Miracle-dz/UniFAR-FTUs huggingface dataset:
Aberrant gene expression in autism

Autism spectrum disorder (ASD) is a complex neurodevelopmental condition characterized by substantial phenotypic and genetic heterogeneity. Analyzing gene expression may reveal specific patterns of gene activation and repression associated with the disorder. For this, we developed a new analysis method based on a multivariate distance measure commonly used for outlier detection. Our method detects the discrepancies in gene expression dispersion between populations and allows the identification of aberrantly expressed genes in a two-group setting. Using this method, we re-visited RNA sequencing data previously generated from postmortem brain tissues of 47 autistic and 57 control samples and identified a number of sets of genes with increased expression variability in autistics. The expression dispersion of these genes is more pronounced in autistics than controls. Many of these genes are known to be implicated in ASD, including those expressed in the synapse and those with neuropeptide binding function. Furthermore, we detected co-expressed gene modules among non-autistic controls and found that many of these modules disappear among autistics, due to the aberrant gene expression exclusively affecting ASD subjects. For the diagnostic purposes, we developed a greedy algorithm to globally search for classifier gene sets, for which the expression in peripheral blood samples of autistics is maximally deviant from that of non-autistic controls. We identified three classifier gene sets producing prominent and specific signals, which allowed the distinguishing of ASD from non-ASD samples. In summary, we have developed the aberrant gene expression analysis based on the multivariate, dispersion-specific measure, which is powerful in detecting increased gene expression variability functionally associated with ASD. CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi. org/10.1101/029488 doi: bioRxiv preprint first posted online Oct. 19, 2015;
Molecular Bases of Odor Discrimination: Reconstitution of Olfactory Receptors that Recognize Overlapping Sets of Odorants

The vertebrate olfactory system discriminates a wide variety of odorants by relaying coded information from olfactory sensory neurons in the olfactory epithelium to olfactory cortical areas of the brain. Recent studies have shown that the first step in odor discrimination is mediated by ∼1000 distinct olfactory receptors, which comprise the largest family of G-protein-coupled receptors. In the present study, we used Ca2+ imaging and single-cell reverse transcription-PCR techniques to identify mouse olfactory neurons responding to an odorant and subsequently to clone a receptor gene from the responsive cell. The functionally cloned receptors were expressed in heterologous systems, demonstrating that structurally related olfactory receptors recognized overlapping sets of odorants with distinct affinities and specificities. Our results provide direct evidence for the existence of a receptor code in which the identities of different odorants are specified by distinct combinations of odorant receptors that possess unique molecular receptive ranges. We further demonstrate that the receptor code for an odorant changes with odorant concentration. Finally, we show that odorant receptors in human embryonic kidney 293 cells couple to stimulatory G-proteins such as Gαolf, resulting in odorant-dependent increases in cAMP. Odor discrimination is thus determined by differences in the receptive ranges of the odorant receptors that together encode specific odorant molecules.
Survey of Image Retrieval Techniques and Algorithms for Image-rich Information Networks

Social networking sites allow users to share images, Ecommerce web sites also contains millions of images and thus forms image-rich information networks. Retrieving images from image-rich information networks is very challenging task, due to existence of information like text, user, image, feature, tags and group. The concept of image-rich information networks, image retrieval system and techniques like CBIR and TBIR are explained in this paper. The comparative study of image ranking and retrieval algorithms like simrank, k-simrank, HMOK-simrank is also mentioned in this paper. General Terms Image-rich information networks, CBIR, TBIR.
International Journal of Nephrology and Renovascular Disease Dovepress Blood Oxygenation Level-dependent Mri for Assessment of Renal Oxygenation

Blood oxygen level-dependent magnetic resonance imaging (BOLD MRI) has recently emerged as an important noninvasive technique to assess intrarenal oxygenation under physiologic and pathophysiologic conditions. Although this tool represents a major addition to our armamentarium of methodologies to investigate the role of hypoxia in the pathogenesis of acute kidney injury and progressive chronic kidney disease, numerous technical limitations confound interpretation of data derived from this approach. BOLD MRI has been utilized to assess intrarenal oxygenation in numerous experimental models of kidney disease and in human subjects with diabetic and nondiabetic chronic kidney disease, acute kidney injury, renal allograft rejection, contrast-associated nephropathy, and obstructive uropathy. However, confidence in conclusions based on data derived from BOLD MRI measurements will require continuing advances and technical refinements in the use of this technique.
Capping of the N‐terminus of PSD‐95 by calmodulin triggers its postsynaptic release

Postsynaptic density protein‐95 (PSD‐95) is a central element of the postsynaptic architecture of glutamatergic synapses. PSD‐95 mediates postsynaptic localization of AMPA receptors and NMDA receptors and plays an important role in synaptic plasticity. PSD‐95 is released from postsynaptic membranes in response to Ca2+ influx via NMDA receptors. Here, we show that Ca2+/calmodulin (CaM) binds at the N‐terminus of PSD‐95. Our NMR structure reveals that both lobes of CaM collapse onto a helical structure of PSD‐95 formed at its N‐terminus (residues 1–16). This N‐terminal capping of PSD‐95 by CaM blocks palmitoylation of C3 and C5, which is required for postsynaptic PSD‐95 targeting and the binding of CDKL5, a kinase important for synapse stability. CaM forms extensive hydrophobic contacts with Y12 of PSD‐95. The PSD‐95 mutant Y12E strongly impairs binding to CaM and Ca2+‐induced release of PSD‐95 from the postsynaptic membrane in dendritic spines. Our data indicate that CaM binding to PSD‐95 serves to block palmitoylation of PSD‐95, which in turn promotes Ca2+‐induced dissociation of PSD‐95 from the postsynaptic membrane.
Metaheuristic algorithms based Flow Anomaly Detector

Increasing throughput of modern high-speed networks needs accurate real-time Intrusion Detection System (IDS). A traditional packet-based Network IDS (NIDS) is time-intensive as it inspects all packets. A flow-based anomaly detector addresses scalability issues by monitoring only packet headers. This method is capable of detecting unknown attacks in high speed networks. An Artificial Neural Network (ANN) is employed in this research to detect anomalies in flow-based traffic. Metaheuristic optimization algorithms have the potential to achieve global optimal solution. In this paper, two metaheuristic algorithms, Cuckoo and PSOGSA, are examined to optimize the interconnection weights of a Multi-Layer Perceptron (MLP) neural network. This optimized MLP is evaluated with two different flow-based data sets. We then compare the performance of these algorithms. The results show that Cuckoo and PSOGSA algorithms enable high accuracy in classifying benign and malicious flows. However, the Cuckoo has lower training time.
New Chondrocyte Genes Discovered by Representational Difference Analysis of Chondroinduced Human Fibroblasts

This report includes a review of the potential for gene expression analyses to provide new information for solving problems in skeletal repair and regeneration. It focuses on two approaches: high-throughput gene array methods and representational difference analysis (RDA). The principles underlying these methods are presented with experimental tutorials and some applications. Second, this report includes a review of results from applying both approaches to an in vitro model of postnatal chondroinduction by demineralized bone powder (DBP). Human dermal fibroblasts (hDFs) cultured with DBP acquire a chondroblast phenotype and express cartilage-specific matrix proteins after 7 days. We used cDNA macroarrays and RDA to identify the genes that were altered prior to expression of the chondroblast phenotype, i.e., after only 3 days’ culture with DBP. Using a strategy of data management and reduction based upon biological functions, we reported several functional families of genes (cytoskeletal elements, protein synthesis/trafficking, and matrix molecules and their modifiers) that are upregulated during chondroinduction of hDFs. Together with histological and biochemical evidence of the chondroblast phenotype, the gene expression patterns indicate that there are specific stages of induced chondrocyte differentiation in this experimental system. Third, this report includes a new study, in which DBP-regulated genes were used as a data base to derive new information on the cell biology of chondrocytes. The objective was to determine whether a set of genes expressed during induction of chondrocyte differentiation is also expressed by mature articular chondrocytes. Our search of the literature for 59 of the DBP-regulated genes disclosed that expression of 20 of them (33%) had been documented in mature cartilage or chondrocytes. Of the 39 genes not previously documented in cartilage, 11 were tested by RT-PCR and all were found to be expressed in freshly isolated adult human chondrocytes. This review and these new data show how the strategy of high-throughput methods and functional data reduction can expand our knowledge of chondrocyte cell biology.
Multidimensional Recurrence Quantification Analysis (MdRQA) for the Analysis of Multidimensional Time-Series: A Software Implementation in MATLAB and Its Application to Group-Level Data in Joint Action

We introduce Multidimensional Recurrence Quantification Analysis (MdRQA) as a tool to analyze multidimensional time-series data. We show how MdRQA can be used to capture the dynamics of high-dimensional signals, and how MdRQA can be used to assess coupling between two or more variables. In particular, we describe applications of the method in research on joint and collective action, as it provides a coherent analysis framework to systematically investigate dynamics at different group levels—from individual dynamics, to dyadic dynamics, up to global group-level of arbitrary size. The Appendix in Supplementary Material contains a software implementation in MATLAB to calculate MdRQA measures.
Occupational Choice and the Private Equity Premium Puzzle

This paper suggests a solution to what has become known as the "private equity premium puzzle" (Moskowitz and Vissing-Jorgensen (2002)). We interpret occupational choice as a dynamic portfolio choice problem of a life-cycle investor facing a liquidity constraint and imperfect information about the profitability of potential businesses. In this setting, becoming an entrepreneur is equivalent to investing in non-traded private equity capital subject to transaction costs. We model the return on private equity as the sum of two components, the individual ability of the entrepreneur and idiosyncratic business risk. Information is imperfect, because only entrepreneurs observe their own business risk realizations. Using numerical techniques we find that the model generates the observed return structure for private equity using standard CRRA-preferences and fully rational expectations.
Facial stimulation induces long-term depression at cerebellar molecular layer interneuron–Purkinje cell synapses in vivo in mice

Cerebellar long-term synaptic plasticity has been proposed to provide a cellular mechanism for motor learning. Numerous studies have demonstrated the induction and mechanisms of synaptic plasticity at parallel fiber–Purkinje cell (PF–PC), parallel fiber–molecular layer interneurons (PF–MLI) and mossy fiber–granule cell (MF–GC) synapses, but no study has investigated sensory stimulation-evoked synaptic plasticity at MLI–PC synapses in the cerebellar cortex of living animals. We studied the expression and mechanism of MLI–PC GABAergic synaptic plasticity induced by a train of facial stimulation in urethane-anesthetized mice by cell-attached recordings and pharmacological methods. We found that 1 Hz, but not a 2 Hz or 4 Hz, facial stimulation induced a long-term depression (LTD) of GABAergic transmission at MLI–PC synapses, which was accompanied with a decrease in the stimulation-evoked pause of spike firing in PCs, but did not induce a significant change in the properties of the sensory-evoked spike events of MLIs. The MLI–PC GABAergic LTD could be prevented by blocking cannabinoid type 1 (CB1) receptors, and could be pharmacologically induced by a CB1 receptor agonist. Additionally, 1 Hz facial stimulation delivered in the presence of a metabotropic glutamate receptor 1 (mGluR1) antagonist, JNJ16259685, still induced the MLI–PC GABAergic LTD, whereas blocking N-methyl-D-aspartate (NMDA) receptors during 1 Hz facial stimulation abolished the expression of MLI–PC GABAergic LTD. These results indicate that sensory stimulation can induce an endocannabinoid (eCB)-dependent LTD of GABAergic transmission at MLI–PC synapses via activation of NMDA receptors in cerebellar cortical Crus II in vivo in mice. Our results suggest that the sensory stimulation-evoked MLI–PC GABAergic synaptic plasticity may play a critical role in motor learning in animals.
Elucidating the Behavioral Phenotype of Drosophila melanogaster Larvae : Correlations Between Larval Foraging Strategies and Pupation Height

Larvae which demonstrated long trails covering a large area while feeding (rover foragers) pupated significantly higher than those covering a relatively small area and exhibiting short paths (sitter foragers). Pupation height and density of larvae per vial were positively correlated. Under the condition o f equal larval density per vial, rovers were found to pupate significantly higher than sitter larval foragers. The effect of three light regimes (constant light, constant darkness, and 12 h light followed by 12 h dark) indicated a more complex relationship between pupation height and larval foraging behavior.
Iris segmentation methodology for non-cooperative recognition

An overview of the iris image segmentation methodologies for biometric purposes is presented. The main focus is on the analysis of the ability of segmentation algorithms to process images with heterogeneous characteristics, simulating the dynamics of a non-cooperative environment. The accuracy of the four selected methodologies on the UBIRIS database is tested and, having concluded about their weak robustness when dealing with non-optimal images regarding focus, reflections, brightness or eyelid obstruction, the authors introduce a new and more robust iris image segmentation methodology. This new methodology could contribute to the aim of non-cooperative biometric iris recognition, where the ability to process this type of image is required.
Brief Report Results and Discussion

Increased angiogenic sprouting in poor prognosis FL is associated with elevated numbers of CD163 ϩ macrophages within the immediate sprouting microenvironment Follicular lymphoma has considerable clinical heterogeneity, and there is a need for easily quantifiable prognostic biomar-kers. Microvessel density has been shown to be a useful prognostic factor based on numerical assessment of vessel numbers within histologic sections in some studies , but assessment of tumor neovascular-ization through angiogenic sprouting may be more relevant. We therefore examined the smallest vessels, single-staining structures measuring less than 30 ␮m 2 in area, seen within histologic sections, and confirmed that they were neovascular an-giogenic sprouts using extended focal imaging. Tissue microarrays composing diagnostic biopsies from patients at the extremes of survival of follicular lym-phoma were analyzed with respect to numbers of these sprouts. This analysis revealed higher angiogenic activity in the poor prognostic group and demonstrated an association between increased sprouting and elevated numbers of infiltrating CD163 ؉ macrophages within the immediate microenvironment surrounding the neovascular sprout. Introduction Follicular lymphoma (FL) patients have an indolent clinical course with a median survival of 10 years, but the clinical course is very heterogeneous; some patients have rapid disease progression and short survival, 1 with worse prognosis in those patients who transform to a more aggressive histology. 2,3 The Follicular Lym-phoma International Prognostic Index 4,5 helps to risk-stratify patients but has limited discriminative power, and additional prognostic biomarkers providing insight into underlying disease biology are urgently required. The use of simple, numerical quantification of blood vessels in histologic sections as a prognostic marker in FL has provided conflicting results. 6,7 An inherent limitation of conventional microvessel density analyses on histologic sections is that it provides only a relatively thin, 2-dimensional representation of the 3-dimensional, branching network of tumor vasculature and a static snapshot of the dynamic process of tumor neovascular-ization. We sought to establish whether the smallest-sized vascular structures, lacking a lumen, which are seen in routine sections, correspond to angiogenic sprouts; and whether quantifying these vascular sprouts could provide an improved surro-gate measure of angiogenic activity and its effect on subsequent clinical outcome. The immune microenvironment in FL is intimately linked to clinical behavior and response to treatment, 8-10 and increased numbers of tumor-associated macrophages (TAMs) in FL diagnostic biopsies indicate adverse prognosis, 11 although this appears to be dependent on treatment used. 12,13 Macrophages adapt to activation signals in their environment and display plasticity …
Diarrhea recurrence in patients with Clostridium difficile-associated diarrhea: Role of concurrent antibiotics.

OBJECTIVE To monitor prospectively patients with Clostridium difficile-associated diarrhea (CAD) in a six hundred bed tertiary care hospital to determine which factors influenced the recurrence of the diarrhea. DESIGN A prospective, nonrandomized study. After an initial diagnosis of CAD, patients were interviewed, and each week stool samples and environmental samples were monitored for the presence of toxigenic C difficile for as long as the patients remained in hospital. The relationship of concurrent antibiotics, prolonged fecal excretion of organism or toxin, and environmental contamination was assessed. PATIENTS Over a two-and-a-half year period, 75 consecutive patients with CAD were selected and those who gave their written informed consent were enrolled. A control group to evaluate environmental contamination consisted of 75 patients with diarrhea not associated with C difficile. RESULTS Of the 75 CAD patients, 11 (14.7%) had a recurrence of their diarrhea. Diarrhea recurrence was associated with an increased rate of prolonged excretion of toxigenic organism and/or C difficile toxin(s) (nine of 11 [81.8%] compared with nine of 64 [14.1%]; P≤0.0001; relative risk 14.25; 95% CI 3.383 to 60.023). The risk of diarrhea recurrence was not related to a specific antibiotic but to concurrent therapy. Treatment within 30 days of initial CAD-specific treatment with an antibiotic other than metronidazole or vancomycin occurred significantly more frequently in patients with recurrence of diarrhea compared with those who did not have a recurrence (eight of 11 [72.7%] compared with 22 of 64 [34.4%], P=0.022; relative risk 4; 95% CI 1.153 to 13.881). The environmental contamination rate for toxigenic C difficile in week one in the rooms of patients with diarrhea not caused by C difficile was low (two of 75 [2.6%]) compared with week one data for patients with CAD (14 of 75 [18.7%], P=0.002; relative risk 1.922; 95% CI 1.479 to 2.498). The most frequent site contaminated was the bedpan sprayer (eight of 14 [57.1%]). Pulsed field gel electrophoresis analysis of stool and environmental toxigenic isolates indicated that there was not a single endemic strain of C difficile. CONCLUSIONS This study indicates that the recurrence of diarrhea may be related to concurrent 'other' antibiotics. Although data indicated that there was a correlation between diarrhea recurrence and prolonged fecal excretion of toxin, further studies are required to clarify the clinical significance.
Drosophila homeodomain-interacting protein kinase inhibits the Skp1-Cul1-F-box E3 ligase complex to dually promote Wingless and Hedgehog signaling

Drosophila Homeodomain-interacting protein kinase (Hipk) has been shown to regulate in vivo, the stability of Armadillo, the transcriptional effector of Wingless signaling. The Wingless pathway culminates in the stabilization of Armadillo that, in the absence of signaling, is sequentially phosphorylated, polyubiquitinated and degraded. Loss-of-function clones for hipk result in reduced stabilized Armadillo, whereas overexpression of hipk elevates Armadillo levels to promote Wingless-responsive target gene expression. Here, we show that overexpression of hipk can suppress the effects of negative regulators of Armadillo to prevent its degradation in the wing imaginal disc. Hipk acts to stabilize Armadillo by impeding the function of the E3 ubiquitin ligase Skp1-Cul1-F-box (SCF)Slimb, thereby inhibiting Armadillo ubiquitination and subsequent degradation. Vertebrate Hipk2 displays a similar ability to prevent β-catenin ubiquitination in a functionally conserved mechanism. We find that Hipk's ability to inhibit SCFSlimb-mediated ubiquitination is not restricted to Armadillo and extends to other substrates of SCFSlimb, including the Hedgehog signaling effector Ci. Thus, similar to casein kinase 1 and glycogen synthase kinase 3, Hipk dually regulates both Wingless and Hedgehog signaling by controlling the stability of their respective signaling effectors, but it is the first kinase to our knowledge identified that promotes the stability of both Armadillo and Ci.