bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional regulation of Satb1 in mouse trophoblast stem cells
Authors: Yu Wei , Chakravarthi V. Praveen , Borosha Shaon , Dilower Iman , Lee Eun Bee , Ratri Anamika , Starks Rebekah R. , Fields Patrick E. , Wolfe Michael W. , Faruque M. Omar , Tuteja Geetu , Rumi M. A. Karim 
Published: December 2022

SATB homeobox proteins are important regulators of developmental gene expression. Among the stem cell lineages that emerge during early embryonic development, trophoblast stem (TS) cells exhibit robust SATB expression. Both SATB1 and SATB2 act to maintain the trophoblast stem-state. However, the molecular mechanisms that regulate TS-specific Satb expression are not yet known. We identified Satb1 variant 2 as the predominant transcript in trophoblasts. Histone marks, and RNA polymerase II occupancy in TS cells indicated an active state of the promoter. A novel cis-regulatory region with active histone marks was identified ∼21 kbp upstream of the variant 2 promoter. CRISPR/Cas9 mediated disruption of this sequence decreased Satb1 expression in TS cells and chromosome conformation capture analysis confirmed looping of this distant regulatory region into the proximal promoter. Scanning position weight matrices across the enhancer predicted two ELF5 binding sites in close proximity to SATB1 sites, which were confirmed by chromatin immunoprecipitation. Knockdown of ELF5 downregulated Satb1 expression in TS cells and overexpression of ELF5 increased the enhancer-reporter activity. Interestingly, ELF5 interacts with SATB1 in TS cells, and the enhancer activity was upregulated following SATB overexpression. Our findings indicate that trophoblast-specific Satb1 expression is regulated by long-range chromatin looping of an enhancer that interacts with ELF5 and SATB proteins.
Evolution of marine gravel dunes on the open shelf under multi-directional currents conditions
Authors: Ribó Marta , Watson Sally J. , Macdonald Helen , Strachan Lorna J. 
Published: December 2022

On inner continental shelves, a variety of coarse grained bedforms, such as gravel dunes, are shaped by hydrodynamic and morphodynamic processes. The formation and evolution of bedforms reflect a balance between seabed and coastal morphology, sediment type and availability, and regional hydrodynamics. Yet, observing bedform evolution directly in the marine environment is rare, mostly due to the lack of repeat seafloor mapping surveys. In this study we use repeat bathymetry from 3 surveys over 4 years from the western Cook Strait/Te Moana-o-Raukawakawa region, New Zealand/Aotearoa. We integrate seabed morphology characterisation with sediment classification and regional hydrodynamic modelling, to investigate the evolution of gravel dunes under multi-directional current conditions. The repeat seafloor mapping reveals morphological changes to plan-view dune geometry and bifurcation of crestlines, with maximum observed vertical changes up to 3 m at water depths between 60 and 80 m. However, no dune migration was detected. Our hydrodynamic model shows that the most prominent morphological changes over the gravel dunes are spatially correlated with eddy formation, and high multi-directional near-bottom currents, reaching maximum speeds of ∼4 m s−1 and bottom stress of &gt;25 N m−2 in each tidal cycle. We demonstrate that the average hydrodynamic conditions in this region are capable of mobilising coarse-grained sediment (i.e., sand to gravel), indicating that the observed morphological changes over multi-year time scales are a result of continuous remobilisation by currents, rather than extreme or storm events. Our findings demonstrate the highly dynamic nature of the seabed in Cook Strait, and the need for regular, repeat mapping surveys to ensure up-to-date seabed morphology information.
Infertile human endometrial organoid apical protein secretions are dysregulated and impair trophoblast progenitor cell adhesion
Authors: Zhou Wei , Barton Siena , Cui Jinwei , Santos Leilani L. , Yang Guannan , Stern Catharyn , Kieu Violet , Teh Wan Tinn , Ang Catarina , Lucky Tarana , Sgroi Joseph , Ye Louie , Dimitriadis Evdokia 
Published: December 2022

IntroductionEmbryo implantation failure leads to infertility. As an important approach to regulate implantation, endometrial epithelial cells produce and secrete factors apically into the uterine cavity in the receptive phase to prepare the initial blastocyst adhesion and implantation. Organoids were recently developed from human endometrial epithelium with similar apical-basal polarity compared to endometrial gland making it an ideal model to study endometrial epithelial secretions.MethodsEndometrial organoids were established using endometrial biopsies from women with primary infertility and normal fertility. Fertile and infertile organoids were treated with hormones to model receptive phase of the endometrial epithelium and intra-organoid fluid (IOF) was collected to compare the apical protein secretion profile and function on trophoblast cell adhesion.ResultsOur data show that infertile organoids were dysregulated in their response to estrogen and progesterone treatment. Proteomic analysis of organoid apical secretions identified 150 dysregulated proteins between fertile and infertile groups (&gt;1.5-fold change). Trophoblast progenitor spheroids (blastocyst surrogates) treated with infertile organoid apical secretions significantly compromised their adhesion to organoid epithelial cell monolayers compared to fertile group (P &lt; 0.0001).DiscussionThis study revealed that endometrial organoid apical secretions alter trophoblast cell adhesiveness relative to fertility status of women. It paves the way to determine the molecular mechanisms by which endometrial epithelial apical released factors regulate blastocyst initial attachment and implantation.
Serum spexin differed in newly diagnosed type 2 diabetes patients according to body mass index and increased with the improvement of metabolic status
Authors: Gu Liping , Yan Shuai , Huang Yunhong , Yang Jiaying , Peng Yongde , Wang Yufan 
Published: December 2022

ObjectiveThe aim of this study was to explore serum spexin levels in newly diagnosed type 2 diabetes mellitus (T2DM) patients with different body mass indexes (BMIs) and to investigate the changes of spexin after improvement of metabolic indicators.MethodsA total of 323 newly diagnosed T2DM patients from national Metabolic Management Center (MMC) in Shanghai General Hospital were recruited. T2DM patients were categorized into three groups: diabetes with obesity group (DM-OB group, BMI≥28 kg/m2, n=89), diabetes with overweight group (DM-OV group, 24≤BMI&lt;28 kg/m2, n=161), and diabetes with normal weight group (DM-NW group, 18≤BMI&lt;24 kg/m2, n=73). In addition, 41 volunteers with normal glucose tolerance (NGT) were used as controls. Spexin and metabolic parameters were compared at baseline, and changes after MMC follow-up in 100 DM patients were investigated.ResultsIn the DM-OB group, the level of spexin was significantly lower than that in the DM-OV group and the DM-NW group (P &lt; 0.01). Spexin was significantly negatively related to body mass index (BMI, β=-0.214, P&lt;0.001), waist circumference (β=-0.249, P&lt;0.001), visceral fat area (VFA, β=-0.214, P&lt;0.001), and subcutaneous fat area (SFA, β=-0.265, P&lt;0.001) after adjustment for age and sex. Among all the metabolic indicators, the decline in BMI in the DM-OB group was the most obvious among those in the three groups (-3.7 ± 0.8 kg/m2 vs. -0.9 ± 0.3 kg/m2 vs. 0.7 ± 0.6 kg/m2, P&lt;0.01) after one year of MMC standardized management. The serum spexin level in the DM-OB group increased the most (1.00 ± 0.10 ng/mL vs. 0.49 ± 0.06 ng/mL in DM-OV group and 0.58 ± 0.09 ng/mL in DM-NW group, P &lt; 0.001).ConclusionsSerum spexin differed in newly diagnosed T2DM patients according to BMI and was lowest in the DM-OB group. With the improvement of metabolic indicators, especially the decline in BMI, serum spexin increased significantly after MMC management.
A cost-efficient DC active load laboratory solution
Authors: Santoro Danilo , Delmonte Nicola , Cova Paolo , Toscani Andrea 
Published: December 2022

The increased use of DC renewable energy resources and DC storage systems, combined with the necessary reduction of energy waste, is boosting the development of DC smart grids. In this scenario, DC load emulation is of great importance. From the hardware point of view, DC buses stability of smart grids and the different DC/DC converter topologies must be tested. From the software point of view, smart grid strategies and job schedulers must be tested with different power absorption profiles. Moreover, DC load emulation can be useful for many other purposes, such as battery characterization, power supply testing, photovoltaic I-V curve measurements, etc. In this work, a cost-efficient DC Active Load (AL) solution is proposed. The principle of the circuit topology is a buck-boost-derived converter. This solution can be designed and tested considering the required voltage, current, and maximum input power. Both simulation and experimental results are shown on a 400 W size prototype. Thermal and electrical results validate the simulation model and the AL feasibility.
Nest-site choice by loggerhead sea turtles as a risk-management adaptation to offset hatching failure by unpredictable storms and predators
Authors: Cassill Deby L. , Watkins Alison 
Published: December 2022

IntroductionAlong the coasts of Florida, United States, the nesting season of the loggerhead sea turtle, Caretta caretta, overlaps with the hurricane season. Nesting loggerhead females do not extend parental protection beyond depositing eggs in sandy, excavated nests in locations that provide a viable range of temperatures, moisture, and respiratory gas exchange. Thereafter, a female’s clutches are subjected to the uncertainties of desiccation, predation, flooding, or beach erosion.MethodsHere, we used data from a 1996-2004 study of 94 tagged loggerhead females nesting on a small barrier island off the Gulf Coast of south Florida, United States. We tested the hypothesis that the distribution of nest sites by loggerhead females was a randomized response to unpredictable hatching failure.ResultsWe show that nest site choice accounted for 19.2% of variation in hatching success whereas breeding year and breeding month accounted for the remaining 81.8% of variation in hatching success. We show that the emergence site along the beach-length axis, nest site choice along the beach-width axis, and distances between nest locations did not fit a uniform-random distribution or a normal distribution. Instead, we show that loggerhead females employed a “Goldilocks” distribution in which nest sites were “neither too clustered nor too dispersed.” Moreover, loggerhead females selected nest sites with limited overlap with nest sites from previous breeding seasons.DiscussionWe propose that nest site choice by this population of loggerhead females constitutes a significant maternal risk-management adaptation that deserves thoughtful consideration as we continue to assess the impacts of climate change on the future of loggerhead sea turtles.
EPC infusion ameliorates acute graft-versus-host disease-related endothelial injury after allogeneic bone marrow transplantation
Authors: Wang Weiwei , Ye Yali , Du Yuwei , Xu Zhengqing , Yuan Ke , Wang Yizhou , Adzraku Seyram Yao , Li Yue , Xu Kailin , Qiao Jianlin , Ju Wen , Zeng Lingyu 
Published: December 2022

IntroductionGraft-versus-host disease (GVHD) damages vascular endothelium. Endothelial progenitor cell (EPC) can differentiate to endothelial cell and promote angiogenesis, but its role in endothelial damage in GVHD is unclear.MethodsIn this study, we intend to assess whether EPC infusion promotes the repair of endothelial injury in GVHD mouse model. Male BALB/c mice were randomly divided into 5 groups: control group, total body irradiation group (TBI group), allogeneic bone marrow transplantation group (Allo-BMT group), acute graft versus host disease group (GVHD group), EPC infusion group (GVHD+EPC group) followed by analysis of mice survival, acute GVHD (aGVHD) score, T cell infiltration by immunofluorescence, as well as continuity of vascular endothelium in liver.ResultsCompared with Allo-BMT group, the clinical and pathological score of aGVHD mice were higher. On day 21 after transplantation, a large number of mononuclear cell infiltrations were seen in the target tissues of aGVHD mice and mice died within 30 days. In addition, aGVHD group also presented increased subendothelial infiltration of CD3+ T cells in the liver, decreased VE-cadherin expression and elevated major histocompatibility complex (MHC) II molecule expression in the endothelium. Moreover, expression of MHC-II molecule increased in endothelial cell after irradiation injury and LPS stimulation, indicating abnormally activated endothelial cell with antigen-presenting function. Interestingly, infusion of EPC reduced the clinical and pathological score of aGVHD, decreased infiltration of mononuclear cells, improved survival as well as upregulated VE-cadherin and downregulated MHC-II molecule.DiscussionEPC infusion can mobilize to affected endothelium to decrease the infiltration of T cells and pathological endothelial activation contributing to ameliorating the damage of endothelium. EPC infusion combined with bone marrow transplantation might be a perspective strategy for the prevention and treatment of aGVHD.
Altered serum human cytomegalovirus microRNA levels are common and closely associated with the inflammatory status in patients with fever
Authors: Wang Cheng , Zhu Yunhua , Chen Penglu , Wang Chen , Zhou Wanqing , Zhang Cuiping , Wang Jing , Chen Xi , Ding Meng , Zhang Chunni , Wang Jun-Jun , Zhang Chen-Yu 
Published: December 2022

BackgroundFever has a complicated etiology, and diagnosing its causative factor is clinically challenging. Human cytomegalovirus (HCMV) infection causes various diseases. However, the clinical relevance, prevalence, and significance of HCMV microRNAs (miRNA) in association with fever remain unclear. In the present study, we analyzed the HCMV miRNA expression pattern in the serum of patients with fever and evaluate its clinical associations with occult HCMV infection status in immune disorders.MethodsWe included serum samples from 138 patients with fever and 151 age-gender-matched controls in this study. First, the serum levels of 24 HCMV miRNAs were determined using a hydrolysis probe-based stem-loop quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay in the training set. The markedly altered miRNAs were verified in the validation and testing sets. The serum HCMV IgG/IgM and DNA titers in the testing cohort were also assessed using enzyme-linked immunosorbent assay (ELISA) and RT-qPCR, respectively.ResultsThe majority of HCMV miRNAs were markedly upregulated in the serum of fever patients. We selected the five most significantly altered HCMV miRNAs: hcmv-miR-US4-3p, hcmv-miR-US29-3p, hcmv-miR-US5-2-3p, hcmv-miR-UL112-3p, and hcmv-miR-US33-3p for validation. These miRNAs were also significantly elevated in the serum of fever patients in the validation and testing sets compared with the controls. Logistic regression analysis revealed that the five miRNAs were novel potential risk factors for fever. Notably, the serum levels of four of the five confirmed HCMV miRNAs were significantly associated with blood C-reaction protein concentrations. Moreover, the five HCMV miRNA levels were closely correlated with the HCMV DNA titers in the testing cohort.ConclusionHCMV infection and activation are common in fever patients and could be novel risk factors for fever. These differentially expressed HCMV miRNAs could enable HCMV activation status monitoring in immune disorders.
Integration analysis identifies MYBL1 as a novel immunotherapy biomarker affecting the immune microenvironment in clear cell renal cell carcinoma: Evidence based on machine learning and experiments
Authors: Wang Tengda , Jian Wengang , Xue Wei , Meng Yuyang , Xia Zhinan , Li Qinchen , Xu Shenhao , Dong Yu , Mao Anli , Zhang Cheng 
Published: December 2022

BackgroundPrevious studies have identified MYBL1 as a cancer-promoting molecule in numerous types of cancer. Nevertheless, the role of MYBL in renal cancer remains unclear.MethodsGenomic and clinical data of clear cell renal cell carcinoma (ccRCC) was get from the Cancer Genome Atlas (TCGA) database. CCK8, colony formation, and 5-ethynyl-2’-deoxyuridine assay were utilized to evaluate the performance of cell proliferation. Cell apoptosis was detected using the flow cytometric analysis. The protein level of MYBL1 in different tissues was evaluated using immunohistochemistry. A machine learning algorithm was utilized to identify the prognosis signature based on MYBL1-derived molecules.ResultsHere, we comprehensively investigated the role of MYBL1 in ccRCC. Here, we noticed a higher level of MYBL1 in ccRCC patients in both RNA and protein levels. Further analysis showed that MYBL1 was correlated with progressive clinical characteristics and worse prognosis performance. Biological enrichment analysis showed that MYBL1 can activate multiple oncogenic pathways in ccRCC. Moreover, we found that MYBL1 can remodel the immune microenvironment of ccRCC and affect the immunotherapy response. In vitro and in vivo assays indicated that MYBL1 was upregulated in ccRCC cells and can promote cellular malignant behaviors of ccRCC. Ultimately, an machine learning algorithm – LASSO logistics regression was utilized to identify a prognosis signature based on the MYBL1-derived molecules, which showed satisfactory prediction ability on patient prognosis in both training and validation cohorts.ConclusionsOur result indicated that MYBL1 is a novel biomarker of ccRCC, which can remodel the tumor microenvironment, affect immunotherapy response and guide precision medicine in ccRCC.
The consistency of invasive and non-invasive arterial blood pressure for the assessment of dynamic cerebral autoregulation in NICU patients
Authors: Zhang Weijun , Lu Hongji , Liu Jia , Ou Aihua , Zhang Pandeng , Zhong Jingxin 
Published: December 2022

BackgroundStudies of the clinical application of dynamic cerebral autoregulation show considerable variations, and differences in blood pressure devices may be one of the reasons for this variation. Few studies have examined the consistency of invasive and non-invasive arterial blood pressure for evaluating cerebral autoregulation. We attempted to investigate the agreement between invasive and non-invasive blood pressure methods in the assessment of dynamic cerebral autoregulation with transfer function analysis.MethodsContinuous cerebral blood flow velocity and continuous invasive and non-invasive arterial blood pressure were simultaneously recorded for 15 min. Transfer function analysis was applied to derive the phase shift, gain and coherence function at all frequency bands from the first 5, 10, and 15 min of the 15-min recordings. The consistency was assessed with Bland–Altman analysis and intraclass correlation coefficient.ResultsThe consistency of invasive and noninvasive blood pressure methods for the assessment of dynamic cerebral autoregulation was poor at 5 min, slightly improved at 10 min, and good at 15 min. The values of the phase shift at the low-frequency band measured by the non-invasive device were higher than those measured with invasive equipment. The coherence function values measured by the invasive technique were higher than the values derived from the non-invasive method.ConclusionBoth invasive and non-invasive arterial blood pressure methods have good agreement in evaluating dynamic cerebral autoregulation when the recording duration reaches 15 min. The phase shift values measured with non-invasive techniques are higher than those measured with invasive devices. We recommend selecting the most appropriate blood pressure device to measure cerebral autoregulation based on the disease, purpose, and design.
A prognostic estimation model based on mRNA-sequence data for patients with oligodendroglioma
Authors: Zhu Qinghui , Shen Shaoping , Yang Chuanwei , Li Mingxiao , Zhang Xiaokang , Li Haoyi , Zhao Xuzhe , Li Ming , Cui Yong , Ren Xiaohui , Lin Song 
Published: December 2022

BackgroundThe diagnosis of oligodendroglioma based on the latest World Health Organization Classification of Tumors of the Central Nervous System (WHO CNS 5) criteria requires the codeletion of chromosome arms 1p and 19q and isocitrate dehydrogenase gene (IDH) mutation (mut). Previously identified prognostic indicators may not be completely suitable for patients with oligodendroglioma based on the new diagnostic criteria. To find potential prognostic indicators for oligodendroglioma, we analyzed the expression of mRNAs of oligodendrogliomas in Chinese Glioma Genome Atlas (CGGA).MethodsWe collected 165 CGGA oligodendroglioma mRNA-sequence datasets and divided them into two cohorts. Patients in the two cohorts were further classified into long-survival and short-survival subgroups. The most predictive mRNAs were filtered out of differentially expressed mRNAs (DE mRNAs) between long-survival and short-survival patients in the training cohort by least absolute shrinkage and selection operator (LASSO), and risk scores of patients were calculated. Univariate and multivariate analyses were performed to screen factors associated with survival and establish the prognostic model. qRT-PCR was used to validate the expression differences of mRNAs.ResultsA total of 88 DE mRNAs were identified between the long-survival and the short-survival groups in the training cohort. Seven RNAs were selected to calculate risk scores. Univariate analysis showed that risk level, age, and primary-or-recurrent status (PRS) type were statistically correlated with survival and were used as factors to establish a prognostic model for patients with oligodendroglioma. The model showed an optimal predictive accuracy with a C-index of 0.912 (95% CI, 0.679–0.981) and harbored a good agreement between the predictions and observations in both training and validation cohorts.ConclusionWe established a prognostic model based on mRNA-sequence data for patients with oligodendroglioma. The predictive ability of this model was validated in a validation cohort, which demonstrated optimal accuracy. The 7 mRNAs included in the model would help predict the prognosis of patients and guide personalized treatment.