bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimizing Nodal, Wnt and BMP signaling pathways for robust and efficient differentiation of human induced pluripotent stem cells to intermediate mesoderm cells
Authors: Magro-Lopez Esmeralda , Vazquez-Alejo Elena , Espinar-Buitrago María de la Sierra , Muñoz-Fernández María Ángeles 
Published: June 2024

Several differentiation protocols have enabled the generation of intermediate mesoderm (IM)-derived cells from human pluripotent stem cells (hPSC). However, the substantial variability between existing protocols for generating IM cells compromises their efficiency, reproducibility, and overall success, potentially hindering the utility of urogenital system organoids. Here, we examined the role of high levels of Nodal signaling and BMP activity, as well as WNT signaling in the specification of IM cells derived from a UCSD167i-99-1 human induced pluripotent stem cells (hiPSC) line. We demonstrate that precise modulation of WNT and BMP signaling significantly enhances IM differentiation efficiency. Treatment of hPSC with 3 μM CHIR99021 induced TBXT+/MIXL1+ mesoderm progenitor (MP) cells after 48 h of differentiation. Further treatment with a combination of 3 μM CHIR99021 and 4 ng/mL BMP4 resulted in the generation of OSR1+/GATA3+/PAX2+ IM cells within a subsequent 48 h period. Molecular characterization of differentiated cells was confirmed through immunofluorescence staining and RT-qPCR. Hence, this study establishes a consistent and reproducible protocol for differentiating hiPSC into IM cells that faithfully recapitulates the molecular signatures of IM development. This protocol holds promise for improving the success of protocols designed to generate urogenital system organoids in vitro, with potential applications in regenerative medicine, drug discovery, and disease modeling.
Investigating gut microbiota–blood and urine metabolite correlations in early sepsis-induced acute kidney injury: insights from targeted KEGG analyses
Authors: Xu Yaya , Xu Jiayue , Zhu Yueniu , Mao Haoyun , Li Jiru , Kong Xiangmei , Zhu Xiaodong , Zhang Jianhua 
Published: June 2024

BackgroundThe interplay between gut microbiota and metabolites in the early stages of sepsis-induced acute kidney injury (SA-AKI) is not yet clearly understood. This study explores the characteristics and interactions of gut microbiota, and blood and urinary metabolites in patients with SA-AKI.MethodsUtilizing a prospective observational approach, we conducted comparative analyses of gut microbiota and metabolites via metabolomics and metagenomics in individuals diagnosed with SA-AKI compared to those without AKI (NCT06197828). Pearson correlations were used to identify associations between microbiota, metabolites, and clinical indicators. The Comprehensive Antibiotic Resistance Database was employed to detect antibiotic resistance genes (ARGs), while Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways informed on metabolic processes and microbial resistance patterns.ResultsOur study included analysis of four patients with SA-AKI and five without AKI. Significant disparities in bacterial composition were observed, illustrated by diversity indices (Shannon index: 2.0 ± 0.4 vs. 1.4 ± 0.6, P = 0.230; Simpson index: 0.8 ± 0.1 vs. 0.6 ± 0.2, P = 0.494) between the SA-AKI group and the non-AKI group. N6, N6, N6-Trimethyl-L-lysine was detected in both blood and urine metabolites, and also showed significant correlations with specific gut microbiota (Campylobacter hominis and Bacteroides caccae, R &gt; 0, P &lt; 0.05). Both blood and urine metabolites were enriched in the lysine degradation pathway. We also identified the citrate cycle (TCA cycle) as a KEGG pathway enriched in sets of differentially expressed ARGs in the gut microbiota, which exhibits an association with lysine degradation.ConclusionsSignificant differences in gut microbiota and metabolites were observed between the SA-AKI and non-AKI groups, uncovering potential biomarkers and metabolic changes linked to SA-AKI. The lysine degradation pathway may serve as a crucial link connecting gut microbiota and metabolites.
A Mendelian randomization study of the effect of mental disorders on cardiovascular disease
Authors: Yu Yunfeng , Yang Xinyu , Wu Jingyi , Hu Gang , Bai Siyang , Yu Rong 
Published: June 2024

ObjectiveThe effect of mental disorders (MD) on cardiovascular disease (CVD) remains controversial, and this study aims to analyze the causal relationship between eight MD and CVD by Mendelian randomization (MR).MethodsSingle nucleotide polymorphisms of attention-deficit/hyperactivity disorder (ADHD), anorexia nervosa (AN), anxiety disorder (ANX), autism spectrum disorder (ASD), bipolar disorder (BD), depression, obsessive-compulsive disorder (OCD), schizophrenia (SCZ), and CVD were obtained from UK Biobank and FinnGen. Exposure-outcome causality was tested using inverse variance weighted (IVW), MR-Egger, and weighted median. Horizontal pleiotropy and heterogeneity were assessed by MR-Egger intercept and Cochran's Q, respectively, while stability of results was assessed by leave-one-out sensitivity analysis.ResultsMR analysis showed that ANX (IVW [odds ratio (OR) 1.11, 95% confidence intervals (CI) 1.07–1.15, p &lt; 0.001]; MR-Egger [OR 1.03, 95% CI 0.92–1.14, p = 0.652]; weighted median [OR 1.09, 95% CI 1.03–1.14, p = 0.001]), ASD (IVW [OR 1.05, 95% CI 1.00–1.09, p = 0.039]; MR-Egger [OR 0.95, 95% CI 0.84–1.07, p = 0.411]; weighted median [OR 1.01, 95% CI 0.96–1.06, p = 0.805]), depression (IVW [OR 1.15, 95% CI 1.10–1.19, p &lt; 0.001]; MR-Egger [OR 1.10, 95% CI 0.96–1.26, p = 0.169]; weighted median [OR 1.13, 95% CI 1.08–1.19, p &lt; 0.001]) were significantly associated with increased risk of CVD, whereas ADHD, AN, BD, OCD, and SCZ were not significantly associated with CVD (p &gt; 0.05). Intercept analysis showed no horizontal pleiotropy (p &gt; 0.05). Cochran's Q showed no heterogeneity except for BD (p = 0.035). Sensitivity analysis suggested that these results were robust.ConclusionsANX, ASD, and depression are associated with an increased risk of CVD, whereas AN, ADHD, BD, OCD, and SCZ are not causally associated with CVD. Active prevention and treatment of ANX, ASD, and depression may help reduce the risk of CVD.
Gastroesophageal reflux disease may causally associate with the increased atrial fibrillation risk: evidence from two-sample Mendelian randomization analyses
Authors: Wang Lei , Lu Yi Wei 
Published: June 2024

BackgroundThe risk of atrial fibrillation (AF) is increased in individuals with gastroesophageal reflux disease (GERD), according to observational research. The causal significance of this association is still unclear. This study sought to assess GERD's role as a potential contributing factor in AF.MethodsWith the use of a two-sample Mendelian randomization (MR) technique, we assessed the causal relationship between GERD and AF. The association of genetic variants with GERD was examined using data from a recent genome-wide association study (GWAS) that included 602,604 people. Data on the association between genetic variations and AF was obtained from a second GWAS with 1,030,836 participants. The effect sizes were examined based on the inverse-variance weighted method. Additional statistical techniques, including MR-Egger, simple mode, weighted mode, MR Pleiotropy Residual Sum, outlier, and weighted median were used in the sensitivity analysis.ResultsMR analyses in inverse-variance weighted models, using 76 single nucleotide polymorphisms (SNPs) as markers, revealed a relationship between genetically predicted GERD and a greater AF incidence [odds ratio (OR): 1.165, 95% CI 1.102–1.231; P = 7.637 × 10−8]. According to MR-Egger, there was no evidence of gene pleiotropy that could be found (intercept = 0.003, P = 0.581). The findings of the sensitivity study, which used several MR methods, were found to be reliable.ConclusionThe MR analysis revealed a correlation between GERD and increased AF incidence, supporting the idea that treating patients with GERD as early as possible might reduce their chance of developing AF.
Hydrological and climate intensification induces conservative behavior in the Hydrochorea corymbosa xylem production in a Central Amazon floodplain forest
Authors: de Sá Priscila Amaral , Schöngart Jochen , Wittmann Florian , Piedade Maria Teresa Fernandez , Tomazello-Filho Mario , Oliveira Rafael S. , Horna Viviana , Parolin Pia , Durgante Flavia Machado 
Published: June 2024

IntroductionTrees from flooded forests have to adjust their xylem hydraulic structure to face the annual flooding and the climatic conditions of the atmosphere. Usually, this adjustment of anatomical tissues in the tropics is driven by drought events inducing conservative behavior and can be recorded annually in tree rings. However, how the flood pulse and the climatic conditions influence the xylem hydraulic structure in floodplain trees is unknown.MethodsTo fill this gap, we explore if flooded periods and monthly climate variation affect the annual tree growth and xylem anatomy structure for the tree species Hydrochorea corymbosa (Fabaceae) from the várzea flooded forest in the Central Amazon. We developed a 41-year ring width chronology (1971–2018) and a 30-year time series of xylem anatomy parameters (1988–2018) as mean hydraulic vessel diameter (Dh), vessel frequency (VF), and parenchyma quantity (PQ). We correlated the series with monthly hydrological and climatic data.ResultsThe hydrological regime did not correlate with annual tree growth in that species as we previously expected but showed correlations with the xylem anatomical structure. High flood levels during the end of the flooding period induced conservative patterns of the anatomical structure, with a negative correlation with Dh (rho June = −0.40, p &lt; 0.05) and a positive correlation with the PQ (rho September/October = 0.42, p &lt; 0.05). These responses show that these trees are responding to flooding similar to the tree responses to drought. Regarding the climatic variation, the annual tree growth showed a negative correlation with the vapor pressure deficit (VPD), after the second half of the flooded period with the strongest correlation happening during the non-flooded period (rho December = −0.66, p &lt; 0. 01). These conservative patterns in tree behavior also happened when the maximum temperature negatively affected the vessel diameter (rho September = −0.42, p &lt; 0.05).DiscussionIn that case, we recognized two different moments that the environment is inducing conservative patterns in the xylem structure of those trees: 1) increasing the flood levels and 2) the high evaporative demand during the non-flooded period. In this way, the intensification of the hydrological regime, as well as the strong drought conditions during the non-flooded periods, can be a risk for H. corymbosa in the Central Amazonian floodplains.
Regulatory and memory T lymphocytes infiltrating prostate tumors predict long term clinical outcomes
Authors: Molina Oscar Eduardo , LaRue Hélène , Simonyan David , Hovington Hélène , Vittrant Benjamin , Têtu Bernard , Fradet Vincent , Lacombe Louis , Bergeron Alain , Fradet Yves 
Published: June 2024

IntroductionThe localization, density but mostly the phenotype of tumor infiltrating lymphocytes (TIL) provide important information on the initial interaction between the host immune system and the tumor. Our objective was to assess the prognostic significance of T (CD3+), T regulatory (Treg) (FoxP3+) and T memory (Tmem) (CD45RO+) infiltrating lymphocytes and of genes associated with TIL in prostate cancer (PCa).MethodsImmunohistochemistry (IHC) was used to assess the infiltration of CD3+, FoxP3+ and CD45RO+ cells in the tumor area, tumor margin and adjacent normal-like epithelium of a series of 98 PCa samples with long clinical follow-up. Expression of a panel of 31 TIL-associated genes was analyzed by Taqman Low-Density Array (TLDA) technology in another series of 50 tumors with long clinical follow-up. Kaplan-Meier and Cox proportional hazards regression analyses were performed to determine association of these markers with biochemical recurrence (BCR), need for definitive androgen deprivation therapy (ADT) or lethal PCa.ResultsTIL subtypes were present at different densities in the tumor, tumor margin and adjacent normal-like epithelium, but their density and phenotype in the tumor area were the most predictive of clinical outcomes. In multivariate analyses, a high density of Treg (high FoxP3+/CD3+ cell ratio) predicted a higher risk for need of definitive ADT (HR=7.69, p=0.001) and lethal PCa (HR=4.37, p=0.04). Conversely, a high density of Tmem (high CD45RO+/CD3+ cell ratio) predicted a reduced risk of lethal PCa (HR=0.06, p=0.04). TLDA analyses showed that a high expression of FoxP3 was associated with a higher risk of lethal PCa (HR=5.26, p=0.02). Expression of CTLA-4, PD-1, TIM-3 and LAG-3 were correlated with that of FoxP3. Amongst these, only a high expression of TIM-3 was associated with a significant higher risk for definitive ADT in univariate Cox regression analysis (HR=3.11, p=0.01).ConclusionThese results show that the proportion of Treg and Tmem found within the tumor area is a strong and independent predictor of late systemic progression of PCa. Our results also suggest that inhibition of TIM-3 might be a potential approach to counter the immunosuppressive functions of Treg in order to improve the anti-tumor immune response against PCa.
A local drug delivery system prolongs graft survival by dampening T cell infiltration and neutrophil extracellular trap formation in vascularized composite allografts
Authors: Arenas Hoyos Isabel , Helmer Anja , Yerly Anaïs , Lese Ioana , Hirsiger Stefanie , Zhang Lei , Casoni Daniela , Garcia Luisana , Petrucci MariaFrancesca , Hammer Sabine E. , Duckova Tereza , Banz Yara , Montani Matteo , Constantinescu Mihai , Vögelin Esther , Bordon Gregor , Aleandri Simone , Prost Jean-Christophe , Taddeo Adriano , Luciani Paola , Rieben Robert , Sorvillo Nicoletta , Olariu Radu 
Published: June 2024

IntroductionThe standard treatment for preventing rejection in vascularized composite allotransplantation (VCA) currently relies on systemic immunosuppression, which exposes the host to well-known side effects. Locally administered immunosuppression strategies have shown promising results to bypass this hurdle. Nevertheless, their progress has been slow, partially attributed to a limited understanding of the essential mechanisms underlying graft rejection. Recent discoveries highlight the crucial involvement of innate immune components, such as neutrophil extracellular traps (NETs), in organ transplantation. Here we aimed to prolong graft survival through a tacrolimus-based drug delivery system and to understand the role of NETs in VCA graft rejection.MethodsTo prevent off-target toxicity and promote graft survival, we tested a locally administered tacrolimus-loaded on-demand drug delivery system (TGMS-TAC) in a multiple MHC-mismatched porcine VCA model. Off-target toxicity was assessed in tissue and blood. Graft rejection was evaluated macroscopically while the complement system, T cells, neutrophils and NETs were analyzed in graft tissues by immunofluorescence and/or western blot. Plasmatic levels of inflammatory cytokines were measured using a Luminex magnetic-bead porcine panel, and NETs were measured in plasma and tissue using DNA-MPO ELISA. Lastly, to evaluate the effect of tacrolimus on NET formation, NETs were induced in-vitro in porcine and human peripheral neutrophils following incubation with tacrolimus.ResultsRepeated intra-graft administrations of TGMS-TAC minimized systemic toxicity and prolonged graft survival. Nevertheless, signs of rejection were observed at endpoint. Systemically, there were no increases in cytokine levels, complement anaphylatoxins, T-cell subpopulations, or neutrophils during rejection. Yet, tissue analysis showed local infiltration of T cells and neutrophils, together with neutrophil extracellular traps (NETs) in rejected grafts. Interestingly, intra-graft administration of tacrolimus contributed to a reduction in both T-cellular infiltration and NETs. In fact, in-vitro NETosis assessment showed a 62–84% reduction in NETs after stimulated neutrophils were treated with tacrolimus.ConclusionOur data indicate that the proposed local delivery of immunosuppression avoids off-target toxicity while prolonging graft survival in a multiple MHC-mismatch VCA model. Furthermore, NETs are found to play a role in graft rejection and could therefore be a potential innovative therapeutic target.
Effects of an ergothioneine-rich Pleurotus sp. on skin moisturizing functions and facial conditions: a randomized, double-blind, placebo-controlled trial
Authors: Hanayama Motoki , Mori Koichiro , Ishimoto Takahiro , Kato Yukio , Kawai Junya 
Published: June 2024

BackgroundL-ergothioneine (EGT), an antioxidative and anti-inflammatory amino acid, is abundant in various mushroom fruiting bodies. Meanwhile, the effects of EGT-containing mushrooms on human skin are unknown. This study investigated the effects of oral ingestion of a novel EGT-rich strain of Pleurotus species (hiratake) on skin conditions in humans.MethodsWe conducted a 12-week, randomized, double-blind, placebo-controlled, parallel-group trial to evaluate skin moisturizing functions and facial conditions in 80 healthy women who were randomly assigned to either a group that was supplemented with hiratake tablets containing 25 mg of EGT/day or a placebo group. Skin moisture content, transepidermal water loss (TEWL), and facial scores (VISIA scores) were measured at baseline, 8 weeks, and 12 weeks of supplementation.ResultsAt 8 weeks, the skin moisture content was significantly higher on the temple in the hiratake group than in the placebo group. The hiratake group also exhibited a significant increase in skin moisture content on the arm at 8 and 12 weeks compared with baseline. At 12 weeks, wrinkle and texture scores were significantly better in the hiratake group than in the placebo group, and plasma EGT concentrations in the hiratake group were 4.7-fold higher than baseline (from 3.4 to 15.9 μM). Furthermore, EGT concentrations in plasma were significantly correlated with improvements in skin moisture content and TEWL on the arm, implying that these skin moisturizing benefits could be partly attributed to EGT. A stratified analysis of participants with a low baseline plasma EGT concentration (&lt; 3.3 μM) revealed that skin moisture content on the temple was significantly higher at 8 and 12 weeks, and skin moisture content on the arm at 12 weeks tended to be higher (p = 0.074), in the hiratake group than in the placebo group. These findings suggested that oral ingestion of EGT-rich hiratake can improve skin moisturizing functions.ConclusionEGT-rich hiratake may help maintain skin conditions in healthy women, and EGT may play a role in these beneficial effects.
Morphological variation and expressed sequence tags-simple sequence repeats-based genetic diversity of Aspergillus cristatus in Chinese dark tea
Authors: Hu Zhiyuan , Liu Shiquan , Zhou Xiaohong , Liu Zhanjun , Li Taotao , Yu Songlin , Zhang Xinyu , Xu Zhenggang 
Published: June 2024

IntroductionAspergillus cristatus is a homothallic fungus that is used in the natural fermentation process of Chinese Fuzhuan tea and has been linked to the production of bioactive components. However, not much is known about the variations present in the fungus. To understand the variation of the dominant microorganism, A. cristatus, within dark tea, the present study investigated the genetic and morphological diversity of 70 A. cristatus collected across six provinces of China.MethodsExpressed sequence tags-simple sequence repeats (EST-SSR) loci for A. cristatus were identified and corresponding primers were developed. Subsequently, 15 specimens were selected for PCR amplification.ResultsThe phylogenetic tree obtained revealed four distinct clusters with a genetic similarity coefficient of 0.983, corresponding to previously identified morphological groups. Five strains (A1, A11, B1, D1, and JH1805) with considerable differences in EST-SSR results were selected for further physiological variation investigation. Microstructural examinations revealed no apparent differentiation among the representative strains. However, colony morphology under a range of culture media varied substantially between strains, as did the extracellular enzymatic activity (cellulase, pectinase, protease, and polyphenol oxidase); the data indicate that there are differences in physiological metabolic capacity among A. cristatus strains.DiscussionNotably, JH1805, B1, and A11 exhibited higher enzymatic activity, indicating their potential application in the production of genetically improved strains. The findings provide valuable insights into species identification, genetic diversity determination, and marker-assisted breeding strategies for A. cristatus.
Low levels of Vitamin D during pregnancy associated with gestational diabetes mellitus and low birth weight: results from the MAASTHI birth cohort
Authors: Deepa R. , Schayck Onno C. P. Van , Babu Giridhara R. 
Published: June 2024

IntroductionIndia has a high prevalence of Vitamin D insufficiency among women of childbearing age. In this study, we aimed to evaluate the potential relationship between Vitamin D deficiency and gestational diabetes mellitus (GDM) and low birth weight (LBW) of newborns in the “Maternal antecedents of adiposity and studying the transgenerational role of hyperglycaemia and insulin” (MAASTHI) birth cohort.MethodsA prospective cohort study involving 230 participants was conducted in public hospitals located in urban Bengaluru, India. Healthy pregnant women who visited these hospitals for antenatal care (ANC) and who were between 14 and 36 weeks of gestational age were recruited after obtaining their informed consent. An oral glucose tolerance test (OGTT) was administered between 24 and 36 weeks of pregnancy and blood samples were preserved at −80°C for Vitamin D analysis. Follow-up at birth included recording the child's birth weight.ResultsWe found that 178 (77.4%) of the study participants were vitamin D deficient, 44 (19.1%) were diagnosed with GDM, and 64 (27.8%) gave birth to LBW babies. Women in the lowest quartile of serum Vitamin D levels had three times higher odds of developing GDM than women in the higher quartiles [OR = 3.22 (95% CI: 1.03, 10.07), p = 0.04] after adjusting for age, parity, socioeconomic status, season, and adiposity. For every one-unit increase in Vitamin D levels, Homeostatic Model Assessment for Insulin Resistance (HOMA-IR) decreased by nearly 18%. Furthermore, causal mediation analysis showed that a decrease in one unit of Vitamin D is associated with a decrease of 0.015 units of fasting blood sugar (FBS) and 0.019 units of postprandial blood sugar (PPBS) as it flows through the mediator variable insulin resistance. Vitamin D-deficient women were twice at risk of giving birth to LBW babies (OR 2.04, 95% CI 0.99, 4.19, p = 0.05).DiscussionsLow levels of Vitamin D during pregnancy are associated with a greater risk of pregnant women developing GDM and giving birth to LBW babies in urban Bengaluru.