Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of Myf5 Early Enhancer by Histone Acetyltransferase p300 during Stem Cell Differentiation

Skeletal myogenesis is an intricate process coordinated temporally by multiple myogenic regulatory factors (MRF) including Myf5, which is the first MRF expressed and marks the commitment of skeletal muscle lineage. The expression of Myf5 gene during early embryogenesis is controlled by a set of enhancer elements, and requires the histone acetyltransferase (HAT) activity of transcriptional coactivator p300. However, it is unclear as to how different regulatory signals converge at enhancer elements to regulate early Myf5 gene expression, and if p300 is directly involved. We show here that p300 associates with the Myf5 early enhancer at the early stage of stem cell differentiation, and its HAT activity is important for the recruitment of β-catenin to this early enhancer. In addition, histone H3-K27 acetylation, but not H3-K9/14, is intimately connected to the p300 HAT activity. Thus, p300 is directly involved in the regulation of the Myf5 early enhancer, and is important for specific histone acetylation and transcription factor recruitment. This connection of p300 HAT activity with H3-K27 acetylation and β-catenin signalling during myogenic differentiation in vitro offers a molecular insight into the enhancer-elements participation observed in embryonic development. In addition, pluripotent stem cell differentiation is a valuable system to dissect the signal-dependent regulation of specific enhancer element during cell fate determinations.
Growth and optimization of carbon nanotubes in powder activated carbon for an efficient removal of methylene blue from aqueous solution

ABSTRACT This work demonstrated the synthesis of carbon nanotubes (CNTs) on powder activated carbon (PAC) impregnated with Ni-catalyst through chemical vapour deposition. The optimized effects of reaction temperature, time and feedstock flow rates on CNT growth were examined. Potassium permanganate (KMnO4) and potassium permanganate in acidic solution (KMnO4/H2SO4) were used to functionalize CNTs samples. A primary screening of methylene blue (MB) adsorption was conducted. The chemical, physical and morphological properties of the adsorbent with the highest removal efficiency were investigated using FESEM, EDX, TEM, BET surface area, RAMAN, TGA, FTIR, and zeta potential. The resulting carbon nanotube-loaded activated carbons possessed abundant pore structure and large surface area. The MB removal by the as-synthesized CNTs was more remarkable than that by the modified samples. Adsorption studies were carried out to evaluate the optimum conditions, kinetics and isotherms for MB adsorption process. The response surface methodology-central composite design (RSM-CCD) was used to optimize the adsorption process parameters, including pH, adsorbent dosage and contact time. The investigation of the adsorption behaviour demonstrated that the adsorption was well fitted with the pseudo-second-order model and Langmuir isotherm with the maximum monolayer adsorption capacity of 174.5 mg/g. Meanwhile, the adsorption of MB onto adsorbent was driven by the electrostatic attraction and π-π interaction. Moreover, the as-obtained CNT-PAC exhibited good reusability after four repeated operations. In view of these empirical findings, the low-cost CNT-PAC has potential for removal of MB from aqueous solution.
Bats' Conquest of a Formidable Foraging Niche: The Myriads of Nocturnally Migrating Songbirds

Along food chains, i.e., at different trophic levels, the most abundant taxa often represent exceptional food reservoirs, and are hence the main target of consumers and predators. The capacity of an individual consumer to opportunistically switch towards an abundant food source, for instance, a prey that suddenly becomes available in its environment, may offer such strong selective advantages that ecological innovations may appear and spread rapidly. New predator-prey relationships are likely to evolve even faster when a diet switch involves the exploitation of an unsaturated resource for which few or no other species compete. Using stable isotopes of carbon and nitrogen as dietary tracers, we provide here strong support to the controversial hypothesis that the giant noctule bat Nyctalus lasiopterus feeds on the wing upon the multitude of flying passerines during their nocturnal migratory journeys, a resource which, while showing a predictable distribution in space and time, is only seasonally available. So far, no predator had been reported to exploit this extraordinarily diverse and abundant food reservoir represented by nocturnally migrating passerines.
Chronic Kidney Disease Induces Inflammatory CD40+ Monocyte Differentiation via Homocysteine Elevation and DNA Hypomethylation.

RATIONALE Patients with chronic kidney disease (CKD) develop hyperhomocysteinemia and have a higher cardiovascular mortality than those without hyperhomocysteinemia by 10-fold. OBJECTIVE We investigated monocyte differentiation in human CKD and cardiovascular disease (CVD). METHODS AND RESULTS We identified CD40 as a CKD-related monocyte activation gene using CKD-monocyte -mRNA array analysis and classified CD40 monocyte (CD40+CD14+) as a stronger inflammatory subset than the intermediate monocyte (CD14++CD16+) subset. We recruited 27 patients with CVD/CKD and 14 healthy subjects and found that CD40/CD40 classical/CD40 intermediate monocyte (CD40+CD14+/CD40+CD14++CD16-/CD40+CD14++CD16+), plasma homocysteine, S-adenosylhomocysteine, and S-adenosylmethionine levels were higher in CVD and further elevated in CVD+CKD. CD40 and CD40 intermediate subsets were positively correlated with plasma/cellular homocysteine levels, S-adenosylhomocysteine and S-adenosylmethionine but negatively correlated with estimated glomerular filtration rate. Hyperhomocysteinemia was established as a likely mediator for CKD-induced CD40 intermediate monocyte, and reduced S-adenosylhomocysteine/S-adenosylmethionine was established for CKD-induced CD40/CD40 intermediate monocyte. Soluble CD40 ligand, tumor necrosis factor (TNF)-α/interleukin (IL)-6/interferon (IFN)-γ levels were elevated in CVD/CKD. CKD serum/homocysteine/CD40L/increased TNF-α/IL-6/IFN-γ-induced CD40/CD40 intermediate monocyte in peripheral blood monocyte. Homocysteine and CKD serum-induced CD40 monocyte were prevented by neutralizing antibodies against CD40L/TNF-α/IL-6. DNA hypomethylation was found on nuclear factor-κB consensus element in CD40 promoter in white blood cells from patients with CKD with lower S-adenosylmethionine / S-adenosylhomocysteine ratios. Finally, homocysteine inhibited DNA methyltransferase-1 activity and promoted CD40 intermediate monocyte differentiation, which was reversed by folic acid in peripheral blood monocyte. CONCLUSIONS CD40 monocyte is a novel inflammatory monocyte subset that appears to be a biomarker for CKD severity. Hyperhomocysteinemia mediates CD40 monocyte differentiation via soluble CD40 ligand induction and CD40 DNA hypomethylation in CKD.
Digging deep into Golgi phenotypic diversity with unsupervised machine learning

Structural alterations of the Golgi apparatus may lead to phenotypes that human vision cannot easily discriminate. In this work, we present a high-content analysis framework including an unsupervised clustering step to automatically uncover Golgi phenotypic diversity. We use this deep phenotyping to quantitatively compare the effects of gene depletion.
Differential mRNA expression of acetylcholinesterase in the central nervous system of rats with acute and chronic exposure of sarin & physostigmine

A time‐course study was carried out to measure the acetylcholinesterase (AChE) gene expression in the brain of female rats exposed to different doses of sarin and physostigmine. Short‐term effects were studied with an acute single subcutaneous dose (s.c.) of 80 µg kg−1 (0.5 × LD50) sarin. Cortex and cerebellum showed a significant decline in AChE mRNA expression at 2.5, 24 and 72 h. Biochemical studies showed that plasma butrylcholinesterase (BChE) and brain AChE activities were significantly decreased at 2.5 h, which came back to near control values by 24 h in both cases. For long‐term chronic studies, three groups of female rats received daily doses of physostigmine (0.1 mg kg−1 day−1) intramuscularly (i.m.), sarin (15 µg kg−1 day−1) s.c. independently and a combined dose of physostigmine (i.m.) (0.1 mg kg−1 day−1) followed by sarin (s.c.) (15 µg kg−1 day−1) continuously for 30 days. Differential AChE mRNA levels in cortex and cerebellum of rat brain were observed after 30 days and after a lag period of another 30 days with no further administration. Plasma (BChE) and brain (AChE) showed irregular inhibition profile in biochemical studies at 30 days and returned to control levels after 60 days. The acute single subcutaneous administration of sarin for short‐term as well as chronic long‐term studies showed that AChE inhibition alone does not lead to observed changes in mRNA expression of AChE gene. These observations further suggest that route of administration as well as dose exposure regimen also contributes to the regulation of AChE mRNA expression. Copyright © 2009 John Wiley & Sons, Ltd.
Missing peroxy radical sources within a rural forest canopy

Organic peroxy (RO2) and hydroperoxy (HO2) radicals are key intermediates in the photochemical processes that generate ozone, secondary organic aerosol and reactive nitrogen reservoirs throughout the troposphere. In regions with ample biogenic hydrocarbons, the richness and complexity of peroxy radical chemistry presents a significant challenge to current-generation models, especially given the scarcity of measurements in such environments. We present peroxy radical observations acquired within a Ponderosa pine forest during the summer 2010 Bio-hydro-atmosphere interactions of Energy, Aerosols, Carbon, H2O, Organics and Nitrogen - Rocky Mountain Organic Carbon Study (BEACHON-ROCS). Total peroxy radical mixing ratios reach as high as 180 pptv and are among the highest yet recorded. Using the comprehensive measurement suite to constrain a near-explicit 0-D box model, we investigate the sources, sinks and distribution of peroxy radicals below the forest canopy. The base chemical mechanism underestimates total peroxy radicals by as much as a factor of 3. Since primary reaction partners for peroxy radicals are either measured (NO) or under-predicted (HO2 and RO2, i.e. self-reaction), missing sources are the most likely explanation for this result. A close comparison of model output with observations reveals at least two distinct source signatures. The first missing source, characterized by a sharp midday maximum and a strong dependence on solar radiation, is consistent with photolytic production of HO2. The diel profile of the second missing source peaks in the afternoon and suggests a process that generates RO2 independently of sun-driven photochemistry, such as ozonolysis of reactive hydrocarbons. The maximum magnitudes of these missing sources (approximately 120 and 50 pptv min1, respectively) are consistent with previous observations alluding to unexpectedly intense oxidation within forests. We conclude that a similar mechanism may underlie many such observations.
HIV Alters Gap Junction-Mediated Intercellular Communication in Human Brain Pericytes

Despite successful control of viremia by combined antiretroviral therapy, brain infection and its resulting neurocognitive impairment remain a prevalent comorbidity in HIV infected individuals. HIV invades the brain early in the course of infection via penetration through the blood-brain barrier (BBB). While the impact of HIV on BBB astrocytes and endothelial cells is relatively well studied, the role of pericytes in BBB regulation during HIV infection remains unclear; however, it is known that a selective population of pericytes is prone to infection. In the present study, we hypothesize that injury signals are propagated from infected pericytes to neighboring cells via gap junction (GJ)-mediated intercellular communication. Among a variety of studied GJ proteins, HIV infection of human brain pericytes specifically increased expression of connexin 43 as determined by immunoblotting and immunostaining. This effect was confirmed in the brains of mice infected with EcoHIV, a mouse-specific HIV strain. In addition, HIV infection enhanced functional GJ-mediated intercellular communication in pericytes. The importance of this process was confirmed in experiments in which inhibition of GJs by carbenoxolone attenuated HIV infection. In addition to GJs, an extracellular ATP release assay revealed that HIV may also play a role in opening of connexin (Cx)-containing hemichannels (HCs). Overall, these findings indicate an important role of GJs in the propagation of HIV infection in human brain pericytes that may contribute to BBB dysfunction in brain infection and the pathogenesis of NeuroAIDS.
Differential vocational rehabilitation service patterns and outcomes for transition‐age youth with autism

BACKGROUND It is important to investigate receipt of vocational rehabilitation (VR) services, service patterns and outcomes for youth with autism, so that limited public resources can be used more efficiently. METHOD This study used chi-squared automatic interaction detector, and multivariate logistic regression analysis to investigate relationships between demographic variables, receipt of VR services and employment outcomes for transition-age youth (TAY) with Autism. RESULTS The results indicate that gender, education level and cash benefits are significant predictors of employment outcomes. After controlling for the effect of demographic variables, several VR services (i.e., job placement, on-the-job support, on-the-job training, maintenance, other services, information referral, and diagnostic and treatment services) were significantly associated with competitive employment. CONCLUSIONS Overall, the results indicate that job-related services were significantly related to employment outcomes for TAY with Autism; therefore, it is important these youths are provided with more targeted job placements and supported employment services (Wehman et al., ).
Clinical characteristics and cytokine changes in children with pneumonia requiring mechanical ventilation

Objective To assess clinical characteristics and cytokine levels in children with severe pneumonia who required ventilatory support. Methods In this prospective, descriptive, cross-sectional study, blood and endotracheal fluid samples were obtained from patients with severe pneumonia, aged <5 years, within 24 h following intubation. Blood samples were also obtained from age-matched healthy controls. Cytokine levels were investigated using flow cytometry-assisted immunoassay. Results Forty-five patients with severe pneumonia requiring mechanical ventilation (aged 10 ± 5 months) and 35 healthy age-matched controls were included. Patients with severe pneumonia had significantly increased serum interleukin (IL)-6, IL-8, and granulocyte/macrophage colony-stimulating factor concentrations compared with controls (80.84 pg/ml versus 2.06 pg/ml, 90.03 pg/ml versus 6.62 pg/ml, and 115.58 pg/ml versus 11.47 pg/ml, respectively). In the severe pneumonia group, serum IL-10 levels were significantly higher in patients aged <6 months versus those aged 6–12 months. Age-group differences in serum cytokine levels did not correspond to age-group differences in endotracheal-fluid cytokine levels. Serum IL-6 levels were significantly higher in patients who subsequently died versus those who survived (267.12 pg/ml versus 20.75 pg/ml, respectively). Conclusion High IL-6 concentrations were associated with mortality in patients <5 years of age with severe pneumonia requiring mechanical ventilation.
Intake Levels of Fish in the UK Paediatric Population

The United Kingdom (UK) is an island and its culture, including diet, is heavily influenced by the maritime resources. Dietary guidance in the UK recommends intake of fish, which provides important nutrients, such as long-chain omega-3 polyunsaturated fatty acids (n-3 PUFA). This study was designed to describe the fish intake habits of UK children using a nationally representative sample. Dietary and socio-demographic data of children 2–18 (N = 2096) in the National Diet and Nutrition Survey Rolling Program (NDNS) Years 1–4 (2008–2012) were extracted. Average nutrient and food intakes were estimated. Logistic regression models were used to predict the meeting of fish intake recommendations, controlling for age, sex, income, total energy intake, and survey year. All analyses were conducted using survey routines and dietary survey weights. In this nationally representative study, 4.7% of children met the fish and 4.5% the oily fish intake recommendations; only 1.3% of the population met both recommendations. Fish intake levels did not significantly change with children’s increasing age. Higher vegetable but lower meat consumption predicted meeting the fish intake recommendations, indicating that children eating fish have better diet quality than non-consumers. Further research is needed to explore how intake behaviours can be changed to improve children’s diet quality.
Pressure distribution of the high-redshift cluster of galaxies CL J1226.9+3332 with NIKA ?

The thermal Sunyaev-Zel’dovich (tSZ) e ect is expected to provide a low scatter mass proxy for galaxy clusters since it is directly proportional to the cluster thermal energy. The tSZ observations have proven to be a powerful tool for detecting and studying them, but high angular resolution observations are now needed to push their investigation to a higher redshift. In this paper, we report high angular (<20 arcsec) resolution tSZ observations of the high-redshift cluster CL J1226.9+3332 (z = 0:89). It was imaged at 150 and 260 GHz using the NIKA camera at the IRAM 30-m telescope. The 150 GHz map shows that CL J1226.9+3332 is morphologically relaxed on large scales with evidence of a disturbed core, while the 260 GHz channel is used mostly to identify point source contamination. NIKA data are combined with those of Planck and X-ray from Chandra to infer the cluster’s radial pressure, density, temperature, and entropy distributions. The total mass profile of the cluster is derived, and we find M500 = 5:96 +1:02 0:79 10 14 M within the radius R500 = 930 +50 kpc, at a 68% confidence level. (R500 is the radius within which the average density is 500 times the critical density at the cluster’s redshift.) NIKA is the prototype camera of NIKA2, a KIDs (kinetic inductance detectors) based instrument to be installed at the end of 2015. This work is, therefore, part of a pilot study aiming at optimizing tSZ NIKA2 large programs.
Narrow-band imaging with magnifying endoscopy for Peyer's patches is useful in predicting the recurrence of remissive patients with ulcerative colitis

Background/Aims Peyer's patches (PPs) are aggregates of lymphoid follicles that are mainly located in the distal ileum; they play a major role in mucosal immunity. We recently reported that patients with ulcerative colitis (UC) have alterations in PPs that can be detected using narrow-band imaging with magnifying endoscopy (NBI-ME). However, the usefulness of NBI-ME in UC treatment as a whole is still unknown. Methods We collected NBI-ME images of PPs from 67 UC patients who had undergone ileocolonoscopy. We evaluated changes in the villi using the "villi index," which is based on three categories: irregular formation, hyperemia, and altered vascular network pattern. The patients were divided into two groups on the basis of villi index: low (L)- and high (H)-types. We then determined the correlation between morphological alteration of the PPs and various clinical characteristics. In 52 patients who were in clinical remission, we also analyzed the correlation between NBI-ME findings of PPs and clinical recurrence. Results The time to clinical recurrence was significantly shorter in remissive UC patients with H-type PPs than in those with L-type PPs (P<0.01). Moreover, PP alterations were not correlated with age, sex, disease duration, clinical activity, endoscopic score, or extent of disease involvement. Multivariate analysis revealed that the existence of H-type PPs was an independent risk factor for clinical recurrence (hazard ratio, 3.3; P<0.01). Conclusions UC patients with morphological alterations in PPs were at high risk of clinical relapse. Therefore, to predict the clinical course of UC, it may be useful to evaluate NBI-ME images of PPs.
The imposition of participation?: the case of participatory water management in coastal Bangladesh

Community-based Natural Resources Management (CBNRM) has been promoted as part of the development discourse on sustainable natural resources management since the mid-1980s. It has influenced recent water policy in Bangladesh through the Guidelines for Participatory Water Management (GPWM) where community-based organisations are to participate in the management of water resources. This paper reviews the extent of success of such participatory water management. It does so by first discussing the changing discourses of participation in Bangladesh’s water policy from social mobilisation to decentralised CBNRM. Second, Bangladesh is used as a case study to draw attention to how the creation of separate water management organisations has been unable to promote inclusive participation. It argues that the current form of decentralisation through a CBNRM framework has not resulted in its stated aims of equitable, efficient, and sustainable management of natural resources; rather it has duplicated existing local government institutions. Finally, it questions the current investments into community-based organisations and recommends that the role of local government in water management be formally recognised.
Posttraumatic growth in breast cancer survivors and their husbands based on the actor‐partner interdependence model

This study aimed to verify actor and partner effects, by examining the effects of self‐esteem, relationship quality, and subjective distress on posttraumatic growth in breast cancer survivors and their spouses, and involved a structural analysis of descriptive cause‐and‐effect relationships to verify the suitability of the actor‐partner interdependence model.
ABO blood group and venous thromboembolism a ) Single studies

ABO blood group antigens are complex carbohydrate molecules expressed on red blood cells and a variety of tissues. The ABO blood type is implicated in the development of a number of human diseases and there is increasing evidence regarding its involvement in the pathogenesis of cardiovascular disorders, mainly through its effect on von Willebrand factor levels. In this review, after a brief analysis of the potential molecular mechanisms by which the blood group influences haemostasis, we focus on the clinical implications of such interaction. Overall, the literature data document the close relationship between venous thromboembolism (VTE) and non-O blood type, which is associated with an approximately two-fold increased risk of venous thrombosis. A supra-additive effect on VTE risk is observed when an inherited thrombophilic condition is associated with non-O blood group. A weaker association exists between non-O blood type and arterial thrombosis, which needs to be further investigated.