Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of domain correlations in yeast protein complexes

MOTIVATION A growing body of research has concentrated on the identification and definition of conserved sequence motifs. It is widely recognized that these conserved sequence and structural units often mediate protein functions and interactions. The continuing advancements in high-throughput experiments necessitate the development of computational methods to critically assess the results. In this work, we analyzed high-throughput protein complexes using the domain composition of their protein constituents. Domains that mediate similar or related functions may consistently co-occur in protein complexes. RESULTS We analyzed Saccharomyces cerevisiae protein complexes from curated and high-throughput experimental datasets to identify statistically significant functional associations between domains. The resulting correlations are represented as domain networks that form the basis of comparison between the datasets, as well as to binary protein interactions. The results show that the curated datasets produce domain networks that map to known biological assemblies, such as ribosome, RNA polymerase, proteasome regulators, transcription initiation and histones. Furthermore, many of these domain correlations were also found in binary protein interactions. In contrast, the high-throughput datasets contain one large network of domain associations. High connectivity of RNA processing and binding domains in the high-throughput datasets reflects the abundance of RNA binding proteins in yeast, in agreement with a previous report that identified a nucleolar protein cluster, possibly mediated by rRNA, from these complexes. AVAILABILITY The software is available upon request from the authors and is dependent on the NCBI C++ toolkit.
Modelling the elastic behaviour of real chains in polymer networks

Monte-Carlo simulations of the elastic behaviour of PDMS networks, using a realistic (R-I-S) network-chain model, are able to reproduce experimentally observed deviations from Gaussian network behaviour in uniaxial extension. The finite extensibility of the network chains is shown to cause non-affine deformation of the mean-square network-chain end-to-end distance, even at moderate sample deformations (λ≈1.5). An increase in the proportion of fully-extended chains with increasing macroscopic strain gives rise to a steady decrease in the rate of network free-energy change, causing a reduction in the network modulus at moderate macroscopic strains. There is no need to invoke a transition from affine to phantom chain behaviour as deformation increases.
Extracting Placeness from Social Media: an Ontology-Based System

The recent popularity of location-based social (LBS) networking services has resulted in huge volumes of geo-tagged data from social media, allowing us to monitor massive lifelogs from a real-world space. Also, the characteristics of urban areas, placeness, were identified from the lifelogs attained.Based on this concern, in this paper, we propose a new approach of placeness extraction with an ontology-based urban area placeness identification system. The suggested technique uses the textual, temporal, and spatial information of a LBS post from a specific area, and combines this information with the help of ontology. This combination measures the areas occasion-oriented placeness, which can be subdivided into time or companions. Our work focuses on a case study of Twitter data from the city of Seoul. The results show that our system is able to extract subdividable placeness and suitable correspondences when compared to real world socio-geographic features.
A voting-based computational framework for visual motion analysis and interpretation

Most approaches for motion analysis and interpretation rely on restrictive parametric models and involve iterative methods which depend heavily on initial conditions and are subject to instability. Further difficulties are encountered in image regions where motion is not smooth-typically around motion boundaries. This work addresses the problem of visual motion analysis and interpretation by formulating it as an inference of motion layers from a noisy and possibly sparse point set in a 4D space. The core of the method is based on a layered 4D representation of data and a voting scheme for affinity propagation. The inherent problem caused by the ambiguity of 2D to 3D interpretation is usually handled by adding additional constraints, such as rigidity. However, enforcing such a global constraint has been problematic in the combined presence of noise and multiple independent motions. By decoupling the processes of matching, outlier rejection, segmentation, and interpretation, we extract accurate motion layers based on the smoothness of image motion, and then locally enforce rigidity for each layer in order to infer its 3D structure and motion. The proposed framework is noniterative and consistently handles both smooth moving regions and motion discontinuities without using any prior knowledge of the motion model.
Eurographics/siggraph Symposium on Computer Animation (2003) a Sketching Interface for Articulated Figure Animation

We introduce a new interface for rapidly creating 3D articulated figure animation, from 2D sketches of the character in the desired key frame poses. Since the exact 3D animation corresponding to a set of 2D drawings is ambiguous we first reconstruct the possible 3D configurations and then apply a set of constraints and assumptions to present the user with the most likely 3D pose. The user can refine this candidate pose by choosing among alternate poses proposed by the system. This interface is supported by pose reconstruction and optimization methods specifically designed to work with imprecise hand drawn figures. Our system provides a simple, intuitive and fast interface for creating rough animations that leverages our users' existing ability to draw. The resulting key framed sequence can be exported to commercial animation packages for interpolation and additional refinement.
THE PSYCHIATRIC PATIENT IN THE NURSING HOME: A RETROSPECTIVE STUDY *

With considerable ambivalence not immediately evident from the increasing numbers of patient~ di~charged from state hospitals to nur~ing home~, p~yrhi­ utric trcatmrnt tcamtl in mental hotlpitaltl arc utilizing nurtling homes a~ a major community 1'<'1-'0Ur<·r for the aftercare of aged patiPnt:-;. Oo! dfarb t 1.1 pay;; particular attention to 2 categorirs of patirnts who are di~chargt•d to nursing honw;;: Ia) tho:-;c who have ngt>d in the hospital (P.g. patient~ with chronic schizophrenia), and (b) those who first come to psyc hiatrie attt•n tion in their old age, often with physical illness and impairt>d phy~ieal function. Davis (2) n•ports a succc~,;ful program for placing patiPnt~ from psychiatric hospitals in nursing homes. Shore (3) and Kaplan ( 4) discus:-;, from the ;;tandpoint of the administrator, the problems of mixing the mentally ill and the mentally well in the same home. Cohen (5) focuses on 3 questions in the issue of placement in a nursing home versus retention of the patient in the mental hospital: 1. Does the nursing home program meet the patient's needs in a precise way? 2. Does a nursing home or docs a state hospital offer the best chance for achieving the goal of a therapeutic program? 3. Does the choice of a nursing home or mental hospital conserve the use of the already short supply of professional personnel, while meeting the patient's needs? Survey studies in Kansas (6), Maryland (7) and North Carolina (8) have shown that from 30 to 43 per cent of the patients admitted to nursing homes, regardless of source, carry psychiatric diagnoses. Miller (9) in a careful study of one horne in New York found that careful post-admission examination raised this proportion to 64 per cent. Goldfarb (10) reported that 87 per cent of the patients in nursing homes, when studied by objective measures of mental status, manifest a significant degree of chronic brain syndrome. Clearly, if the foregoing statistics are accepted, the existence in nursing homes of such large numbers of psychiatric patients raises many questions regarding the factors that contribute to either the success or failure of the patient's adjustment to these facilities.
Biomass and Biological Activity during the Production of Compost Used as a Substrate in Mushroom Cultivation

The production of a suitable substrate for the cultivation of the common white button mushroom, Agaricus bisporus, is referred to as composting. High microbiological activity causes temperatures of the composting material to rise as high as 80°C. At stacking, an optimal oxygen consumption rate of 140 μmol of O2 h−1 g (dry weight)−1 was found in the compost at 50°C, whereas the oxygen consumption rate of the end product was lower at all temperatures tested. No significant differences were observed between biomass content and mineralization rate of 14C-labeled glutamate of the two composts. Biomass content was shown to be a major function of both temperature and the sampling site position in the stack. On the basis of the results reported here, a minimal composting time of 3.3 days for the phase I process was calculated. Further suggestions are made to reduce the time necessary for the production of a substrate for A. bisporus considerably.
RTSVM: Real time support vector machines

In this paper, we propose a new classification method that improves the support vector machines technique (SVM). It consists of the real time SVM (RTSVM) that uses an incremental version of SVM which is the LASVM. It also takes into account of new data over time. Actually, current classification techniques suffer from scalability problem. There is a permanent growing and evolution of data. Besides, there is a need of important memory capacity and execution time to deal with data stream. Although the improvement made to SVM to reduce the memory use and computational time in training phase, the obtained model in training phase cannot be applied to new observations in test phase without using the hole data. To overcome this issue and improve classification task in test phase, the RTSVM adapts the initial model produced by the LASVM. After that, the RTSVM updates and improves it in test phase by only using new data for re-training. As a result, our proposal considerably reduces the execution time and improves the accuracy especially in test phase. Empirical study shows RTSVM to be effective when using real-world datasets.
Auditory distraction transmitted by a cochlear implant alters allocation of attentional resources

Cochlear implants (CIs) are auditory prostheses which restore hearing via electrical stimulation of the auditory nerve. The successful adaptation of auditory cognition to the CI input depends to a substantial degree on individual factors. We pursued an electrophysiological approach toward an analysis of cortical responses that reflect perceptual processing stages and higher-level responses to CI input. Performance and event-related potentials on two cross-modal discrimination-following-distraction (DFD) tasks from CI users and normal-hearing (NH) individuals were compared. The visual-auditory distraction task combined visual distraction with following auditory discrimination performance. Here, we observed similar cortical responses to visual distractors (Novelty-N2) and slowed, less accurate auditory discrimination performance in CI users when compared to NH individuals. Conversely, the auditory-visual distraction task was used to combine auditory distraction with visual discrimination performance. In this task we found attenuated cortical responses to auditory distractors (Novelty-P3), slowed visual discrimination performance, and attenuated cortical P3-responses to visual targets in CI users compared to NH individuals. These results suggest that CI users process auditory distractors differently than NH individuals and that the presence of auditory CI input has an adverse effect on the processing of visual targets and the visual discrimination ability in implanted individuals. We propose that this attenuation of the visual modality occurs through the allocation of neural resources to the CI input.
New membrane technologies for dialysis

Hemodialysis, developed in 1960s, has served as a treatment for patients with end stage renal disease. However, the 5 year mortality rate of hemodialysis patients is 65%. Research shows that some protein-bound toxins, which cannot to be cleared by hemodialysis, play an important role in mortality of hemodialysis patients. In order to improve the mortality rate of hemodialysis patients, we created a new type of hemodialysis membranes, which can remove more toxins than current hemodialysis membranes. In this thesis, we first adopted electrospinning technology to synthesis hemodialysis membranes with adsorptive nanoparticles. Polyacrylonitrile-zeolite nanofiber composite membranes were fabricated and their ability to adsorb water soluble uremic toxins was tested. The results show that both the free zeolite powder and membranes with zeolite can adsorb creatinine at high level and fast speed. The creatinine adsorption level of 940-zeolite powders is 25423 μg g in 625 μmol L creatinine solution. 0.025 g of 940-zeolite powders can eliminate 91% of 2 μmol creatinine in 5 min. In order to choose good zeolites, we also carried out experiments to study how their size and shape influence the creatinine uptake level. Spherical micro-particle 840, spherical nanoparticle P-87 and rod-like nanoparticle P-371 zeolites were tested. Experiments show that the zeolites have similar creatinine uptake ability as powders. However, they have significantly different creatinine uptake ability after being incorporated inside the membranes. Micro-particle and sphere-shaped particles perform better inside the membranes. Although the membranes we fabricated through electrospinning can adsorb water soluble toxins, their pore size is too large for hemodialysis. In another part of the thesis, we used spin-coating technologies to synthesize polyethersulphone
Two-step diagonal Newton method for large-scale systems of nonlinear equations

We propose some improvements on a diagonal Newton's method for solving large-scale systems of nonlinear equations. In this approach, we use data from two preceding steps to improve the current approximate Jacobian in diagonal form. Via this approach, we can achieve a higher order of accuracy for Jacobian approximation when compares to other existing diagonal-type Newton's method. The results of our numerical tests, demonstrate a clear enhancement in numerical performance of our proposed method
Instrumenting Bitstreams for Debugging FPGA Circuits

Since FPGAs are frequently used to improve the time to market for products, shortening the time for validating and debugging FPGA designs is, thus, important. Our paper discusses how directly instrumenting FPGA programming data, or bitstreams, with debugging hardware can improve the debugging productivity for designers and, thus, reduce a design’s time to market. We also provide some background relating to the current state of the art in debugging FPGA designs and describe how bitstream instrumentation can be automated using JHDL, JBits and JRoute. When instrumenting designs with embedded logic analyzers at the bitstream level, we have witnessed design modification speed-ups ranging from about 6 to 19 times over more conventional techniques. We will also briefly mention other applications of bitstream modification in debugging FPGA designs.
Role of Natural Killer Cells in Innate Protection against Lethal Ebola Virus Infection

Ebola virus is a highly lethal human pathogen and is rapidly driving many wild primate populations toward extinction. Several lines of evidence suggest that innate, nonspecific host factors are potentially critical for survival after Ebola virus infection. Here, we show that nonreplicating Ebola virus-like particles (VLPs), containing the glycoprotein (GP) and matrix protein virus protein (VP)40, administered 1–3 d before Ebola virus infection rapidly induced protective immunity. VLP injection enhanced the numbers of natural killer (NK) cells in lymphoid tissues. In contrast to live Ebola virus, VLP treatment of NK cells enhanced cytokine secretion and cytolytic activity against NK-sensitive targets. Unlike wild-type mice, treatment of NK-deficient or -depleted mice with VLPs had no protective effect against Ebola virus infection and NK cells treated with VLPs protected against Ebola virus infection when adoptively transferred to naive mice. The mechanism of NK cell–mediated protection clearly depended on perforin, but not interferon-γ secretion. Particles containing only VP40 were sufficient to induce NK cell responses and provide protection from infection in the absence of the viral GP. These findings revealed a decisive role for NK cells during lethal Ebola virus infection. This work should open new doors for better understanding of Ebola virus pathogenesis and direct the development of immunotherapeutics, which target the innate immune system, for treatment of Ebola virus infection.
Platelet-derived growth factor B induces senescence and transformation in normal human fibroblasts

Normal cells enter a senescent state upon aberrant oncogenic signals and this response inhibits tumor initiation and progression. It is now well admitted that intracellular and membrane localized oncogenes can illicit oncogene induced senescence. However, the effect of mitogenic growth factor on cellular senescence is so far largely unknown. Here we show that normal human dermal fibroblasts display a complex response to Platelet derived growth factor B (PDGFB) expression. Indeed, PDGFB expression induces, in the same cell population, both senescence and cellular transformation. Remarkably both populations are sustained with passages suggesting that transformed cells eventually enter a senescent state. This senescence state is p53 dependent as inhibiting the p53 pathway blocks the ability of PDGFB to induce senescence and results in strong cellular transformation increase upon PDGFB expression. The relevance of these observations is supported by the fact that human dermatofibrosarcoma protuberans, skin tumors arising from constitutive PDGFB production with little aggressiveness, also display some senescence hallmarks. Together these data support the view that PDGFB, a mitogenic growth factor, has a limited ability to induce senescence. We propose that this low level of senescence might decrease the transforming ability of this factor without totally abolishing it.
Pollen flow in the wildservice tree, Sorbus torminalis (L.) Crantz. IV. Whole interindividual variance of male fecundity estimated jointly with the dispersal kernel

Interindividual variance of male reproductive success (MRS) contributes to genetic drift, which in turn interacts with selection and migration to determine the short‐term response of populations to rapid changes in their environment. Individual relative MRS can be estimated through paternity analysis and can be further dissected into fecundity and spatial components. Existing methods to achieve this decomposition either rely on the strong assumption of a random distribution of pollen donors (TwoGener) or estimate only the part of the variance of male fecundity that is explained by few covariates. We developed here a method to estimate jointly the whole variance of male fecundity and the pollen dispersal curve from the genotypic information of sampled seeds and their putative fathers and geographical information of all individuals in the study area. We modelled the relative individual fecundities as a log‐normally distributed random effect. We used a Bayesian approach, well suited to the hierarchical nature of the model, to estimate these fecundities. When applied to Sorbus torminalis, the estimated variance of male fecundity corresponded to an effective density of trees 13 times lower than the observed density (dobs/dep ~ 13). This value is between the value (~2) estimated with a classical mating model including three covariates (neighbourhood density, diameter, flowering intensity) that affect fecundity and the value (~30) estimated with TwoGener. The estimated dispersal kernel was close to previous results. This approach allows fine monitoring of ongoing genetic drift in natural populations, and quantitative dissection of the processes contributing to drift, including human actions.
Island Pedicle Flap for Repair of the Lower Helical Rim and Earlobe

The island pedicle flap, also known as the V-Y advancement flap, is a well-described technique of repairing cutaneous defects. The flap is an island of tissue adjacent to the wound defect that closely matches the original tissue of the defect in color, texture, and sebaceous and follicular qualities. The flap has the advantages of maximizing tissue concordance, eliminating the need to remove excessive tissue in Burow’s triangles, and often making the closure possible within one cosmetic unit.
A Semi-Supervised Approach for Gender Identification

In most of the research studies on Author Profiling, large quantities of correctly labeled data are used to train the models. However, this does not reflect the reality in forensic scenarios: in practical linguistic forensic investigations, the resources that are available to profile the author of a text are usually scarce. To pay tribute to this fact, we implemented a Semi-Supervised Learning variant of the k nearest neighbors algorithm that uses small sets of labeled data and a larger amount of unlabeled data to classify the authors of texts by gender (man vs woman). We describe the enriched KNN algorithm and show that the use of unlabeled instances improves the accuracy of our gender identification model. We also present a feature set that facilitates the use of a very small number of instances, reaching accuracies higher than 70% with only 113 instances to train the model. It is also shown that the algorithm also performs well using publicly available data.
Conformational analysis of peptides corresponding to all the secondary structure elements of protein L B1 domain: Secondary structure propensities are not conserved in proteins with the same fold

The solution conformation of three peptides corresponding to the two β‐hairpins and the α‐helix of the protein L B1 domain have been analyzed by circular dichroism (CD) and nuclear magnetic resonance spectroscopy (NMR). In aqueous solution, the three peptides show low populations of native and non‐native locally folded structures, but no well‐defined hairpin or helix structures are formed. In 30% aqueous trifluoroethanol (TFE), the peptide corresponding to the α‐helix adopts a high populated helical conformation three residues longer than in the protein. The hairpin peptides aggregate in TFE, and no significant conformational change occurs in the NMR observable fraction of molecules. These results indicate that the helical peptide has a significant intrinsic tendency to adopt its native structure and that the hairpin sequences seem to be selected as non‐helical. This suggests that these sequences favor the structure finally attained in the protein, but the contribution of the local interactions alone is not enough to drive the formation of a detectable population of native secondary structures. This pattern of secondary structure tendencies is different to those observed in two structurally related proteins: ubiquitin and the protein G B1 domain. The only common feature is a certain propensity of the helical segments to form the native structure. These results indicate that for a protein to fold, there is no need for large native‐like secondary structure propensities, although a minimum tendency to avoid non‐native structures and to favor native ones could be required.