bluuebunny/crossref_metadata_2025_split huggingface dataset:
BCL6B-dependent suppression of ETV2 hampers endothelial cell differentiation
Authors: Li Zhonghao , Wu Wei , Li Qiushi , Heng Xin , Zhang Wei , Zhu Yinghong , Chen Lin , Chen Ziqi , Shen Mengcheng , Ma Ning , Xiao Qingzhong , Yan Yi 
Published: July 2024

Abstract
Background
B-cell CLL/lymphoma 6 member B (BCL6B) operates as a sequence-specific transcriptional repressor within the nucleus, playing crucial roles in various biological functions, including tumor suppression, immune response, stem cell self-renew, and vascular angiogenesis. However, whether BCL6B is involved in endothelial cell (EC) development has remained largely unknown. ETS variant transcription factor 2 (ETV2) is well known to facilitate EC differentiation. This study aims to determine the important role of BCL6B in EC differentiation and its potential mechanisms.

Methods
Doxycycline-inducible human induced pluripotent stem cell (hiPSC) lines with BCL6B overexpression or BCL6B knockdown were established and subjected to differentiate into ECs and vessel organoids (VOs). RNA sequencing analysis was performed to identify potential signal pathways regulated by BCL6B during EC differentiation from hiPSCs. Quantitative real-time PCR (qRT-PCR) was used to detect the expression of pluripotency and vascular-specific marker genes expression. EC differentiation efficiency was determined by Flow cytometry analysis. The performance of EC was evaluated by in vitro Tube formation assay. The protein expression and the vessel-like structures were assessed using immunofluorescence analysis or western blot. Luciferase reporter gene assay and chromatin immunoprecipitation (ChIP)-PCR analysis were used to determine the regulatory relationship between BCL6B and ETV2.

Results
Functional ECs and VOs were successfully generated from hiPSCs. Notably, overexpression of BCL6B suppressed while knockdown of BCL6B improved EC differentiation from hiPSCs. Additionally, the overexpression of BCL6B attenuated the capacity of derived hiPSC-ECs to form a tubular structure. Furthermore, compared to the control VOs, BCL6B overexpression repressed the growth of VOs, whereas BCL6B knockdown had little effect on the size of VOs. RNA sequencing analysis confirmed that our differentiation protocol induced landscape changes for cell/tissue/system developmental process, particularly vascular development and tube morphogenesis, which were significantly modulated by BCL6B. Subsequent experiments confirmed the inhibitory effect of BCL6B is facilitated by the binding of BCL6B to the promoter region of ETV2, led to the suppression of ETV2's transcriptional activity. Importantly, the inhibitory effect of BCL6B overexpression on EC differentiation from hiPSCs could be rescued by ETV2 overexpression.

Conclusions
BCL6B inhibits EC differentiation and hinders VO development by repressing the transcriptional activity of ETV2.
HES1 is required for mouse fetal hematopoiesis
Authors: Zhu Anthony Z. , Ma Zhilin , Wolff Emily V. , Lin Zichen , Gao Zhenxia J. , Li Xue , Du Wei 
Published: July 2024

Abstract
Background
Hematopoiesis in mammal is a complex and highly regulated process in which hematopoietic stem cells (HSCs) give rise to all types of differentiated blood cells. Previous studies have shown that hairy and enhancer of split (HES) repressors are essential regulators of adult HSC development downstream of Notch signaling.

Methods
In this study, we investigated the role of HES1, a member of HES family, in fetal hematopoiesis using an embryonic hematopoietic specific Hes1 conditional knockout mouse model by using phenotypic flow cytometry, histopathology analysis, and functional in vitro colony forming unit (CFU) assay and in vivo bone marrow transplant (BMT) assay.

Results
We found that loss of Hes1 in early embryonic stage leads to smaller embryos and fetal livers, decreases hematopoietic stem progenitor cell (HSPC) pool, results in defective multi-lineage differentiation. Functionally, fetal hematopoietic cells deficient for Hes1 exhibit reduced in vitro progenitor activity and compromised in vivo repopulation capacity in the transplanted recipients. Further analysis shows that fetal hematopoiesis defects in Hes1fl/flFlt3Cre embryos are resulted from decreased proliferation and elevated apoptosis, associated with de-repressed HES1 targets, p27 and PTEN in Hes1-KO fetal HSPCs. Finally, pharmacological inhibition of p27 or PTEN improves fetal HSPCs function both in vitro and in vivo.

Conclusion
Together, our findings reveal a previously unappreciated role for HES1 in regulating fetal hematopoiesis, and provide new insight into the differences between fetal and adult HSC maintenance.
Exploring non-viral methods for the delivery of CRISPR-Cas ribonucleoprotein to hematopoietic stem cells
Authors: Molaei Zahra , Jabbarpour Zahra , Omidkhoda Azadeh , Ahmadbeigi Naser 
Published: July 2024

AbstractGene manipulation of hematopoietic stem cells (HSCs) using the CRISPR/Cas system as a potent genome editing tool holds immense promise for addressing hematologic disorders. An essential hurdle in advancing this treatment lies in effectively delivering CRISPR/Cas to HSCs. While various delivery formats exist, Ribonucleoprotein complex (RNP) emerges as a particularly efficient option. RNP complexes offer enhanced gene editing capabilities, devoid of viral vectors, with rapid activity and minimized off-target effects. Nevertheless, novel delivery methods such as microfluidic-based techniques, filtroporation, nanoparticles, and cell-penetrating peptides are continually evolving. This study aims to provide a comprehensive review of these methods and the recent research on delivery approaches of RNP complexes to HSCs.
Fasudil and viscosity of gelatin promote hepatic differentiation by regulating organelles in human umbilical cord matrix-mesenchymal stem cells
Authors: Choi Jiwan , Kang Seoon , An Hye-In , Kim Chae-Eun , Lee Sanghwa , Pack Chan-Gi , Yoon Young-In , Jin Hana , Cho Yong-Pil , Kim Chong Jai , Namgoong Jung-Man , Kim Jun Ki , Tak Eunyoung 
Published: July 2024

Abstract
Background
Human mesenchymal stem cells originating from umbilical cord matrix are a promising therapeutic resource, and their differentiated cells are spotlighted as a tissue regeneration treatment. However, there are limitations to the medical use of differentiated cells from human umbilical cord matrix-mesenchymal stem cells (hUCM-MSCs), such as efficient differentiation methods.

Methods
To effectively differentiate hUCM-MSCs into hepatocyte-like cells (HLCs), we used the ROCK inhibitor, fasudil, which is known to induce endoderm formation, and gelatin, which provides extracellular matrix to the differentiated cells. To estimate a differentiation efficiency of early stage according to combination of gelatin and fasudil, transcription analysis was conducted. Moreover, to demonstrate that organelle states affect differentiation, we performed transcription, tomographic, and mitochondrial function analysis at each stage of hepatic differentiation. Finally, we evaluated hepatocyte function based on the expression of mRNA and protein, secretion of albumin, and activity of CYP3A4 in mature HLCs.

Results
Fasudil induced endoderm-related genes (GATA4, SOX17, and FOXA2) in hUCM-MSCs, and it also induced lipid droplets (LDs) inside the differentiated cells. However, the excessive induction of LDs caused by fasudil inhibited mitochondrial function and prevented differentiation into hepatoblasts. To prevent the excessive LDs formation, we used gelatin as a coating material. When hUCM-MSCs were induced into hepatoblasts with fasudil on high-viscosity (1%) gelatin-coated dishes, hepatoblast-related genes (AFP and HNF4A) showed significant upregulation on high-viscosity gelatin-coated dishes compared to those treated with low-viscosity (0.1%) gelatin. Moreover, other germline cell fates, such as ectoderm and mesoderm, were repressed under these conditions. In addition, LDs abundance was also reduced, whereas mitochondrial function was increased. On the other hand, unlike early stage of the differentiation, low viscosity gelatin was more effective in generating mature HLCs. In this condition, the accumulation of LDs was inhibited in the cells, and mitochondria were activated. Consequently, HLCs originated from hUCM-MSCs were genetically and functionally more matured in low-viscosity gelatin.

Conclusions
This study demonstrated an effective method for differentiating hUCM-MSCs into hepatic cells using fasudil and gelatin of varying viscosities. Moreover, we suggest that efficient hepatic differentiation and the function of hepatic cells differentiated from hUCM-MSCs depend not only on genetic changes but also on the regulation of organelle states.
Donor and recipient hematopoietic stem and progenitor cells mobilization in liver transplantation patients
Authors: Zhi Yao , Qiu Wei , Tian Guangyao , Song Shifei , Zhao Wenchao , Du Xiaodong , Sun Xiaodong , Chen Yuguo , Huang Heyu , Li Jing , Yu Ying , Li Mingqian , Lv Guoyue 
Published: July 2024

Abstract
Background
Hematopoietic stem and progenitor cells (HSPCs) mobilize from bone marrow to peripheral blood in response to stress. The impact of alloresponse-induced stress on HSPCs mobilization in human liver transplantation (LTx) recipients remains under-investigated.

Methods
Peripheral blood mononuclear cell (PBMC) samples were longitudinally collected from pre- to post-LTx for one year from 36 recipients with acute rejection (AR), 74 recipients without rejection (NR), and 5 recipients with graft-versus-host disease (GVHD). 28 PBMC samples from age-matched healthy donors were collected as healthy control (HC). Multi-color flow cytometry (MCFC) was used to immunophenotype HSPCs and their subpopulations. Donor recipient-distinguishable major histocompatibility complex (MHC) antibodies determined cell origin.

Results
Before LTx, patients who developed AR after transplant contained more HSPCs in PBMC samples than HC, while the NR group patients contained fewer HSPCs than HC. After LTx, the HSPC ratio in the AR group sharply decreased and became less than HC within six months, and dropped to a comparable NR level afterward. During the one-year follow-up period, myeloid progenitors (MPs) biased differentiation was observed in all LTx recipients who were under tacrolimus-based immunosuppressive treatment. During both AR and GVHD episodes, the recipient-derived and donor-derived HSPCs mobilized into the recipient’s blood-circulation and migrated to the target tissue, respectively. The HSPCs percentage in blood reduced after the disease was cured.

Conclusions
A preoperative high HSPC ratio in blood characterizes recipients who developed AR after LTx. Recipients exhibited a decline in blood-circulating HSPCs after transplant, the cells mobilized into the blood and migrated to target tissue during alloresponse.
Reproducible MS/MS library cleaning pipeline in matchms
Authors: de Jonge Niek F. , Hecht Helge , Strobel Michael , Wang Mingxun , van der Hooft Justin J. J. , Huber Florian 
Published: July 2024

AbstractMass spectral libraries have proven to be essential for mass spectrum annotation, both for library matching and training new machine learning algorithms. A key step in training machine learning models is the availability of high-quality training data. Public libraries of mass spectrometry data that are open to user submission often suffer from limited metadata curation and harmonization. The resulting variability in data quality makes training of machine learning models challenging. Here we present a library cleaning pipeline designed for cleaning tandem mass spectrometry library data. The pipeline is designed with ease of use, flexibility, and reproducibility as leading principles.Scientific contributionThis pipeline will result in cleaner public mass spectral libraries that will improve library searching and the quality of machine-learning training datasets in mass spectrometry. This pipeline builds on previous work by adding new functionality for curating and correcting annotated libraries, by validating structure annotations. Due to the high quality of our software, the reproducibility, and improved logging, we think our new pipeline has the potential to become the standard in the field for cleaning tandem mass spectrometry libraries.
Graphical Abstract
The effect of remote ischemic conditioning on mortality after kidney transplantation: the systematic review and meta-analysis of randomized controlled trials
Authors: Ko Eunji , Park Ha Yeon , Lim Choon Hak , Kim Hyun Jung , Jang Yookyung , Seong Hyunyoung , Kim Yun Hee , Shin Hyeon Ju 
Published: July 2024

Abstract
Background
Ischemic-reperfusion injury resulting from kidney transplantation declines the post-transplant graft function. Remote ischemic conditioning (RIC) is known to be able to reduce the criticality of ischemic reperfusion injury. This study aimed to meta-analyze whether the application of remote ischemic conditioning to kidney transplantation patients improves clinical outcomes.

Methods
Researchers included randomized controlled studies of the application of RIC to either kidney donors or recipients. Articles were retrieved from PubMed, Embase, Web of Science, and Cochrane Library. The risk of bias was evaluated using RoB 2.0. The primary outcome was mortality after transplantation. Secondary outcomes were the incidence of delayed graft function, graft rejection, and post-transplant laboratory results. All outcomes were integrated by RevMan 5.4.1.

Results
Out of 90 papers, 10 articles (8 studies, 1977 patients) were suitable for inclusion criteria. Mortality collected at all time points did not show a significant difference between the groups. Three-month mortality (RR, 3.11; 95% CI, 0.13–75.51, P = 0.49) tended to increase in the RIC group, but 12-month (RR, 0.70; 95% CI, 0.14–3.45, P = 0.67) or final-reported mortality (RR, 0.49; 95% CI, 0.23–1.06, P = 0.07) was higher in the sham group than the RIC group. There was no significant difference between the RIC and sham group in delayed graft function (RR, 0.64; 95% CI, 0.30–1.35, P = 0.24), graft rejection (RR, 1.13; 95% CI, 0.73–1.73, P = 0.59), and the rate of time required for a 50% reduction in baseline serum creatinine concentration of less than 24 h (RR, 0.98; 95% CI, 0.61–1.56, P = 0.93).

Conclusions
It could not be concluded that the application of RIC is beneficial to kidney transplantation patients. However, it is noteworthy that long-term mortality tended to decrease in the RIC group. Since there were many limitations due to the small number of included articles, researchers hope that large-scale randomized controlled trials will be included in the future.

Systematic review registration
PROSPERO CRD42022336565.
Oral health-related quality of life and loneliness: results based on a cross-sectional survey
Authors: Abdullah Ammar , König Hans-Helmut , Hajek André 
Published: July 2024

Abstract
Background
The aim of this study was to clarify the link between oral health-related quality of life (independent variable) and loneliness (outcome) among the general adult population (also stratified by sex).

Methods
Data were taken from a quota-based survey of the German general adult population (representative in terms of state, sex and age group), with n = 5,000 individuals (mean age was 46.9 years, SD: 15.3 years, ranging from 18 to 74 years). Oral health-related quality of life was quantified using the OHIP-G5. Loneliness was quantified using the De Jong Gierveld tool. Multiple linear regressions were conducted.

Results
After adjusting for several covariates, multiple linear regressions revealed that poor oral health-related quality of life is associated with higher loneliness levels in the total sample (β = 0.12, p < 0.001). Such associations were also found in both sexes (men: β = 0.12, p < 0.001, women: β = 0.12, p < 0.001).

Conclusion
Study findings showed an association between oral health-related quality of life and loneliness. Such knowledge is important for addressing individuals at risk for higher loneliness levels. Future research is required to clarify the underlying mechanisms.
Carbapenemase-producing enterobacterales colonisation status does not lead to more frequent admissions: a linked patient study
Authors: Lydeamore Michael J. , Donker Tjibbe , Wu David , Gorrie Claire , Turner Annabelle , Easton Marion , Hennessy Daneeta , Geard Nicholas , Howden Benjamin P. , Cooper Ben S. , Wilson Andrew , Peleg Anton Y. , Stewardson Andrew J. 
Published: July 2024

Abstract
Background
Hospitals in any given region can be considered as part of a network, where facilities are connected to one another – and hospital pathogens potentially spread – through the movement of patients between them. We sought to describe the hospital admission patterns of patients known to be colonised with carbapenemase-producing Enterobacterales (CPE), and compare them with CPE-negative patient cohorts, matched on comorbidity information.

Methods
We performed a linkage study in Victoria, Australia, including datasets with notifiable diseases (CPE notifications) and hospital admissions (admission dates and diagnostic codes) for the period 2011 to 2020. Where the CPE notification date occurred during a hospital admission for the same patient, we identified this as the ‘index admission’. We determined the number of distinct health services each patient was admitted to, and time to first admission to a different health service. We compared CPE-positive patients with four cohorts of CPE-negative patients, sampled based on different matching criteria.

Results
Of 528 unique patients who had CPE detected during a hospital admission, 222 (42%) were subsequently admitted to a different health service during the study period. Among these patients, CPE diagnosis tended to occur during admission to a metropolitan public hospital (86%, 190/222), whereas there was a greater number of metropolitan private (23%, 52/222) and rural public (18%, 39/222) hospitals for the subsequent admission. Median time to next admission was 4 days (IQR, 0–75 days). Admission patterns for CPE-positive patients was similar to the cohort of CPE-negative patients matched on index admission, time period, and age-adjusted Charlson comorbidity index.

Conclusions
Movement of CPE-positive patients between health services is not a rare event. While the most common movement is from one public metropolitan health service to another, there is also a trend for movement from metropolitan public hospitals into private and rural hospitals. After accounting for clinical comorbidities, CPE colonisation status does not appear to impact on hospital admission frequency or timing. These findings support the potential utility of a centralised notification and outbreak management system for CPE positive patients.
High-tannin food enhances spatial memory and scatter-hoarding in rodents via the microbiota-gut-brain axis
Authors: Zhao Xiangyu , Guo Jiawei , Wang Yiming , Yi Xianfeng 
Published: July 2024

Abstract
Background
The mutually beneficial coevolutionary relationships between rodents and plant seeds have been a theme of research in plant-animal relationships. Seed tannins are important secondary metabolites of plants that regulate the food-hoarding behavior of rodents; however, the underlying molecular mechanisms are not yet clear. In this study, we investigated whether and how seed tannins improve spatial memory and regulate the hoarding behavior of Tamias sibiricus by altering their gut microbiota.

Results
We showed that acorn tannins not only improved spatial memory but also enhanced scatter-hoarding in T. sibiricus. Changes in the composition and function of the gut microbiota in response to tannins from acorns are closely related to these improvements. Metabonomic analyses revealed the role of gut isovaleric acid and isobutyric acid as well as serum L-tryptophan in mediating the spatial memory of T. sibiricus via the gut microbiota. The hippocampal proteome provides further evidence that the microbiota-gut-brain axis regulates spatial memory and scatter-hoarding in animals. Our study is likely the first to report that plant secondary metabolites improve hippocampal function and spatial memory and ultimately modulate food-hoarding behavior via the microbiota-gut-brain axis.

Conclusion
Our findings may have resolved the long-standing puzzle about the hidden role of plant secondary metabolites in manipulating food-hoarding behavior in rodents via the microbiota-gut-brain axis. Our study is important for better understanding the mutualistic coevolution between plants and animals.
Exploring the relationships between ASS indices and CAF and the impact on Chinese college students’ oral English performance
Authors: Shi Xiaoqin , Wang Xiaoqing , Zhang Wei 
Published: July 2024

AbstractAutomatic Speech Scoring (ASS) has increasingly become a useful tool in oral proficiency testing for Second Language (L2) learners. However, limited studies investigate the alignment of ASS indices with the Complexity, Accuracy, and Fluency (CAF)—the three dimensions in evaluating L2 speakers’ oral proficiency, and the subsequent impact indices on the oral performance of Chinese college students. To bridge this gap, this study used comparative analysis, Pearson analysis, and linear regression analysis to delve into the relationship and correlations between paired ASS indicators of “pronunciation”, “fluency”, “integrity”, “speed”, “duration”, and “overall”, while also analyzing the relationships between “overall” and other variables. These analyses were conducted using 956 audio clips of freshmen who took the College English Test-Spoken English Test Band 4 (CET-SET-4) in May 2022 in China. The findings reveal that (1) the ASS indicators and evaluation methods are similar but not identical to those employed in prior studies; (2) “pronunciation” encapsulates both the accuracy and fluency dimensions of CAF; (3) “pronunciation” and “integrity” have significant impacts on Chinese college students’ oral English performance in read-aloud tasks. The study suggests that future research should further investigate the specific pronunciation challenges faced by Chinese college students, such as phonetics, stress, and intonation. Additionally, it highlights the need to comprehend teachers’ attitudes and preferences towards ASS to enhance its effectiveness in assessing second language (L2) learners’ oral proficiency. The study would provide some references to teachers for oral English teaching design and students for their self-assessment of oral English proficiencies.
Nutritional therapy for the prevention of post-intensive care syndrome
Authors: Oshima Taku , Hatakeyama Junji 
Published: July 2024

AbstractPost-intensive care syndrome (PICS) is a triad of physical, cognitive, and mental impairments that occur during or following the intensive care unit (ICU) stay, affecting the long-term prognosis of the patient and also the mental health of the patient’s family. While the severity and duration of the systemic inflammation are associated with the occurrence of ICU-acquired weakness (ICU-AW), malnutrition and immobility during the treatment can exacerbate the symptoms. The goal of nutrition therapy in critically ill patients is to provide an adequate amount of energy and protein while addressing specific nutrient deficiencies to survive the inflammatory response and promote recovery from organ dysfunctions. Feeding strategy to prevent ICU-AW and PICS as nutrition therapy involves administering sufficient amounts of amino acids or proteins later in the acute phase after the hyperacute phase has passed, with specific attention to avoid energy overfeeding. Physiotherapy can also help mitigate muscle loss and subsequent physical impairment. However, many questions remain to be answered regarding the potential role and methods of nutrition therapy in association with ICU-AW and PICS, and further research is warranted.