bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of Higher Intake of Plant-Based Foods and Protein With Slower Kidney Function Decline in Women With HIV
Authors: Banerjee Tanushree , Frongillo Edward A. , Turan Janet M. , Sheira Lila A. , Adedimeji Adebola , Wilson Tracey , Merenstein Daniel , Cohen Mardge , Adimora Adaora A. , Ofotokun Igho , Metsch Lisa , D'Souza Gypsyamber , Fischl Margaret A. , Fisher Molly C. , Tien Phyllis C. , Weiser Sheri D. 
Published: October 2023

Background:
We investigated whether there exists an association between dietary acid load and kidney function decline in women living with HIV (WLWH) receiving antiretroviral therapy (ART).

Setting:
One thousand six hundred eight WLWH receiving ART in the WIHS cohort with available diet data and a baseline estimated glomerular filtration rate (eGFR) ≥15 mL/minute/1.73 m2.

Methods:
A brief dietary instrument conducted from 2013 to 2016 under the Food Insecurity Sub-Study was used for assessing fruits and vegetables (FV) and protein intake. A mixed-effects model with random intercept and slope was used to estimate subjects' annual decline rate in eGFR and the association between FV intake and eGFR decline, adjusting for sociodemographics, serum albumin, comorbidities, time on ART, ART drugs, HIV markers, and baseline eGFR. We evaluated whether markers of inflammation mediated the effect of FV intake on decline in eGFR, using causal mediation analysis.

Results:
We found a dose–response relationship for the association of FV intake and eGFR decline, with lesser annual decline in eGFR in the middle and highest tertiles of FV intake. An increase of 5 servings of FV intake per day was associated with a lower annual eGFR decline (−1.18 [−1.43, −0.94]). On average, 39% of the association between higher FV intake and slower eGFR decline was explained by decreased levels of inflammation.

Conclusions:
Plant-rich diet was associated with slower decline in kidney function. Inflammation is a potential path through which diet may affect kidney function. The findings support an emerging body of literature on the potential benefits of plant-rich diets for prevention of chronic kidney disease.
Increasing Spiritual Beliefs are Associated With Lower HIV Incidence Among Black Men Who Have Sex With Men: Results From HPTN 061 Longitudinal Study
Authors: Ransome Yusuf , Taggart Tamara , Huang Amber Shu , Vermund Sten H. , Mayer Kenneth H. , Nunn Amy S. 
Published: October 2023

Background:
There is a limited understanding about the impact of spiritual beliefs and activities on HIV seroconversion among black men who have sex with men (BMSM), which we investigate in this study.

Setting:
United States.

Methods:
The HIV Prevention Trials Network Study 061 collected demographic and biomedical assessments among BMSM across 6 United States cities for longitudinal analysis. Spiritual beliefs and spiritual activities are constructed composite scales. Bivariate analyses among 894 who provided data at 12-month follow-up compared men who seroconverted to HIV between baseline and 6 months with those who remained uninfected with HIV at 12 months. Cox proportional hazard regression among 944 men tested spiritual beliefs and activities on the longitudinal risk of HIV seroconversion adjusting for age and any sexually transmitted infection (STI).

Results:
Among this sample, HIV incidence between baseline and 6 months was 1.69%, (95% confidence intervals [CI]: 1.04 to 2.77). Men who seroconverted to HIV were significantly younger than those who remained uninfected at the 12-month follow-up: (mean age 27, SD = 11 vs 37, SD = 12) and a higher proportion reported any STI (46.67% vs 11.39%, P < 0.01). A one-unit increase in spiritual beliefs was associated with lower hazard rate of seroconverting to HIV at follow-up [adjusted hazard ratio (aHR) = 0.37, 95% CI: = (0.16 to 0.87)]. Religious service attendance and spiritual activities were unrelated to seroconverting.

Conclusions:
Spirituality is important in the lives of BMSM. Biomedical and behavioral HIV prevention interventions should consider assessing spiritual beliefs in HIV care among BMSM.
Brief Report: Outcomes of Individuals Using HIV Postexposure Prophylaxis-In-Pocket (“PIP”) for Low-Frequency, High-Risk Exposures in Toronto, Canada
Authors: Billick Maxime J. , Fisher Karla N. , Myers Samantha , Tan Darrell H. S. , Bogoch Isaac I. 
Published: October 2023

Background:
HIV postexposure prophylaxis-in-pocket (“PIP”) is a self-initiated, event-driven HIV prevention modality for individuals with a low frequency of HIV exposures.

Methods:
A cohort of 111 patients using PIP as their primary HIV prevention modality was longitudinally evaluated for PIP self-initiation, HIV and sexual transmitted infections, and switching to other HIV prevention modalities between February 2016 and December 2022.

Results:
A total of 111 patients had 178.7 cumulative patient-years of PIP use. PIP was self-initiated 69 times by 35 (31.5%) individuals, with 0 HIV seroconversions identified. Thirty four individuals (30.6%) transitioned from PIP to pre-exposure prophylaxis and 33 individuals (29.7%) switched from pre-exposure prophylaxis to PIP.

Conclusions:
PIP is a useful addition to other pharmacologic HIV prevention tools, and may help prevent infection in those with a lower frequency of unanticipated HIV exposures.
Laparoscopic Inguinal Hernia Repair for Female Patients: Experience from a High-volume Center in 20 years
Authors: Lu Jingfeng , Zhao Xuan , Yue Fei , Xue Pei , Feng Bo , Chen Qian , Li Jianwen 
Published: October 2023

Background:
Although laparoscopic inguinal hernia repair (LIHR) is widely performed worldwide, few studies have focused on the procedure in female patients. This study investigated the characteristics and outcomes of female patients with inguinal hernias who underwent LIHR.

Materials and Methods:
This study retrospectively analyzed the data of 7380 patients with inguinal hernia admitted to the General Surgery Department of Ruijin Hospital and underwent LIHR from January 2001 to December 2020. The clinical characteristics, surgical outcomes, and complications were assessed.

Results:
In total, 572 female patients were enrolled in this study. The proportion of femoral hernias in female patients was higher in women than in male patients (17.4% vs. 0.3%, respectively). Mesothelial cysts of the round uterine ligament (MCURL) were noted in 74 patients. The mean age of patients with MCURL was lower than that of patients without MCURL (46.4 vs. 55.6, P=0.018). Seventy cases (93.3%) of MCURL were resected laparoscopically, and 5 cases were resected through an auxiliary small incision. The round ligament was cut off in 335 patients and preserved in 237. No significant differences were observed in the number of hospitalization days, recurrence rates, or complications between the transection and preservation groups. None of the cases were converted to laparotomy, and no recurrence was noted during follow-up.

Conclusion:
LIHR is safe and feasible in female patients. Treatment of femoral hernia, MCURL, and the round ligament of the uterus should be carefully considered during LIHR in female patients.
PD-L1 Restrains the PD-1hiNrp1loTGFβ+Treg to block IL6+Neutrophil tumor infiltration to Suppress Inflammation-driven Colorectal Cancer
Authors: Poschel Dakota B. , Klement John D. , Merting Alyssa D. , Lu Chunwan , Zhao Yang , Yang Dafeng , Xiao Wei , Zhu Huabin , Rajeshwari Ponnala , Toscano Michael , Jones Kimya , Madwani Kiran , Barrett Amanda , Bollag Roni J. , Fallon Padraic G. , Shi Huidong , Liu Kebin 
Published: October 2023

SummaryPD-L1 functions as a suppressor of T cell activation and colonic inflammation. The consequence of and mechanism underlying these opposite functions of PD-L1 in colorectal cancer remains unknown. We report that globalCd274deletion promotes inflammation-driven colorectal tumorigenesis. 16S rRNA and shotgun metagenomic sequencing revealed that loss of host PD-L1 leads to expansion of gutLigilactobacillus murinusand activation of the AhR pathway in tumor-bearing mice. scRNA-seq analysis revealed that PD-L1 regulates PD-189Nrp11215Treg, IL6+neutrophils, and B cells in colorectal tumor. Treg expresses high level of TGFβ to recruit IL6+neutrophils. IL6 inhibits activation of B and T cells. IL6 blockade or B cell activation via CD40 agonist increases CTL activation and suppresses colon tumor growth in vivo. Our findings determine that PD-L1 functions as a tumor suppressor in the context of inflammation-driven colorectal cancer and the PD-L1/L. murius/PD-189Nrp11215TGFβ+Treg/IL6+neutrophils pathway controls host cancer immunosurveillance and colorectal tumorigenesis.Key pointsGlobal deletion ofCd274promotes inflammation-driven colorectal tumorigenesis.Loss of PD-L1 increases gutL. murinusand activates AhR pathway in colorectal tumor.PD-1hiTGFβ+Nrp1loTreg recruits IL6+neutrophils to inhibit B and T cell function in colorectal tumor.L. murinusand tryptophan metabolites connect PD-L1 and colorectal tumor immunosurveillance.Graphic summary
Evidence of spatial regime shifts: contrasting spatial dynamics of three Atlantic cod (Gadusmorhua) populations in the North Sea
Authors: Cecapolli Enrico , Romagnoni Giovanni , Blöcker Alexandra M. , Möllmann Christian , Sguotti Camilla 
Published: October 2023

AbstractRecent scientific assessments have started to consider the presence of multiple populations of Atlantic cod (Gadus morhua) in the North Sea due to genetic evidence. The Atlantic cod stock as a whole has experienced a regime shift in the North Sea and is now considered to be in a persistent depleted state. Here we investigated if the regime shift detected for North Sea cod manifested differently across areas (South, North-West and Viking (North-East)), revealing different dynamics and recovery potential for the corresponding populations. Methods from change point analyses to stochastic cusp models were applied to detect the regime shifts. We found that cod in the Southern North Sea has undergone a regime shift and is now in a persistent depleted state. The Viking population is in a low state but with high resilience, making its dynamics more predictable and thus easier to manage. Finally, the north-western population did not show signs of a regime shift and is in a high biomass level. Several abiotic and biotic drivers (e.g. fishing, warming) contribute to these differences. Our study provides useful information for the restructuring of management units of cod in the North Sea and highlights the importance of looking at regime shifts spatially.
A fluid-walled microfluidic platform for human neuron microcircuits and directed axotomy
Authors: Nebuloni Federico , Do Quyen B. , Cook Peter R. , Walsh Edmond J. , Wade-Martins Richard 
Published: October 2023

AbstractIn our brains, different neurons make appropriate connections; however, there remain fewin vitromodels of such circuits. We use an open microfluidic approach to build and study neuronal circuitsin vitroin ways that fit easily into existing bio-medical workflows. Dumbbell-shaped circuits are built in minutes in standard Petri dishes; the aqueous phase is confined by fluid walls – interfaces between cell-growth medium and an immiscible fluorocarbon, FC40. Conditions are established that ensure post-mitotic neurons derived from human induced pluripotent stem cells (iPSCs) plated in one chamber of a dumbbell remain where deposited. After seeding cortical neurons on one side, axons grow through the connecting conduit to ramify amongst striatal neurons on the other – an arrangement mimicking unidirectional cortico-striatal connectivity. We also develop a moderate-throughput non-contact axotomy assay. Cortical axons in conduits are severed by a media jet; then, brain-derived neurotrophic factor and striatal neurons in distal chambers promote axon regeneration. As additional conduits and chambers are easily added, this opens up the possibility of mimicking complex neuronal networks, and screening drugs for their effects on connectivity.
An Automated and Robust Tool for Musculoskeletal and Finite Element Modeling of the Knee Joint
Authors: Esrafilian Amir , Chandra Shekhar S. , Gatti Anthony A. , Nissi Mikko , Mustonen Anne-Mari , Säisänen Laura , Reijonen Jusa , Nieminen Petteri , Julkunen Petro , Töyräs Juha , Saxby David J. , Lloyd David G. , Korhonen Rami K. 
Published: October 2023

AbstractObjectiveTo develop and assess an automatic and robust knee musculoskeletal finite element (MSK-FE) modeling pipeline.MethodsMagnetic resonance images (MRI) were used to train nnU-Net networks for auto-segmentation of knee bones (femur, tibia, patella, and fibula), cartilages (femur, tibia, and patella), menisci, and major knee ligaments. Two different MRI sequences were used to broaden applicability. Next, we created MSK-FE models of an unseen dataset using two MSK-FE modeling pipelines: template-based and auto-meshing. MSK models had personalized knee geometries with multi-degree-of-freedom elastic foundation contacts. FE models used fibril-reinforced poroviscoelastic swelling material models for cartilages and menisci.ResultsVolumes of knee bones, cartilages, and menisci did not significantly differ (p>0.05) across MRI sequences. MSK models estimated secondary knee kinematics during passive knee flexion tests consistent within vivoand simulation-based values from the literature. Between the template-based and auto-meshing FE models, estimated cartilage mechanics often differed significantly (p<0.05), though differences were <15% (considering peaks during walking), i.e., <1.5 MPa for maximum principal stress, <1 percentage point for collagen fibril strain, and <3 percentage points for maximum shear strain.ConclusionThe template-based modeling provided a more rapid and robust tool than the auto-meshing approach, while the estimated knee biomechanics were comparable. Nonetheless, the auto-meshing approach might provide more accurate estimates in subjects with distinct knee irregularities, e.g., cartilage lesions.SignificanceThe MSK-FE modeling tool provides a rapid, easy-to-use, and robust approach to investigating task- and person-specific mechanical responses of the knee cartilage and menisci, holding significant promise, e.g., in personalized rehabilitation planning.
MADAME: a user-friendly bioinformatic tool for data and metadata retrieval in microbiome research
Authors: Fumagalli Sara , Soletta Giulia , Agostinetto Giulia , Striani Manuel , Labra Massimo , Casiraghi Maurizio , Bruno Antonia 
Published: October 2023

AbstractMicrobiome research advancements have provided countless insights. Despite the massive amount of data currently stored in public repositories, these resources remain vastly underutilized due to the intricacy of data and metadata retrieval from these databases. However, leveraging data-driven approaches is crucial for microbiome research progress by overcoming variations between studies and identifying generalizable trends.We designed the open-access and user-friendly bioinformatic tool MADAME (MetADAta MicrobiomE) to streamline the data and metadata retrieval process. MADAME addresses the challenges posed by the public repositories’ current limitations, allowing users to retrieve publications associated with the accession codes of interest. Additionally, MADAME allows users to visually explore retrieved results through the generation of a comprehensive report with plots and statistics. These unique features of MADAME let users maximize their time and resources, enabling them to assess metadata suitability before pursuing data download. To showcase its diverse functionalities, we recreate several scenarios to meet the diverse requirements that researchers may have.
Epigenome erosion in Alzheimer’s disease brain cells and induced neurons
Authors: Wang Bang-An , Jones Jeffrey R. , Zhou Jingtian , Tian Wei , Wu Yue , Wang Wenliang , Berube Peter , Bartlett Anna , Castanon Rosa , Nery Joseph R. , Chen Huaming , Kenworthy Mia , Altshul Jordan , Valadon Cynthia , Wang Yichen , Kang Austin , Goodman Ryan , Liem Michelle , Claffey Naomi , O’Connor Caz , Metcalf Jeffrey , Luo Chongyuan , Gage Fred H. , Ecker Joseph R. 
Published: October 2023

ABSTRACTLate-onset Alzheimer’s disease (LOAD) is typically sporadic, correlated only to advanced age, and has no clear genetic risk factors. The sporadic nature of LOAD presents a challenge to understanding its pathogenesis and mechanisms. Here, we comprehensively investigated the epigenome of LOAD primary entorhinal cortex brain tissues via single-cell multi-omics technologies, simultaneously capturing DNA methylation and 3D chromatin conformation. We identified AD-specific DNA methylation signatures and found they interact with bivalent promoters of AD differentially expressed genes. In addition, we discovered global chromosomal epigenome erosion of 3D genome structure within and across brain cell types. Furthermore, to evaluate whether these age- and disease-dependent molecular signatures could be detected in thein vitrocellular models, we derived induced neurons (iNs) converted directly from AD patients’ fibroblasts and found a set of conserved methylation signatures and shared molecular processes. We developed a machine-learning algorithm to identify robust and consistent methylation signatures of LOADin vivoprimary brain tissues andin vitrofibroblast-derived iNs. The results recapitulate the age- and disease-related epigenetic features in iNs and highlight the power of epigenome and chromatin conformation for identifying molecular mechanisms of neuronal aging and generating biomarkers for LOAD.HIGHLIGHTAD-specific DNA methylation signatures are identified in entorhinal cortex brain cell typesThe AD differentially expressed genes linked with differentially methylated regions via loop interactions are enriched in a bivalent chromatin stateChromosomal epigenome erosion of 3D genome structures occurs in LOAD brain cell types.Shared and reliable methylation signatures are observed in bothin vitrocellular iN models and primary brain tissues.Machine learning models identify robust and reliable methylation loci as AD biomarkers across cell types.
Neural activity ramps in frontal cortex signal extended motivation during learning
Authors: Regalado Josue M. , Asensio Ariadna Corredera , Haunold Theresa , Toader Andrew C. , Li Yan Ran , Neal Lauren A. , Rajasethupathy Priya 
Published: October 2023

SUMMARYLearning requires the ability to link actions to outcomes. How motivation facilitates learning is not well understood. We designed a behavioral task in which mice self-initiate trials to learn cue-reward contingencies and found that the anterior cingulate region of the prefrontal cortex (ACC) contains motivation-related signals to maximize rewards. In particular, we found that ACC neural activity was consistently tied to trial initiations where mice seek to leave unrewarded cues to reach reward-associated cues. Notably, this neural signal persisted over consecutive unrewarded cues until reward associated cues were reached, and was required for learning. To determine how ACC inherits this motivational signal we performed projection specific photometry recordings from several inputs to ACC during learning. In doing so, we identified a ramp in bulk neural activity in orbitofrontal cortex (OFC) -to-ACC projections as mice received unrewarded cues, which continued ramping across consecutive unrewarded cues, and finally peaked upon reaching a reward associated cue, thus maintaining an extended motivational state. Cellular resolution imaging of OFC confirmed these neural correlates of motivation, and further delineated separate ensembles of neurons that sequentially tiled the ramp. Together, these results identify a mechanism by which OFC maps out task structure to convey an extended motivational state to ACC to facilitate goal-directed learning.
High-density recording reveals sparse clusters (but not columns) for shape and texture encoding in macaque V4
Authors: Namima Tomoyuki , Kempkes Erin , Zamarashkina Polina , Owen Natalia , Pasupathy Anitha 
Published: October 2023

AbstractMacaque area V4 includes neurons that exhibit exquisite selectivity for visual form and surface texture, but their functional organization across laminae is unknown. We used high-density Neuropixels probes in two awake monkeys to characterize shape and texture tuning of dozens of neurons simultaneously across layers. We found sporadic clusters of neurons that exhibit similar tuning for shape and texture: ∼20% exhibited similar tuning with their neighbors. Importantly, these clusters were confined to a few layers, seldom ‘columnar’ in structure. This was the case even when neurons were strongly driven, and exhibited robust contrast invariance for shape and texture tuning. We conclude that functional organization in area V4 is not columnar for shape and texture stimulus features and in general organization maybe at a coarse scale (e.g. encoding of 2D vs 3D shape) rather than at a fine scale in terms of similarity in tuning for specific features (as in the orientation columns in V1). We speculate that this may be a direct consequence of the great diversity of inputs integrated by V4 neurons to build variegated tuning manifolds in a high-dimensional space.Significance StatementIn primary visual cortex of the macaque monkey, studies have demonstrated columnar functional organization, i.e. shared tuning across layers for stimulus orientation, spatial frequency, ocular dominance, etc. In mid and higher level visual form processing stages, where neurons exhibit high-dimensional tuning, functional organization has been harder to evaluate. Here, leveraging the use of the high-density Neuropixels probes to record simultaneously from dozens of neurons across cortical layers, we demonstrate that functional organization is not columnar for shape and texture tuning in area V4, a midlevel stage critical for form processing. Our results contribute to the debate about the functional significance of cortical columns providing support to the idea that they emerge due to one-to-many representational expansion.
NCOR1+/CD4+ T cells in tertiary lymphoid organs suppresses tumor growth and predicts favourable prognosis in pancreatic ductal adenocarcinoma
Authors: Dong Tiangeng , Yi Tuo , Gong Yuda , Gao Weidong , Zhang Bo , Sheng Weizhong 
Published: October 2023

AbstractCD4+ T cells have critical roles in anti-tumour immunity and its differentiation is known to be regulated by the nuclear receptor co-repressor 1 (NCOR1). Previous studies suggested that high CD4+ T cells are associated with a favourable prognosis in patients with pancreatic ductal adenocarcinoma (PDAC). However, the prognostic significance of NCOR1 in PDAC is still missing. In this study, the pathological impact of NCOR1 and CD4 has been analysed by multiplex immunohistochemistry in 100 PADC patients. NCOR1 expression in tertiary lymphoid organs is positively associated with the good prognosis of PDAC patients, while its expression in tumour tissue is not. Furthermore, the presence of NCOR1+/CD4+ T cells in tertiary lymphoid organs predicts a favourable prognosis in PDAC. Mechanistically, upregulation of NCOR1 expression in CD4+ T cells increases the release of TNF-α, which induces the apoptosis of the tumor cellsin vitro. Together, our data highlighted the tumour suppressive role of NCOR1+/CD4+ T cells in PDAC.