bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of long-range chromatin contacts, compartments and looping between mouse embryonic stem cells, lens epithelium and lens fibers
Authors: Camerino Michael , Chang William , Cvekl Ales 
Published: April 2024

Abstract
Background
Nuclear organization of interphase chromosomes involves individual chromosome territories, “open” and “closed” chromatin compartments, topologically associated domains (TADs) and chromatin loops. The DNA- and RNA-binding transcription factor CTCF together with the cohesin complex serve as major organizers of chromatin architecture. Cellular differentiation is driven by temporally and spatially coordinated gene expression that requires chromatin changes of individual loci of various complexities. Lens differentiation represents an advantageous system to probe transcriptional mechanisms underlying tissue-specific gene expression including high transcriptional outputs of individual crystallin genes until the mature lens fiber cells degrade their nuclei.

Results
Chromatin organization between mouse embryonic stem (ES) cells, newborn (P0.5) lens epithelium and fiber cells were analyzed using Hi-C. Localization of CTCF in both lens chromatins was determined by ChIP-seq and compared with ES cells. Quantitative analyses show major differences between number and size of TADs and chromatin loop size between these three cell types. In depth analyses show similarities between lens samples exemplified by overlaps between compartments A and B. Lens epithelium-specific CTCF peaks are found in mostly methylated genomic regions while lens fiber-specific and shared peaks occur mostly within unmethylated DNA regions. Major differences in TADs and loops are illustrated at the ~ 500 kb Pax6 locus, encoding the critical lens regulatory transcription factor and within a larger ~ 15 Mb WAGR locus, containing Pax6 and other loci linked to human congenital diseases. Lens and ES cell Hi-C data (TADs and loops) together with ATAC-seq, CTCF, H3K27ac, H3K27me3 and ENCODE cis-regulatory sites are shown in detail for the Pax6, Sox1 and Hif1a loci, multiple crystallin genes and other important loci required for lens morphogenesis. The majority of crystallin loci are marked by unexpectedly high CTCF-binding across their transcribed regions.

Conclusions
Our study has generated the first data on 3-dimensional (3D) nuclear organization in lens epithelium and lens fibers and directly compared these data with ES cells. These findings generate novel insights into lens-specific transcriptional gene control, open new research avenues to study transcriptional condensates in lens fiber cells, and enable studies of non-coding genetic variants linked to cataract and other lens and ocular abnormalities.
Unraveling the interplay of ferroptosis and immune dysregulation in diabetic kidney disease: a comprehensive molecular analysis
Authors: Jiao Yuanyuan , Liu Xinze , Shi Jingxuan , An Jiaqi , Yu Tianyu , Zou Guming , Li Wenge , Zhuo Li 
Published: April 2024

Abstract
Background
Diabetic kidney disease (DKD) is a primary microvascular complication of diabetes with limited therapeutic effects. Delving into the pathogenic mechanisms of DKD and identifying new therapeutic targets is crucial. Emerging studies reveal the implication of ferroptosis and immune dysregulation in the pathogenesis of DKD, however, the precise relationship between them remains not fully elucidated. Investigating their interplay is pivotal to unraveling the pathogenesis of diabetic kidney disease, offering insights crucial for targeted interventions and improved patient outcomes.

Methods
Integrated analysis, Consensus clustering, Machine learning including Generalized Linear Models (GLM), RandomForest (RF), Support Vector Machine (SVM) and Extreme Gradient Boosting (xGB), Artificial neural network (ANN) methods of DKD glomerular mRNA sequencing were performed to screen DKD-related ferroptosis genes.CIBERSORT, ESTIMATE and ssGSEA algorithm were used to assess the infiltration of immune cells between DKD and control groups and in two distinct ferroptosis phenotypes. The ferroptosis hub genes were verified in patients with DKD and in the db/db spontaneous type 2 diabetes mouse model via immunohistochemical and Western blotting analyses in mouse podocyte MPC5 and mesangial SV40-MES-13 cells under high-glucose (HG) conditions.

Results
We obtained 16 differentially expressed ferroptosis related genes and patients with DKD were clustered into two subgroups by consensus clustering. Five ferroptosis genes (DUSP1,ZFP36,PDK4,CD44 and RGS4) were identified to construct a diagnostic model with a good diagnosis performance in external validation. Analysis of immune infiltration revealed immune heterogeneity between DKD patients and controls.Moreover, a notable differentiation in immune landscape, comprised of Immune cells, ESTIMATE Score, Immune Score and Stromal Score was observed between two FRG clusters. GSVA analysis indicated that autophagy, apoptosis and complement activation can participate in the regulation of ferroptosis phenotypes. Experiment results showed that ZFP36 was significantly overexpressed in both tissue and cells while CD44 was on the contrary.Meanwhile,spearman analysis showed both ZFP36 and CD44 has a strong correlation with different immune cells,especially macrophage.

Conclusion
The regulation of the immune landscape in DKD is significantly influenced by the focal point on ferroptosis. Newly identified ferroptosis markers, CD44 and ZFP36, are poised to play essential roles through their interactions with macrophages, adding substantial value to this regulatory landscape.
Mutation analysis of BCR-ABL1 kinase domain in chronic myeloid leukemia patients with tyrosine kinase inhibitors resistance: a Malaysian cohort study
Authors: Seman Zahidah Abu , Ahid Fadly , Kamaluddin Nor Rizan , Sahid Ermi Neiza Mohd , Esa Ezalia , Said Siti Shahrum Muhamed , Azman Norazlina , Mat Wan Khairull Dhalila Wan , Abdullah Julia , Ali Nurul Aqilah , Khalid Mohd Khairul Nizam Mohd , Yusoff Yuslina Mat 
Published: April 2024

Abstract
Objective
Mutational analysis of BCR::ABL1 kinase domain (KD) is a crucial component of clinical decision algorithms for chronic myeloid leukemia (CML) patients with failure or warning responses to tyrosine kinase inhibitor (TKI) therapy. This study aimed to detect BCR::ABL1 KD mutations in CML patients with treatment resistance and assess the concordance between NGS (next generation sequencing) and Sanger sequencing (SS) in detecting these mutations.

Results
In total, 12 different BCR::ABL1 KD mutations were identified by SS in 22.6% (19/84) of patients who were resistant to TKI treatment. Interestingly, NGS analysis of the same patient group revealed an additional four different BCR::ABL1 KD mutations in 27.4% (23/84) of patients. These mutations are M244V, A344V, E355A, and E459K with variant read frequency below 15%. No mutation was detected in 18 patients with optimal response to TKI therapy. Resistance to TKIs is associated with the acquisition of additional mutations in BCR::ABL1 KD after treatment with TKIs. Additionally, the use of NGS is advised for accurately determining the mutation status of BCR::ABL1 KD, particularly in cases where the allele frequency is low, and for identifying mutations across multiple exons simultaneously. Therefore, the utilization of NGS as a diagnostic platform for this test is very promising to guide therapeutic decision-making.
Endoplasmic reticulum stress-related genes as prognostic and immunogenic biomarkers in prostate cancer
Authors: Wan Lilin , Fan Yunxia , Wu Tiange , Liu Yifan , Zhang Ruixin , Chen Saisai , Zhao Chenggui , Xue Yifeng 
Published: April 2024

Abstract
Background
The metastasis and aggressive nature of prostate cancer (PCa) has become a major malignancy related threat that concerns men’s health. The efficacy of immune monotherapy against PCa is questionable due to its lymphocyte-suppressive nature.

Method
Endoplasmic reticulum stress- (ERS-) and PCa-prognosis-related genes were obtained from the Molecular Signatures Database and the Cancer Genome Atlas database. The expression, prognosis and immune infiltration values of key genes were explored by “survival R package”, “rms”, “xCELL algorithm”, and univariate–multivariate Cox and LASSO regression analyses. The “consensus cluster plus R package” was used for cluster analysis.

Result
As ERS-related genes, ERLIN2 and CDK5RAP3 showed significant expressional, prognostic and clinic-pathologic values. They were defined as the key genes significantly correlated with immune infiltration and response. The nomogram was constructed with T-stage and primary treatment outcome, and the risk-prognostic model was constructed in the following way: Riskscore = (− 0.1918) * ERLIN2 + (0.5254) * CDK5RAP3. Subsequently, prognostic subgroups based on key genes classified the high-risk group as a pro-cancer subgroup that had lower mutation rates of critical genes (SPOP and MUC16), multiple low-expression immune-relevant molecules, and differences in macrophages (M1 and M2) expressions. Finally, ERLIN2 as an anti-oncogene and CDK5RAP3 as a pro-oncogene were further confirmed by cell phenotype assays and immunohistochemistry.

Conclusion
We identified ERLIN2 and CDK5RAP3 as ERS-related genes with important prognostic and immunologic values, and classified patients between high- and low-risk subgroups, which provided new prognostic markers, immunotherapeutic targets, and basis for prognostic assessments.
Influence of vaccination on critical COVID-19 patients with acute respiratory failure: a retrospective cohort study
Authors: Shen Hsiao-Chin , Huang Jhong-Ru , Sun Chuan-Yen , Liao Ying-Ting , Ko Hung-Jui , Chang Chih-Jung , Feng Jia-Yih , Chen Yuh-Min , Chen Wei-Chih , Yang Kuang-Yao 
Published: April 2024

Abstract
Background
Despite vaccines’ effectiveness in reducing COVID-19 infection rates and disease severity, their impact on critical patients presenting with acute respiratory failure is elusive. The aim of this study was to further investigate the influence of vaccination on mortality rates among severely ill COVID-19 patients experiencing acute respiratory failure.

Methods
This retrospective cohort study was carried out at a tertiary medical center in Taiwan. From April to September 2022, patients who tested positive for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through reverse transcription polymerase chain reaction (RT-PCR) and subsequently experienced acute respiratory failure were included in the study. Baseline characteristics, including vaccination history, along with information regarding critical illness and clinical outcomes, were gathered and compared between patients who received the vaccine and those who did not.

Results
A total of 215 patients with COVID-19 exhibiting acute respiratory failure, as confirmed via RT‒PCR, were included in the analysis. Of this cohort, sixty-six (30.7%) patients died within 28 days. Neither administration of the vaccine nor achievement of primary series vaccination status had a significantly different effect on 28 day mortality, number of viral shedding events, acute respiratory distress syndrome (ARDS) incidence or other clinical outcomes. Patients who received the booster vaccine and completed the primary series showed a tendency of increased 28 days of ventilator-free status, though this difference was not statistically significant (p = 0.815).

Conclusions
Vaccination status did not significantly influence mortality rates, the occurrence of ARDS, or the viral shedding duration in COVID-19 patients with acute respiratory failure.
Allostatic load and frailty do not covary significantly among older residents of Greater Poland
Authors: Jeszka Jan , Hummel Darian , Woźniewicz Malgorzata , Morinaka Tomoko , Sone Yoshiaki , Crews Douglas E. 
Published: April 2024

Abstract
Background
Physiological dysregulation/allostatic load and the geriatric syndrome frailty increase with age. As a neurophysiological response system, allostasis supports survival by limiting stressor-related damage. Frailty reflects decreased strength, endurance, and physical abilities secondary to losses of muscle and bone with age. One suggestion, based on large cohort studies of person’s ages 70 + years, is that frailty contributes to allostatic load at older ages. However, small community-based research has not confirmed this specific association.

Methods
To further explore possible associations between allostatic load and frailty, we enrolled 211 residents of Greater Poland aged 55–91 years living in a small village (Nekla, N = 104) and an urban center and capital of Greater Poland (Poznan, N = 107). For each, we recorded age, self-reported sex, and residence and estimated a 10-biomarker allostatic load score (ALS) and an 8-biomarker frailty index. We anticipated the following: higher ALS and frailty among men and rural residents; for frailty but not ALS to be higher at older ages; significant associations of ALS with sex and place of residence, but not with age or frailty. The significance of observed associations was evaluated by t-tests and multivariate regression.

Results
ALS did not vary significantly between men and women nor between Nekla and Poznan residents overall. However, women showed significantly higher frailty than men. Nekla men showed significantly higher ALS but not frailty, while Nekla women showed nonsignificantly higher ALS and lower frailty than Poznan. In multivariate analyses, neither age, nor sex, nor residence was associated with ALS. Conversely, age, sex, and residence, but not ALS, are associated significantly with frailty. In Nekla, both age and sex, but in Poznan only age, are associated with ALS. Among women, both age and residence, but among men, neither associated with ALS. In no case did ALS associate significantly with frailty.

Conclusion
In this sample, lifestyle factors associated with residence, age, and sex influence stress-related physiology, less so in women, while ALS and frailty do not covary, suggesting their underlying promoters are distinct. Similar complex associations of physiological dysregulation with frailty, age, sex, and residence likely exist within many local settings. Knowledge of this variation likely will aid in supporting health and healthcare services among seniors.
Personality of organizational social media accounts and its relationship with characteristics of their photos: analyses of startups’ Instagram photos
Authors: Kim Yunhwan 
Published: April 2024

Abstract
Background
Organizational accounts of social networking sites (SNSs) are similar to individual accounts in terms of their online behaviors. Thus, they can be investigated from the perspective of personality, as individual accounts have been in the literature. Focusing on startups’ Instagram accounts, this study aimed to investigate the characteristics of Big Five personality traits and the relationships between the traits and the characteristics of photos in organizational SNS accounts.

Methods
The personality traits of 108 startups’ accounts were assessed with an online artificial intelligence service, and a correspondence analysis was performed to identify the key dimensions where the account were distributed by their personality. Photo features were extracted at the content and pixel levels, and correlational analyses between personality traits and photo features were conducted. Moreover, predictive analyses were performed using random forest regression models.

Results
The results indicated that personality of the accounts had high openness, agreeableness, and conscientiousness and moderate extraversion and neuroticism. In addition, the two dimensions of high vs. low in neuroticism and extraversion/openness vs. conscientiousness/agreeableness in the accounts’ distribution by their personality traits were identified. Conscientiousness was the trait most associated with photo features—in particular, with content category, pixel-color, and visual features, while agreeableness was the trait least associated with photo features. Neuroticism was mainly correlated with pixel-level features, openness was correlated mainly with pixel-color features, and extraversion was correlated mainly with facial features. The personality traits, except neuroticism, were predicted from the photo features.

Conclusions
This study applied the theoretical lens of personality, which has been mainly used to examine individuals’ behaviors, to investigate the SNS communication of startups. Moreover, it focused on the visual communication of organizational accounts, which has not been actively studied in the literature. This study has implications for expanding the realm of personality research to organizational SNS accounts.
Phosphorus fractions affect fungal compositions and functions under land use conversions in saline-alkali soil in northeastern China
Authors: Hu Juan , Huang Yingxin , Zhou Daowei 
Published: April 2024

Abstract
Background
Little is known about the link between the fungal community and phosphorus fractions when land use is converted from cropland to grassland in saline-alkali soil in northeastern China. Therefore, in this study, the diversity, composition, and function of fungi, as well as phosphorus fractions including Olsen-P and inorganic phosphorus (Pi), were investigated under land use conversions from maize cropland (MC) to alfalfa (Medicago sativa L.) (AG), Leymus chinensis (LG), and natural restored grasslands (RG).

Results
The results showed that the Pi fractions of Ca8-P, Fe-P, Ca2-P, and Ca10-P were closely related with Olsen-P. Significantly increased Olsen-P content was found in 0–10 cm soil layer in the AG treatment, relative to LG and RG treatments (P < 0.05). The occluded P content in 0–10 cm and the Al-P content in 10–20 cm in the RG treatment were the highest. The RG treatment increased the Shannon index of fungi, as well as the abundances of phyla Mortierellomycota and phyla Glomeromycota. Higher abundance of genus Mortierella and lower abundance of genus Cladosporium were observed at RG treatment. Moreover, the RG treatment greatly reduced the abundance of plant pathogens and enhanced the abundances of mycorrhizal and ectomycorrhizal. The Olsen-P was positively correlated with the abundance of plant pathogen (P < 0.01), and the Olsen-P, Ca2-P, and Fe–P were negatively correlated with both the abundances of mycorrhizal and ectomycorrhizal (P < 0.05).

Conclusion
Land use conversion from maize cropland to natural restored grassland could reduce plant pathogens and enhance useful fungi by decreasing the availability of phosphorus.

Graphical Abstract
Indian voters’ attitude and behavior toward a political brand for producing green products: a mediation model
Authors: Yadav Parul , Agarwal Bhawna , Mathew Jones 
Published: April 2024

AbstractThis study explores the attitude–behavior relationship among voters for political party brands that use a sustainable or green marketing approach. A structural equation modeling is used to analyze data collected from 1771 respondents who are registered Indian voters in this case. A positive attitude toward a political brand is compared to intentions to vote for the same brand. According to the findings, political brands create a more environmentally friendly product in the form of green actions because doing so encourages consumers to think favorably of the political brand, which results in them voting for it. As a result, authors are able to identify a positive attitude–behavior relationship for political brands among voters.
Hemostatic Effects of Exercise-related Hypoglycemia in Male Persons With Type 1 Diabetes
Authors: Hagelqvist Per Gustav , Andersen Andreas , Maytham Kaisar , Andreasen Christine Rode , Engberg Susanne , Pedersen-Bjergaard Ulrik , Forman Julie Lyng , Johansson Pär , Lykkesfeldt Jens , Knop Filip Krag , Vilsbøll Tina 
Published: April 2024

Abstract

Context
People with type 1 diabetes (T1D) are at increased risk of thrombosis compared to the general population; however, the underlying mechanisms remain unclear. Hypoglycemia induced at rest can induce coagulation activation, but little is known about the hemostatic effects of exercise-related hypoglycemia in people with T1D.

Objective
We compared hemostatic profiles of individuals with T1D with healthy controls and explored hemostatic effects of hypoglycemia, induced with or without exercise, in participants with T1D.

Methods
Thrombelastography was used for a baseline hemostatic comparison between fifteen men with T1D and matched healthy controls. In addition, the participants with T1D underwent two euglycemic-hypoglycemic clamp days in a randomized, crossover fashion. Hypoglycemia was induced with the participants at rest (Hypo-rest) or during exercise (Hypo-exercise). Thrombelastography provides data on the rate of coagulation activation (R-time), the rate of clot formation (K-time, α-Angle), the maximum clot amplitude (MA), the functional fibrinogen contribution to the clot strength (MA-FF) and the fibrinolysis (LY-30).

Results
The T1D group exhibited a faster rate of coagulation activation (shorter R-time) and a faster clot formation (greater α-Angle) compared with the controls. During the clamp experiments, Hypo-exercise induced an increased clot strength (MA) with a mean difference from baseline of 2.77 mm (95% CI, 2.04-3.51) accompanied with a decreased fibrinolysis (LY-30) of −0.45 percentage point (−0.60 to −0.29). Hypo-rest resulted in increased functional fibrinogen (MA-FF) of 0.74 mm (0.13-1.36) along with an increased fibrinolysis (LY-30) of 0.54 percentage point (0.11-0.98).

Conclusion
Individuals with T1D exhibit a hypercoagulable hemostatic profile compared with healthy controls and exercise-related hypoglycemia may increase the susceptibility to thrombosis via both procoagulant and antifibrinolytic effects.
The Transformation of Prewar Blues into Postwar Rhythm and Blues
Authors: Stoia Nicholas 
Published: April 2024

Abstract
The transformation of blues into rhythm and blues in the mid-twentieth century mirrored the experience of migrants who traveled from the South and adapted to bustling city life in the North and Midwest. When millions of Black Americans moved to cities during the Great Migration, traditional blues traveled with them, but the faster pace of urban life engendered new approaches to blues that reflected the new environment, and rhythm and blues emerged in the early postwar period as an urbanized transformation of the earlier genre.
Rhythm and blues was loud, emphatically energetic, and, through greater use of new modern instruments, highly electrified. These attributes were, as many have observed, artistic responses to the new urban setting and marked a distinct divergence from the genre's prewar origins.
What have received less attention than timbre, tempo, and volume, though, are the many new formal approaches that mark the new style: the urban environment engendered a corresponding creative explosion of new variants on the traditional twelve-bar form, many of them characterized by faster textual pacing, greater phrase-rhythmic density, and elaborate stylization. These transformations are the formal counterparts to the electrification and livelier tempos that mark the urbanization of blues and its metamorphosis into a new postwar genre, and they appear throughout the work of many pivotal rhythm and blues musicians, including Willie Dixon, Ruth Brown, Howlin' Wolf, Ray Charles, Big Mama Thornton, Fats Domino, Chuck Berry, and Little Richard, the main artists explored in this study.