Miracle-dz/UniFAR-FTUs huggingface dataset:
Poly(3‐hydroxybutyrate) fuels the tricarboxylic acid cycle and de novo lipid biosynthesis during Bacillus anthracis sporulation

Numerous bacteria accumulate poly(3‐hydroxybutyrate) (PHB) as an intracellular reservoir of carbon and energy in response to imbalanced nutritional conditions. In Bacillus spp. , where PHB biosynthesis precedes the formation of the dormant cell type called the spore (sporulation), the direct link between PHB accumulation and efficiency of sporulation was observed in multiple studies. Although the idea of PHB as an intracellular carbon and energy source fueling sporulation was proposed several decades ago, the mechanisms underlying PHB contribution to sporulation have not been defined. Here, we demonstrate that PHB deficiency impairs Bacillus anthracis sporulation through diminishing the energy status of the cells and by reducing carbon flux into the tricarboxylic acid (TCA) cycle and de novo lipid biosynthesis. Consequently, this metabolic imbalance decreased biosynthesis of the critical components required for spore integrity and resistance, such as dipicolinic acid (DPA) and the spore's inner membrane. Supplementation of the PHB deficient mutant with exogenous fatty acids overcame these sporulation defects, highlighting the importance of the TCA cycle and lipid biosynthesis during sporulation. Combined, the results of this work reveal the molecular mechanisms of PHB contribution to B. anthracis sporulation and provide valuable insight into the metabolic requirements for this developmental process in Bacillus species.
Intracellular nicotinamide phosphoribosyltransferase protects against hepatocyte apoptosis and is down-regulated in nonalcoholic fatty liver disease.

CONTEXT Nonalcoholic fatty liver disease (NAFLD) is the most common liver disease in Western and non-Western countries, but its pathogenesis is not fully understood. OBJECTIVE Based on the role of nicotinamide phosphoribosyltransferase (NAMPT) in fat and glucose metabolism and cell survival, we hypothesized a role for NAMPT/visfatin in the pathogenesis of NAFLD-related disease. DESIGN AND SETTING We conducted clinical studies at a referral medical center in well-characterized NAFLD patients (n = 58) and healthy controls (n = 27). In addition we performed experimental in vitro studies in hepatocytes. MAIN OUTCOME MEASURES We examined 1) the hepatic and systemic expression of NAMPT/visfatin in patients with NAFLD and control subjects, 2) the hepatic regulation of NAMPT/visfatin, and 3) the effect of NAMPT/visfatin on hepatocyte apoptosis. RESULTS Our main findings were as follows. 1) Patients with NAFLD had decreased NAMPT/visfatin expression both systemically in serum and within the hepatic tissue, with no difference between simple steatosis and nonalcoholic steatohepatitis. 2) By studying the hepatic regulation of NAMPT/visfatin in wild-type and peroxisome proliferators-activated receptor (PPAR)alpha(-/-) mice as well as in hepatocytes, we showed that PPARalpha activation and glucose may be involved in the down-regulation of hepatic NAMPT/visfatin expression in NAFLD. 4) Within the liver, NAMPT/visfatin was located to hepatocytes, and our in vitro studies showed that NAMPT/visfatin exerts antiapoptotic effects in these cells, involving enzymatic synthesis of nicotinamide adenine dinucleotide. CONCLUSION Based on these findings, we suggest a role for decreased NAMPT/visfatin levels in hepatocyte apoptosis in NAFLD-related disease.
Nicotine exposure refines visual map topography through an NMDA receptor‐mediated pathway

The precise mapping of one surface onto another is fundamental to visual system organization and depends upon adequate stimulation of postsynaptic targets to stabilize correctly placed synapses. As exogenous nicotine alters neuronal activity, we investigated whether it would affect the visual map created by retinal ganglion cell terminals in the frog optic tectum. Chronic exposure of the tectum to nicotine decreased the retinal area from which cells project to a given tectal site. This map refinement was also produced by exposure to either the α‐bungarotoxin sensitive nicotinic receptor agonist, anatoxin‐a or the α‐bungarotoxin‐insensitive nicotinic receptor agonist epiboxidine. Immunocytochemical studies using mAb306 and mAb22 demonstrated that α‐bungarotoxin‐sensitive and ‐insensitive nicotinic receptors, respectively, occupied different tectal sites. Choline acetyltransferase immunoreactivity overlapped with mAb306, but not mAb22, staining. The developing optic tectum was more sensitive to nicotine than the adult tectum and nicotine induced both map refinements and map disruptions in a concentration‐dependent manner. Blockade of the N‐methyl‐d‐aspartate (NMDA) receptor with D(–)‐2‐amino‐5‐phosphonopentanoic acid (D‐APV) prevented nicotine from refining the map in the adult tectum. Exposure to the use‐dependent NMDA antagonist MK801 alone had no effect on retinotectal topography but in combination with either NMDA or nicotine it disrupted the map. Exposure to NMDA alone produced refinement. We conclude that the map refinement induced by chronic nicotine treatment has as its basis an increase in the level of NMDA receptor activity. The data are consistent with a model whereby map topography can be bidirectionally affected by either increasing or decreasing NMDA receptor activity.
Conservation Abilities in Middle-Aged and Elderly Adults

The conservation abilities of middle-aged and elderly adults were compared. The design was a 3 (noninstitutionalized middle-aged, noninstitutionalized elderly, and institutionalized elderly) × 2 (male and female) × 3 (substance, weight, and volume conservation) × 2 (judgment and explanation responses) factorial design. The results of both an analysis of variance and correlational analyses indicated that age was not significantly related to conservation performance. Likewise, no significant institutionalization or sex effects were obtained. However, correlational analyses yielded a significant positive relationship between education and conservation.
Endothelin‐1 gene regulation

Over two decades of research have demonstrated that the peptide hormone endothelin‐1 (ET‐1) plays multiple, complex roles in cardiovascular, neural, pulmonary, reproductive, and renal physiology. Differential and tissue‐specific production of ET‐1 must be tightly regulated in order to preserve these biologically diverse actions. The primary mechanism thought to control ET‐1 bioavailability is the rate of transcription from the ET‐1 gene (ednl). Studies conducted on a variety of cell types have identified key transcription factors that govern ednl expression. With few exceptions, the cts‐acting elements bound by these factors have been mapped in the ednl regulatory region. Recent evidence has revealed new roles for some factors originally believed to regulate ednl in a tissue or hormone‐specific manner. In addition, other mechanisms involved in epigenetic regulation and mRNA stability have emerged as important processes for regulated ednl expression. The goal of this review is to provide a comprehensive overview of the specific factors and signaling systems that govern ednl activity at the molecular level. —Stow, L. R. , Jacobs, M. E. , Wingo, C. S. , Cain, B. D. Endothelin‐1 gene regulation. FASEB J. 25, 16–28 (2011). www.fasebj. org
Exercise Rehabilitation for Patients with Peripheral Arterial Disease

Intermittent claudication, resulting from PAD, impairs functional status. Reducing the disability result from the disease is therefore an important goal of treatment. To evaluate the efficacy of an intervention designed to improve functional status requires that appropriate outcome measures be developed to assess all treatments. Such outcome measures include graded treadmill testing and questionnaire assessment. These methodologies are important because they have a high degree of precision and accuracy and are practical and reproducible. Thus, functional status changes resulting from any intervention can be evaluated, and interventions can be compared with one another using the same methodologies. Currently, interventional therapies are often used to treat a portion of patients with claudication [49]. Such therapies restore blood flow and improve functional status, but with a high associated cost: morbidity and mortality. Pharmacological therapies currently are being developed, but the role of drugs in the overall management of claudication needs further study. Importantly, exercise therapy has been shown in numerous studies to be efficacious and very well tolerated by patients. Patients improve both their walking ability in the laboratory and their community-based functional status. Because of the efficacy of this treatment, in addition to the low associated morbidity, exercise therapy is recommended as a major treatment option for persons with intermittent claudication due to PAD.
Transient voltage stability constrained optimal sizing of wind farm considering uncertainty of wind speed

The rapid increase in wind farms' penetration level is remarkable. Hence, the investigation of the impact of wind farms on the stability of the system has become more important. In this paper, a new approach for optimal sizing of wind farm with consideration of transient voltage stability and uncertainty of wind speed is presented. For this purpose, PSO algorithm is adopted as search engine for finding the most proper generation capacity of wind farm. In this respect, the operation benefit of wind farms and the transient voltage stability of the system are regarded as two components of the objective function for maximization. Also, in order to consider the uncertainty due to wind speed, the Monte Carlo method has been used to model the uncertainty of the wind speed into planning process. The simulation studies have been performed on the IEEE 39-Bus (New England) system. The simulation results show that when the wind power penetration level increases, the transient security margin reduces but the operation benefit increases.
[LC-ESI-MS metabolic profiling analysis of taxanes from the extracts of Taxus chinensis cell cultures].

AIM To develop a rapid analytical method for small amount biological samples of taxanes by using liquid chromatography coupled with electrospray ionization tandem mass spectrometry (LC-ESI-MS) in small amount biological samples. METHODS A solution containing five given taxane constituents and the extract from cell cultures of Taxus chinensis were analysed separately. According to the performance of the given taxanes in ESI-MS/MS, run parameters of the mass spectrometer were optimized. Positive and negative electrospray modes were employed to simultaneously scan the cell cultures sample, and the full ion chromatogram and the molecular weight of individual peak were obtained. The qualitative analysis of taxanes was achieved by comparison of the retention time and molecular weight with those of the reference substances or was based on the interpretation of the MS/MS spectra of the analytes and the knowledge of the concerning genetic backgrounds of taxanes published in literatures. RESULTS The taxanes with several acetyl substituents tended to produce ammonium adduct ions peak, while multi-hydroxy taxanes were subject to give protonized molecular ion peaks in positive ion ESI-MS. Thirteen taxanes in cell samples were assigned. Eight compounds of them were identified to be 1 -acetyl-5, 7, 10-deacetyl-baccatin I (DAB-I, 1) , baccatin III (B-III, 3), baccatin VI (B-VI, 8), taxol (9), yunnanxane (10 ), taxuyunnanine C (Tc, 11), sinenxane B (12), sinenxane C (13), separately. For the other five constituents, character of taxane and the number of substituents were deduced. CONCLUSION The results confirm the feasibility of characterizing taxanes in biological samples by LC-ESI-MS analysis. The analytical methodology provided a rapid, conventional and reliable tool to study metabolic profiling of taxanes for structural elucidation in taxol biosynthesis.
Genes Involved in Viral Carcinogenesis and Tumor Initiation in Hepatitis C Virus-Induced Hepatocellular Carcinoma

The role of chronic hepatitis C virus (HCV) in the pathogenesis of HCV-associated hepatocellular carcinoma (HCC) remains controversial. To understand the transition from benign to malignant, we studied the gene expression patterns in liver tissues at different stages, including normal, cirrhosis, and different HCC stages. We studied 108 liver tissue samples obtained from 88 distinct patients (41 HCV-cirrhotic tissues, 17 HCV-cirrhotic tissues from patients with HCC, and 47 HCV-HCC tissues). Differentially expressed genes (DEG) were studied by use of high-density oligonucleotide arrays. Among probe sets identified as differentially expressed via the F test, all pairwise comparisons were performed. Cirrhotic tissues with and without concomitant HCC were further evaluated, and a classifier was used to predict whether the tissue type was associated with HCC. Differential expression profiles were analyzed using Interaction Networks and Functional Analysis. Characteristic gene signatures were identified when normal tissue was compared with cirrhosis, cirrhosis with early HCC, and normal with HCC. Pathway analysis classified the cellular and biological functions of the DEG as related to cellular growth and proliferation, cell death and inflammatory disease in cirrhosis; cell death, cell cycle, DNA replication, and immune response in early HCCs; and cell death, cell growth and proliferation, cell cycle, and DNA repair in advanced HCCs. Characteristic gene signatures were identified at different stages of HCV-HCC progression. A set of genes were identified to predict whether the cirrhotic tissue was associated with HCC.
A Study on User Selection in Dual-Polarized Antenna Systems

Dual-polarized antenna (DPA) systems can provide two independent data transmissions in line-of-sight wireless channel environments. The capacity of each data stream can be affected by a rotation angle between transmitter and receiver DPAs and channel gains of vertical and horizontal receiver antennas. In this paper, we propose a user selection scheme for the DPA system. In the proposed scheme, the best DPA user is selected based on both the rotation angle and the channel gains. By using this scheme, the capacity of the DPA system increases two times when the selection order is three. The selected best user can even achieve 3 times of capacity when the selection order is six.
Action-related objects influence the distribution of visuospatial attention

Previous studies have shown that attention is drawn to the location of manipulable objects and is distributed across pairs of objects that are positioned for action. Here, we investigate whether central, action-related objects can cue attention to peripheral targets. Experiment 1 compared the effect of uninformative arrow and object cues on a letter discrimination task. Arrow cues led to spatial-cueing benefits across a range of stimulus onset asynchronies (SOAs: 0 ms, 120 ms, 400 ms), but object-cueing benefits were slow to build and were only significant at the 400-ms SOA. Similar results were found in Experiment 2, in which the targets were objects that could be either congruent or incongruent with the cue (e.g., screwdriver and screw versus screwdriver and glass). Cueing benefits were not influenced by the congruence between the cue and target, suggesting that the cueing effects reflected the action implied by the central object, not the interaction between the objects. For Experiment 3 participants decided whether the cue and target objects were related. Here, the interaction between congruent (but not incongruent) targets led to significant cueing/positioning benefits at all three SOAs. Reduced cueing benefits were obtained in all three experiments when the object cue did not portray a legitimate action (e.g., a bottle pointing towards an upper location, since a bottle cannot pour upwards), suggesting that it is the perceived action that is critical, rather than the structural properties of individual objects. The data suggest that affordance for action modulates the allocation of visual attention.
Review of uses of network and graph theory concepts within proteomics

The size and nature of data collected on gene and protein interactions has led to a rapid growth of interest in graph theory and modern techniques for describing, characterizing and comparing networks. Simultaneously, this is a field of growth within mathematics and theoretical physics, where the global properties, and emergent behavior of networks, as a function of the local properties has long been studied. In this review, a number of approaches for exploiting modern network theory to help describe and analyze different data sets and problems associated with proteomic data are considered. This review aims to help biologists find their way towards useful ideas and references, yet may also help scientists from a mathematics and physics background to understand where they may apply their expertise.
Quality of Service Driven Runtime Resource Allocation in Reconfigurable HPC Architectures

Heterogeneous System Architectures (HSA) are gaining importance in the High Performance Computing (HPC) domain due to increasing computational requirements coupled with energy consumption concerns, which conventional CPU architectures fail to effectively address. Systems based on Field Programmable Gate Array (FPGA) recently emerged as an effective alternative to Graphical Processing Units (GPUs) for demanding HPC applications, although they lack the abstractions available in conventional CPU-based systems. This work tackles the problem of runtime resource management of a system using FPGA-based co-processors to accelerate multiprogrammed HPC workloads. We propose a novel resource manager able to dynamically vary the number of FPGAs allocated to each of the jobs running in a multi-accelerator system, with the goal of meeting a given Quality of Service metric for the running jobs measured in terms of deadline or throughput. We implement the proposed resource manager in a commercial HPC system, evaluating its behavior with representative workloads.
SimRank on Uncertain Graphs

SimRank is a similarity measure between vertices in a graph. Recently, many algorithms have been proposed to efficiently evaluate SimRank similarities. However, the existing algorithms either overlook uncertainty in graph structures or depends on an unreasonable assumption. In this paper, we study SimRank on uncertain graphs. Following the random-walk-based formulation of SimRank on deterministic graphs and the possible world model of uncertain graphs, we first define random walks on uncertain graphs and show that our definition of random walks satisfies Markov’s property. We formulate our SimRank measure based on random walks on uncertain graphs. We discover a critical difference between random walks on uncertain graphs and random walks on deterministic graphs, which makes all existing SimRank computation algorithms on deterministic graphs inapplicable to uncertain graphs. For SimRank computation, we consider computing both single-pair SimRank and single-source top-<inline-formula><tex-math notation="LaTeX">$K$ </tex-math><alternatives><inline-graphic xlink:href="zou-ieq1-2725275.gif"/></alternatives></inline-formula> SimRank. We propose three algorithms, namely the sampling algorithm with high efficiency, the two-phase algorithm with comparable efficiency and higher accuracy, and a speeding-up algorithm with much higher efficiency. Meanwhile, we present an optimized algorithm for efficient computing the single-source top-<inline-formula> <tex-math notation="LaTeX">$K$</tex-math><alternatives><inline-graphic xlink:href="zou-ieq2-2725275.gif"/> </alternatives></inline-formula> SimRank. The experimental results verify the effectiveness of our SimRank measure and the efficiency of the proposed SimRank computation algorithms.
Heat-directed tumor cell fusion.

In previous studies we demonstrated that a modified human HSP70b promoter (HSE.70b) directs high levels of gene expression to tumor cells after mild hyperthermia treatment in the range of 41.5-44 degrees C. This transcriptional targeting system exhibits low basal activity at 37 degrees C, is highly induced (950-fold) after mild heat treatment (43 degrees C/30 min), and returns to basal activity levels within 12-24 hours of activation. Here we describe heat-directed targeting of an activated form of the Gibbon ape leukemia virus env protein (GALV FMG) to tumor cells. GALV FMG mediates cell-cell fusion, and when expressed in tumor cells can produce bystander effects of up to 1:200. Transient transfection of a HSE70b.GALV FMG minigene caused extensive syncytia formation in HeLa and HT-1080 cells following mild heat treatment (44 degrees C/30 min). Stable transfection into HT-1080 cells produced a cell line (HG5) that exhibits massive syncytia formation and a 60% reduction in viability relative to a vector-only control (CI1) following heat treatment in vitro. Mild hyperthermia also resulted in syncytia formation, necrosis, and complete macroscopic regression of HG5 xenograft tumors grown in the footpads of mice with severe combined immunodeficiency disorders (SCID). Median survival increased from 12.5 (in heated CI1 controls) to 52 days after a single heat treatment. Heat-directed tumor cell fusion may prove to be a highly beneficial adjunct to existing cancer treatment strategies that take advantage of the synergistic interaction between mild hyperthermia and radiation or chemotherapeutic drugs.
TreePOD: Sensitivity-Aware Selection of Pareto-Optimal Decision Trees

Balancing accuracy gains with other objectives such as interpretability is a key challenge when building decision trees. However, this process is difficult to automate because it involves know-how about the domain as well as the purpose of the model. This paper presents TreePOD, a new approach for sensitivity-aware model selection along trade-offs. TreePOD is based on exploring a large set of candidate trees generated by sampling the parameters of tree construction algorithms. Based on this set, visualizations of quantitative and qualitative tree aspects provide a comprehensive overview of possible tree characteristics. Along trade-offs between two objectives, TreePOD provides efficient selection guidance by focusing on Pareto-optimal tree candidates. TreePOD also conveys the sensitivities of tree characteristics on variations of selected parameters by extending the tree generation process with a full-factorial sampling. We demonstrate how TreePOD supports a variety of tasks involved in decision tree selection and describe its integration in a holistic workflow for building and selecting decision trees. For evaluation, we illustrate a case study for predicting critical power grid states, and we report qualitative feedback from domain experts in the energy sector. This feedback suggests that TreePOD enables users with and without statistical background a confident and efficient identification of suitable decision trees.