Miracle-dz/UniFAR-FTUs huggingface dataset:
Identifying Hierarchical and Overlapping Protein Complexes Based on Essential Protein-Protein Interactions and “Seed-Expanding” Method

Many evidences have demonstrated that protein complexes are overlapping and hierarchically organized in PPI networks. Meanwhile, the large size of PPI network wants complex detection methods have low time complexity. Up to now, few methods can identify overlapping and hierarchical protein complexes in a PPI network quickly. In this paper, a novel method, called MCSE, is proposed based on λ-module and “seed-expanding. ” First, it chooses seeds as essential PPIs or edges with high edge clustering values. Then, it identifies protein complexes by expanding each seed to a λ-module. MCSE is suitable for large PPI networks because of its low time complexity. MCSE can identify overlapping protein complexes naturally because a protein can be visited by different seeds. MCSE uses the parameter λ_th to control the range of seed expanding and can detect a hierarchical organization of protein complexes by tuning the value of λ_th. Experimental results of S. cerevisiae show that this hierarchical organization is similar to that of known complexes in MIPS database. The experimental results also show that MCSE outperforms other previous competing algorithms, such as CPM, CMC, Core-Attachment, Dpclus, HC-PIN, MCL, and NFC, in terms of the functional enrichment and matching with known protein complexes.
Optimizing insulin secretagogue therapy in patients with type 2 diabetes: a randomized double-blind study with repaglinide.

OBJECTIVE Repaglinide, a novel antidiabetic agent that has a rapid onset and short duration of action, was developed for mealtime dosing. The purpose of this pharmacodynamic study was to validate a prandial regimen of repaglinide by comparing meal-related dosing with a regimen in which the same total daily dose was divided into only two doses at morning and evening meals. RESEARCH DESIGN AND METHODS The study was a double-blind, randomized, parallel-group trial in 19 antidiabetic agent-naive subjects with type 2 diabetes (mean age 58 years, known duration of diabetes 3.5 years, HbA(1c) 7.3%, and BMI 32 kg/m(2)). Patients were randomly assigned to receive repaglinide either before each of the three main meals or before breakfast and before the evening meal. Patients in both groups received the same total daily dose of repaglinide. Twenty-four hour profiles of blood glucose, plasma insulin, and plasma C-peptide concentrations were measured at baseline and after 4 weeks of treatment. RESULTS Repaglinide increased postprandial insulin levels and markedly reduced postprandial glucose levels relative to baseline in both groups. Significant reductions were also recorded in fasting blood glucose and HbA(1c) levels. The repaglinide regimen, in which a dose was taken before each main meal, was more effective in improving glycemic control (including postprandial glucose and HbA(1c) levels) than the same total dose of repaglinide divided into morning and evening mealtime doses. CONCLUSIONS These data support the strategy of mealtime dosing with repaglinide. The improvements in glycemic control observed in these patients are encouraging. In addition to classic parameters of glycemic control, improvements in postprandial glucose excursions may prove to be important because postprandial hyperglycemia has been suggested to be an independent risk factor for cardiovascular disease in diabetes.
Optimized design of top-hat filter based on algorithms of support vector machine

A novel method for self adapting morphological top-hat operator was presented. The structural elements of opening top-hat are trained by utilizing the support vector machine from a mass of sample sets. Once the machine is trained by the samples of structural elements, it can implement background suppressing in the following frames. Practical infrared image sequence background suppressing shows that the proposed method based on support vector machine was fit for lower signal noise ratio image. Experimental results of the actual measurement show that using the improved top-hat operator, the detection probability of image with sbr (sbrap0.9 dB) is higher than 96%, compared with fixed top-hat filter, the detection probability is improved by nearly 7%.
Strain rates and contemporary deformation in the Snake River Plain and surrounding Basin and Range from GPS and seismicity

We used new horizontal global positioning system (GPS) velocities along with earthquakes, faults, and volcanic features to assess how strain is accommodated in the northern Basin and Range Province. We estimated horizontal velocities for 132 stations within the Snake River Plain and the surrounding Basin and Range from GPS phase data collected from 1994 to 2007. These velocities show regional-scale clockwise rotation suggestive of driving forces beyond those associated with the Yellowstone hotspot. Within the western Centennial tectonic belt, the GPS measurements indicate that the Basin and Range is extending at a rate an order of magnitude greater than the Snake River Plain, which explains its low seismicity. Between these two regions, we discern the “Centennial shear zone,” a NE-trending zone of right-lateral shear with estimated slip rates that increase northeastward from 0.9 ± 0.3 mm/yr in the SW to 1.7 ± 0.2 mm/yr in NE. We interpret the new GPS velocities to indicate: (1) right-lateral shear may be accommodated by strike-slip earthquakes on NE-trending faults in the Centennial shear zone; (2) three Basin and Range faults (Lost River, Lemhi, and Beaverhead) terminate at the Snake River Plain margin; and (3) extension in the Snake River Plain occurs at a much lower rate than the rate of normal faulting in the western Centennial tectonic belt.
Induction of controlled hypoxic pregnancy in large mammalian species

Progress in the study of pregnancy complicated by chronic hypoxia in large mammals has been held back by the inability to measure long‐term significant reductions in fetal oxygenation at values similar to those measured in human pregnancy complicated by fetal growth restriction. Here, we introduce a technique for physiological research able to maintain chronically instrumented maternal and fetal sheep for prolonged periods of gestation under significant and controlled isolated chronic hypoxia beyond levels that can be achieved by habitable high altitude. This model of chronic hypoxia permits measurement of materno‐fetal blood gases as the challenge is actually occurring. Chronic hypoxia of this magnitude and duration using this model recapitulates the significant asymmetric growth restriction, the pronounced cardiomyopathy, and the loss of endothelial function measured in offspring of high‐risk pregnancy in humans, opening a new window of therapeutic research.
Efficient Bregman Range Search

We develop an algorithm for efficient range search when the notion of dissimilarity is given by a Bregman divergence. The range search task is to return all points in a potentially large database that are within some specified distance of a query. It arises in many learning algorithms such as locally-weighted regression, kernel density estimation, neighborhood graph-based algorithms, and in tasks like outlier detection and information retrieval. In metric spaces, efficient range search-like algorithms based on spatial data structures have been deployed on a variety of statistical tasks. Here we describe an algorithm for range search for an arbitrary Bregman divergence. This broad class of dissimilarity measures includes the relative entropy, Mahalanobis distance, Itakura-Saito divergence, and a variety of matrix divergences. Metric methods cannot be directly applied since Bregman divergences do not in general satisfy the triangle inequality. We derive geometric properties of Bregman divergences that yield an efficient algorithm for range search based on a recently proposed space decomposition for Bregman divergences.
Convergent Evolution of Ribonuclease H in LTR Retrotransposons and Retroviruses

Ty3/Gypsy long terminals repeat (LTR) retrotransposons are structurally and phylogenetically close to retroviruses. Two notable structural differences between these groups of genetic elements are 1) the presence in retroviruses of an additional envelope gene, env, which mediates infection, and 2) a specific dual ribonuclease H (RNH) domain encoded by the retroviral pol gene. However, similar to retroviruses, many Ty3/Gypsy LTR retrotransposons harbor additional env-like genes, promoting concepts of the infective mode of these retrotransposons. Here, we provide a further line of evidence of similarity between retroviruses and some Ty3/Gypsy LTR retrotransposons. We identify that, together with their additional genes, plant Ty3/Gypsy LTR retrotransposons of the Tat group have a second RNH, as do retroviruses. Most importantly, we show that the resulting dual RNHs of Tat LTR retrotransposons and retroviruses emerged independently, providing strong evidence for their convergent evolution. The convergent resemblance of Tat LTR retrotransposons and retroviruses may indicate similar selection pressures acting on these diverse groups of elements and reveal potential evolutionary constraints on their structure. We speculate that dual RNH is required to accelerate retrotransposon evolution through increased rates of strand transfer events and subsequent recombination events.
Design and Architecture for Web Graph Mining Base Recommender System for Query, Image and Social Network using Query Suggestion Algorithm and Heat Diffusion Method

Recommendation techniques is now a day's very important. various kinds of recommendations are done on the Web, example movies, music, images, books recommendations, query suggestions and tags recommendations, etc. it is not important that what kind of data sources are used for the recommendations, these data sources can be modeled or taken in the various types of graphs. In this paper, We are discussing a general framework on Web graphs mining based recommender system for Query, Image-tags and Social Network using Query Suggestion Algorithm and Heat Diffusion Method 1) we first propose a novel diffusion method which shows similarities between different nodes and generates recommendations; 2) secondly we illustrate Architecture of web graph mining base recommender system which function for query, image and social network using three different data sets respectively 3) And at the end we illustrate the design using UML diagrams as a Visual models for the same; Hao Ma, Irwin King et al in their paper "Mining Web Graphs for Recommendations" have proposed a system for query suggestion and image recommendation using heat diffusion by taking reference of that we are adding a social recommendation. Aim of this paper is to review heat diffusion and depict the architecture and design for the proposed system.
TAZ promotes epithelial to mesenchymal transition via the upregulation of connective tissue growth factor expression in neuroblastoma cells

Neuroblastoma (NB) is a neuroendocrine cancer that occurs most commonly in infants and young children. The Hippo signaling pathway regulates cell proliferation and apoptosis, and its primary downstream effectors are TAZ and yes-associated protein 1 (YAP). The effect of TAZ on the metastatic progression of neuroblastoma and the underlying mechanisms involved remain elusive. In the current study, it was determined by western blot analysis that the migratory and invasive properties of SK-N-BE(2) human neuroblastoma cells are associated with high expression levels of TAZ. Repressed expression of TAZ in SK-N-BE(2) cells was shown to result in a reduction in aggressiveness of the cell line, by Transwell migration and invasion assay. In contrast, overexpression of TAZ in SK-N-SH human neuroblastoma cells was shown by Transwell migration and invasion assays, and western blot analysis, to result in epithelial-mesenchymal transition (EMT) and increased invasiveness. Mechanistically, the overexpression of TAZ was demonstrated to upregulate the expression levels of connective tissue growth factor (CTGF), by western blot analysis and chromatin immunoprecipitation assay, while the knockdown of TAZ downregulated it. Furthermore, TAZ was shown by luciferase assay to induce CTGF expression by modulating the activation of the TGF-β/Smad3 signaling pathway. In conclusion, the present study is, to the best of our knowledge, the first to demonstrate that the overexpression of TAZ induces EMT, increasing the invasive abilities of neuroblastoma cells. This suggests that TAZ may serve as a potential target in the development of novel therapies for the treatment of neuroblastoma.
Construction a DNA Vaccine Containing Human Papillomavirus Type 16 Early Genes as a Potential Vaccine for Cervical Cancer Prevention and Therapy

Background and Objectives: Some of the human papillomaviruses (HPVs) can infect genital tracts and are sometimes associated with anogenital tract cancers. HPVs induced cervical cancers through the expression of E6 and E7 genes by inactivating the tumor suppressor proteins. In this study, E6 and E7 genes were chosen in order to construct an expression vector which is able to express target proteins. Patients and Methods: This experimental investigation was performed in Virology Department of Tarbiat Modares University. An expression vector containing human papillomavirus type 16 E6 and E7 genes was constructed. The accuracy of the plasmid was confirmed by polymerase chain reaction (PCR) and restriction enzyme analysis. The construct was transfected into the eukaryotic cells and its ability for protein production was confirmed by Western blotting. Results: The colonies containing desired plasmid have the fragment about 995 bp. For confirming the ability of the construct for protein production in eukaryotic cells, Western blotting was done using the lyses-cells as antigen and they showed the desired bands using monoclonal antibodies. Conclusion: The designed vector can consider as a based vaccine for construction a therapeutic vaccine in suitable vectors for gene therapy in order to administration in Iranian patients with cervical cancer.
Emotional Processing, P50 Sensory Gating, and Social Functioning in Bipolar Disorder

Emotional processing has been reported to effect sensory gating as measured by the event-related potential known as P50. Because both P50 and emotional processing are dysfunctional in bipolar disorder (BD), we sought to investigate the impact that concurrent emotional processing has on sensory gating in this psychiatric population. P50 was recorded using a paired-click paradigm. Peak-to-peak amplitudes for stimulus 1 (S1) and stimulus 2 (S2) were acquired during the presentation of disgust and neutral faces to young adults with BD (n = 19) and controls (n = 20). Social functioning and quality-of-life self-reported measures were also obtained. The BD group had significantly larger P50 amplitudes elicited by the S2-disgust response compared with controls, but no significant difference in overall P50 sensory gating was found between the groups. There were also no differences between groups in S1-disgust or in either of the neutral P50 amplitudes. The BD group showed significant associations between sensory gating to disgust and measures of social functioning. Importantly, BD showed impaired filtering of auditory information when paired with an emotionally salient image. Thus, it appears that patients with the greatest impairment in sensory gating also have the most difficulty engaging in social situations.
Brushless DC motor design using harmony search optimization

This paper presents the design and optimization procedure for slotless brushless DC (BLDC) motors. The motor optimization is achieved using a modified harmony search technique, though other optimization methods can also be used. The expressions of motor electromagnetic torque, speed, voltage, current, power losses, volume and cost are analytically represented as functions of motor geometric parameters. The objective function is a combination of motor power losses, volume and cost, and needs to be minimized subject to a set of electrical and mechanical requirements and limitations. Ten design parameters are considered including the number of poles, current density and the dimensions of magnet, stator, rotor, winding and air-gap. The effects of each design parameter on the brushless DC motor performance have been investigated. The method was originally conceived for the design of a small motor for a biomedical application, but in this paper one sample case of a larger motor illustrates the general use of the technique.
Minimizing Regret : The General Case

In repeated games with differential information on one side, the labelling "general case" refers to games in which the action of the informed player is not known to the uninformed, who can only observe a signal which is the random outcome of his and his opponent's action. Here we consider the problem of minimizing regret (in the sense first formulated by Hannan [8]) when the information available is of this type. We give a simple condition describing the approachable set.
Data Placement and Replica Selection for Improving Co-location in Distributed Environments

Increasing need for large-scale data analytics in a number of application domains has led to a dramatic rise in the number of distributed data management systems, both parallel relational databases, and systems that support alternative frameworks like MapReduce. There is thus an increasing contention on scarce data center resources like network bandwidth; further, the energy requirements for powering the computing equipment are also growing dramatically. As we show empirically, increasing the execution parallelism by spreading out data across a large number of machines may achieve the intended goal of decreasing query latencies, but in most cases, may increase the total resource and energy consumption significantly. For many analytical workloads, however, minimizing query latencies is often not critical; in such scenarios, we argue that we should instead focus on minimizing the average query span, i.e., the average number of machines that are involved in processing of a query, through colocation of data items that are frequently accessed together. In this work, we exploit the fact that most distributed environments need to use replication for fault tolerance, and we devise workload-driven replica selection and placement algorithms that attempt to minimize the average query span. We model a historical query workload trace as a hypergraph over a set of data items, and formulate and analyze the problem of replica placement by drawing connections to several well-studied graph theoretic concepts. We develop a series of algorithms to decide which data items to replicate, and where to place the replicas. We show effectiveness of our proposed approach by presenting results on a collection of synthetic and real workloads. Our experiments show that careful data placement and replication can dramatically reduce the average query spans resulting in significant reductions in the resource consumption.
ICA FEATURES OF IMAGE DATA IN ONE, TWO AND THREE DIMENSIONS

In this paper we study image features obtained by independent component analysis (ICA) in one, two and three dimensions. As three-dimensional data we use an image of a human head obtained with magnetic resonance imaging (MRI). We also study the features when cutting one or two dimensions from the data, and make comparisons to ordinary optical natural image data. Additionally, we look at feature distributions and scale invariance in both data types.
Space-Time Block Codes in Nakagami Fading Channels with Non-Identical m-Distributions

Space-time block codes are known to be a powerful tool to achieve full spatial diversity gain while maintaining a very simple receiver structure. In this paper, the authors analyze the asymptotic error performance of orthogonal space-time block codes over flat Nakagami-m fading channels. Both identical and non-identical m-distributions are considered. Based on the moment generation function (MGF) approach, the closed-form asymptotic symbol error probabilities over Nakagami-m fading channels are derived. Compared to the previous works in literature, our results are more accurate and more general. Simulation results are provided to verify our analytical results.
A Novel Fast Fuzzy C-Means Clustering Technique for Segmentation of Human- Brain Magnetic Resonance Images

In medical applications all effectual agents in patient health must be fast, even medical algorithms such as clustering ones. In this paper an optimized technique is presented to decrease execution time and iterations of standard Fuzzy C-Means (FCM) alghorythm. New approach calculates cluster center in each iteration by new formula. Applying proposed method decreases the complexity of FCM algorithm. A type of averaging among cluster centers is applied in each iteration step however, membership function is a fuzzy coefficient. By proposed approach intensity of pixels in a cluster is averaged in each time step. Simulation results show that the proposed Fast FCM (FFCM) spends moderately half time of standard FCM and decreases iteration numbers. Moreover, to decrease the time of convergence considerably and decline the number of iterations significantly, cluster centroids are initialized by an algorithm. FCM and FFCM techniques are applied to segment magnetic resonance (MR) images. Accuracy of the proposed approach is significantly same as standard FCM. Applying fuzzy validity functions to quantitative assessment of FFCM in comparison with FCM verifies efficient performance of the proposed approach.
Testicular Differentiation Occurs in Absence of R-spondin1 and Sox9 in Mouse Sex Reversals

In mammals, male sex determination is governed by SRY-dependent activation of Sox9, whereas female development involves R-spondin1 (RSPO1), an activator of the WNT/beta-catenin signaling pathway. Genetic analyses in mice have demonstrated Sry and Sox9 to be both required and sufficient to induce testicular development. These genes are therefore considered as master regulators of the male pathway. Indeed, female-to-male sex reversal in XX Rspo1 mutant mice correlates with Sox9 expression, suggesting that this transcription factor induces testicular differentiation in pathological conditions. Unexpectedly, here we show that testicular differentiation can occur in XX mutants lacking both Rspo1 and Sox9 (referred to as XX Rspo1KOSox9cKO ), indicating that Sry and Sox9 are dispensable to induce female-to-male sex reversal. Molecular analyses show expression of both Sox8 and Sox10, suggesting that activation of Sox genes other than Sox9 can induce male differentiation in Rspo1KOSox9cKO mice. Moreover, since testis development occurs in XY Rspo1KOSox9cKO mice, our data show that Rspo1 is the main effector for male-to-female sex reversal in XY Sox9cKO mice. Thus, Rspo1 is an essential activator of ovarian development not only in normal situations, but also in sex reversal situations. Taken together these data demonstrate that both male and female sex differentiation is induced by distinct, active, genetic pathways. The dogma that considers female differentiation as a default pathway therefore needs to be definitively revised.