Miracle-dz/UniFAR-FTUs huggingface dataset:
Overproduction of Acetyl-CoA Carboxylase Activity Increases the Rate of Fatty Acid Biosynthesis in Escherichia coli *

Acetyl-CoA carboxylase (ACC) catalyzes the first committed step of the fatty acid synthetic pathway. Although ACC has often been proposed to be a major rate-controlling enzyme of this pathway, no direct tests of this proposal in vivo have been reported. We have tested this proposal in Escherichia coli.The genes encoding the four subunits of E. coli ACC were cloned in a single plasmid under the control of a bacteriophage T7 promoter. Upon induction of gene expression, the four ACC subunits were overproduced in equimolar amounts. Overproduction of the proteins resulted in greatly increased ACC activity with a concomitant increase in the intracellular level of malonyl-CoA. The effects of ACC overexpression on the rate of fatty acid synthesis were examined in the presence of a thioesterase, which provided a metabolic sink for fatty acid overproduction. Under these conditions ACC overproduction resulted in a 6-fold increase in the rate of fatty acid synthesis.
Effect of particle size on the hydration kinetics and microstructural development of tricalcium silicate

Impure tricalcium silicate (Alite, C3S) is the most important and abundant phase of Portland cement. It reacts quickly with water to give calcium hydroxide (CH) and calcium silicate hydrate (C-S-H) which is the most important phase for strength development. It is well known that the C3S particle size distribution plays an important role on the hydration kinetics, microstructural development and final properties of hydrated cement pastes. The general aim of the present investigation was to gain insight on the effect of particle size on the hydration kinetics and microstructural development of alite pastes. In this study, alite was synthesized and separated into different gradations. The hydration kinetics was investigated by means of isothermal calorimetry and chemical shrinkage. The microstructural developments of the different gradations of alite were studied and compared using different techniques such as: SEM, TEM, XRD, He pycnometry, N2 adsorption, etc. The hydration kinetics during the different stages of the hydration was observed to be dependent on the initial particle size of the grains and also related with the defect concentration on the surface of the grains. Higher rates of reaction were observed for powders with higher specific surface area. A linear relationship between the rate constant and the specific surface area was observed. Further, it was observed that the hydration kinetics of multi-sized system during the nucleation and growth process can be modeled as the linear addition of individual particles. The microstructural development of C3S pastes at later ages was found to be poorly affected by the initial particle size; the nature of the hydration products is the same. The only differences concern the capillary porosity and the C-S-H density. Slightly higher values of capillary porosity and C-S-H density were measured for smaller particles. The most likely explanation can be related with a different initial arrangement of the grains.
Detecting Epistasis in Genome-wide Association Studies with the Marginal EPIstasis Test

Epistasis, commonly defined as the interaction between multiple genes, is an important genetic component underlying phenotypic variation. Many statistical methods have been developed to model and identify epistatic interactions between genetic variants. However, because of the large combinatorial search space of interactions, most epistasis mapping methods face enormous computational challenges and often suffer from low statistical power. Here, we present a novel, alternative strategy for mapping epistasis: instead of directly identifying individual pairwise or higher-order interactions, we focus on mapping variants that have non-zero marginal epistatic effects — the combined pairwise interaction effects between the given variant and all other variants. By testing marginal epistatic effects, we can identify candidate variants that are involved in epistasis without the need to identify the exact partners with which the variants interact, thus potentially alleviating much of the statistical and computational burden associated with standard epistatic mapping procedures. Our method is based on the variance component model, and relies on a recently developed variance component estimation method for efficient parameter inference and p-value computation. We refer to our method as the “Marginal EPIstasis Test”, or MEPIT. With simulations, we show how MEPIT can be used to robustly estimate marginal epistatic effects, produce calibrated test statistics under the null, and facilitate the detection of pairwise epistatic interactions. We further illustrate the benefits of MEPIT on several real datasets, including seven common diseases from the Wellcome Trust Case Control Consortium, as well as body composition traits from a swine genome-wide association study.
The disc-jet coupling in the neutron star X-ray binary Aquila X-1

We study the accretion/ejection processes (i.e. disc/jet coupling) in the neutron star X-ray binary Aquila X-1 via a multiwavelength approach. We use in the radio band the publicly available Very Large Array archive containing observations of the object between 1986 and 2005, in the X-ray band the archival Rossi X-ray Timing Explorer data (Proportional Counter Array and High Energy X-ray Timing Experiment) between 1997 and 2008, and in optical (R band) observations with the Small and Moderate Aperture Research Telescope System recorded between 1998 and 2007. In the combined data set, we find three outbursts for which quasi-simultaneous radio, optical (R band) and X-ray data exist and focus on them to some extent. We provide evidence that the disc/jet coupling in Aquila X-1 is similar to what has been observed in black hole X-ray binaries, at least from the point of view of the behaviour in the hardness-intensity diagrams (the hysteresis effect included), when the phenomenology of the jet is taken into account. Although based on a very small number of observations, a radio/X-ray correlation seems to exist for this system, with a slope of α= 0.40 ± 0.07 (Fradio∝FαX), which is different than the slope of α= 1.40 ± 0.25 found for another atoll source, 4U 1728−34, but interestingly enough is relatively close to the values obtained for several black hole X-ray binaries. No significant correlation is found between the radio and optical (R-band) emissions. We also report a significant drop in the radio flux from Aquila X-1 above an X-ray flux of ∼5 × 10−9 erg cm−2 s−1. This behaviour, also reported in the neutron star X-ray binary 4U 1728−34, may be analogous to the suppression of radio emission in black hole X-ray binaries in bright, soft X-ray states. It suggests that from this point of view neutron star X-ray binaries can mimic the behaviour of black hole X-ray binaries in suppressing the jet in soft/disc-dominated X-ray states.
Presolar Graphite from AGB Stars: Microstructure and s-Process Enrichment

Correlated transmission electron microscopy and secondary ion mass spectrometry with submicron spatial resolution (NanoSIMS) investigations of the same presolar graphites spherules from the Murchison meteorite were conducted, to link the isotopic anomalies with the mineralogy and chemical composition of the graphite and its internal grains. Refractory carbide grains (especially titanium carbide) are commonly found within the graphite spherules, and most have significant concentrations of Zr, Mo, and Ru in solid solution, elements primarily produced by s-process nucleosynthesis. The effect of chemical fractionation on the Mo/Ti ratio in these carbides is limited, and therefore from this ratio one can infer the degree of s-process enrichment in the gas from which the graphite condensed. The resulting s-process enrichments within carbides are large (~200 times solar on average), showing that most of the carbide-containing graphites formed in the mass outflows of asymptotic giant branch (AGB) stars. NanoSIMS measurements of these graphites also show isotopically light carbon (mostly in the 100 < 12C/13C < 400 range). The enrichment of these presolar graphites in both s-process elements and 12C considerably exceeds that astronomically observed around carbon stars. However, a natural correlation exists between 12C and s-process elements, as both form in the He intershell region of thermally pulsing AGB stars and are dredged up together to the surface. Their observation together suggests that these graphites may have formed in chemically and isotopically inhomogeneous regions around AGB stars, such as high-density knots or jets. As shown in the companion paper, a gas density exceeding that expected for smooth mass outflows is required for graphite of the observed size to condense at all in circumstellar environments, and the spatially inhomogeneous, high-density regions from which they condense may also be incompletely mixed with the surrounding gas. We have greatly expanded the available data set of presolar graphites (N = 847) and characterized them by their morphology (onion type and cauliflower type). This effort has also revealed two new, rare presolar phases (iron carbide and metallic osmium). Due to the peculiar gas composition needed to form these rare presolar grain types, the graphites containing them are more likely to originate in supernova outflows.
RECQ5 helicase associates with the C-terminal repeat domain of RNA polymerase II during productive elongation phase of transcription

It is known that transcription can induce DNA recombination, thus compromising genomic stability. RECQ5 DNA helicase promotes genomic stability by regulating homologous recombination. Recent studies have shown that RECQ5 forms a stable complex with RNA polymerase II (RNAPII) in human cells, but the cellular role of this association is not understood. Here, we provide evidence that RECQ5 specifically binds to the Ser2,5-phosphorylated C-terminal repeat domain (CTD) of the largest subunit of RNAPII, RPB1, by means of a Set2–Rpb1-interacting (SRI) motif located at the C-terminus of RECQ5. We also show that RECQ5 associates with RNAPII-transcribed genes in a manner dependent on the SRI motif. Notably, RECQ5 density on transcribed genes correlates with the density of Ser2-CTD phosphorylation, which is associated with the productive elongation phase of transcription. Furthermore, we show that RECQ5 negatively affects cell viability upon inhibition of spliceosome assembly, which can lead to the formation of mutagenic R-loop structures. These data indicate that RECQ5 binds to the elongating RNAPII complex and support the idea that RECQ5 plays a role in the maintenance of genomic stability during transcription.
Learning Video Manifolds for Content Analysis of Crowded Scenes

In this paper, we propose a new approach for recognizing group events and abnormality detection in a crowded scene. A manifold learning algorithm with temporal-constraints is proposed to embed a video of a crowded scene in a low-dimensional space. Our low dimensional representation of a video preserves the spatial temporal property of a video as well as the characteristic of the video. Recognizing video events and abnormality detection in a crowded scene is achieved by studying the video trajectory in the manifold space. We evaluate our proposed method on the state-of-the-art public data-sets containing different crowd events. Qualitative and quantitative results show the promising performance of the proposed method.
Size effect regarding fatigue evaluation of asphalt mixtures

ABSTRACT Experimental results for fatigue tests on three size geometrically similar asphalt concrete specimen are presented. Effect on fatigue life is analyzed and compared to trends given by a fatigue damage model. This innovative laboratory campaign points out a size effect on fatigue assessment of asphalt mixture. In a second part, the application of a nonlocal fatigue damage model for asphalt mixtures is presented. A qualitative agreement is obtained between experimental results and non local damage fatigue predictions trends. This agreement validates the nonlocal modelling that allows to model the influence of the heterogeneous nature of the material on fatigue failure. Differences observed between laboratory data and model predictions may be attributed to viscoelasticity induced thermal softening which had to be quantified and coupled to damage in order to properly study these fatigue test data.
Interaction Between ACE and ADD1 Gene Polymorphisms in the Progression of IgA Nephropathy in Japanese Patients

Abstract—An interaction effect between the angiotensin-converting enzyme insertion/deletion (ACE I/D) and &agr;-adducin (ADD1) Gly460Trp polymorphisms (G460W) on blood pressure regulation has recently been suggested, although its significance in the prognosis of renal function in IgA nephropathy (IgAN) has not been fully investigated. Therefore, we evaluated the clinical manifestations and renal prognosis in 276 Japanese patients with histologically proven IgAN with respect to their ACE I/D and ADD1 G460W polymorphisms. The prognosis of renal function was analyzed by Kaplan-Meier survival curves and multivariate Cox proportional-hazards regression models. Baseline data, including blood pressures, proteinuria, renal function, and incidence of hypertension, were similar for the different genotypes of ACE and ADD1. The individual genotypes taken alone were not associated with the progression of renal dysfunction. However, renal survival of patients with the 460WW polymorphism of ADD1 was significantly worse within the group with the II genotype of ACE (Kaplan-Meier, log rank test; &khgr;2=6.062, P =0.0138) but not for those with other ACE genotypes. In the Cox proportional-hazards regression model with adjustment for clinical risk factors, including hypertension, proteinuria, and no administration of an angiotensin-converting enzyme inhibitors or angiotensin II receptor blockers, the 460WW variant of ADD1 was a highly significant and independent risk factor only for patients with the ACE II genotype, with a hazard ratio of 3.65 (P =0.0016), but not for those with other ACE genotypes (hazard ratio=0.65, P =0.2902). These findings suggest an interaction between ACE and ADD1 polymorphisms not only on blood pressure regulation but also on the progression of renal dysfunction in patients with IgAN.
Neurobiological substrates of Tourette's disorder.

OBJECTIVE This article reviews the available scientific literature concerning the neurobiological substrates of Tourette's disorder (TD). METHODS The electronic databases of PubMed, ScienceDirect, and PsycINFO were searched for relevant studies using relevant search terms. RESULTS Neuropathological as well as structural and functional neuroimaging studies of TD implicate not only the sensorimotor corticostriatal circuit, but also the limbic and associative circuits as well. Preliminary evidence also points to abnormalities in the frontoparietal network that is thought to maintain adaptive online control. Evidence supporting abnormalities in dopaminergic and noradrenergic neurotransmission remains strong, although the precise mechanisms remain the subject of speculation. CONCLUSION Structural and functional abnormalities in multiple parallel corticostriatal circuits may underlie the behavioral manifestations of TD and related neuropsychiatric disorders over the course of development. Further longitudinal research is needed to elucidate these neurobiological substrates.
A Spatial Clustering Method With Edge Weighting for Image Segmentation

As one of the best image clustering methods, fuzzy local information C-means is often used for image segmentation. The effects of noise are avoided by utilizing the spatial relationship among pixels, but it often generates boundary zones for the mix pixels around the edges. This letter presents an image spatial clustering method, called fuzzy C-means with edge and local information (FELICM), which reduces the edge degradation by introducing the weights of pixels within local neighbor windows. The edges are extracted at first by Canny edge detection. During detection, two adaptive thresholds obtained by multi-Otsu method are used. Then, different weights are set according to whether the window center and the local neighbors are separated by an edge or not. Pixels, together with different weighted local neighbors, are clustered iteratively, until the final clustering result is obtained. The method can be directly applied to the image without any filter preprocessing, and the experimental results over remote sensing images show that FELICM not only effectively solves the problem of isolated and random distribution of pixels inside regions but also obtains high edge accuracies.
A Ka-band MMIC Doherty Power Amplifier using GaAs pHEMT technology

A fully integrated Ka-band Monolithic microwave integrated circuit (MMIC) Doherty Power Amplifier (PA) is designed and demonstrated in this paper. The proposed Doherty PA maily consists of a Lange coupler, carrier amplifier branch, peaking amplifier branch and impedance transformer network. offset lines are introduced in each branch to overcome the inherent defects of conventional Doherty PA. Electromagnetic (EM) simulated results show the proposed Doherty PA obtains a small signal gain over 5.5dB from 31GHz to 35GHz with a compact die size of 2mm×1.7mm. Power added efficiency (PAE) is over 19.8% at 6dB back-off with saturated output power over 26dBm.
Effect of activation of protein kinase C on CD45 isoform expression and CD45 protein tyrosine phosphatase activity in T cells

The T200/leukocyte common antigen (CD45) is a family of at least five large‐molecular weight glycoproteins, which are differentially expressed on T cell subsets. The CD45 antigen consists of a variable heavily glycosylated exterior domain, a single membrane‐spanning region, and a large cytoplasmic domain that has protein tyrosine phosphatase (PTPase) activity. In this study, we examined the effects of activation of protein kinase C (PKC) on the phosphorylation and expression of CD45 isoforms and PTPase activity in human T cells. After activation of PKC by phorbol 12‐myristate 13‐acetate (PMA), CD45RA expression rapidly increased within the first 24 h, whereas CD45RO expression did not change within this time. However by 48 h, expression of CD45RO also began to increase. Metabolic labeling showed that the rapid increment in CD45RA expression observed after PMA stimulation is primarily due to increased de novo synthesis of the 205‐kDa and not the 220‐kDa molecule. PMA treatment resulted in the phosphorylation of each CD45 isoform to a degree corresponding to its relative surface expression. Significantly, we found that the phosphorylation of CD45 by PKC activation down‐regulated CD45 PTPase activity.
Substrate delivery by the AAA+ ClpX and ClpC1 unfoldases activates the mycobacterial ClpP1P2 peptidase

Mycobacterial Clp‐family proteases function via collaboration of the heteromeric ClpP1P2 peptidase with a AAA+ partner, ClpX or ClpC1. These enzymes are essential for M. tuberculosis viability and are validated antibacterial drug targets, but the requirements for assembly and regulation of functional proteolytic complexes are poorly understood. Here, we report the reconstitution of protein degradation by mycobacterial Clp proteases in vitro and describe novel features of these enzymes that distinguish them from orthologues in other bacteria. Both ClpX and ClpC1 catalyse ATP‐dependent unfolding and degradation of native protein substrates in conjunction with ClpP1P2, but neither mediates protein degradation with just ClpP1 or ClpP2. ClpP1P2 alone has negligible peptidase activity, but is strongly stimulated by translocation of protein substrates into ClpP1P2 by either AAA+ partner. Interestingly, our results support a model in which both binding of a AAA+ partner and protein‐substrate delivery are required to stabilize active ClpP1P2. Our model has implications for therapeutically targeting ClpP1P2 in dormant M. tuberculosis, and our reconstituted systems should facilitate identification of novel Clp protease inhibitors and activators.
Early Parallel Activation of Semantics and Phonology in Picture Naming: Evidence from a Multiple Linear Regression MEG Study

The time course of brain activation during word production has become an area of increasingly intense investigation in cognitive neuroscience. The predominant view has been that semantic and phonological processes are activated sequentially, at about 150 and 200–400 ms after picture onset. Although evidence from prior studies has been interpreted as supporting this view, these studies were arguably not ideally suited to detect early brain activation of semantic and phonological processes. We here used a multiple linear regression approach to magnetoencephalography (MEG) analysis of picture naming in order to investigate early effects of variables specifically related to visual, semantic, and phonological processing. This was combined with distributed minimum-norm source estimation and region-of-interest analysis. Brain activation associated with visual image complexity appeared in occipital cortex at about 100 ms after picture presentation onset. At about 150 ms, semantic variables became physiologically manifest in left frontotemporal regions. In the same latency range, we found an effect of phonological variables in the left middle temporal gyrus. Our results demonstrate that multiple linear regression analysis is sensitive to early effects of multiple psycholinguistic variables in picture naming. Crucially, our results suggest that access to phonological information might begin in parallel with semantic processing around 150 ms after picture onset.
Improved Semi Analytical Model of Effective Area for a Step and ParabolicIndex Optical Fiber: Introduction of Increased Parameters in Fundamental Modal Field

An accurate three parameter approximate solution of fundamental mode, to describe different propagation parameter of graded-index optical fiber has been presented. Due to three parameter optimization of the fundamental modal solution, the results are much more accurate for a wide range of optical fiber specifications. Employing variational technique, an estimation of effective area and effective index with proposed fundamental modal field are carried out. It has been shown that the results match identically with the exact available results for step and parabolic refractive index profile optical fiber. The accurate analytical expressions for the evaluation of effective area and effective index are formulated. Optimization of three parameters has been carried out for a wide range of normalized frequencies. Data for these parameters are also provided, which can be used directly while calculating different design parameters of an optical fiber.