibrosis. We suggested that moderate autophagy induced by rapamycin contribute to enhanced ischemic tolerance and long term survival of fat grafts through mitochondrial quality control.
Weathering the Storm: Syringe Services Program Laws and Human Immunodeficiency Virus During the COVID-19 Pandemic
Authors: Jackson Hannah , Dunphy Christopher , Grist Mary Blain , Jiang Xinyi , Xu Likang , Guy Gery P. , Salvant-Valentine Sheila 
Published: November 2023

Background:
Syringe services programs (SSPs) are community-based prevention programs that provide a range of harm reduction services to persons who inject drugs. Despite their benefits, SSP laws vary across the United States. Little is known regarding how legislation surrounding SSPs may have influenced HIV transmission over the COVID-19 pandemic, a period in which drug use increased. This study examined associations between state SSP laws and HIV transmission among the Medicaid population before and after the COVID-19 pandemic.

Methods:
State-by-month counts of new HIV diagnoses among the Medicaid population were produced using administrative claims data from the Transformed Medicaid Statistical Information System from 2019 to 2020. Data on SSP laws were collected from the Prescription Drug Abuse Policy System. Associations between state SSP laws and HIV transmission before and after the start of the COVID-19 pandemic were evaluated using an event study design, controlling for the implementation of COVID-19 nonpharmaceutical interventions and state and time fixed effects.

Results:
State laws allowing the operation of SSPs were associated with 0.54 (P = 0.044) to 1.18 (P = 0.001) fewer new monthly HIV diagnoses per 100,000 Medicaid enrollees relative to states without such laws in place during the 9 months after the start of the COVID-19 pandemic. The largest effects manifested for population subgroups disproportionately affected by HIV, such as male and non-Hispanic Black Medicaid enrollees.

Conclusion:
Less restrictive laws on SSPs may have helped mitigate HIV transmission among the Medicaid population throughout the COVID-19 pandemic. Policymakers can consider implementing less restrictive SSP laws to mitigate HIV transmission resulting from future increases in injection drug use.

Disclaimer:
The findings and conclusions in this report are those of the author(s) and do not necessarily represent the official position of the Centers for Disease Control and Prevention.
More Frequent HIV Viral Load Testing With Point-Of-Care Tests Detects Elevated Viral Load Earlier in Postpartum HIV-Positive Women in a Randomized Controlled Trial in Two Clinics in Johannesburg, South Africa
Authors: Fairlie Lee , Sawry Shobna , Pals Sherri , Sherman Gayle , Williamson Dhelia , Le Roux Jean , Ngeno Bernadette , Berrie Leigh , Diallo Karidia , Cox Mackenzie Hurlston , Mogashoa Mary , Chersich Matthew , Modi Surbhi ,   For the OPPTIM (Optimised Postpartum PMTCT Testing for Infants and their Mothers) Study Team
Published: November 2023

Background:
Elevated maternal HIV viral load (VL) increases vertical transmission risk for breastfeeding children. This randomized controlled trial in Johannesburg primarily evaluated whether 3-monthly point-of-care testing, with laboratory-based standard-of-care testing (arm 2), compared with 6-monthly laboratory-based VL testing (arm 1) in postpartum women living with HIV receiving first-line tenofovir–emtricitabine–efavirenz antiretroviral treatment improved VL suppression, factors associated with nonsuppression, and drug resistance in those with virologic failure.

Methods:
Mother–child pairs were enrolled July 2018–April 2019 at the child's 6/10/14-week clinic visit. Women were randomized 1:1 to arm 1 or 2. Trained staff performed point-of-care VL testing using the Cepheid's Xpert HIV-1 VL assay. We fitted a generalized linear mixed model with VL suppression (<50 copies/mL (cps/mL) and <1000 cps/mL) at enrollment and 6, 12, and 18 months postpartum as the outcome and indicator variables for time, study site, study arm, and interaction variables. The final model tested for a difference by study arm, pooling across time points.

Results:
Of 405 women enrolled (204 arm 1 and 201 arm 2), 249 (61%) remained in follow-up through 18 months. There was no difference in VL suppression between arms at 6, 12, or 18 months. VL suppression rate (<50 cps/mL) at 18 months was 64.8% in arm 1 and 63.0% in arm 2 (P = 0.27). On bivariate analysis, there was an association with late antenatal booking and being in arm 2 for nonsuppressed VL, but no significant association with breastfeeding. HIV drug resistance was found in 12 of 23 participants (52.2%).

Conclusion:
We found no significant difference in VL suppression with more frequent VL testing in postpartum women living with HIV receiving first-line efavirenz-based antiretroviral treatment.
Cancer Treatment Decision-Making for People Living With HIV: Physician-Reported Barriers, Facilitators, and Recommendations
Authors: Khouri Ashley , Stephens Maya J. , Young Jeanette , Galyean Patrick , Knettel Brandon A. , Cherenack Emily M. , Zickmund Susan , Watt Melissa H. , Bartlett John , Pollak Kathryn I. , Ubel Peter A. , Fagerlin Angela , Suneja Gita 
Published: November 2023

Background:
Compared with the general cancer population, people living with HIV (PLWH) and cancer are less likely to receive treatment and have significantly elevated cancer-specific mortality for many common cancer types. Physician recommendations drive the cancer therapy that patients receive, yet there is limited information assessing how cancer treatment decisions are made for people living with HIV and cancer. We sought to understand oncologist decision-making in PLWH and cancer by eliciting barriers, facilitators, and recommendations for enhancing care delivery.

Setting:
Participants were recruited between May 2019 and May 2021 from one academic medical center in the western United States (n = 13), another in the southeastern United States (n = 7), and community practices nationwide (n = 5).

Methods:
Using an inductive qualitative approach, we conducted in-depth interviews with 25 oncologists from two academic medical centers and community practices.

Results:
Facilitators of cancer care delivery included readily available information regarding HIV status and stage, interdepartmental communication, and antiviral therapy adherence. Barriers included a lack of formal education on HIV malignancies, perceptions of decreased life expectancy, fear of inadvertent disclosure, and drug–drug interactions. Recommendations included improved provider communication, patient social and mental health resources, and continuing education opportunities.

Conclusion:
The study revealed drivers of cancer treatment decision-making, highlighting physician-reported barriers and facilitators, and recommendations to support treatment decision-making. This is the first known study examining oncologists' perceptions of caring for PLWH. Given that cancer is a leading cause of death among PLWH, there is an urgent need to improve care and outcomes.
Preferences of Pregnant and Postpartum Women for Differentiated Service Delivery in Kenya
Authors: Humphrey John , Wanjama Esther , Carlucci James G. , Naanyu Violet , Were Edwin , Muli Lindah , Alera Marsha , McGuire Alan , Nyandiko Winstone , Songok Julia , Wools-Kaloustian Kara , Zimet Gregory 
Published: November 2023

Background:
Differentiated service delivery models are implemented by HIV care programs globally, but models for pregnant and postpartum women living with HIV (PPWH) are lacking. We conducted a discrete choice experiment to determine women's preferences for differentiated service delivery.

Setting:
Five public health facilities in western Kenya.

Methods:
PPWH were enrolled from April to December 2022 and asked to choose between pairs of hypothetical clinics that differed across 5 attributes: clinic visit frequency during pregnancy (monthly vs. every 2 months), postpartum visit frequency (monthly vs. only with routine infant immunizations), seeing a mentor mother (each visit vs. as needed), seeing a clinician (each visit vs. as needed), and basic consultation cost (0, 50, or 100 Kenya Shillings [KSh]). We used multinomial logit modeling to determine the relative effects (β) of each attribute on clinic choice.

Results:
Among 250 PPWH (median age 31 years, 42% pregnant, 58% postpartum, 20% with a gap in care), preferences were for pregnancy visits every 2 months (β = 0.15), postpartum visits with infant immunizations (β = 0.36), seeing a mentor mother and clinician each visit (β = 0.05 and 0.08, respectively), and 0 KSh cost (β = 0.39). Preferences were similar when stratified by age, pregnancy, and retention status. At the same cost, predicted market choice for a clinic model with fewer pregnant/postpartum visits was 75% versus 25% for the standard of care (ie, monthly visits during pregnancy/postpartum).

Conclusion:
PPWH prefer fewer clinic visits than currently provided within the standard of care in Kenya, supporting the need for implementation of differentiated service delivery for this population.
Cirscan: a shiny application to identify differentially active sponge mechanisms and visualize circRNA-miRNA-mRNA networks
Authors: Fraboulet Rose-Marie , Ahmed Yanis Si , Aubry Marc , Corre Sebastien , Galibert Marie-Dominique , Blum Yuna 
Published: November 2023

AbstractBackgroundNon-coding RNAs represent a large part of the human transcriptome and have been shown to play an important role in disease such as cancer. However, their biological functions are still incompletely understood. Among noncoding RNAs, circular RNAs (circRNAs) have recently been identified for their microRNA (miRNA) sponge function which allows them to modulate the expression of miRNA target genes by taking on the role of competitive endogenous RNAs (ce-circRNAs). Today, most computational tools are not adapted to the search for ce-circRNAs or have not been developed for the search for ce-circRNAs from user’s transcriptomic data.ResultsIn this study, we present Cirscan (CIRcular RNA Sponge CANdidates), an interactive Shiny application that automatically infers circRNA-miRNA-mRNA networks from human multi-level transcript expression data from two biological conditions (e.g. tumor versus normal conditions in the case of cancer study) in order to identify on a large scale, potential sponge mechanisms active in a specific condition. Cirscan ranks each circRNA-miRNA-mRNA subnetwork according to a sponge score that integrates multiple criteria based on interaction reliability and expression level. Finally, the top ranked sponge mechanisms can be visualized as networks and an enrichment analysis is performed to help its biological interpretation. We showed on two real case studies that Cirscan is capable of retrieving sponge mechanisms previously described, as well as identifying potential novel circRNA sponge candidates.ConclusionsCirscan can be considered as a companion tool for biologists, facilitating their ability to prioritize sponge mechanisms for experimental validations and identifying potential therapeutic targets. Cirscan is implemented in R, released under the license GPL-3 and accessible on GitLab (https://gitlab.com/geobioinfo/cirscan_Rshiny). The scripts used in this paper are also provided on Gitlab (https://gitlab.com/geobioinfo/cirscan_paper).
Prefrontal cortex signals value category while basal ganglia represent learned values in value learning
Authors: Reza Heydari M. , Ravandi Mohammad Ali Kheirkhah , Hikosaka Okihide , Ghazizadeh Ali 
Published: November 2023

AbstractValue learning can be variable for objects with the exact same reward but the underlying neural mechanism for such variability is not known. We have addressed this question by recording single-unit activity in the prefrontal cortex (PFC) and substantia nigra reticulata (SNr), two key nodes in cortex-basal ganglia circuitry with crucial roles in value learning, as macaque monkeys learned to associate novel objects with either high or low rewards. Estimating the trial by trial learned values based on choice performance, revealed stark differences between learned values across objects with the same reward outcome. Importantly, while PFC neurons rapidly learned to differentiate objects based on their value category, the firing in SNr correlated with the variability in learned values within a value category. Our results suggest that the variation in objects’ learned values is more likely to be a readout of SNr firing while PFC may provide a top-down teaching signal to basal ganglia to demarcate the value categories.
Chimeric Antigen Cytotoxic Receptors for In-Vivo Engineering of Tumor-targeting Natural Killer Cells
Authors: Diwanji Neha , Getts Daniel , Wang Yuxiao 
Published: November 2023

ABSTRACTEx vivo chimeric antigen receptor (CAR) NK cells face challenges in manufacturing, and have limited tumor infiltration and in vivo persistency. A method leveraging mRNA-based delivery for in-vivo engineering of human NK cells could address these issues but has not been established. Here we developed an in-vivo NK cell engineering method by designing CARs that capitalize on inherent NK receptor biology for specific expression and function. These CARs utilize the Immunoreceptor Tyrosine-based Activation Motif (ITAM)-containing signaling adaptor in human NK cells for tumor destruction and cytokine response. We demonstrated that an NKp44-based CAR’s expression and function depend on the signaling adaptor DAP12. This approach enables precise mRNA-driven in-vivo NK cell programming against tumors, ensuring specificity and reducing off-target expression in non-immune healthy tissues.
Integrated Proteomics analysis of baseline protein expression in pig tissues
Authors: Wang Shengbo , Collins Andrew , Prakash Ananth , Fexova Silvie , Papatheodorou Irene , Jones Andrew R. , Vizcaíno Juan Antonio 
Published: November 2023

AbstractThe availability of an increasingly large amount of public proteomics datasets presents an opportunity for performing combined analyses to generate comprehensive organism-wide protein expression maps across different organisms and biological conditions.Sus scrofa, the domestic pig, is a model organism relevant for food production and for human biomedical research. Here we reanalyzed 14 public proteomics datasets from the PRIDE database coming from pig tissues to assess baseline (without any biological perturbation) protein abundance in 14 organs, encompassing a total of 20 healthy tissues from 128 samples. The analysis involved the quantification of protein abundance in 599 mass spectrometry runs.We compared protein expression patterns among different pig organs and examined the distribution of proteins across these organs. Then, we studied how protein abundances compared across different datasets and studied the tissue specificity of the detected proteins. Of particular interest, we conducted a comparative analysis of protein expression between pig and human tissues, revealing a high degree of correlation in protein expression among orthologs, particularly in brain, kidney, heart, and liver samples.We have integrated the protein expression results into the Expression Atlas resource for easy access and visualisation of the protein expression data individually or alongside gene expression data.
Adipose-derived exosomal miR-421 targets CBX7 and promotes metastatic potential in ovarian cancer cells
Authors: Zhang Yi , Tedja Roslyn , Millman Michael , Wong Terrence , Fox Alexandra , Chehade Hussein , Gershater Meyer , Adzibolosu Nicholas , Gogoi Radhika , Anderson Matthew , Rutherford Thomas , Zhang Zhenggang , Chopp Michael , Mor Gil , Alvero Ayesha B. 
Published: November 2023

AbstractBackgroundChromobox protein homolog 7 (CBX7), a member of the Polycomb repressor complex, is a potent epigenetic regulator and gene silencer. Our group has previously reported that CBX7 functions as a tumor suppressor in ovarian cancer cells and its loss accelerated formation of carcinomatosis and drove tumor progression in an ovarian cancer mouse model. The goal of this study is to identify specific signaling pathways in the ovarian tumor microenvironment that down-regulate CBX7. Given that adipocytes are an integral component of the peritoneal cavity and the ovarian tumor microenvironment, we hypothesize that the adipose microenvironment is an important regulator of CBX7 expression.ResultsUsing conditioned media from human omental explants, we found that adipose-derived exosomes mediate CBX7 downregulation and enhance migratory potential of human ovarian cancer cells. Further, we identified adipose-derived exosomal miR-421 as a novel regulator of CBX7 expression and the main effector that downregulates CBX7.ConclusionIn this study, we identified miR-421 as a specific signaling pathway in the ovarian tumor microenvironment that can downregulate CBX7 to induce epigenetic change in OC cells, which can drive disease progression. These findings suggest that targeting exosomal miR-421 may curtail ovarian cancer progression.
Connecting Chromatin Structures to Gene Regulation Using Dynamic Polymer Simulations
Authors: Fu Yi , Zhao Tianxiao , Clark Finnegan , Nomikou Sofia , Tsirigos Aristotelis , Lionnet Timothée 
Published: November 2023

AbstractThe transfer of regulatory information between distal loci on chromatin is thought to involve physical proximity, but key biophysical features of these contacts remain unclear. For instance, it is unknown how close and for how long two loci need to be in order to productively interact. The main challenge is that it is currently impossible to measure chromatin dynamics with high spatiotemporal resolution at scale. Polymer simulations provide an accessible and rigorous way to test biophysical models of chromatin regulation, yet there is a lack of simple and general methods for extracting the values of model parameters. Here we adapt the Nelder-Mead simplex optimization algorithm to select the best polymer model matching a given Hi-C dataset, using theMYClocus as an example. The model’s biophysical parameters predict a compartmental rearrangement of theMYClocus in leukemia, which we validate with single-cell measurements. Leveraging trajectories predicted by the model, we find that loci with similar Hi-C contact frequencies can exhibit widely different contact dynamics. Interestingly, the frequency of productive interactions between loci exhibits a non-linear relationship with their Hi-C contact frequency when we enforce a specific capture radius and contact duration. These observations are consistent with recent experimental observations and suggest that the dynamic ensemble of chromatin configurations, rather than average contact matrices, is required to fully predict productive long-range chromatin interactions.