bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epigenetic deregulation of lamina-associated domains in Hutchinson-Gilford progeria syndrome
Authors: Köhler Florian , Bormann Felix , Raddatz Günter , Gutekunst Julian , Corless Samuel , Musch Tanja , Lonsdorf Anke S. , Erhardt Sylvia , Lyko Frank , Rodríguez-Paredes Manuel 
Published: May 2020

Abstract
Background
Hutchinson-Gilford progeria syndrome (HGPS) is a progeroid disease characterized by the early onset of age-related phenotypes including arthritis, loss of body fat and hair, and atherosclerosis. Cells from affected individuals express a mutant version of the nuclear envelope protein lamin A (termed progerin) and have previously been shown to exhibit prominent histone modification changes.

Methods
Here, we analyze the possibility that epigenetic deregulation of lamina-associated domains (LADs) is involved in the molecular pathology of HGPS. To do so, we studied chromatin accessibility (Assay for Transposase-accessible Chromatin (ATAC)-see/-seq), DNA methylation profiles (Infinium MethylationEPIC BeadChips), and transcriptomes (RNA-seq) of nine primary HGPS fibroblast cell lines and six additional controls, two parental and four age-matched healthy fibroblast cell lines.

Results
Our ATAC-see/-seq data demonstrate that primary dermal fibroblasts from HGPS patients exhibit chromatin accessibility changes that are enriched in LADs. Infinium MethylationEPIC BeadChip profiling further reveals that DNA methylation alterations observed in HGPS fibroblasts are similarly enriched in LADs and different from those occurring during healthy aging and Werner syndrome (WS), another premature aging disease. Moreover, HGPS patients can be stratified into two different subgroups according to their DNA methylation profiles. Finally, we show that the epigenetic deregulation of LADs is associated with HGPS-specific gene expression changes.

Conclusions
Taken together, our results strongly implicate epigenetic deregulation of LADs as an important and previously unrecognized feature of HGPS, which contributes to disease-specific gene expression. Therefore, they not only add a new layer to the study of epigenetic changes in the progeroid syndrome, but also advance our understanding of the disease’s pathology at the cellular level.
Metabolic syndrome is associated with better quality of sleep in the oldest old: results from the “Mugello Study”
Authors:   the Mugello Study Working Group, Laudisio Alice , Giovannini Silvia , Finamore Panaiotis , Navarini Luca , Margiotta Domenico Paolo Emanuele , Vannetti Federica , Macchi Claudio , Coraci Daniele , Imbimbo Isabella , Molino-Lova Raffaello , Loreti Claudia , Antonelli Incalzi Raffaele , Zuccalà Giuseppe , Padua Luca 
Published: May 2020

Abstract
Background and aims
Reduced sleep quality is common in advanced age. Poor sleep quality is associated with adverse outcomes, chiefly cardiovascular, in young and middle-aged subjects, possibly because of its association with metabolic syndrome (MetS). However, the correlates of sleep quality in oldest populations are unknown. We evaluated the association of sleep quality with MetS in a cohort of subjects aged 90+.

Methods and results
We analysed data of 343 subjects aged 90+ living in the Mugello area (Tuscany, Italy). Quality of sleep was assessed using the Pittsburgh Sleep Quality Assessment Index (PSQI). Good quality of sleep was defined by a PSQI score < 5. MetS was diagnosed according to the National Cholesterol Education Program’s ATP-III criteria; 83 (24%) participants reported good quality of sleep. MetS was diagnosed in 110 (24%) participants. In linear and logistic models, MetS was inversely associated with PSQI score ((B = − 1.04; 95% CI − 2.06 to − .03; P = .044), with increased probability of good sleep quality (OR = 2.52; 95% CI 1.26–5.02; P = .009), and with a PSQI below the median (OR = 2.11; 95% CI 1.11–3.40, P = .022), after adjusting. None of the single components of MetS were associated with PSQI (all P values > .050). However, an increasing number of MetS components was associated with increasing probability of good quality of sleep (P for trend = .002), and of PSQI below the median (P for trend = .007). Generalized Additive Model analysis documented no smoothing function suggestive of nonlinear association between PSQI and MetS.

Conclusion
Our results confirm a high prevalence of poor sleep quality in oldest age; however, in these subjects, MetS seems to be associated with better sleep quality. Additional larger, dedicated studies are required to confirm our results, and, if so, to identify the subsystems involved and the potential therapeutic implications of such an association.
Phenotyping individuals with newly-diagnosed type 2 diabetes at risk for all-cause mortality: a single centre observational, prospective study
Authors: Biancalana Edoardo , Parolini Federico , Mengozzi Alessandro , Solini Anna 
Published: May 2020

Abstract
Background
Type 2 diabetes (T2D) shows a high mortality rate, dependent on disease duration, comorbidities and glucose control over time. Data on patients with short disease duration are scanty.

Methods
We prospectively followed a cohort of newly-diagnosed T2D patients referring to a single diabetes centre, treated according to the international guidelines and checked every 6–12 months. All-cause mortality and major cardiovascular (CV) events were registered.

Results
289 patients out of 3019 consecutive first attendances matched inclusion criteria and were included in the observation. Mean follow-up was 51.2 months. At 31 December 2018, 253 patients were alive and 36 deceased. At baseline, deceased individuals were older, with lower eGFR and lower uric acid, higher prevalence of atrial fibrillation. During the follow-up, 18 non-fatal CV events were adjudicated; patients with incident CV disease (CVD) differed at baseline for sex, previous history of CVD and retinopathy, higher use of secretagogues and lower use of metformin. At multivariate analysis, age and previous CVD were the only independent determinants of all-cause mortality and incident CVD, respectively. In deceased individuals, eGFR slope was markedly unstable and ΔeGFR at the end of the follow-up was higher (p < 0.001), and predicted mortality.

Conclusion
Newly-diagnosed T2D patients followed according to the best clinical practice show a mortality rate similar to that reported in more complicated patients with longer disease duration; none of the clinical and biochemical variables commonly measured at baseline can predict mortality or incident CVD; early metformin use seems to be associated with no risk of prevalent or incident retinopathy.
Study on biodegradation kinetics of di-2-ethylhexyl phthalate by newly isolated halotolerant Ochrobactrum anthropi strain L1-W
Authors: Nshimiyimana Jean Bosco , Khadka Sujan , Zou Piao , Adhikari Sanjib , Proshad Ram , Thapa Alina , Xiong Li 
Published: May 2020

Abstract
Objective
Di-2-ethylhexyl phthalate (DEHP) pollution is one of the major environmental concerns all over the world. This research aimed at studying the biodegradation kinetics of DEHP by a newly isolated bacterial strain. Water and sediment samples were collected from Wuhan South Lake and potent bacterial isolates were screened for DEHP degradation, characterized by biochemical, physiological, morphological and 16S rDNA gene sequencing, and optimized under suitable pH, temperature, NaCl and DEHP concentrations. DEHP and its metabolites were quantified by High Performance Liquid Chromatography and their degradation kinetics were studied.

Results
The newly isolated bacterium was identified as Ochrobactrum anthropi strain L1-W with 99.63% similarity to Ochrobactrum anthropi ATCC 49188. It was capable of utilizing DEHP as the carbon source. The optimum growth temperature, pH, DEHP and NaCl concentration for the strain L1-W were 30 °C, 6, 400 mg/L and 10 g/L respectively. Strain L1-W was capable of degrading almost all (98.7%) of DEHP when the initial concentration was 200 mg/L within a period of 72 h. Besides, it was also found capable of degrading five other phthalates, thus making it a possible candidate for bioremediation of phthalates in the environmental settings.
Structure-based screening of chemical libraries to identify small molecules that are likely to bind with the SET and RING-associated (SRA) domain of Ubiquitin-like, PHD and Ring Finger-containing 1 (UHRF1)
Authors: Patnaik Debasis 
Published: May 2020

Abstract
Objectives
UHRF1 is a multi-domain protein that recognizes both histone and DNA modification marks on chromatin. UHRF1 is involved in various cellular processes that lead to tumorigenesis and thus attracted considerable attention as a potential anti-cancer drug target. The SRA domain is a unique to the UHRF family. SRA domain recognizes 5-methylcytosine in hemimethylated DNA and necessary for maintenance DNA methylation mediated by DNMT1. Small molecules capable of interacting with the SRA domain may reduce aberrant methylation levels by preventing the interaction of 5-methylcytosine with the SRA domain and thereby blocking substrate access to the catalytic center of DNMT1. The data were collected to identify and predict an initial set of small molecules that are expected to bind to the SRA domain.

Data description
Nearly 2.4 million molecules from various chemical libraries were screened with the SRA domain of UHRF1 using Schrodinger’s Small Molecule Drug Discovery Suite. The data is available in the form of a methodology presentation, MS Excel files listing the top hits, and Maestro pose viewer files that provide visualization of how the identified ligands interact with the SRA domain.
Transgenerational inheritance of fetal alcohol exposure adverse effects on immune gene interferon-ϒ
Authors: Gangisetty Omkaram , Palagani Ajay , Sarkar Dipak K. 
Published: May 2020

Abstract
Background
Alcohol exposures in utero have been shown to alter immune system functions in the offspring which persists into adulthood. However, it is not apparent why the in utero alcohol effect on the immune system persists into adulthood of fetal alcohol-exposed offspring. The objective of this study was to determine the long-term effects of fetal alcohol exposure on the production of interferon-ϒ (IFN-ϒ), a cytokine known to regulate both innate and adaptive immunity.

Methods
Isogenic Fisher 344 rats were bred to produce pregnant dams, which were fed with a liquid diet containing 6.7% alcohol between gestation days 7 and 21 and pair-fed with an isocaloric liquid diet or fed ad libitum with rat chow; their male and female offspring were used for the study. F1-F3 generation rats were used when they were 2 to 3 months old. Fetal alcohol exposure effects on the Ifn-ɣ gene was determined by measuring the gene promoter methylation and mRNA and protein expression in the spleen. Additionally, transgenerational studies were conducted to evaluate the germline-transmitted effects of fetal alcohol exposure on the Ifn-ɣ gene.

Results
Fetal alcohol exposure reduced the expression of Ifn-ɣ mRNA and IFN-ϒ protein while it increased the proximal promoter methylation of the Ifn-ɣ gene in both male and female offspring during the adult period. Transgenerational studies revealed that the reduced levels of Ifn-ɣ expression and increased levels of its promoter methylation persisted only in F2 and F3 generation males derived from the male germ line.

Conclusion
Overall, these findings provide the evidence that fetal alcohol exposures produce an epigenetic mark on the Ifn-ɣ gene that passes through multiple generations via the male germ line. These data provide the first evidence that the male germ line transmits fetal alcohol exposure's adverse effects on the immune system.
Symphony of epigenetic and metabolic regulation—interaction between the histone methyltransferase EZH2 and metabolism of tumor
Authors: Zhang Tengrui , Gong Yueqing , Meng Hui , Li Chen , Xue Lixiang 
Published: May 2020

AbstractIncreasing evidence has suggested that epigenetic and metabolic alterations in cancer cells are highly intertwined. As the master epigenetic regulator, enhancer of zeste homolog 2 (EZH2) suppresses gene transcription mainly by catalyzing the trimethylation of histone H3 at lysine 27 (H3K27me3) and exerts highly enzymatic activity in cancer cells. Cancer cells undergo the profound metabolic reprogramming and manifest the distinct metabolic profile. The emerging studies have explored that EZH2 is involved in altering the metabolic profiles of tumor cells by multiple pathways, which cover glucose, lipid, and amino acid metabolism. Meanwhile, the stability and methyltransferase activity of EZH2 can be also affected by the metabolic activity of tumor cells through various mechanisms, including post-translational modification. In this review, we have summarized the correlation between EZH2 and cellular metabolic activity during tumor progression and drug treatment. Finally, as a promising target, we proposed a novel strategy through a combination of EZH2 inhibitors with metabolic regulators for future cancer therapy.
Cell therapy approaches to autism: a review of clinical trial data
Authors: Price Jack 
Published: May 2020

AbstractA number of clinical trials of cell therapies for autism spectrum disorder have been conducted, and some have published their outcomes. This review considers the data that have emerged from this small set of published trials, evaluates their success, and proposes further steps that could be taken if this field of endeavour is to be pursued further. A number of reservations arise from this tranche of studies, specifically the absence of identified therapeutic targets, and deficiencies in the therapeutic approach that is being employed. If this therapeutic direction is to be pursued further, then additional pre-clinical studies are recommended that might lead to improvements in patient stratification, biomarkers, the defined mode of action, and the preparation and identification of the therapeutic cells themselves.
Broken-crescent sign at CT indicates impending aortic rupture in patients with acute aortic intramural hematoma
Authors: Ko Sheung-Fat , Lu Chia-Yin , Sheu Jiunn-Jye , Yip Hon-Kan , Huang Chung-Cheng , Ng Shu-Hang 
Published: May 2020

Abstract
Background
This retrospective study evaluated the computed tomography (CT) features and clinical implications of a novel broken-crescent sign in patients with acute aortic intramural hematoma (IMH).

Methods
Out of 104 patients with aortic IMH encountered in our institution between 2003 and 2018, nine patients exhibited a positive broken-crescent sign, which was defined as a focal defect within the hyper-attenuating crescentic IMH on unenhanced CT, corresponding to a smooth out-bulging of the aortic lumen on enhanced study. The clinical findings, CT features, and outcomes of these nine patients were analyzed.

Results
Of five males and four females (age range 48–84 years, mean 69.7 years), six had type A and three had type B IMH. Five patients who had medical treatment and stable status for 1 to 3 days suffered sudden death, two of whom showed ascending aortic rupture with hemopericardium in one and adventitial tear with outward spillage of IMH in another at follow-up CT. The other four patients had early surgical or endovascular management survived; two demonstrated ascending aorta ecchymosis with adventitial tear and intact intima at surgery. Our results support the supposition that aortic IMH complicated with adventitial tear and partial outward seepage of IMH may generate a broken-crescent sign in CT. Despite initially stable clinical status, the residual intact inner aortic wall carries a high risk of sudden aortic rupture.

Conclusions
In patients with acute aortic IMH, identification of a broken-crescent sign in CT is highly suggestive of impending aortic rupture, and early aggressive treatment is mandatory.
Stem cell therapy: a potential approach for treatment of influenza virus and coronavirus-induced acute lung injury
Authors: Du Jiang , Li Han , Lian Jie , Zhu Xinxing , Qiao Liang , Lin Juntang 
Published: May 2020

AbstractAcute lung injury (ALI), an increasingly devastating human disorder, is characterized by a multitude of lung changes arising from a wide variety of lung injuries. Viral infection is the main cause of morbidity and mortality in ALI and acute respiratory distress syndrome (ARDS) patients. In particular, influenza virus, coronavirus, and other respiratory viruses circulate in nature in various animal species and can cause severe and rapidly spread human infections. Although scientific advancements have allowed for rapid progress to be made to understand the pathogenesis and develop therapeutics after each viral pandemic, few effective methods to treat virus-induced ALI have been described. Recently, stem cell therapy has been widely used in the treatment of various diseases, including ALI. In this review, we detail the present stem cell-based therapeutics for lung injury caused by influenza virus and the outlook for the future state of stem cell therapy to deal with emerging influenza and coronaviruses.
Intracellular functions of RNA-binding protein, Musashi1, in stem and cancer cells
Authors: Forouzanfar Mahboobeh , Lachinani Liana , Dormiani Kianoush , Nasr-Esfahani Mohammad Hossein , Gure Ali Osmay , Ghaedi Kamran 
Published: May 2020

AbstractRNA-binding protein, musashi1 (MSI1), is a main protein in asymmetric cell division of the sensory organ precursor cells, whereas its expression is reported to be upregulated in cancers. This protein is a critical element in proliferation of stem and cancer stem cells, which acts through Wnt and Notch signaling pathways. Moreover, MSI1 modulates malignancy and chemoresistance of lung cancer cells via activating the Akt signaling. Due to the main role of MSI1 in metastasis and cancer development, MSI1 would be an appropriate candidate for cancer therapy. Downregulation of MSI1 inhibits proliferation of cancer stem cells and reduces the growth of solid tumors in several cancers. On the other hand, MSI1 expression is regulated by microRNAs in such a way that several different tumor suppressor miRNAs negatively regulate oncogenic MSI1 and inhibit migration and tumor metastasis. The aim of this review is summarizing the role of MSI1 in stem cell proliferation and cancer promotion.
TATA box-binding protein-related factor 3 drives the mesendoderm specification of human embryonic stem cells by globally interacting with the TATA box of key mesendodermal genes
Authors: Liang He , Zhang Peng , Bai Hua-Jun , Huang Jijun , Yang Huang-Tian 
Published: May 2020

Abstract
Background
Mesendodermal formation during early gastrulation requires the expression of lineage-specific genes, while the regulatory mechanisms during this process have not yet been fully illustrated. TATA box-binding protein (TBP) and TBP-like factors are general transcription factors responsible for the transcription initiation by recruiting the preinitiation complex to promoter regions. However, the role of TBP family members in the regulation of mesendodermal specification remains largely unknown.

Methods
We used an in vitro mesendodermal differentiation system of human embryonic stem cells (hESCs), combining with the microarray and quantitative polymerase chain reaction (qRT-PCR) analysis, loss of function and gain of function to determine the function of the TBP family member TBP-related factor 3 (TRF3) during mesendodermal differentiation of hESCs. The chromatin immunoprecipitation (ChIP) and biochemistry analysis were used to determine the binding of TRF3 to the promoter region of key mesendodermal genes.

Results
The mesendodermal differentiation of hESCs was confirmed by the microarray gene expression profile, qRT-PCR, and immunocytochemical staining. The expression of TRF3 mRNA was enhanced during mesendodermal differentiation of hESCs. The TRF3 deficiency did not affect the pluripotent marker expression, alkaline phosphatase activity, and cell cycle distribution of undifferentiated hESCs or the expression of early neuroectodermal genes during neuroectodermal differentiation. During the mesendodermal differentiation, the expression of pluripotency markers decreased in both wild-type and TRF3 knockout (TRF3−/−) cells, while the TRF3 deficiency crippled the expression of the mesendodermal markers. The reintroduction of TRF3 into the TRF3−/− hESCs rescued inhibited mesendodermal differentiation. Mechanistically, the TRF3 binding profile was significantly shifted to the mesendodermal specification during mesendodermal differentiation of hESCs based on the ChIP-seq data. Moreover, ChIP and ChIP-qPCR analysis showed that TRF3 was enriched at core promoter regions of mesendodermal developmental genes, EOMESODERMIN, BRACHYURY, mix paired-like homeobox, and GOOSECOID homeobox, during mesendodermal differentiation of hESCs.

Conclusions
These results reveal that the TBP family member TRF3 is dispensable in the undifferentiated hESCs and the early neuroectodermal differentiation. However, it directs mesendodermal lineage commitment of hESCs via specifically promoting the transcription of key mesendodermal transcription factors. These findings provide new insights into the function and mechanisms of the TBP family member in hESC early lineage specification.
Improvement in circulating endothelial progenitor cells pool after cardiac resynchronization therapy: increasing the list of benefits
Authors: Cristóvão Gonçalo , Milner James , Sousa Pedro , Ventura Miguel , Cristóvão João , Elvas Luís , Paiva Artur , Gonçalves Lino , Ribeiro Carlos Fontes , António Natália 
Published: May 2020

Abstract
Background
Recent studies suggest that circulating endothelial progenitor cells (EPCs) may influence the response to cardiac resynchronization therapy (CRT). The aim of this study was to evaluate the effect of CRT on EPC levels and to assess the impact of EPCs on long-term clinical outcomes.

Population and methods
Prospective study of 50 patients submitted to CRT. Two populations of circulating EPCs were quantified previously to CRT implantation: CD34+KDR+ and CD133+KDR+ cells. EPC levels were reassessed 6 months after CRT. Endpoints during the long-term follow-up were all-cause mortality, heart transplantation, and hospitalization for heart failure (HF) management.

Results
The proportion of non-responders to CRT was 42% and tended to be higher in patients with an ischemic vs non-ischemic etiology (64% vs 35%, p = 0.098). Patients with ischemic cardiomyopathy (ICM) showed significantly lower CD34+KDR+ EPC levels when compared to non-ischemic dilated cardiomyopathy patients (DCM) (0.0010 ± 0.0007 vs 0.0030 ± 0.0024 cells/100 leukocytes, p = 0.032). There were no significant differences in baseline EPC levels between survivors and non-survivors nor between patients who were rehospitalized for HF management during follow-up or not. At 6-month follow-up, circulating EPC levels were significantly higher than baseline levels (0.0024 ± 0.0023 vs 0.0047 ± 0.0041 CD34+KDR+ cells/100 leukocytes, p = 0.010 and 0.0007 ± 0.0004 vs 0.0016 vs 0.0013 CD133+/KDR+ cells/100 leukocytes, p = 0.007).

Conclusions
Patients with ICM showed significantly lower levels of circulating EPCs when compared to their counterparts. CRT seems to improve the pool of endogenously circulating EPCs and reduced baseline EPC levels seem not to influence long-term outcomes after CRT.

Graphical abstract