bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insights into the clinical impact of complete blood cell inflammatory markers on body composition variations and fatty liver grading in Iranian adults undergoing bariatric surgery: a retrospective longitudinal study
Authors: Radkhah Hanieh , Alirezaei Ali , Parhizkar Peyvand , Khalooeifard Razieh , Khoundabi Batoul , Najjari Khosrow , Talebpour Mohammad , Hajabi Reza 
Published: July 2024

Background:
In bariatric surgery, inflammatory biomarkers predict outcomes. Limited research on complete blood cell (CBC) markers stresses the need for correlation study. This research explores links between CBC inflammatory markers, body changes, and fatty liver grades in Iranian bariatric patients.

Materials and methods:
This retrospective longitudinal study examined 237 bariatric surgery patients who satisfied the inclusion criteria and were deemed eligible for participation. These criteria encompassed patients who had undergone sleeve or mini-bypass surgery and were aged between 18 and 65 years. The study gathered demographic data, pre and post-surgery changes in CBC inflammatory biomarkers [neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), and monocyte-to-lymphocyte ratio (MLR), mean platelet volume (MPV), MPV-to-platelet count ratio (MPV/PC), and red cell distribution width (RDW)] and fatty liver grades. Additionally, it recorded pre and post-surgery changes in body composition, such as weight, muscle mass (MM), fat mass (FM), and fat-free mass (FFM).

Results:
The pre-surgery RDW marker significantly associated with FM changes, highlighting its predictive nature. While no significant association was found between changes in patients’ fatty liver grade and baseline marker values, it’s worth noting that individuals with higher MM at 3 months achieved a fatty liver grade of zero. Also, at 6 months, higher FFM and MM were also associated with reaching a fatty liver grade of zero.

Conclusions:
While the retrospective design of this study limits its findings to existing clinical data, future prospective research should collect additional samples, extend the observation time, and examine the long-term predictive value of these markers.
Parent Perspectives on Social Risk Screening in the PICU*
Authors: Asp Rebecca A. , Paquette Erin T. 
Published: July 2024

OBJECTIVE:
Health inequities are widespread and associated with avoidable poor health outcomes. In the PICU, we are increasingly understanding how health inequities relate to critical illness and health outcomes. Experts recommend assessing for health inequities by screening for social determinants of health (SDOH) and adverse childhood experiences (ACEs); however, guidance on screening is limited and screening has not been universally implemented. Our study aimed to understand parent perspectives on screening for SDOH/ACEs in the PICU, with the primary objective of determining whether screening would be acceptable in this setting.

DESIGN:
We conducted a qualitative study using semistructured interviews with a convenience sample of eleven PICU parents between November 2021 and January 2022.

SETTING:
Urban, quaternary free-standing children’s hospital.

SUBJECTS:
Parents of children with a PICU hospitalization between November 2020 and October 2021.

INTERVENTIONS:
None.

MEASUREMENTS AND MAIN RESULTS:
Domains of interest included experience with and attitudes toward SDOH/ACEs screening, perspectives on addressing needs with/without resources and their relationship to health, and recommendations for screening. Interviews were transcribed verbatim and coded with an inductive approach using thematic analysis and constant comparative methods. Ann & Robert H. Lurie Children’s Institutional Review Board approved this study (2021- 4781, Approved September 13, 2021). Ten participants found SDOH/ACEs screening to be acceptable and valuable in the PICU, even for topics without a readily available resource. Participants did not have broad experience with ACEs screening, though all believed this provided the medical team with valuable context regarding their child. Ten participants recommended screening occur after their child has been stabilized and that they are notified that screening is universal.

CONCLUSIONS:
Participants found screening for SDOH/ACES to be acceptable and valuable in the PICU. Families have important insight that should be leveraged to improve the support of unmet needs through the development of strengths-based, parent-informed screening initiatives.
Multimodal Imaging Approach for Tumor Treatment Response Evaluation in the Era of Immunotherapy
Authors: Lee Geewon , Moon Seung Hwan , Kim Jong Hoon , Jeong Dong Young , Choi Jihwan , Choi Joon Young , Lee Ho Yun 
Published: July 2024

Abstract
Immunotherapy is likely the most remarkable advancement in lung cancer treatment during the past decade. Although immunotherapy provides substantial benefits, their therapeutic responses differ from those of conventional chemotherapy and targeted therapy, and some patients present unique immunotherapy response patterns that cannot be judged under the current measurement standards. Therefore, the response monitoring of immunotherapy can be challenging, such as the differentiation between real response and pseudo-response. This review outlines the various tumor response patterns to immunotherapy and discusses methods for quantifying computed tomography (CT) and 18F-fluorodeoxyglucose positron emission tomography (PET) in the field of lung cancer. Emerging technologies in magnetic resonance imaging (MRI) and non-FDG PET tracers are also explored. With immunotherapy responses, the role for imaging is essential in both anatomical radiological responses (CT/MRI) and molecular changes (PET imaging). Multiple aspects must be considered when assessing treatment responses using CT and PET. Finally, we introduce multimodal approaches that integrate imaging and nonimaging data, and we discuss future directions for the assessment and prediction of lung cancer responses to immunotherapy.
Three Molecular Developmental Pathways of Remnant Pancreatic Cancer after Resection
Authors: Suzuki Shuji , Omori Yuko , Ono Yusuke , Hirose Katsuya , Itoh Taito , Karasaki Hidenori , Shimoda Mitsugi , Nagakawa Yuichi , Higuchi Ryota , Endo Itaru , Rikiyama Toshiki , Unno Michiaki , Fujii Tsutomu , Sunagawa Yuki , Eguchi Hidetoshi , Sasanuma Hideki , Akahori Takahiro , Okano Keiichi , Tani Masaji , Hirano Satoshi , Shimizu Yasuhiro , Kitago Minoru , Mizuno Shugo , Yamamoto Tomohisa , Furukawa Masayuki , Ohtsuka Masayuki , Sugimoto Motokazu , Matsushita Akira , Hakamada Kenichi , Igarashi Hisato , Kuroki Tamotsu , Tanno Satoshi , Tsuji Yoshihisa , Masamune Atsushi , Mizumoto Kazuhiro , Hirooka Yoshiki , Yamaue Hiroki , Okazaki Kazuichi , Satoi Sohei , Takeyama Yoshifumi , Mizukami Yusuke , Furukawa Toru 
Published: July 2024

Objective:
This study aimed to clarify the molecular mechanism of remnant pancreatic cancer (PC) development after primary PC resection.

Summary Background Data:
Molecular mechanisms of the development of remnant PCs following primary PC resection are largely unknown.

Methods:
Forty-three patients undergoing remnant PC resection after primary PC resection between 2001 and 2017 at 26 institutes were retrospectively analyzed. Clinicopathological features and molecular alterations detected by targeted amplicon sequencing of 36 PC-associated genes were evaluated.

Results:
These patients showed significantly lower body mass indices and higher hemoglobin A1c values at remnant PC resection than at primary PC resection. A comparison of the molecular features between primary and remnant PCs indicated that remnant PCs were likely to develop via three different molecular pathways: successional, showing identical and accumulated alterations (n=14); phylogenic, showing identical and distinct alterations (n=26); and distinct, showing independent distinctive alterations (n=3). The similarity of gene alterations was associated with time to the remnant PC development (r=－0.384, P=0.0173). Phylogenic pathways were significantly associated with the intraductal spread of carcinoma (P=0.007). Patient survival did not differ significantly depending on these molecular pathways.

Conclusion:
Molecular profiling uncovered three pathways for the development of remnant PCs, namely, successional, phylogenic, and distinct pathways. The vast majority of remnant PCs are likely to be molecularly associated with primary PCs either in the successional or phylogenic way. This information could impact the design of a strategy for monitoring and treating remnant PCs.
Geographic Access to Urogynecology Care in the United States
Authors: Schmidt Eleanor M. , Ward Lucy , Gregory W. Thomas , Cichowski Sara B. 
Published: July 2024

Importance
Although access to urogynecologic care is known to influence patient outcomes, less is known regarding geographic access to care and how it may vary by population characteristics.

Objective
The primary objective of this study was to estimate geographic accessibility of urogynecologic services in terms of drive time and by population demographics.

Study Design
We performed a descriptive study using practice location data by zip code for all board-certified urogynecologists who are American Urogynecologic Society members (n = 497) and pelvic floor physical therapists (n = 985). Drive times from each zip code to the nearest health care professional zip code were calculated. These data were then overlaid onto a map of the continental United States. Race/ethnicity, age, education, poverty status, disability status, health insurance coverage, and rurality were compared across travel times.

Results
Of the 31,754 zip codes of the continental United States, 389 (1.23%) had at least 1 urogynecologist, and 785 (2.47%) had at least 1 pelvic floor physical therapist; 92.29 million women older than 35 years were represented in the demographic analyses. Seventy-nine percent of the studied population live within 1 hour of a urogynecologist, and 85% live within 1 hour of a pelvic floor physical therapist. Seven percent and 3% live >2 hours from urogynecologic services, respectively. Values for drive times to all health care professionals indicate that American Indian/Alaska Native individuals have a much greater travel burden than other racial/ethnic groups.

Conclusions
There are population groups with limited geographic access to urogynecologic services. Pelvic floor physical therapists are more geographically accessible to the population studied than urogynecologists.
Structural comparisons of human and mouse fungiform taste buds
Authors: High Brigit , Finger Thomas E. 
Published: July 2024

AbstractTaste buds are commonly studied in rodent models, but some differences exist between mice and humans in terms of gustatory mechanisms and sensitivities. Whether these functional differences are reflected in structural differences between species is unclear. Using immunofluorescent image stacks, we compared morphological and molecular characteristics of mouse and human fungiform taste buds. The results suggest that while the general features of fungiform taste buds are similar between mice and humans, several characteristics differ significantly. Human taste buds are larger and taller than those of mice, yet they contain similar numbers of taste cells. Taste buds in humans are more heavily innervated by gustatory nerve fibers expressing the purinergic receptor P2X3 showing a 40% higher innervation density than in mice. Like Type II cells of mice, a subset (about 30%) of cells in human taste buds is immunoreactive for PLCβ2. These PLCβ2-immunoreactive cells display CALHM1-immunoreactive puncta closely apposed to gustatory nerve fibers suggestive of channel-type synapses described in mice. These puncta, used as a measure of synaptic contact, are however significantly larger in humans compared to mice. Altogether these findings suggest that while many similarities exist in the structural organization of murine and human fungiform taste buds, significant differences do exist in taste bud size, innervation density, and size of synaptic contacts that may impact gustatory signal transmission.
Improving rigor and reproducibility in chromatin immunoprecipitation assay data analysis workflows with Rocketchip
Authors: Haghani Viktoria , Goyal Aditi , Zhang Alan , Sharifi Osman , Mariano Natasha , Yasui Dag , Korf Ian , LaSalle Janine 
Published: July 2024

AbstractAs genome sequencing technologies advance, the accumulation of sequencing data in public databases necessitates more robust and adaptable data analysis workflows. Here, we present Rocketchip, which aims to offer a solution to this problem by allowing researchers to easily compare and swap out different components of ChIP-seq, CUT&RUN, and CUT&Tag data analysis, thereby facilitating the identification of reliable analysis methodologies. Rocketchip enables researchers to efficiently process large datasets while ensuring reproducibility and allowing for the reanalysis of existing data. By supporting comparative analyses across different datasets and methodologies, Rocketchip contributes to the rigor and reproducibility of scientific findings. Furthermore, Rocketchip serves as a platform for benchmarking algorithms, allowing researchers to identify the most accurate and efficient analytical approaches to be applied to their data. In emphasizing reproducibility and adaptability, Rocketchip represents a significant step towards fostering robust scientific research practices.
Antibody-dependent DENV infection induces distinct transcriptomic responses in infected and bystander human macrophages
Authors: Hardy Céline S. C. , Wegman Adam D. , Waldran Mitchell J. , Waickman Adam T. 
Published: July 2024

ABSTRACTDengue virus (DENV) is a mosquito-borne flavivirus which coexists as four genetically and immunologically distinct serotypes (DENV1-4). In secondary heterologous DENV infection, pre-existing immunity is believed to contribute to severe disease through antibody dependent enhancement (ADE). Although the elevated pathology observed in ADE conditions has been described, the cell intrinsic mechanisms governing this process remain unclear. Using scRNAseq, we investigated the transcriptomic profiles of human monocyte-derived macrophages infected by DENV via ADE compared to conventional infection conditions. Unsupervised analysis of scRNAseq data enabled the identification and differentiation of infected and bystander/uninfected cells in a heterogeneous cell culture. Differential gene expression and Ingenuity Pathway analyses revealed a number of significantly up- and down-regulated genes and gene networks between cells infected by ADE compared to conventional infection. Specifically, these pathways indicated mechanisms such as suppressed interferon signaling and inflammatory chemokine transcription in cells infected via ADE. Further analysis revealed that transcriptomic changes were independent of viral RNA within infected cells, suggesting that the observed changes are reflective of cell-intrinsic responses and not simply a function of per-cell viral burden. Bystander cells in ADE conditions also demonstrated distinct profiles, indicating an immunologically activated phenotype enriched for the expression of gene networks involved with protein translation, cytokine production, and antigen presentation. Together, these findings support the concept that DENV infection via ADE induces a qualitatively different transcriptomic response in infected and bystander cells, contributing to our understanding of ADE as a mechanistic driver of disease and pathogenesis.IMPORTANCEDengue virus (DENV) is a mosquito-borne human pathogen with a significant and growing global health burden. Although correlates of severe dengue disease are poorly understood, pre-existing immunity to DENV has been associated with severe disease risk and known to contribute to an alternative route of viral entry termed antibody-dependent enhancement (ADE). Using single cell RNA sequencing, we identified distinct transcriptomic processes involved in antibody-mediated DENV entry compared to conventional receptor mediated entry. These data provide meaningful insight into the discrete processes contributing to DENV pathogenesis in ADE conditions.
T3SS translocon induces pyroptosis by direct interaction with NLRC4/NAIP inflammasome
Authors: Zhao Yan , Zhu Hanshuo , Li Jinqian , Xu Hang , Sun Li 
Published: July 2024

AbstractType III secretion system (T3SS) is a virulence apparatus existing in many bacterial pathogens. Structurally, T3SS consists of the base, needle, tip, and translocon. The NLRC4 inflammasome is the major receptor for T3SS needle and basal rod proteins. Whether other T3SS components are recognized by NLRC4 is unclear. In this study, usingEdwardsiella tardaas a model intracellular pathogen, we examined T3SS−inflammasome interaction and its effect on cell death.E. tardainduced pyroptosis in a manner that required the bacterial translocon and the host inflammasome proteins of NLRC4, NLRP3, ASC, and caspase 1/4. The translocon protein EseB triggered NLRC4/NAIP-mediated pyroptosis by binding NAIP via its C-terminal region, particularly the terminal 6 residues (T6R). EseB homologs exist widely in T3SS-positive bacteria and share high identities in T6R. LikeE. tardaEseB, all of the representatives of the EseB homologs exhibited T6R-dependent NLRC4 activation ability. Together these results revealed the function and molecular mechanism of EseB to induce host cell pyroptosis and suggested a highly conserved inflammasome-activation mechanism of T3SS translocon in bacterial pathogens.
Emergence of sympatric host-specific lineages of the fungal plant pathogenZymoseptoria passeriniiin natural ecosystems
Authors: Rojas-Barrera Idalia C. , Flores-Núñez Victor M. , Haueisen Janine , Alizadeh Alireza , Salimi Fatemeh , Stukenbrock Eva H. 
Published: July 2024

SummaryThe barley disease Septoria Speckled Leaf Blotch, caused by the fungal pathogenZymoseptoria passerinii,had its last outbreak in North America in the early 2000s. Although rare in agricultural settings, field sampling of wild grasses in the Middle East revealed the disease persistence in wild barley.Identification ofZ. passeriniiin distinct wild barley species led us to investigate signatures of host specialization using genomics to address the mode of emergence by host tracking or host range expansion. Furthermore, we applied virulence assays and confocal laser microscopy to evaluate if the disease development differs between wild and domesticated barley.Wild- and domesticated-host infecting populations have diverged, and phylogenetic relationships support the emergence of sympatric host-specific lineages. Cross-virulence assays showed thatZymoseptoriapasserinii from domesticated hosts infect domesticated barley and its wild ancestor,Hordeum spontaneum. However, wild isolates from Iran did not infect domesticated barley. Wild and domesticated pathosystems have similar disease timing and progression, suggesting its persistence in natural ecosystems might be tied to environmental conditions.The study supports that a wide range of hosts can foster the emergence of host-specific lineages in sympatry and provide novel insights into the evolution of understudied fungal pathogens on wild crop relatives.
High fat diet induces differential age- and gender-dependent changes in neuronal function linked to redox stress
Authors: de Lange Megan , Yarosh Vladyslava , Farell Kevin , Oates Caitlin , Patil Renee , Hawthorn Isabel , Jung Mok-Min , Wenje Sophie , Steinert Joern R 
Published: July 2024

AbstractThe prevalence of neurodegenerative diseases, such as Alzheimer’s disease and Parkinson’s disease, is steadily increasing, posing significant challenges to global healthcare systems. Emerging evidence suggests that dietary habits, particularly consumption of high-fat diets specify which fats, may play a pivotal role in the development and progression of neurodegenerative disorders. Moreover, several studies have shed light on the intricate communication between the gut and the brain, known as the gut-brain axis and its involvement in neurodegenerative processes.This study aims to assess the effects of a high-fat dietary intake on various aspects of neuronal function during aging and following gender separation to help understand the potential contributions of diet to neuronal function.To investigate the effects of a high-fat diet,Drosophila melanogasterwas used and exposed to standard normal food diet (NF) and high-fat diet (HF). Adults were grouped at 10 and 45 days of age in male and female flies reared under the same conditions. Multiple assays were conducted, showing differential gender- and HF diet-induced oxidative stress levels as determined by malondialdehyde (MDA) measurements, enhanced caspase-3 expression and reduced climbing activity. Adult lifespan under both dietary conditions was unchanged but odour-associated learning ability was reduced in larvae reared in a HF diet.This is the first study to characterise effects of diet on neuronal phenotypes in an age- and gender-specific manner in aDrosophilamodel. Our findings suggest a HF diet induces differential forms of neuronal dysfunction with age and sex-specific outcomes, characterised by enhanced oxidative stress and cell death which impacts on neuronal and behavioural functions.
Single-cell transcriptomics reveal differences between chorionic and basal plate cytotrophoblasts and trophoblast stem cells
Authors: Morey Robert , Soncin Francesca , Kallol Sampada , Sah Nirvay , Manalo Zoe , Bui Tony , Slamecka Jaroslav , Cheung Virginia Chu , Pizzo Don , Requena Daniela F. , Chang Ching-Wen , Farah Omar , Kittle Ryan , Meads Morgan , Horii Mariko , Fisch Kathleen , Parast Mana M. 
Published: July 2024

AbstractCytotrophoblast (CTB) of the early gestation human placenta are bipotent progenitor epithelial cells, which can differentiate into invasive extravillous trophoblast (EVT) and multinucleated syncytiotrophoblast (STB). Trophoblast stem cells (TSC), derived from early first trimester placentae, have also been shown to be bipotential. In this study, we set out to probe the transcriptional diversity of first trimester CTB and compare TSC to various subgroups of CTB. We performed single-cell RNA sequencing on six normal placentae, four from early (6-8 weeks) and two from late (12-14 weeks) first trimester, of which two of the early first trimester cases were separated into basal (maternal) and chorionic (fetal) fractions prior to sequencing. We also sequenced three TSC lines, derived from 6-8 week placentae, to evaluate similarities and differences between primary CTB and TSC. CTB clusters displayed notable distinctions based on gestational age, with early first trimester placentae showing enrichment for specific CTB subtypes, further influenced by origin from the basal or chorionic plate. Differential expression analysis of CTB from basal versus chorionic plate highlighted pathways associated with proliferation, unfolded protein response, and oxidative phosphorylation. We identified trophoblast states representing initial progenitor CTB, precursor STB, precursor and mature EVT, and multiple CTB subtypes. CTB progenitors were enriched in early first trimester placentae, with basal plate cells biased toward EVT, and chorionic plate cells toward STB, precursors. Clustering and trajectory inference analysis indicated that TSC were most like EVT precursor cells, with only a small percentage of TSC on the pre-STB differentiation trajectory. This was confirmed by flow cytometric analysis of 6 different TSC lines, which showed uniform expression of proximal column markers ITGA2 and ITGA5. Additionally, we found that ITGA5+ CTB could be plated in 2D, forming only EVT upon spontaneous differentiation, but failed to form self-renewing organoids; conversely, ITGA5-CTB could not be plated in 2D, but readily formed organoids. Our findings suggest that distinct CTB states exist in different regions of the placenta as early as six weeks gestation and that current TSC lines most closely resemble ITGA5+ CTB, biased toward the EVT lineage.