Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficacy of Bacillus thuringiensis Cry14 Toxin against Root Knot Nematode, Meloidogyne javanica

Two Bacillus thuringiensis strains including ToIr65 and ToIr67 with nematicidal activity against hatched juveniles and eggs of Meloidogyne javanica were identified by phenotypic, microscopic, 16s rDNA sequencing and nematode cry gene specific PCR. Two forms of bacterial isolates including bacterial suspension (BS) and spore/crystal mixture (SCM) were tested in lab and pot conditions to evaluate their efficacy in M. javanica management. The BS of ToIr65 and ToIr67 showed 70% nematicidal activity in comparison to SCM in vitro . In pot experiments, two forms of ToIr65 significantly (by 51%) decreased number of gall over infested control and also increased growth parameters on tomato plants, but ToIr67 did not. Our results suggested that Bt-ToIr65 could be employed as a biocontrol agent for the management of M. javanica .
Learning Topographic Sparse Coding through Similarity Function

In this paper, we present a novel method to learn the topographic and sparse representation from the natural images. By using two kinds of similarity functions onto the sparse coding bases learned from natural images respectively, we find that these Gabor-like bases inherently contain the topographic information. This method makes those similar bases be close to each other and a topographic organization emerged in the 2-D space. These two kinds of similarity functions are: basis functions similarity in classical sparse model [7] and analysis vectors similarity in encoder/decoder model [2]. Traditional topographic ICA [3] and topographic sparse coding [6] that contain two layer network, however, our proposed model can generate the topographic visualization by using one layer network. The simulation results demonstrate that these two kinds of similarity functions can produce distinct topographic organization of bases, and the analysis vectors similarity provides better results.
Training to use a commercial brain-computer interface as access technology: a case study

Abstract Purpose: This case study describes how an individual with spastic quadriplegic cerebral palsy was trained over a period of four weeks to use a commercial electroencephalography (EEG)-based brain-computer interface (BCI). Method: The participant spent three sessions exploring the system, and seven sessions playing a game focused on EEG feedback training of left and right arm motor imagery and a customised, training game paradigm was employed. Results: The participant showed improvement in the production of two distinct EEG patterns. The participant’s performance was influenced by motivation, fatigue and concentration. Six weeks post-training the participant could still control the BCI and used this to type a sentence using an augmentative and alternative communication application on a wirelessly linked device. Conclusions: The results from this case study highlight the importance of creating a dynamic, relevant and engaging training environment for BCIs. Implications for Rehabilitation Customising a training paradigm to suit the users’ interests can influence adherence to assistive technology training. Mood, fatigue, physical illness and motivation influence the usability of a brain-computer interface. Commercial brain-computer interfaces, which require little set up time, may be used as access technology for individuals with severe disabilities
Photovoltaic ground fault and blind spot electrical simulations.

Ground faults in photovoltaic (PV) systems pose a fire and shock hazard. To mitigate these risks, AC-isolated, DC grounded PV systems in the United States use Ground Fault Protection Devices (GFPDs), e.g., fuses, to de-energize the PV system when there is a ground fault. Recently the effectiveness of these protection devices has come under question because multiple fires have started when ground faults went undetected. In order to understand the limitations of fuse-based ground fault protection in PV systems, analytical and numerical simulations of different ground faults were performed. The numerical simulations were conducted with Simulation Program with Integrated Circuit Emphasis (SPICE) using a circuit model of the PV system which included the modules, wiring, switchgear, grounded or ungrounded components, and the inverter. The derivation of the SPICE model and the results of parametric fault current studies are provided with varying array topologies, fuse sizes, and fault impedances. Closed-form analytical approximations for GFPD currents from faults to the grounded current carrying conductor-known as %E2%80%9Cblind spot%E2%80%9D ground faults-are derived to provide greater understanding of the influence of array impedances on fault currents. The behavior of the array during various ground faults is studied for a range of ground fault fuse sizesmore » to determine if reducing the size of the fuse improves ground fault detection sensitivity. The results of the simulations show that reducing the amperage rating of the protective fuse does increase fault current detection sensitivity without increasing the likelihood of nuisance trips to a degree. Unfortunately, this benefit reaches a limit as fuses become smaller and their internal resistance increases to the point of becoming a major element in the fault current circuit. « less
Aiding Sentiment Evaluation with Social Network

One challenge for sentiment analysis as well as many other natural language processing task is the language variation. In this project, based on the intuition of language homophily, we aim to solve this problem by combing social network information. We propose a new model that measure the interaction between author embedding and sentence words’ embeddings. This model is based on the current state-of-the-art methodology that does not consider social network information. The authors’ embeddings are pretrained with three different yet most popular network node embedding methods, and their performances are compared.
Periplasmic enzymes in Bdellovibrio bacteriovorus and Bdellovibrio stolpii

When cells of either Bdellovibrio bacteriovorus 109J or Bdellovibrio stolpii UKi2 were subjected to osmotic shock by treatment with sucrose-EDTA and MgCl2 solutions, only trace amounts of proteins or enzyme activities were released into the shock fluid. In contrast, when nongrowing cells were converted to motile, osmotically stable, peptidoglycan-free spheroplasts by penicillin treatment, numerous proteins were released into the suspending fluid. For both species, this suspending fluid contained substantial levels of 5'-nucleotidase, purine phosphorylase, and deoxyribose-phosphate aldolase. Penicillin treatment also released aminoendopeptidase N from B. bacteriovorus, but not from B. stolpii. Penicillin treatment did not cause release of cytoplasmic enzymes such as malate dehydrogenase. The data indicated that bdellovibrios possess periplasmic enzymes or peripheral enzymes associated with the cell wall complex. During intraperiplasmic bdellovibrio growth, periplasmic and cytoplasmic enzymes of the Escherichia coli substrate cell were not released upon formation of the spherical bdelloplast during bdellovibrio penetration. Most of the E. coli enzymes were retained within the bdelloplast until later in the growth cycle, when they became inactivated or released into the suspending buffer or both.
CERAMIC: Case-Control Association Testing in Samples with Related Individuals, Based on Retrospective Mixed Model Analysis with Adjustment for Covariates

We consider the problem of genetic association testing of a binary trait in a sample that contains related individuals, where we adjust for relevant covariates and allow for missing data. We propose CERAMIC, an estimating equation approach that can be viewed as a hybrid of logistic regression and linear mixed-effects model (LMM) approaches. CERAMIC extends the recently proposed CARAT method to allow samples with related individuals and to incorporate partially missing data. In simulations, we show that CERAMIC outperforms existing LMM and generalized LMM approaches, maintaining high power and correct type 1 error across a wider range of scenarios. CERAMIC results in a particularly large power increase over existing methods when the sample includes related individuals with some missing data (e.g., when some individuals with phenotype and covariate information have missing genotype), because CERAMIC is able to make use of the relationship information to incorporate partially missing data in the analysis while correcting for dependence. Because CERAMIC is based on a retrospective analysis, it is robust to misspecification of the phenotype model, resulting in better control of type 1 error and higher power than that of prospective methods, such as GMMAT, when the phenotype model is misspecified. CERAMIC is computationally efficient for genomewide analysis in samples of related individuals of almost any configuration, including small families, unrelated individuals and even large, complex pedigrees. We apply CERAMIC to data on type 2 diabetes (T2D) from the Framingham Heart Study. In a genome scan, 9 of the 10 smallest CERAMIC p-values occur in or near either known T2D susceptibility loci or plausible candidates, verifying that CERAMIC is able to home in on the important loci in a genome scan.
Myocardial Infarction and Cardiac Remodelling in Mice

We established a mouse model of cardiac dysfunction due to myocardial infarction (MI). For this we ligated the left anterior descending coronary artery in male C57BL/6J mice and assessed healing and left ventricular (LV) remodelling at 1, 2 and 4 days and 1, 2 and 4 weeks after MI. Echocardiography was performed at 1 and 2 weeks and 1, 2, 4 and 6 months after MI. We found that neutrophil infiltration of the infarct border was noticeable at 1‐2 days. Marked macrophage infiltration occurred at day 4, while lymphocyte infiltration was apparent at 7‐14 days. Massive proliferation of fibroblasts and collagen accumulation began by day 7‐14, and scar formation was completed by day 21. LV diastolic dimension increased markedly at 2 weeks and remained at the same level thereafter. LV shortening fraction decreased significantly at 2 weeks and then slowly decreased. In non‐infarcted areas of the LV, myocyte cross‐sectional area and interstitial collagen fraction increased progressively, reaching a maximum at 4 months. This study provides important qualitative and quantitative information about the natural history of cardiac remodelling after MI in mice.
High performance sensorless controls based on HF excitation: A viable solution for future AC motor drives?

Sensorless AC motor control strategies exploiting the injection of high frequency signals to detect magnetic, or geometrical, saliencies have been investigated since '90s, in order to overcome key deficiencies of model based methodologies. However, even if several techniques are nowadays practically used on some market available industrial AC drives, the development of a methodology of general applicability is still an open problem. In this paper the authors outline the state of the art in the development of control strategies based on the injection of high frequency signals. Implementation issues are then described, highlighting the challenges that must be won, in order to made sensorless motor drives exploiting high frequency signal injection, fully pursuing their sensored counterparts, in terms of operating range extension, performance, robustness and reliability.
Simulation of LED lighting system under ALSE test setup

In this paper, we demonstrate a methodology for fast virtual testing of LED lighting system under ALSE test setup. We use simulation software for generation of setup models according to ISO 11452-2 standard [1] and prediction of currents induced in LEDs. The levels of the currents are analyzed to check the possible malfunction of the system.
Discovery of phenotypic networks from genotypic association studies with application to obesity

Genome-wide Association Studies (GWAS) have resulted in many discovered risk variants for several obesity-related traits. However, before clinical relevance of these discoveries can be achieved, molecular or physiological mechanisms of these risk variants needs to be discovered. One strategy is to perform data mining of phenotypically-rich data sources such as those present in dbGAP (database of Genotypes and Phenotypes) for hypothesis generation. Here we propose a technique that combines the power of existing Bayesian Network (BN) learning algorithms with the statistical rigour of Structural Equation Modelling (SEM) to produce an overall phenotypic network discovery system with optimal properties. We illustrate our method using the analysis of a candidate SNP data set from the AMERICO sample, a multi-ethnic cross-sectional cohort of roughly 300 children with detailed obesity-related phenotypes. We demonstrate our approach by showing genetic mechanisms for three obesity-related SNPs.
An overhaul of the species–area approach for predicting biodiversity loss: incorporating matrix and edge effects

Summary 1. Species–area (SA) models have often been used to predict biodiversity loss resulting from habitat loss. This application of SA models hinges on two fundamental assumptions: the resultant landscape matrix is inhospitable to the taxa of interest; and edge effects do not factor into extinction risks. Despite growing consensus that these assumptions are unrealistic, the SA approach continues to be used in assessments of biodiversity decline and conservation planning. 2. We propose an overhaul of the SA approach by accounting for taxon-specific responses to landscape-specific matrix quality and deleterious effects of habitat edges. We pitted nine variants of an improved SA model (calibrated for edge and ⁄ or matrix) against two variants of the conventional model (calibrated with island or continental z values) to predict species extinction and endangerment in 15 tropical biodiversity hotspots. 3. The matrix-calibrated SA model received the highest Akaike’s Information Criterion weight (birds: 66AE8%; mammals: 63AE3%), which reflects the weight of evidence in support of it being the most parsimonious model given the set of candidate models and data considered. Additionally, the matrix-calibrated (MC) model produced species extinction predictions that were the most accurate and least biased. 4. The second best model (for both birds and mammals) was one that simultaneously corrected for matrix and edge effects. 5. The conventional SA model (particularly when calibrated with an island z value) performed worse than the matrix-calibrated and ⁄ or edge-corrected models. 6. Synthesis and applications. Our results suggest that accounting for the landscape matrix per se is a sufficient and significant improvement to the SA approach in terms of assessing species extinction risks from land-use change. More importantly, given that the MC model was also the most parsimonious model (in that it requires only one additional model parameter than the conventional SA model), it could prove to be a cost-effective heuristic tool for conservation scientists and decision makers to accurately evaluate extinction risks resulting from land-use decisions. We argue that, henceforth, the MC model, which takes account of both the extent of deforestation and quality of the resultant matrix, should replace the conventional SA model for predicting biodiversity loss.
Analysis of a Switched Impedance Transformer-Type Nonsuperconducting Fault Current Limiter

This paper proposes a nonsuperconducting fault current limiter (NSFCL) topology and control strategy. The switched impedance transformer-type NSFCL topology is optimized to protect against short transients and to work in conjunction with other fuses or circuit breakers, hence has the merits of being simple, low cost, and compact. A prototype has been designed and built for a three-phase 600-VRMS,L-L system. It has been tested in a UL-certified high-power test lab with 5-A normal current and 100-kA potential fault current.
Comparing Dimensionality Reduction Methods Using Data Descriptor Landscapes

Dimensionality reduction (DR) methods are commonly used in data science to turn high-dimensional data into 2D representations. Since data sets contain different structural features that need to be preserved by this process, there is a multitude of DR methods, each geared towards preserving a separate aspect. This makes choosing a suitable algorithm for a given data set a challenging task. In this paper, we propose a comparative analysis of DR methods based on how well their embedding preserves structural features in the high-dimensional point cloud. To this end, we develop a set of data descriptors that assess local and global structural features of point clouds. These features are computed for the high-D point cloud and the 2D embedding. We then use persistent homology to robustly compare the feature functions. An interactive landscape of the data descriptors, based on their topological differences, permits visually exploring the embeddings and their quality. We demonstrate the utility of our workflow by analysing multiple embeddings of high-dimensional data sets from real-world applications.
Optical Properties of Non-Malignant and Malignant Breast Tissue Determined by Surface Displacement of Laser-Induced Photoacoustic Generation

Citation: El-Sharkawy YH (2016) Optical Properties of Non-Malignant and Malignant Breast Tissue Determined by Surface Displacement of Laser-Induced Photoacoustic Generation. Int J Opt Photonic Eng 1:002 Copyright: © 2016 El-Sharkawy YH, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. *Corresponding author: Yasser. H. El-Sharkawy, Military Technical College, Department of Biomedical Engineering, MTC, Cairo, Egypt, E-mail: yhmelsharkawy@yahoo.com Received: March 17, 2016: Accepted: May 24, 2016: Published: May 27, 2016 VIBGYOR ISSN: 2631-5092
Going Global with Innovations from Emerging Economies: Investment in Customer Support Capabilities Pays Off

Globalization of innovation calls for entrepreneurial new ventures from emerging economies to develop customer-focused dynamic capabilities. The authors argue that firms with proprietary technology and a strategic intent to internationalize invest in international customer support capabilities to satisfy the demands of their most important international customers. Using a unique sample of 173 international new ventures from China and India, the authors show that such investments are associated with improved organizational learning and performance. The results suggest that globalization pays off when entrepreneurial firms from emerging economies invest in ongoing support of their most important international customers.
T-ray relevant frequencies for osteosarcoma classification

We investigate the classification of the T-ray response of normal human bone cells and human osteosarcoma cells, grown in culture. Given the magnitude and phase responses within a reliable spectral range as features for input vectors, a trained support vector machine can correctly classify the two cell types to some extent. Performance of the support vector machine is deteriorated by the curse of dimensionality, resulting from the comparatively large number of features in the input vectors. Feature subset selection methods are used to select only an optimal number of relevant features for inputs. As a result, an improvement in generalization performance is attainable, and the selected frequencies can be used for further describing different mechanisms of the cells, responding to T-rays. We demonstrate a consistent classification accuracy of 89.6%, while the only one fifth of the original features are retained in the data set.
Bioinformatics Consensus by Democracy . Using Meta-Analyses of Microarray and Genomic Data to Model the Cold Acclimation Signaling Pathway in Arabidopsis 1 [ W ]

The whole-genome response of Arabidopsis (Arabidopsis thaliana) exposed to different types and durations of abiotic stress has now been described by a wealth of publicly available microarray data. When combined with studies of how gene expression is affected in mutant and transgenic Arabidopsis with altered ability to transduce the low temperature signal, these data can be used to test the interactions between various low temperature-associated transcription factors and their regulons. We quantized a collection of Affymetrix microarray data so that each gene in a particular regulon could vote on whether a ciselement found in its promoter conferred induction (11), repression (21), or no transcriptional change (0) during cold stress. By statistically comparing these election results with the voting behavior of all genes on the same gene chip, we verified the bioactivity of novel cis-elements and defined whether they were inductive or repressive. Using in silico mutagenesis we identified functional binding consensus variants for the transcription factors studied. Our results suggest that the previously identified ICEr1 (induction of CBF expression region 1) consensus does not correlate with cold gene induction, while the ICEr3/ICEr4 consensuses identified using our algorithms are present in regulons of genes that were induced coordinate with observed ICE1 transcript accumulation and temporally preceding genes containing the dehydration response element. Statistical analysis of overlap and cis-element enrichment in the ICE1, CBF2, ZAT12, HOS9, and PHYA regulons enabled us to construct a regulatory network supported by multiple lines of evidence that can be used for future hypothesis testing.
Investigation of the catalytic and structural roles of conserved histidines of human coproporphyrinogen oxidase using site-directed mutagenesis.

BACKGROUND The catalytic contribution of four conserved histidines of human coproporphyrinogen oxidase (CPO) has been investigated using site-directed mutagenesis to change histidine (H) into alanine (A). MATERIAL/METHODS The wild-type and mutant enzyme forms were analyzed for their ability to utilize coproporphyrinogen-III, mesoporphyrinogen-VI, and harderoporphyrinogen as substrates. RESULTS Wild-type CPO had specific activities of 4.9+/-0.9 nmole product/min/mg for coproporphyrinogen-III, 1.7+/-0.7 nmole product/min/mg for mesoporphyrinogen-VI, and 5.1+/-1.8 nmole product/min/mg for harderoporphyrinogen. The four mutant enzymes were catalytically competent with all three substrates, but to varying degrees. The most affected mutant was the H158A enzyme which exhibited approximately 50-fold lower activity than wild-type recombinant CPO. CONCLUSIONS Thus, His158 of human CPO may have a role in the active site, but none of the conserved histidine residues of human coproporphyrinogen oxidase is essential for catalytic activity although changes in histidines have been implicated in the disease state hereditary coproporphyria.