Miracle-dz/UniFAR-FTUs huggingface dataset:
ExPASy: the proteomics server for in-depth protein knowledge and analysis

The ExPASy (the Expert Protein Analysis System) World Wide Web server (http://www.expasy.org), is provided as a service to the life science community by a multidisciplinary team at the Swiss Institute of Bioinformatics (SIB). It provides access to a variety of databases and analytical tools dedicated to proteins and proteomics. ExPASy databases include SWISS-PROT and TrEMBL, SWISS-2DPAGE, PROSITE, ENZYME and the SWISS-MODEL repository. Analysis tools are available for specific tasks relevant to proteomics, similarity searches, pattern and profile searches, post-translational modification prediction, topology prediction, primary, secondary and tertiary structure analysis and sequence alignment. These databases and tools are tightly interlinked: a special emphasis is placed on integration of database entries with related resources developed at the SIB and elsewhere, and the proteomics tools have been designed to read the annotations in SWISS-PROT in order to enhance their predictions. ExPASy started to operate in 1993, as the first WWW server in the field of life sciences. In addition to the main site in Switzerland, seven mirror sites in different continents currently serve the user community.
Interstitial Perfusion Culture with Specific Soluble Factors Inhibits Type I Collagen Production from Human Osteoarthritic Chondrocytes in Clinical-Grade Collagen Sponges

Articular cartilage has poor healing ability and cartilage injuries often evolve to osteoarthritis. Cell-based strategies aiming to engineer cartilaginous tissue through the combination of biocompatible scaffolds and articular chondrocytes represent an alternative to standard surgical techniques. In this context, perfusion bioreactors have been introduced to enhance cellular access to oxygen and nutrients, hence overcoming the limitations of static culture and improving matrix deposition. Here, we combined an optimized cocktail of soluble factors, the BIT (BMP-2, Insulin, Thyroxin), and clinical-grade collagen sponges with a bidirectional perfusion bioreactor, namely the oscillating perfusion bioreactor (OPB), to engineer in vitro articular cartilage by human articular chondrocytes (HACs) obtained from osteoarthritic patients. After amplification, HACs were seeded and cultivated in collagen sponges either in static or dynamic conditions. Chondrocyte phenotype and the nature of the matrix synthesized by HACs were assessed using western blotting and immunohistochemistry analyses. Finally, the stability of the cartilaginous tissue produced by HACs was evaluated in vivo by subcutaneous implantation in nude mice. Our results showed that perfusion improved the distribution and quality of cartilaginous matrix deposited within the sponges, compared to static conditions. Specifically, dynamic culture in the OPB, in combination with the BIT cocktail, resulted in the homogeneous production of extracellular matrix rich in type II collagen. Remarkably, the production of type I collagen, a marker of fibrous tissues, was also inhibited, indicating that the association of the OPB with the BIT cocktail limits fibrocartilage formation, favoring the reconstruction of hyaline cartilage.
Reflection on a legacy transaction processing monitor

In this paper we describe our experience applying the concepts of re ection to a legacy transaction processing TP monitor in order to support the implementation of extended transaction models In the past ten years numerous extended transaction models have been proposed to address the challenges posed by new advanced applications Few practical implementations of these extended transaction models exist and none are being used in a commercial TP monitor We believe the reason for this state of a airs is that the interface and functionality of commercial TP monitors is locked in to a xed transaction model We have developed the Re ective Transaction Framework as a practical method to implement extended transaction models on a commercial TP monitor The design of our framework is based on the principles of computational re ection and in particular open implementation The implementation of our framework introduces transaction adapters which are re ective software modules that provide a meta interface to the underlying TP monitor allowing ap plication developers the exibility to adjust both the application programming interface and system functionality Unlike classic re ective systems the Re ective Transaction Frame work applies re ection to a legacy TP monitor written in a non re ective programming language This paper focuses on the ability of the Re ective Transaction Framework to perform re ective computation and on the extent to which the legacy TP monitor supports this computation
Preparation and Characterization of Chitosan Thin Films on Mixed-Matrix Membranes for Complete Removal of Chromium

Herein we present a new approach for the complete removal of CrVI species, through reduction of CrVI to CrIII, followed by adsorption of CrIII. Reduction of chromium from water is an important challenge, as CrIV is one of the most toxic substances emitted from industrial processes. Chitosan (CS) thin films were developed on plain polysulfone (PSf) and PSf/TiO2 membrane substrates by a temperature-induced technique using polyvinyl alcohol as a binder. Structure property elucidation was carried out by X-ray diffraction, microscopy, spectroscopy, contact angle measurement, and water uptake studies. The increase in hydrophilicity followed the order: PSf < PSf/TiO2 < PSf/TiO2/CS membranes. Use of this thin-film composite membrane for chromium removal was investigated with regards to the effects of light and pH. The observations reveal 100 % reduction of CrVI to CrIII through electrons and protons donated from OH and NH2 groups of the CS layer; the reduced CrIII species are adsorbed onto the CS layer via complexation to give chromium-free water.
AB-Chord: An Efficient Approach for Resource Location in Structured P2P Networks

Recently, P2P (Peer-to-Peer) technology has witnessed a rapid development. Basically, one of key components in successful P2P applications is how to efficiently look up resources. Considering that structured P2P is a relatively efficient way to locate resources, this paper conducted two improvements to increase the search efficiency in Chord-based algorithms, one of the most popular structured P2P resource lookup protocols. In detail, our contributions are twofold. First, considering the fact that routing information in Chord is not abundant enough for efficient resource search, and looking up resource can only be enforced in clockwise direction, a new algorithm called AB-Chord is proposed to reconstruct the finger tables in Chord, in which counter-clockwise finger table is added to achieve resource queries in both directions, and the density of neighboring fingers is increased. Additionally, AB-Chord implements a new operation to remove the redundant fingers introduced by adding fingers in AB-Chord. Experimental results show that AB-Chord's query efficiency has been improved in terms of the average lookup hops and average lookup delay. And furthermore, considering that the proposed AB-Chord algorithm enlarged the finger table which may cause the forwarding-storm of routing maintenance messages, we further propose AB-Chord+, which appropriately extends the periodic time of updating finger tables and makes the joining and leaving nodes actively send updating messages, to reduce the number of messages forwarded in the network. Simulated results show that AB-Chord+ reduced the network bandwidth consumption.
Locally constant functors

Abstract We study locally constant coefficients. We first study the theory of homotopy Kan extensions with locally constant coefficients in model categories, and explain how it characterizes the homotopy theory of small categories. We explain how to interpret this in terms of left Bousfield localization of categories of diagrams with values in a combinatorial model category. Finally, we explain how the theory of homotopy Kan extensions in derivators can be used to understand locally constant functors.
Multiscale Feature Extraction of Finger-Vein Patterns Based on Curvelets and Local Interconnection Structure Neural Network

In this paper, we originally propose a multiscale feature extraction method of finger-vein patterns based on curvelets and local interconnection structure neural networks. The curvelets is used to perform the multiscale self-adaptive enhancement transform on the finger-vein image and a neural network with local interconnection structure is designed to extract the features of the finger-vein pattern. This method has the following features: firstly, the feature of finger-vein is line feature, or anisotropy, which is more suitable to be processed by curvelets than wavelets, especially when dealing with the obscure anisotropic features. Secondly, when the multiscale self-adaptive enhancement transform is applied to the finger-vein image, the finger-vein pattern is emphasized and noises are refrained greatly. Thirdly, a local interconnection neural network with linear receptive field is designed to deal with finger-vein patterns of different thickness and capture the patterns. Fourthly, the method is very fast by using the integral image method. The experimental results show the proposed method is superior to other methods in finger-vein feature extraction and solve the problem of how to extract features from obscure images efficiently. The EER of the proposed method is 0.128%
Divided Attention Improves Delayed, but Not Immediate Retrieval of a Consolidated Memory

A well-documented dissociation between memory encoding and retrieval concerns the role of attention in the two processes. The typical finding is that divided attention (DA) during encoding impairs future memory, but retrieval is relatively robust to attentional manipulations. However, memory research in the past 20 years had demonstrated that retrieval is a memory-changing process, in which the strength and availability of information are modified by various characteristics of the retrieval process. Based on this logic, several studies examined the effects of DA during retrieval (Test 1) on a future memory test (Test 2). These studies yielded inconsistent results. The present study examined the role of memory consolidation in accounting for the after-effect of DA during retrieval. Initial learning required a classification of visual stimuli, and hence involved incidental learning. Test 1 was administered 24 hours after initial learning, and therefore required retrieval of consolidated information. Test 2 was administered either immediately following Test 1 or after a 24-hour delay. Our results show that the effect of DA on Test 2 depended on this delay. DA during Test 1 did not affect performance on Test 2 when it was administered immediately, but improved performance when Test 2 was given 24-hours later. The results are consistent with other findings showing long-term benefits of retrieval difficulty. Implications for theories of reconsolidation in human episodic memory are discussed.
Is there specificity in a defensive mutualism against soil versus laboratory nematodes, Dictyostelium discoideum farmers and their bacteria?

Background: The social amoeba Dictyostelium discoideum is a soil-dwelling microbe, which lives most of its life cycle in the vegetative stage as a predator of bacteria and as prey for nematodes. When bacteria are sparse, amoebae aggregate into a multicellular fruiting body. Some clones of D. discoideum have agriculture (Brock et al., 2011). They carry bacteria through the social stage, eat them prudently, and use some bacteria as defence against non-farming D. discoideum competitors. Caenorhabditis elegans preys on D. discoideum in the laboratory but does not encounter it in nature because C. elegans lives on rotten fruit. The nematode Oscheius tipulae is abundant in the soil. Questions: Do the defensive bacteria that farmers carry also protect farmers from nematodes? Is this protection specific to nematodes that reside with D. discoideum? Hypotheses: Many organisms evolve defensive mutualisms against predators. The natural habitat of D. discoideum is populated with nematodes. Therefore, we hypothesize that farming D. discoideum clones use non-food bacteria for protection from nematodes. We predicted higher fitness of farmers than non-farmers in the presence of nematodes. We also predicted to see this change of fitness only in the presence of the soil nematode, O. tipulae. Organisms: Amoeba Dictyostelium discoideum, nematodes Caenorhabditis elegans and Oscheius tipulae, bacteria Klebsiella pneumoniae and Burkholderia xenovorans. Methods: We compared spore production of D. discoideum farmers and non-farmers with and without nematodes. We also looked at nematode proliferation in the presence of farmers, non-farmers, K. pneumonia, and B. xenovorans. Results: Overall, farmer D. discoideum produced fewer spores than non-farmers. There was a decrease in the spore counts in the presence of nematodes for both farmers and non-farmers. There was a significant decrease in the percentage change in spore production for the farmers in the presence of soil nematodes but not laboratory nematodes. Nematode proliferation with the laboratory nematode and soil nematode did not vary in the presence of farmers, non-farmers, K. pneumoniae or B. xenovorans. Conclusion: The non-food bacteria that farmers carry do not provide defence against nematodes. In fact, it was a disadvantage for farmers to carry bacteria, since the soil nematode decreased spore production for farmers compared with non-farmers. However, the differences Correspondence: B. Adu-Oppong, Department of Biology, CB 1137, Washington University in St. Louis, St. Louis, MO 63130, USA. e-mail: badu-oppong@wustl.edu Consult the copyright statement on the inside front cover for non-commercial copying policies. Evolutionary Ecology Research, 2014, 16: 351–361 © 2014 Boahemaa Adu-Oppong between the laboratory nematode and the soil nematode are marked enough to conclude that different species of nematodes respond differently to D. discoideum as a food source.
The effect of violent video game exposure on emotion modulation of startle and aggression

Video games are quickly becoming the most widely accessible, and used, form of entertainment, with those that contain violence have consistently been the most popular. Building on previous research examining other forms of media, a growing body of literature suggests a connection between violent video game exposure and increased aggression. The General Aggression Model (GAM), has been developed to help explain this relationship, which combines decades of aggression research into a single model. While the GAM describes several routes to increased aggression there are only two cognitive routes. These cognitive routes are desensitization (diminished natural negative response) and priming (pre-activation of neural circuitry related to aggression), and the current study competitively tests these two routes in relation to violent video game exposure (VVGE) using Emotion Modulated Startle (EMS). The objective psychophysiological measure EMS assesses emotional state through either potentiation, or inhibition of the startle response. The startle response is a negative-defensive response, a negative emotional state enhances the startle response through priming, while a positive emotional state diminishes the startle response. In the context of VVGE, if priming is
Magnetic resonance-guided near-infrared tomography of the breast

The design and implementation of a multispectral, frequency-domain near infrared tomography system is outlined, which operates in a MRI magnet for utilization of MR-guided image reconstruction of tissue optical properties. Using long silica optical fiber bundles, measurements of light transmission through up to 12 cm of female breast tissue can be acquired simultaneously with MRI scans. The NIR system utilizes six optical wavelengths from 660 to 850 nm using intensity modulated diode lasers nominally working at 100 MHz. Photomultiplier tube detector gain levels are electronically controlled on a time scale of 200 ms, thereby allowing rapid switching of the source to locations around the tissue. There are no moving parts in the detection channels and for each source position, 15 PMTs operating in parallel allow sensitivity down to 0.5 pW/cm2 at the tissue surface. Images of breast tissue optical absorption and reduced scattering coefficients are obtained using a Newton-type reconstruction algorithm to solv.
Parallel Algorithms for Graph Problems

This work demonstrates good speedups for the Scalable Synthetic Compact Application 2 (SSCA2) and algebraic connectivity for small irregular graphs on the Explicit MultiThreading (XMT) many-core architecture. Previous studies of these algorithms have been focused on using high performance computing architectures to solve large instances of the problems but little work has been done that establishes performance of these parallel algorithms on problem sizes solvable on a smaller scale system. Additionally, analysis of the algorithms is presented that shows how the ease of programming approach for XMT creates a clear path for developers to utilize multi-core resources without having to completely recreate the algorithm for the specific architecture by using the well-studied Parallel Random Access Model (PRAM) of algorithmic thinking. The compiler provided by the UMD XMT research team further makes it possible to trivially parallelize many segments of code and achieve acceptable speedup for the developer time invested. Future innovations from the UMD XMT research team will result in this process becoming even simpler with larger performance gains provided.
Integrity quantification model for object oriented design

Various surveys indicate that over the past several years software security has risen in priority for many software organizations. Security quantification in early stage of software development life cycle assists security experts to address security related problems well in advance. Security assessment using model is proved to be one of the established methods. Keeping in view of the same, an Integrity Quantification Model (IQM) is proposed in this paper. An effort is made by authors to correlate design integrity with complexity factors. Object oriented design metrics are used to quantify complexity factors. The developed model has been validated with realistic (small set of) data to prove the significance.
Automated quantification of coronary plaque with computed tomography: comparison with intravascular ultrasound using a dedicated registration algorithm for fusion-based quantification.

AIMS Previous studies have used semi-automated approaches for coronary plaque quantification on multi-detector row computed tomography (CT), while an automated quantitative approach using a dedicated registration algorithm is currently lacking. Accordingly, the study aimed to demonstrate the feasibility and accuracy of automated coronary plaque quantification on cardiac CT using dedicated software with a novel 3D coregistration algorithm of CT and intravascular ultrasound (IVUS) data sets. METHODS AND RESULTS Patients who had undergone CT and IVUS were enrolled. Automated lumen and vessel wall contour detection was performed for both imaging modalities. Dedicated automated quantitative software (QCT) with a unique registration algorithm was used to fuse a complete IVUS run with a CT angiography volume using true anatomical markers. At the level of the minimal lumen area (MLA), percentage lumen area stenosis, plaque burden, and degree of remodelling were obtained on CT. Additionally, mean plaque burden was assessed for the whole coronary plaque. At the identical level within the coronary artery, the same variables were derived from IVUS. Fifty-one patients (40 men, 58 ± 11 years, 103 coronary arteries) with 146 lesions were evaluated. Quantitative computed tomography and IVUS showed good correlation for MLA (n = 146, r = 0.75, P < 0.001). At the level of the MLA, both techniques were well-correlated for lumen area stenosis (n = 146, r = 0.79, P < 0.001) and plaque burden (n = 146, r = 0.70, P < 0.001). Mean plaque burden (n = 146, r = 0.64, P < 0.001) and remodelling index (n = 146, r = 0.56, P < 0.001) showed significant correlations between QCT and IVUS. CONCLUSION Automated quantification of coronary plaque on CT is feasible using dedicated quantitative software with a novel 3D registration algorithm.
Automatic Photo Annotation Based on Visual Content Analysis

In this paper we describe a novel approach for automatic photo annotation based on visual content analysis. We combine local and global features to ensure robustness and generalization needed by complex queries. We place great emphasis to work in real-time. To cope with the huge number of extracted features, we implemented diskbased locality-sensitive hashing to index descriptors. By searching candidates to extraction of keywords, we focus on photos analysis in terms of probability, that the retrieved photos contain the right keywords for the target photo. The result is that we are able to name key objects directly in the target photo.
Access to Education for Orphans and Vulnerable Children in Uganda: A Multi-District, Cross-Sectional Study Using Lot Quality Assurance Sampling from 2011 to 2013

Objectives This study estimates the proportion of Orphans and Vulnerable Children (OVC) attending school in 89 districts of Uganda from 2011 – 2013 and investigates the factors influencing OVC access to education among this population. Methods This study used secondary survey data from OVCs aged 5 – 17 years, collected using Lot Quality Assurance Sampling in 87 Ugandan districts over a 3-year period (2011 – 2013). Estimates of OVC school attendance were determined for the yearly time periods. Logistic regression was used to investigate the factors influencing OVC access to education. Results 19,354 children aged 5-17 were included in the analysis. We estimated that 79.1% (95% CI: 78.5% – 79.7%) of OVCs attended school during the 3-year period. Logistic regression revealed the odds of attending school were lower among OVCs from Western (OR 0.88; 95% CI: 0.79 – 0.99) and Northern (OR 0.64; 95% CI: 0.56 – 0.73) regions compared to the Central region. Female OVCs had a significantly higher odds of attending school (OR 1.09; 95% CI: 1.02 – 1.17) compared to their male counterparts. When adjusting for all variables simultaneously, we found the odds of school attendance reduced by 12% between 2011 and 2012 among all OVCs (OR 0.88; 95% CI: 0.81 – 0.97). Conclusion Our findings reinforce the need to provide continuing support to OVC in Uganda, ensuring they have the opportunity to attain an education. The data indicate important regional and gender variation that needs to be considered for support strategies and in social policy. The results suggest the need for greater local empowerment to address the needs of OVCs. We recommend further research to understand why OVC access to education and attendance varies between regions and improvement of district level mapping of OVC access to education, and further study to understand the particular factors impacting the lower school attendance of male OVCs.