bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unveiling Cellular Diversity in the Buffalo Corneal Stroma: Insights into Telocytes and Keratocytes Using Light Microscope, Transmission Electron Microscope, and Immunofluorescence Analysis
Authors: Rashwan Ahmed M , Alsafy Mohamed A M , El-Gendy Samir A A , El-Mansi Ahmed A , Ez Elarab Samar M 
Published: November 2023

Abstract
Telocytes and keratocytes are important cells that maintain the structure and function of the cornea. The buffalo cornea, known for its resilience in harsh conditions, has not been extensively studied regarding the presence and role of telocytes and keratocytes. We used light microscopy, transmission electron microscopy (TEM), and immunofluorescence assays with platelet-derived growth factor receptor alpha (PDGFRα), CD34, and Vimentin markers to investigate their expression and localization in the cornea. TEM analysis confirmed the presence of spindle-shaped keratocytes with intercellular connections, while telocytes exhibited small spindle-shaped bodies with long, thin branches connecting to corneal keratocytes. Immunofluorescence findings showed that CD34 was more abundant near the endothelium, Vimentin was prominently expressed near the epithelium, and PDGFRα was uniformly distributed throughout the corneal stroma. Co-expression of CD34 and Vimentin, PDGFRα and Vimentin, as well as CD34 and PDGFRα, was observed in keratocytes and telocytes within the stroma, indicating the potential presence of mesenchymal cells. These results suggest the involvement of telocytes and keratocytes in corneal wound healing, transparency maintenance, and homeostasis. The co-expression of these markers highlights the critical role of telocytes and keratocytes in regulating corneal physiological functions, further enhancing our understanding of corneal biology in the buffalo model.
Convergence of halo statistics: code comparison between rockstar and compaso using scale-free simulations
Authors: Maleubre Sara , Eisenstein Daniel J , Garrison Lehman H , Joyce Michael 
Published: November 2023

ABSTRACT
In this study, we perform a halo-finder code comparison between rockstar and compaso. Based on our previous analysis aiming at quantifying resolution of N-body simulations by exploiting large (up to N = 40963) simulations of scale-free cosmologies run using abacus, we focus on convergence of the halo mass function, two-point correlation function, and mean radial pairwise velocities of halo centres selected with the aforementioned two algorithms. We establish convergence, for both rockstar and compaso, of mass functions at the 1 per cent precision level and of the mean pairwise velocities (and also two-point correlation function) at the 2 per cent level. At small scales and masses, we find that rockstar exhibits greater self-similarity. We also highlight the role played by the merger-tree post-processing of compaso haloes on their convergence. Finally, we give resolution limits expressed as a minimum particle number per halo in a form that can be directly extrapolated to Lambda cold dark matter.
DegronMD: Leveraging Evolutionary and Structural Features for Deciphering Protein-Targeted Degradation, Mutations, and Drug Response to Degrons
Authors: Xu Haodong , Hu Ruifeng , Zhao Zhongming 
Published: November 2023

Abstract
Protein-targeted degradation is an emerging and promising therapeutic approach. The specificity of degradation and the maintenance of cellular homeostasis are determined by the interactions between E3 ubiquitin ligase and degradation signals, known as degrons. The human genome encodes over 600 E3 ligases; however, only a small number of targeted degron instances have been identified so far. In this study, we introduced DegronMD, an open knowledgebase designed for the investigation of degrons, their associated dysfunctional events, and drug responses. We revealed that degrons are evolutionarily conserved and tend to occur near the sites of protein translational modifications, particularly in the regions of disordered structure and higher solvent accessibility. Through pattern recognition and machine learning techniques, we constructed the degrome landscape across the human proteome, yielding over 18,000 new degrons for targeted protein degradation. Furthermore, dysfunction of degrons disrupts the degradation process and leads to the abnormal accumulation of proteins; this process is associated with various types of human cancers. Based on the estimated phenotypic changes induced by somatic mutations, we systematically quantified and assessed the impact of mutations on degron function in pan-cancers; these results helped to build a global mutational map on human degrome, including 89,318 actionable mutations that may induce the dysfunction of degrons and disrupt protein degradation pathways. Multiomics integrative analysis unveiled over 400 drug resistance events associated with the mutations in functional degrons. DegronMD, accessible at https://bioinfo.uth.edu/degronmd, is a useful resource to explore the biological mechanisms, infer protein degradation, and assist with drug discovery and design on degrons.
Aspartate Aminotransferase/Platelet Ratio Index Upon Admission Predicts 24-Week Mortality in Patients With HIV-Associated Talaromyces marneffei
Authors: Wang Qi , Zhao Handan , Tong Yong , Qin Jiaying , Zhou Minghan , Xu Lijun 
Published: November 2023

Abstract

Background
A high aspartate aminotransferase/platelet ratio index (APRI) predicts mortality in patients with severe infection. This study aims to assess the potential of APRI as a predictor for mortality in patients with HIV-associated Talaromyces marneffei (HTM).

Methods
Associations between APRI and CD4 count, white blood cell count, C-reactive protein (CRP) level, procalcitonin (PCT) level, and cytokines were assessed in 119 patients. Univariate and multivariate Cox regression models were used to predict APRI on 24-week mortality.

Results
APRI was positively associated with CRP (r = 0.190, P = .039), PCT (r = 0.220, P = .018), interleukin 6 (r = 0.723, P &lt; .001), interleukin 10 (r = 0.416, P = .006), and tumor necrosis factor α (r = 0.575, P &lt; .001) and negatively associated with CD4 count (r = −0.234, P = .011). In total, 20.2% (24/119) of patients died within the 24-week follow-up. The 24-week survival rate was 88.0% for patients with APRI &lt;5.6% and 61.1% for those with APRI ≥5.6 (log-rank P &lt; .001). After adjustment for sex, age, body mass index, and CD4 count, as well as serum levels of hemoglobin, APRI ≥5.6 (adjusted hazard ratio [95% CI]; 3.0 [1.2–7.1], P = .015), PCT ≥1.7 ng/mL (3.7 [1.5–9.6], P = .006), and non–amphotericin B deoxycholate treatment (2.8 [1.2–6.6], P = .018) were independent risk factors for 24-week mortality.

Conclusions
For patients with HTM, APRI is associated with severity and is an independent risk factor for 24-week mortality.
How will climate change affect ambient air pollution and what can policy-makers do now? Lessons from India
Authors: Ebenstein Avraham , Bansal Sangeeta , Dey Sagnik , Gupta Tanya , Abhay Kakade Kshitij , Simhon Avi 
Published: November 2023

Abstract
Air pollution is a growing concern in India, and its adverse health effects are well documented. Climate change is likely to exacerbate this problem by altering weather patterns and increasing the frequency and severity of extreme events. This paper examines the potential impact of climate change on ambient air pollution in India and its implications for policy design. Our analysis reveals that pollution in India is highly sensitive to variation in weather, particularly in the densely populated Indus-Gangetic Plain. Using our estimated relationship between weather and pollution, we predict that changing weather patterns will increase average PM2.5 concentrations by 3.1 µg/m3, leading to a loss of 364 million years of life expectancy. To address this challenge, we propose an emissions fee calibrated to be highest in regions most vulnerable to persistently high levels of pollution and most sensitive to future deterioration in air quality due to climate change.
How may solar geoengineering impact global prospects for climate change mitigation?
Authors: Ricke Katharine , Harding Anthony 
Published: November 2023

Abstract
As disruptions from climate change increase, so will the urgency to find shorter-term approaches to ameliorating its harms. This may include calls to implement solar geoengineering, an approach to cooling the planet by reflecting incoming sunlight back to space. While the exact effects of solar geoengineering are still highly uncertain, physical science to date suggests that it may be effective at reducing many aspects of climate change in the short term. One of the biggest concerns about solar geoengineering is the extent to which it may interfere with crucial emissions reductions policies, i.e. mitigation. There are multiple channels by which geoengineering could alter mitigation pathways, both financial and behavioural. Here we define three such linkages and present the evidence available to constrain their potential magnitudes. Because solar geoengineering is not a substitute for mitigation, policies to develop or implement technologies that could be used to carry it out should be designed to accentuate its complementary nature to mitigation and deter the possibility it is used to delay decarbonizing the economy.
Transcription factor PpNAC1 and DNA demethylase PpDML1 synergistically regulate peach fruit ripening
Authors: Cao Xiangmei , Li Xinzhao , Su Yike , Zhang Chi , Wei Chunyan , Chen Kunsong , Grierson Donald , Zhang Bo 
Published: November 2023

Abstract
Fruit ripening is accompanied by dramatic changes in color, texture, and flavor and is regulated by transcription factors (TFs) and epigenetic factors. However, the detailed regulatory mechanism remains unclear. Gene expression patterns suggest that PpNAC1 (NAM/ATAF1/2/CUC) TF plays a major role in peach (Prunus persica) fruit ripening. DNA affinity purification (DAP)-seq combined with transactivation tests demonstrated that PpNAC1 can directly activate the expression of multiple ripening-related genes, including ACC synthase1 (PpACS1) and ACC oxidase1 (PpACO1) involved in ethylene biosynthesis, pectinesterase1 (PpPME1), pectate lyase1 (PpPL1), and polygalacturonase1 (PpPG1) related to cell wall modification, and lipase1 (PpLIP1), fatty acid desaturase (PpFAD3-1), and alcohol acyltransferase1 (PpAAT1) involved in volatiles synthesis. Overexpression of PpNAC1 in the tomato (Solanum lycopersicum) nor (nonripening) mutant restored fruit ripening, and its transient overexpression in peach fruit induced target gene expression, supporting a positive role of PpNAC1 in fruit ripening. The enhanced transcript levels of PpNAC1 and its target genes were associated with decreases in their promoter mCG methylation during ripening. Declining DNA methylation was negatively associated with increased transcripts of DNA demethylase1 (PpDML1), whose promoter is recognized and activated by PpNAC1. We propose that decreased methylation of the promoter region of PpNAC1 leads to a subsequent decrease in DNA methylation levels and enhanced transcription of ripening-related genes. These results indicate that positive feedback between PpNAC1 and PpDML1 plays an important role in directly regulating expression of multiple genes required for peach ripening and quality formation.
Optimizing ancestral trait reconstruction of large HIV Subtype C datasets through multiple-trait subsampling
Authors: Li Xingguang , Trovão Nídia S , Wertheim Joel O , Baele Guy , de Bernardi Schneider Adriano 
Published: November 2023

Abstract
Large datasets along with sampling bias represent a challenge for phylodynamic reconstructions, particularly when the study data are obtained from various heterogeneous sources and/or through convenience sampling. In this study, we evaluate the presence of unbalanced sampled distribution by collection date, location, and risk group of human immunodeficiency virus Type 1 Subtype C using a comprehensive subsampling strategy and assess their impact on the reconstruction of the viral spatial and risk group dynamics using phylogenetic comparative methods. Our study shows that a most suitable dataset for ancestral trait reconstruction can be obtained through subsampling by all available traits, particularly using multigene datasets. We also demonstrate that sampling bias is inflated when considerable information for a given trait is unavailable or of poor quality, as we observed for the trait risk group. In conclusion, we suggest that, even if traits are not well recorded, including them deliberately optimizes the representativeness of the original dataset rather than completely excluding them. Therefore, we advise the inclusion of as many traits as possible with the aid of subsampling approaches in order to optimize the dataset for phylodynamic analysis while reducing the computational burden. This will benefit research communities investigating the evolutionary and spatio-temporal patterns of infectious diseases.
A revision of the higher latitude periwinkle species Laevilitorina caliginosa sensu lato
Authors: Rosenfeld Sebastián , Segovia Nicolás I , Maturana Claudia S , Aldea Cristián , Saucède Thomas , Brickle Paul , Spencer Hamish G , Poulin Elie , González-Wevar Claudio A 
Published: November 2023

Abstract
The marine gastropod genus Laevilitorina is exclusive to the Southern Hemisphere, with 21 species from southern South America, Antarctica, Australia, New Zealand, and sub-Antarctic Islands. We present a comprehensive revision of Laevilitorina, using molecular and morphological analyses, to address formally the interspecific divergences within the nominal taxon Laevilitorina caliginosa s.l. We confirm the validity of L. caliginosa and Laevilitorina venusta, and we demonstrate that specimens from the Strait of Magellan and Hornos Island constitute four new species here described: Laevilitorina magellanica sp. nov., Laevilitorina pepita sp. nov., Laevilitorina fueguina sp. nov., and Laevilitorina hicana sp. nov. All six species are clearly distinguishable genetically, morphologically, and through radular tooth shape and configurations. Laevilitorina venusta is broadly distributed across the Antarctic Peninsula, South Georgia, and sub-Antarctic Islands (Marion, Crozet, Kerguelen, and Macquarie), whereas L. caliginosa s.s. appears geographically restricted to Cape Horn, the Falkland/Malvinas Islands, and South Georgia. The identification of populations from Macquarie Island as L. caliginosa is dubious; we suggest that these records are likely to pertain to L. venusta. This detailed revision of Laevilitorina, whereby hidden diversity was detected, significantly enriches our knowledge of the evolutionary history of this group.
Health-Related Quality of Life in Patients With Ventricular Assist Device
Authors: Spielmann Hannah , Tigges-Limmer Katharina , Albert Wolfgang , Spitz-Köberich Christine , Semmig-Könze Sandra , Staus Paulina ,   on behalf of the Selma Study Group, Herrmann-Lingen Christoph , Sandau Kristin E. , Okeson Brynn , Geyer Siegfried , Kugler Christiane 
Published: November 2023

Background
Ventricular assist device (VAD) implantation has become an alternative treatment for patients with end-stage heart failure. In Germany, valid and reliable instruments to assess health-related quality of life in patients with VAD are lacking.

Objective
The aim of this study was to present the psychometric validation of the German version of the Quality of Life with a Ventricular Assist Device questionnaire.

Methods
In a multicenter, cross-sectional study, 393 participants (mean age, 58.3 years; 85.8% male, 60.3% bridge to transplant, and 72.8% living with VAD for ≤2 years) completed the German Quality of Life with a Ventricular Assist Device questionnaire of physical, emotional, social, cognitive, and meaning/spiritual domains. Item and confirmatory factor analyses were conducted to test item difficulty and discrimination and the underlying structure, respectively. To examine internal consistency, Cronbach α was assessed. Convergent construct validity was tested using the Kansas City Cardiomyopathy Questionnaire and the Patient Health Questionnaire-9. Readability was examined using Flesch Reading Ease index and Vienna Factual Text Formula.

Results
The Quality of Life with a Ventricular Assist Device showed reasonable item difficulty (P
total = .67) and mostly moderate to high discriminatory power (r
it > 0.30). In confirmatory factor analysis, root-mean-square error of approximation (0.07) was acceptable for model fit, but no other indices. Acceptable internal consistency was found (α ≥ 0.79), with the exception of the cognitive domain (α = 0.58). The overall questionnaire and single domains demonstrated convergent validity (r ≥ 0.45, P < .001). The questionnaire showed adequate readability (Flesch Reading Ease, 64.11; Vienna Factual Text Formula, 6.91).

Conclusion
Findings indicate a promising standardized clinical instrument to assess health-related quality of life in patients with VAD.
Effects of cardiac rehabilitation on inflammatory biomarkers in unstable ischemic heart disease patients following percutaneous coronary intervention: a randomized controlled study
Authors: Awada Mohamad , Sanaei Shahin , Jameie Mana , Rahnamoun Zahra 
Published: November 2023

Introduction
Several blood inflammatory markers, such as high-sensitivity C-reactive protein (hs-CRP), neutrophil-to-lymphocyte ratio (NLR), and platelet-to-lymphocyte ratio (PLR), are linked to increased risk for cardiovascular diseases. This study aimed to evaluate these inflammatory markers after cardiac rehabilitation (CR) in patients with unstable ischemic heart disease (UIHD) who underwent successful percutaneous coronary intervention (PCI).

Methods
A cohort of 115 patients with successful PCI due to UIHD enrolled in the study from January 2018 to March 2021. We used a permuted block stratified randomization technique (2 : 1 ratio). Seventy-seven patients were randomized to the CR group and 38 patients to the control group. The CR group underwent a 12-week pre-specified CR regimen. Blood samples were taken at baseline and follow-up at 12 weeks for both groups.

Result
Among the 115 patients, 33 patients were female. The mean age was (53 ± 5.55 years) in the control and (53 ± 6.09 years) in the CR group. The two groups were comparable regarding their baseline characteristics and the values of the inflammatory markers. By contrast, at 12 weeks, the inflammatory marker values were significantly lower in the CR group compared to the control group; hs-CRP: 0.11 [0.08–0.14] vs. 0.21 [0.19–0.21], P-value <0.001; NLR: 2.17 [1.42–2.43] vs. 2.26 [2.07–2.6], P-value: 0.016; PLR: 91.2821 [63.3333–103.2000] vs. 92.600 [84.6154–110.0000], P-value: 0.027.

Conclusion
CR after PCI in UIHD patients may attenuate some inflammatory markers, which might benefit cardiovascular health. Further studies are required to evaluate these findings with longer follow-up and the powered to measure major cardiovascular event rates.
Early recovery of leukocyte subsets is associated with progression-free survival in patients with inoperable stage III NSCLC after multimodal treatment: a prospective explorative study
Authors: Hofer Thomas P. , Nieto Alexander E. , Käsmann Lukas , Pelikan Carolyn J. , Taugner Julian , Mathur Saloni , Eze Chukwuka , Belka Claus , Manapov Farkhad , Nößner Elfriede 
Published: November 2023

AbstractBackgroundWe explored the dynamic changes of major leukocyte subsets during definitive treatment of patients with inoperable stage III NSCLC lung cancer and correlated it to survival to identify subpopulations associated with maximal patient benefit.MethodsWe analyzed peripheral blood of 20 patients, either treated with thoracic radiotherapy (RT), concurrent chemo-radiotherapy (cCRT), or cCRT with additional immune-checkpoint inhibition therapy. Blood samples were collected at 9 timepoints before, during, and up to 1 year post treatment and analyzed by multi-color flow cytometry. Statistical analysis was conducted for leukocyte subpopulations, IL-6, progression-free survival (PFS) and overall survival (OS).ResultsIncrease of absolute lymphocyte counts (ALC) after the end of RT until 6 months thereafter was a predictor of PFS. Baseline lymphocyte counts showed no significant correlation to PFS or OS. Early recovery of absolute counts (AC) at 3 weeks after RT, total CD3+ T-cells, and CD8+ cytotoxic T-cells distinguished those patients with favorable PFS (≥12 months) from all other patients. Discriminant analysis identified B-cells, neutrophil-lymphocyte-ratio (NLR), CD4+ T-helper-cells, and NK-cells as predictors of favorable PFS. High variability in IL-6 plasma concentration of consecutive measurements within 6 months after the end of RT correlated negatively with PFS.ConclusionOur results suggest that two parameters commonly assessed in clinical routine, can be used to predict patient outcome. These are: early increase in CD8+ T-cell lymphocyte-count and variability in IL-6 plasma concentration, that are correlated to patients with favorable, respectively, poor outcome after definitive therapy independent of treatment regimen.HighlightsEarly increase within 3 weeks after thoracic radiation therapy (TRT) of CD8+ T cells is associated with favorable progression free survival (PFS).Low standard deviation in IL-6 plasma concentration in consecutive measurements after TRT is associated with favorable PFS.Absolute lymphocyte counts at treatment begin had no predictive value for treatment outcome.Funding statementnone