Miracle-dz/UniFAR-FTUs huggingface dataset:
Schizosaccharomyces pombe ras1 and byr1 are functionally related genes of the ste family that affect starvation-induced transcription of mating-type genes

We have further investigated the function of the ras1 and byr1 genes, which were previously shown to be critical for sexual differentiation in fission yeast cells. Several physiological similarities between strains containing null alleles of these genes supports the idea that ras1 and byr1 are functionally closely related. Furthermore, we have found that byr1 is allelic to ste1, one of at least 10 genes which when mutated can cause sterility. Since ras1 had previously been found to be allelic to ste5, both ras and byr genes are now clearly shown to be a part of the ste gene family, thus confirming their close functional relationship. The observation that the mating-type loci could overcome the sporulation block of ras1 and byr1 mutant strains prompted investigation of the role of the ras-byr pathway in the induction of the mating-type gene transcripts upon nitrogen starvation. By Northern analysis of RNA preparations from strains carrying wild-type or mutant ras1 alleles and grown to different stages of the growth cycle, we have shown that ras1 plays an important role in inducing the Pi transcript of the mating-type loci and the mei3 gene transcript. These observations provide a molecular basis for the role of the ste gene family, including ras1 and byr1, in meiosis and indicate that further characterization of other ste genes would be very useful for elucidating the mechanism of ras1 function in fission yeast cells.
Analysis of Different Pheromone Decay Techniques for ACO based Routing in Ad Hoc Wireless Networks

Ant Colony Optimization (ACO) technique deals with exploratory behavior of ants while finding food by following a path based on the concentration of the pheromone. A major limitation with ACO algorithm is “stagnation”. This occurs when all ants try to follow same path to reach the destination due to higher pheromone concentration and causes congestion when applied to Adhoc Wireless Network (AWN). In the present paper, a detailed analysis of ACO based different pheromone decay techniques such as Discrete, Exponential and Polynomial has been carried out. Pheromone intensity and probability of choosing path for packet transmission are used as parameters for the analysis. It is found that the Discrete decay is not preferable for Congestive network as it leaves large amount of pheromone traces. The polynomial decay technique choose better path and avoid longest path which lead to delay at the time of packet delivery. The Exponential decay has been found to exhibit better performance compared to Discrete and Polynomial decay techniques, However it loses the pheromone traces very fast. The Efficient fine tuning of the exponential decay model can be achieved by using stability factor ‘∆’. The present analysis shows that for values of ‘∆’ 0.09 the probability of selection of the longest optimal path increases to 18%. The
Anti-Inflammatory Effect of the Blueberry Anthocyanins Malvidin-3-Glucoside and Malvidin-3-Galactoside in Endothelial Cells

Blueberry fruits have a wide range of health benefits because of their abundant anthocyanins, which are natural antioxidants. The purpose of this study was to investigate the inhibitory effect of blueberry’s two main anthocyanins (malvidin-3-glucoside and malvidin-3-galactoside) on inflammatory response in endothelial cells. These two malvidin glycosides could inhibit tumor necrosis factor-alpha (TNF-α) induced increases of monocyte chemotactic protein-1 (MCP-1), intercellular adhesion molecule-1 (ICAM-1), and vascular cell adhesion molecule-1 (VCAM-1) production both in the protein and mRNA levels in a concentration-dependent manner. Mv-3-glc at the concentration of 1 μM could inhibit 35.9% increased MCP-1, 54.4% ICAM-1, and 44.7% VCAM-1 protein in supernatant, as well as 9.88% MCP-1 and 48.6% ICAM-1 mRNA expression (p < 0.05). In addition, they could decrease IκBα degradation (Mv-3-glc, Mv-3-gal, and their mixture at the concentration of 50 μM had the inhibition rate of 84.8%, 75.3%, and 43.2%, respectively, p < 0.01) and block the nuclear translocation of p65, which suggested their anti-inflammation mechanism was mediated by the nuclear factor-kappa B (NF-κB) pathway. In general malvidin-3-glucoside had better anti-inflammatory effect than malvidin-3-galactoside. These results indicated that blueberry is good resource of anti-inflammatory anthocyanins, which can be promising molecules for the development of nutraceuticals to prevent chronic inflammation in many diseases.
TraG from RP 4 and TraG and VirD 4 from Ti Plasmids Confer Relaxosome Specificity to the Conjugal Transfer System of pTiC 58

CLAIRE M. HAMILTON,† HYEWON LEE, PEI-LI LI, DAVID M. COOK,‡ KEVIN R. PIPER, SUSANNE BECK VON BODMAN,§ ERICH LANKA, WALT REAM, AND STEPHEN K. FARRAND* Departments of Crop Sciences and Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; Department of Microbiology, Oregon State University, Corvallis, Oregon 97331; and Max-Planck-Institut für Molekulare Genetik, Dahlem, D-14195 Berlin, Germany
Productivity and the Investment Climate: What Matters Most?

The authors explore the links between the investment climate and firm-level productivity and attempt to identify which dimensions of the investment climate matter most for productivity. Their analysis is based on data collected in a recent investment climate survey of garment and food processing firms in five countries in Eastern Europe and Central Asia. The authors use the first principal components of a series of indicators to summarize broad aspects of the investment climate and identify those most important in determining productivity. Their results indicate that competitive pressure is the most critical factor in the investment climate, accounting for more variation in firm-level productivity than infrastructure provision or issues related to government rent seeking and bureaucratic burden. This suggests that to improve productivity, increase output, and reduce poverty, policymakers should focus reform efforts on removing barriers to entry and creating open, highly competitive markets.
Designing a predictive model of student satisfaction in online learning

ABSTRACT Higher education institutions consider student satisfaction to be one of the major elements in determining the quality of their programs. The objective of the study was to develop a model of student satisfaction to identify the influencers that emerged in online higher education settings. The study adopted a mixed method approach to identify issues perceived by students as affecting their satisfaction, using focus groups followed by exploratory and confirmatory factor analyses to develop the study model. Data were collected using an online questionnaire from a campus-wide sample of 834 students enrolled in a generic online course at the University of Mauritius. Using structural equation modeling, the study identified four significant determinants of student satisfaction in decreasing importance: the marketing construct of university reputation; physical facilities; faculty empathy; and student–student interactions. Various theoretical and managerial implications are discussed and directions for further research are proposed.
IDP 3 Encodes a Peroxisomal NADP-dependent Isocitrate Dehydrogenase Required for the b-Oxidation of Unsaturated Fatty Acids

In Saccharomyces cerevisiae the metabolic degradation of saturated fatty acids is exclusively confined to peroxisomes. In addition to a functional b-oxidation system, the degradation of unsaturated fatty acids requires auxiliary enzymes, including a D2,D3-enoyl-CoA isomerase and an NADPH-dependent 2,4-dienoyl-CoA reductase. We found both enzymes to be present in yeast peroxisomes. The impermeability of the peroxisomal membrane for pyrimidine nucleotides led to the question of how the NADPH needed by the reductase is regenerated in the peroxisomal lumen. We report the identification and functional analysis of the IDP3 gene product, which is a yeast peroxisomal NADP-dependent isocitrate dehydrogenase. The newly identified peroxisomal protein is homologous to the mitochondrial Idp1p and cytosolic Idp2p, which both are yeast NADPdependent isocitrate dehydrogenases. Yeast cells lacking Idp3p grow normally on saturated fatty acids, but growth is impaired on unsaturated fatty acids, indicating that the peroxisomal Idp3p is involved in their metabolic utilization. The data presented are consistent with the assumption that peroxisomes of S. cerevisiae contain the enzyme equipment needed for the degradation of unsaturated fatty acids, including an NADPdependent isocitrate dehydrogenase, a putative constituent of a peroxisomal NADPH-regenerating redox system.
Artificial neural networks and signal clipping for Profibus DP diagnostics

This research proposes the use of Artificial Neural Networks to diagnose industrial networks communication via Profibus DP Protocol. These diagnostics are based on information provided by the Physical Layer from the Profibus DP Protocol. In order to analyze the physical layer, an Artificial Neural Network first analyzes signal samples transmitted through the industrial network. In case these signals show some deformation, the Artificial Neural Network indicates a possible cause for the problem, after all, problems from Profibus networks generate specific and distinctive standards imprinted on the digital signal wave formats. Before the Artificial Neural Network analysis, the signal was pre-processed through a clipper methodology. The project was validated by data obtained from concrete Profibus networks created in laboratory. The results were satisfactory, proving the great strength and versatility that intelligent computer systems have when applied to the purposes outlined in this work.
SVD-LDA: A Combined Model for Text Classification

Abstract: Text data has always accounted for a major portion of the world’s information. As the volume of information increases exponentially, the portion of text data also increases significantly. Text classification is therefore still an important area of research. LDA is an updated, probabilistic model which has been used in many applications in many other fields. As regards text data, LDA also has many applications, which has been applied various enhancements. However, it seems that no applications take care of the input for LDA. In this paper, we suggest a way to map the input space to a reduced space, which may avoid the unreliability, ambiguity and redundancy of individual terms as descriptors. The purpose of this paper is to show that LDA can be perfectly performed in a “clean and clear” space. Experiments are conducted on 20 News Groups data sets. The results show that the proposed method can boost the classification results when the appropriate choice of rank of the reduced space is determined.
Automatic Repair of Real Bugs: An Experience Report on the Defects4J Dataset

Automatic software repair aims to reduce human effort for fixing bugs. Various automatic repair approaches have emerged in recent years. In this paper, we report on an experiment on automatically repairing 224 bugs of a real-world and publicly available bug dataset, Defects4J. We investigate the results of three repair methods, GenProg (repair via random search), Kali (repair via exhaustive search), and Nopol (repair via constraint based search). We conduct our investigation with five research questions: fixability, patch correctness, ill-defined bugs, performance, and fault localizability. Our implementations of GenProg, Kali, and Nopol fix together 41 out of 224 (18%) bugs with 59 different patches. This can be viewed as a baseline for future usage of Defects4J for automatic repair research. In addition, manual analysis of sampling 42 of 59 generated patches shows that only 8 patches are undoubtedly correct. This is a novel piece of evidence that there is large room for improvement in the area of test suite based repair.
Pattern Filtering for Detection of Neural Activity, with Examples from HVc Activity During Sleep in Zebra Finches

The detection of patterned spiking activity is important in the study of neural coding. A pattern filtering approach is developed for pattern detection under the framework of point processes, which offers flexibility in combining temporal details and firing rates. The detection combines multiple steps of filtering in a coarse-to-fine manner. Under some conditional Poisson assumptions on the spiking activity, each filtering step is equivalent to classifying by likelihood ratios all the data segments as targets or as background sequences. Unlike previous studies, where global surrogate data were used to evaluate the statistical significance of the detected patterns, a localizedp-test procedure is developed, which better accounts for firing modulation and nonstationarity in spiking activity. Common temporal structures of patterned activity are learned using an entropy-based alignment procedure, without relying on metrics or pair-wise alignment. Applications of pattern filtering to single, presumptive interneurons recorded in the nucleus HVc of zebra finch are illustrated. These demonstrate a match between the auditory-evoked response to playback of the individual bird's own song and spontaneous activity during sleep. Small temporal compression or expansion, or both, is required for optimal matching of spontaneous patterns to stimulus-evoked activity.
A constant power control digital electronic ballast for metal halide lamps

A constant power control digital electronic ballast for metal halide lamp (MHL) is presented in this paper. It is constructed by a three-stage power converter and drives the MHL with a low frequency square-wave to eliminate acoustic resonance. The circuit construction of the ballast is detailedly analyzed in this paper. Control and protection circuit based STC12C5410AD MCU is also designed to ensure stable operation of the MH lamps. According to V-A characteristics of MHL, a corresponding control method is proposed to actualize successfully ignition for MHL's startup, and to ensure the lamp operating safely and stably through detecting working condition of the ballast. The flow chart of software design is also given. Finally, a laboratory prototype of 70-W electronic ballast is implemented. Experimental results show that all electrical parameters satisfy the design requirements.
Visualization of oligonucleotide probes and point mutations in interphase nuclei and DNA fibers using rolling circle DNA amplification

Rolling circle amplification (RCA) is a surface-anchored DNA replication reaction that can be exploited to visualize single molecular recognition events. Here we report the use of RCA to visualize target DNA sequences as small as 50 nts in peripheral blood lymphocytes or in stretched DNA fibers. Three unique target sequences within the cystic fibrosis transmembrane conductance regulator gene could be detected simultaneously in interphase nuclei, and could be ordered in a linear map in stretched DNA. Allele-discriminating oligonucleotide probes in conjunction with RCA also were used to discriminate wild-type and mutant alleles in the cystic fibrosis transmembrane conductance regulator, p53, BRCA-1, and Gorlin syndrome genes in the nuclei of cultured cells or in DNA fibers. These observations demonstrate that signal amplification by RCA can be coupled to nucleic acid hybridization and multicolor fluorescence imaging to detect single nucleotide changes in DNA within a cytological context or in single DNA molecules. This provides a means for direct physical haplotyping and the analysis of somatic mutations on a cell-by-cell basis.
SNARE Protein-Dependent Glutamate Release from Astrocytes

We investigated the cellular mechanisms underlying the Ca2+-dependent release of glutamate from cultured astrocytes isolated from rat hippocampus. Using Ca2+imaging and electrophysiological techniques, we analyzed the effects of disrupting astrocytic vesicle proteins on the ability of astrocytes to release glutamate and to cause neuronal electrophysiological responses, i.e., a slow inward current (SIC) and/or an increase in the frequency of miniature synaptic currents. We found that the Ca2+-dependent glutamate release from astrocytes is not caused by the reverse operation of glutamate transporters, because the astrocyte-induced glutamate-mediated responses in neurons were affected neither by inhibitors of glutamate transporters (β-threo-hydroxyaspartate, dihydrokainate, andl-trans-pyrrolidine-2,4-dicarboxylate) nor by replacement of extracellular sodium with lithium. We show that Ca2+-dependent glutamate release from astrocytes requires an electrochemical gradient necessary for glutamate uptake in vesicles, because bafilomycin A1, a vacuolar-type H+-ATPase inhibitor, reduced glutamate release from astrocytes. Injection of astrocytes with the light chain of the neurotoxin Botulinum B that selectively cleaves the vesicle-associated SNARE protein synaptobrevin inhibited the astrocyte-induced glutamate response in neurons. Therefore, the Ca2+-dependent glutamate release from astrocytes is a SNARE protein-dependent process that requires the presence of functional vesicle-associated proteins, suggesting that astrocytes store glutamate in vesicles and that it is released through an exocytotic pathway.
The effects of surgical levels of sevoflurane and propofol anaesthesia on heart rate variability

Background and objective: We compared heart rate dynamics during surgical levels of propofol and sevoflurane anaesthesia in a highly standardized setting. Methods: We recorded electrocardiography from 24 anaesthetized healthy male subjects. In the first parallel part of the study, the subjects were anaesthetized either with sevoflurane (n = 8) or propofol (n = 8) targeted to match 1.0, 1.5 and 2.0 minimal alveolar concentration/effective concentration 50. In the second part, a separate group (n = 8) underwent four different anaesthetic regimens targeted to bispectral index 40: sevoflurane alone, sevoflurane + 70% nitrous oxide, propofol alone and propofol + 70% nitrous oxide. The electrocardiography data were analysed using conventional time and frequency domain methods, and the approximate entropy method, which estimates the complexity of the data. Results: The induction of anaesthesia was followed by an overall reduction of heart rate variability, evident in all frequency bands in the spectral analysis, and also in the time domain measures. Approximate entropy decreased at 1 effective concentration 50 with propofol and at 2 minimal alveolar concentration with sevoflurane. In the second part of the study, the time domain variables and high‐frequency spectral power were all similarly reduced by sevoflurane and propofol anaesthesia, with and without nitrous oxide. Approximate entropy tended to decrease during propofol anaesthesia. Conclusions: Hypnotic levels of sevoflurane and propofol anaesthesia suppressed the heart rate variability measured using conventional analysis methods. Deeper surgical levels of anaesthesia also reduce the complexity of heart rate variability.
A Technique for Extraction and Analysis of Application Heap Objects within Android Runtime (ART)

This paper describes a technique for analysing objects in memory within the execution environment Android Runtime (ART) using a volatile memory data extraction. A study of the AOSP (Android Open Source Project) source code was necessary to understand the runtime environment used in the modern Android operating system, and software tools were developed allowing the location, extraction and interpretation of useful data for the forensic context. Built by the authors as extensions for the Volatility Framework, these tools help to locate, in a memory extraction from a device compliant with the ARM architecture, arbitrary instances of classes and their data properties.
Understandable models Of music collections based on exhaustive feature generation with temporal statistics

Data mining in large collections of polyphonic music has recently received increasing interest by companies along with the advent of commercial online distribution of music. Important applications include the categorization of songs into genres and the recommendation of songs according to musical similarity and the customer's musical preferences. Modeling genre or timbre of polyphonic music is at the core of these tasks and has been recognized as a difficult problem. Many audio features have been proposed, but they do not provide easily understandable descriptions of music. They do not explain why a genre was chosen or in which way one song is similar to another. We present an approach that combines large scale feature generation with meta learning techniques to obtain meaningful features for musical similarity. We perform exhaustive feature generation based on temporal statistics and train regression models to summarize a subset of these features into a single descriptor of a particular notion of music. Using several such models we produce a concise semantic description of each song. Genre classification models based on these semantic features are shown to be better understandable and almost as accurate as traditional methods.
Use of a small molecule cell cycle inhibitor to control cell growth and improve specific productivity and product quality of recombinant proteins in CHO cell cultures

The continued need to improve therapeutic recombinant protein productivity has led to ongoing assessment of appropriate strategies in the biopharmaceutical industry to establish robust processes with optimized critical variables, that is, viable cell density (VCD) and specific productivity (product per cell, qP). Even though high VCD is a positive factor for titer, uncontrolled proliferation beyond a certain cell mass is also undesirable. To enable efficient process development to achieve consistent and predictable growth arrest while maintaining VCD, as well as improving qP, without negative impacts on product quality from clone to clone, we identified an approach that directly targets the cell cycle G1‐checkpoint by selectively inhibiting the function of cyclin dependent kinases (CDK) 4/6 with a small molecule compound. Results from studies on multiple recombinant Chinese hamster ovary (CHO) cell lines demonstrate that the selective inhibitor can mediate a complete and sustained G0/G1 arrest without impacting G2/M phase. Cell proliferation is consistently and rapidly controlled in all recombinant cell lines at one concentration of this inhibitor throughout the production processes with specific productivities increased up to 110 pg/cell/day. Additionally, the product quality attributes of the mAb, with regard to high molecular weight (HMW) and glycan profile, are not negatively impacted. In fact, high mannose is decreased after treatment, which is in contrast to other established growth control methods such as reducing culture temperature. Microarray analysis showed major differences in expression of regulatory genes of the glycosylation and cell cycle signaling pathways between these different growth control methods. Overall, our observations showed that cell cycle arrest by directly targeting CDK4/6 using selective inhibitor compound can be utilized consistently and rapidly to optimize process parameters, such as cell growth, qP, and glycosylation profile in recombinant antibody production cultures. Biotechnol. Bioeng. 2015;112: 141–155. © 2014 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.