Miracle-dz/UniFAR-FTUs huggingface dataset:
The histone variant H2A.Z promotes initiation of meiotic recombination in fission yeast

Abstract Meiotic recombination is initiated by programmed formation of DNA double strand breaks (DSBs), which are mainly formed at recombination hotspots. Meiotic DSBs require multiple proteins including the conserved protein Spo11 and its cofactors, and are influenced by chromatin structure. For example, local chromatin around hotspots directly impacts DSB formation. Moreover, DSB is proposed to occur in a higher-order chromatin architecture termed ‘axis-loop’, in which many loops protrude from cohesin-enriched axis. However, still much remains unknown about how meiotic DSBs are generated in chromatin. Here, we show that the conserved histone H2A variant H2A.Z promotes meiotic DSB formation in fission yeast. Detailed investigation revealed that H2A.Z is neither enriched around hotspots nor axis sites, and that transcript levels of DSB-promoting factors were maintained without H2A.Z. Moreover, H2A.Z appeared to be dispensable for chromatin binding of meiotic cohesin. Instead, in H2A.Z-lacking mutants, multiple proteins involved in DSB formation, such as the fission yeast Spo11 homolog and its regulators, were less associated with chromatin. Remarkably, nuclei were more compact in the absence of H2A.Z. Based on these, we propose that fission yeast H2A.Z promotes meiotic DSB formation partly through modulating chromosome architecture to enhance interaction between DSB-related proteins and cohesin-loaded chromatin.
Varying Correlation Between 18F-Fluorodeoxyglucose Positron Emission Tomography and Dynamic Contrast-Enhanced MRI in Carotid Atherosclerosis: Implications for Plaque Inflammation

Background and Purpose— 18F-fluorodeoxyglucose positron emission tomography and dynamic contrast-enhanced MRI have been proposed to quantitatively assess plaque inflammation by probing macrophages and neovessels, respectively. We examined their correlation to study the in vivo relationship between macrophage and neovessel activities in atherogenesis. Methods— Forty-one patients (34 men; aged 65±12 years) with a total of 68 carotid plaques (thickness ≥2 mm on ultrasound; 20 symptomatic) were assessed by both 18F-fluorodeoxyglucose positron emission tomography/computed tomography and dynamic contrast-enhanced MRI within 2 weeks, measured as target-to-background ratio and transfer constant (Ktrans), respectively. Results— Overall, the correlation between target-to-background ratio and Ktrans was weak and marginal (r=0.22; P=0.068). They were correlated in the symptomatic plaques (r=0.59; P=0.006) but not in the asymptomatic plaques (r=0.07; P=0.625; P=0.033 for difference in r). Neither target-to-background ratio nor Ktrans was significantly higher in the symptomatic plaques, but both showed an inverse relationship with time since last neurological event (r=−0.94 and −0.69 for target-to-background ratio and Ktrans, respectively). Conclusions— The correlation between 18F-fluorodeoxyglucose positron emission tomography and dynamic contrast-enhanced MRI measurements varied with clinical conditions, pointing to a complex interplay between macrophages and neovessels under different pathophysiological conditions. The moderate correlation shown only in symptomatic plaques indicates the presence of acute plaque inflammation with increased metabolic activity and cytokine production by inflammatory cells.
Cancer Statistics in Korea: Incidence, Mortality, Survival, and Prevalence in 2011

Purpose This study aimed to report nationwide cancer statistics in Korea, including incidence, mortality, survival, and prevalence, and their trends. Materials and Methods Incidence data from 1993 to 2011 were obtained from the Korea National Cancer Incidence Database, and vital status was followed through December 31, 2012. Mortality data from 1983 to 2011 were obtained from Statistics Korea. Crude and age-standardized rates for incidence, mortality, and prevalence, and relative survival were calculated. Results A total of 218,017 cancer cases and 71,579 cancer deaths were reported to have occurred in 2011, and there were 1,097,253 prevalent cases identified in Korea as of January 1, 2012. Over the past 13 years (1999-2011), overall incidence rates have increased by 3.4% per year. The incidence rates of liver and cervical cancers have decreased, while those of thyroid, breast, prostate, and colorectal cancers have increased. Notably, thyroid cancer increased by 23.3% per year in both sexes, and became the most common cancer since 2009. The mortality for all cancers combined decreased by 2.7% per year from 2002 to 2011. Five-year relative survival rates of patients diagnosed in the last 5 years (2007-2011) have improved by 25.1% compared with those from 1993 to 1995. Conclusion Overall cancer mortality rates have declined since 2002 in Korea, while incidence has increased rapidly and survival has improved.
Analysis of Increasing Flash Flood Frequency in the Densely Urbanized Coastline of the Campi Flegrei Volcanic Area, Italy

Climate change is affecting the frequency and severity of extreme meteorological and geo-hydrological events hitting the coastal zone of the Campi Flegrei volcanic district (southern Italy), which is prone to a wide spectrum of natural hazards, including volcanism, earthquakes, ground deformation, flash floods, landslides and coastal erosion. This study documents the trend of flash floods affecting the urban area of Pozzuoli, located along the coastline of the Campi Flegrei volcanic area during 1970-2014 time period. An archive research together with the collection of data published on news websites and social media allowed understanding of the triggering and evolution mechanisms of flash floods in the area, as well as the most recurrent damages. Rainfall data collected by the rain gauge located within the Pozzuoli watershed were also analyzed and rainfall properties estimated. Results of this study show an increased frequency of flash flood events occurred in the study area. The variation in flash flood frequency is likely not related to urbanization changes, as no increase of the urban area occurred after the year 2000. The observed increase in the flash flood events in recent years (2000-2014) can be reasonably ascribed to variations in the rainfall regime. Our research provide a contribution for the understanding of flash flood processes in the study area as well as relevant information for hazard and risk assessment.
Increased coronary atherosclerosis and immune activation in HIV-1 elite controllers

HIV-1 elite controllers spontaneously maintain suppressed levels of viremia, but exhibit significant immune activation. We investigated coronary atherosclerosis by coronary computed tomography angiography (CTA) in elite controllers, nonelite controller, chronically HIV-1 infected, antiretroviral therapy (ART)-treated patients with undetectable viral load (‘chronic HIV’), and HIV-negative controls. Prevalence of atherosclerosis (78 vs. 42%, P < 0.05) and markers of immune activation were increased in elite controllers compared with HIV-negative controls. sCD163, a monocyte activation marker, was increased in elite controllers compared with chronic HIV-1 (P < 0.05) and compared with HIV-negative controls (P < 0.05). These data suggest a significant degree of coronary atherosclerosis and monocyte activation among elite controllers.
Thermodynamic Driving Force of Hydrogen on Rumen Microbial Metabolism: A Theoretical Investigation

Hydrogen is a key product of rumen fermentation and has been suggested to thermodynamically control the production of the various volatile fatty acids (VFA). Previous studies, however, have not accounted for the fact that only thermodynamic near-equilibrium conditions control the magnitude of reaction rate. Furthermore, the role of NAD, which is affected by hydrogen partial pressure (PH2), has often not been considered. The aim of this study was to quantify the control of PH2 on reaction rates of specific fermentation pathways, methanogenesis and NADH oxidation in rumen microbes. The control of PH2 was quantified using the thermodynamic potential factor (FT), which is a dimensionless factor that corrects a predicted kinetic reaction rate for the thermodynamic control exerted. Unity FT was calculated for all glucose fermentation pathways considered, indicating no inhibition of PH2 on the production of a specific type of VFA (e.g., acetate, propionate and butyrate) in the rumen. For NADH oxidation without ferredoxin oxidation, increasing PH2 within the rumen physiological range decreased FT from unity to zero for different NAD+ to NADH ratios and pH of 6.2 and 7.0, which indicates thermodynamic control of PH2. For NADH oxidation with ferredoxin oxidation, increasing PH2 within the rumen physiological range decreased FT from unity at pH of 7.0 only. For the acetate to propionate conversion, FT increased from 0.65 to unity with increasing PH2, which indicates thermodynamic control. For propionate to acetate and butyrate to acetate conversions, FT decreased to zero below the rumen range of PH2, indicating full thermodynamic suppression. For methanogenesis by archaea without cytochromes, FT differed from unity only below the rumen range of PH2, indicating no thermodynamic control. This theoretical investigation shows that thermodynamic control of PH2 on individual VFA produced and associated yield of hydrogen and methane cannot be explained without considering NADH oxidation.
β-Aminobutyric acid increases abscisic acid accumulation and desiccation tolerance and decreases water use but fails to improve grain yield in two spring wheat cultivars under soil drying

A pot experiment was conducted to investigate the effect of the non-protein amino acid, β-aminobutyric acid (BABA), on the homeostasis between reactive oxygen species (ROS) and antioxidant defence during progressive soil drying, and its relationship with the accumulation of abscisic acid (ABA), water use, grain yield, and desiccation tolerance in two spring wheat (Triticum aestivum L.) cultivars released in different decades and with different yields under drought. Drenching the soil with 100 µM BABA increased drought-induced ABA production, leading to a decrease in the lethal leaf water potential (Ψ) used to measure desiccation tolerance, decreased water use, and increased water use efficiency for grain (WUEG) under moderate water stress. In addition, at severe water stress levels, drenching the soil with BABA reduced ROS production, increased antioxidant enzyme activity, and reduced the oxidative damage to lipid membranes. The data suggest that the addition of BABA triggers ABA accumulation that acts as a non-hydraulic root signal, thereby closing stomata, and reducing water use at moderate stress levels, and also reduces the production of ROS and increases the antioxidant defence enzymes at severe stress levels, thus increasing the desiccation tolerance. However, BABA treatment had no effect on grain yield of wheat when water availability was limited. The results suggest that there are ways of effectively priming the pre-existing defence pathways, in addition to genetic means, to improve the desiccation tolerance and WUEG of wheat.
The Dynamics of Democracy, Development and Cultural Values

Over the past decades many countries have experienced rapid changes in their economies, their democratic institutions and the values of their citizens. Comprehensive data measuring these changes across very different countries has recently become openly available. Between country similarities suggest common underlying dynamics in how countries develop in terms of economy, democracy and cultural values. We apply a novel Bayesian dynamical systems approach to identify the model which best captures the complex, mainly non-linear dynamics that underlie these changes. We show that the level of Human Development Index (HDI) in a country drives first democracy and then higher emancipation of citizens. This change occurs once the countries pass a certain threshold in HDI. The data also suggests that there is a limit to the growth of wealth, set by higher emancipation. Having reached a high level of democracy and emancipation, societies tend towards equilibrium that does not support further economic growth. Our findings give strong empirical evidence against a popular political science theory, known as the Human Development Sequence. Contrary to this theory, we find that implementation of human-rights and democratisation precede increases in emancipative values.
Capacity Scaling of Wireless Networks With Inhomogeneous Node Density: Lower Bounds

We consider static ad hoc wireless networks comprising significant inhomogeneities in the node spatial distribution over the area and analyze the scaling laws of their transport capacity as the number of nodes increases. In particular, we consider nodes placed according to a shot-noise Cox process (SNCP), which allows to model the clustering behavior usually recognized in large-scale systems. For this class of networks, we propose novel scheduling and routing schemes that approach previously computed upper bounds to the per-flow throughput as the number of nodes tends to infinity.
Elastically deformable models

The theory of elasticity describes deformable materials such as rubber, cloth, paper, and flexible metals. We employ elasticity theory to construct differential equations that model the behavior of non-rigid curves, surfaces, and solids as a function of time. Elastically deformable models are active: they respond in a natural way to applied forces, constraints, ambient media, and impenetrable obstacles. The models are fundamentally dynamic and realistic animation is created by numerically solving their underlying differential equations. Thus, the description of shape and the description of motion are unified.
Optimizing the Removal of Rhodamine B in Aqueous Solutions by Reduced Graphene Oxide-Supported Nanoscale Zerovalent Iron (nZVI/rGO) Using an Artificial Neural Network-Genetic Algorithm (ANN-GA)

Rhodamine B (Rh B) is a toxic dye that is harmful to the environment, humans, and animals, and thus the discharge of Rh B wastewater has become a critical concern. In the present study, reduced graphene oxide-supported nanoscale zero-valent iron (nZVI/rGO) was used to treat Rh B aqueous solutions. The nZVI/rGO composites were synthesized with the chemical deposition method and were characterized using scanning electron microscopy (SEM), X-ray diffraction (XRD), Raman spectroscopy, N2-sorption, and X-ray photoelectron spectroscopy (XPS) analysis. The effects of several important parameters (initial pH, initial concentration, temperature, and contact time) on the removal of Rh B by nZVI/rGO were optimized by response surface methodology (RSM) and artificial neural network hybridized with genetic algorithm (ANN-GA). The results suggest that the ANN-GA model was more accurate than the RSM model. The predicted optimum value of Rh B removal efficiency (90.0%) was determined using the ANN-GA model, which was compatible with the experimental value (86.4%). Moreover, the Langmuir, Freundlich, and Temkin isotherm equations were applied to fit the adsorption equilibrium data, and the Freundlich isotherm was the most suitable model for describing the process for sorption of Rh B onto the nZVI/rGO composites. The maximum adsorption capacity based on the Langmuir isotherm was 87.72 mg/g. The removal process of Rh B could be completed within 20 min, which was well described by the pseudo-second order kinetic model.
A Hybrid Approach for Predicting PM 2

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Evaluation of Changes in Morphology and Function of Human Induced Pluripotent Stem Cell Derived Cardiomyocytes (HiPSC-CMs) Cultured on an Aligned-Nanofiber Cardiac Patch

Introduction Dilated cardiomyopathy is a major cause of progressive heart failure. Utilization of stem cell therapy offers a potential means of regenerating viable cardiac tissue. However, a major obstacle to stem cell therapy is the delivery and survival of implanted stem cells in the ischemic heart. To address this issue, we have developed a biomimetic aligned nanofibrous cardiac patch and characterized the alignment and function of human inducible pluripotent stem cell derived cardiomyocytes (hiPSC-CMs) cultured on this cardiac patch. This hiPSC-CMs seeded patch was compared with hiPSC-CMs cultured on standard flat cell culture plates. Methods hiPSC-CMs were cultured on; 1) a highly aligned polylactide-co-glycolide (PLGA) nanofiber scaffold (~50 microns thick) and 2) on a standard flat culture plate. Scanning electron microscopy (SEM) was used to determine alignment of PLGA nanofibers and orientation of the cells on the respective surfaces. Analysis of gap junctions (Connexin-43) was performed by confocal imaging in both the groups. Calcium cycling and patch-clamp technique were performed to measure calcium transients and electrical coupling properties of cardiomyocytes. Results SEM demonstrated >90% alignment of the nanofibers in the patch which is similar to the extracellular matrix of decellularized rat myocardium. Confocal imaging of the cardiomyocytes demonstrated symmetrical alignment in the same direction on the aligned nanofiber patch in sharp contrast to the random appearance of cardiomyocytes cultured on a tissue culture plate. The hiPSC-CMs cultured on aligned nanofiber cardiac patches showed more efficient calcium cycling compared with cells cultured on standard flat surface culture plates. Quantification of mRNA with qRT-PCR confirmed that these cardiomyocytes expressed α-actinin, troponin-T and connexin-43 in-vitro. Conclusions Overall, our results demonstrated changes in morphology and function of human induced pluripotent derived cardiomyocytes cultured in an anisotropic environment created by an aligned nanofiber patch. In this environment, these cells better approximate normal cardiac tissue compared with cells cultured on flat surface and can serve as the basis for bioengineering of an implantable cardiac patch.
Relaxin inhibits cardiac fibrosis and endothelial–mesenchymal transition via the Notch pathway

Background Relaxin (RLX) can prevent cardiac fibrosis. We aimed to investigate the possible mechanism and signal transduction pathway of RLX inhibiting cardiac fibrosis. Methods Isoproterenol (5 mg·kg−1·d−1) was used to establish the cardiac fibrosis model in rats, which were administered RLX. The cardiac function, related targets of cardiac fibrosis, and endothelial–mesenchymal transition (EndMT) were measured. Transforming growth factor β (TGF-β) was used to induce EndMT in human umbilical vein endothelial cells, which were pretreated with RLX, 200 ng·mL−1, then with the inhibitor of Notch. Transwell cell migration was used to evaluate cell migration. CD31 and vimentin content was determined by immunofluorescence staining and Western blot analysis. Notch protein level was examined by Western blot analysis. Results RLX improved cardiac function in rats with cardiac fibrosis; it reduced the content of collagen I and III, increased the microvascular density of the myocardium, and suppressed the EndMT in heart tissue. In vitro, RLX decreased the mobility of human umbilical vein endothelial cells induced by TGF-β, increased the expression of endothelial CD31, and decreased vimentin content. Compared to TGF-β and RLX co-culture alone, TGF-β + RLX + Notch inhibitor increased cell mobility and the EndMT, but decreased the levels of Notch-1, HES-1, and Jagged-1 proteins. Conclusion RLX may inhibit the cardiac fibrosis via EndMT by Notch-mediated signaling.
Book Reviews: Foundations of Statistical Natural Language Processing

Statistical approaches to processing natural language text have become dominant in recent years. This foundational text is the first comprehensive introduction to statistical natural language processing (NLP) to appear. The book contains all the theory and algorithms needed for building NLP tools. It provides broad but rigorous coverage of mathematical and linguistic foundations, as well as detailed discussion of statistical methods, allowing students and researchers to construct their own implementations. The book covers collocation finding, word sense disambiguation, probabilistic parsing, information retrieval, and other applications.
APPLICATION OF A GENERIC PHYSIOLOGICALLY BASED PHARMACOKINETIC MODEL TO THE ESTIMATION OF XENOBIOTIC LEVELS IN HUMAN PLASMA

Estimation of xenobiotic kinetics in humans frequently relies upon extrapolation from experimental data generated in animals. In an accompanying paper, we have presented a unique, generic, physiologically based pharmacokinetic model and described its application to the prediction of rat plasma pharmacokinetics from in vitro data alone. Here we demonstrate the application of the same model, parameterized for human physiology, to the estimation of plasma pharmacokinetics in humans and report a comparative evaluation against some recently published predictive methods that involve scaling from in vivo animal data. The model was parameterized through an optimization process, using a training set of in vivo data taken from the literature, and validated using a separate test set of published in vivo data. On average, the vertical divergence of the predicted plasma concentrations from the observed data, on a semilog concentration-time plot, was 0.47 log unit. For the training set, more than 80% of the predicted values of a standardized measure of the area under the concentration-time curve were within 3-fold of the observed values; over 70% of the test set predictions were within the same margin. Furthermore, in terms of predicting human clearance for the test set, the model was found to match or exceed the performance of three published interspecies scaling methods, all of which showed a distinct bias toward overprediction. We conclude that the generic physiologically based pharmacokinetic model, as a means of integrating readily determined in vitro and/or in silico data, is potentially a powerful, cost-effective tool for predicting human xenobiotic kinetics in drug discovery and risk assessment.