Miracle-dz/UniFAR-FTUs huggingface dataset:
CoPS: Comprehensive Peptide Signature Database

UNLABELLED We present the development of a Comprehensive database of 12 076 invariant Peptide Signatures (CoPS) derived from 52 bacterial genomes with a minimum occurrence in at least seven organisms. These peptides were observed in functionally similar proteins and are distributed over nearly 1250 different functional proteins. The database provides function, structure and occurrence in biochemical pathways of the proteins containing these signature peptides. It houses additional information on the signature peptides, such as identical match in other motif/pattern (e.g. PROSITE, BLOCKS, PRINTS and Pfam) databases and the database of interacting proteins, human proteome and mutation effect on these signature peptides. There is a wide applicability of this database in the identification of critical functional residues in proteins. The database also facilitates the identification of folding nucleus/structural determinants in proteins and functional assignment to yet unknown proteins. We demonstrate functional assignment to 2605 hypothetical proteins in bacterial genomes and 112 unknown proteins in human using this database. AVAILABILITY The database can be freely accessed through the following URL: http://203.195. 151.46/copsv2/index.html or http://203.90. 127.70/copsv2/index.html
Incrementally Tracking Reference in Human/Human Dialogue Using Linguistic and Extra-Linguistic Information

A large part of human communication involves referring to entities in the world and often these entities are objects that are visually present for the interlocutors. A system that aims to resolve such references needs to tackle a complex task: objects and their visual features need to be determined, the referring expressions must be recognised, and extra-linguistic information such as eye gaze or pointing gestures need to be incorporated. Systems that can make use of such information sources exist, but have so far only been tested under very constrained settings, such as WOz interactions. In this paper, we apply to a more complex domain a reference resolution model that works incrementally (i.e., word by word), grounds words with visually present properties of objects (such as shape and size), and can incorporate extra-linguistic information. We find that the model works well compared to previous work on the same data, despite using fewer features. We conclude that the model shows potential for use in a realtime interactive dialogue system.
The neural basis of human tool use

In this review, we propose that the neural basis for the spontaneous, diversified human tool use is an area devoted to the execution and observation of tool actions, located in the left anterior supramarginal gyrus (aSMG). The aSMG activation elicited by observing tool use is typical of human subjects, as macaques show no similar activation, even after an extensive training to use tools. The execution of tool actions, as well as their observation, requires the convergence upon aSMG of inputs from different parts of the dorsal and ventral visual streams. Non-semantic features of the target object may be provided by the posterior parietal cortex (PPC) for tool-object interaction, paralleling the well-known PPC input to anterior intraparietal (AIP) for hand-object interaction. Semantic information regarding tool identity, and knowledge of the typical manner of handling the tool, could be provided by inferior and middle regions of the temporal lobe. Somatosensory feedback and technical reasoning, as well as motor and intentional constraints also play roles during the planning of tool actions and consequently their signals likewise converge upon aSMG. We further propose that aSMG may have arisen though duplication of monkey AIP and invasion of the duplicate area by afferents from PPC providing distinct signals depending on the kinematics of the manipulative action. This duplication may have occurred when Homo Habilis or Homo Erectus emerged, generating the Oldowan or Acheulean Industrial complexes respectively. Hence tool use may have emerged during hominid evolution between bipedalism and language. We conclude that humans have two parietal systems involved in tool behavior: a biological circuit for grasping objects, including tools, and an artifactual system devoted specifically to tool use. Only the latter allows humans to understand the causal relationship between tool use and obtaining the goal, and is likely to be the basis of all technological developments.
Gene Therapy of Endothelial Nitric Oxide Synthase and Manganese Superoxide Dismutase Restores Delayed Wound Healing in Type 1 Diabetic Mice

Background—Nitric oxide (NO) deficiency contributes to diabetic wound healing impairment. The present study tested the hypothesis that increased cutaneous superoxide (O2−) levels in type 1 diabetic mice cause NO deficiency and delayed wound healing. Methods and Results—Wound healing was markedly delayed in streptozotocin-induced type 1 diabetic mice compared with the normal controls. There were significantly reduced levels of endothelial NO synthase (eNOS) protein and constitutive NOS activity in diabetic wounds, whereas O2− levels were markedly increased. A single regimen of cutaneous gene therapy of eNOS or manganese superoxide dismutase (MnSOD) restored such healing delay, with a concomitant suppression of wound O2− levels and augmentation of both eNOS protein and constitutive NOS activity. Gene therapy of MnSOD also increased cutaneous MnSOD activity. Cutaneous O2− levels were also increased in Ins2Akita diabetic mice. In vitro glucose treatment of cutaneous tissues from normal mice for 24 hours increased O2− levels in a concentration-dependent manner. The enhanced cutaneous O2− levels induced by high glucose in both normal and diabetic mice were abolished by the NADPH oxidase inhibitor apocynin and the protein kinase C inhibitor chelerythrine. Furthermore, ex vivo gene transfer of dominant-negative HA-tagged N17Rac1, which inhibits NADPH oxidase subunit Rac1, significantly inhibited cutaneous O2− formation induced by high glucose in both normal and Ins2Akita diabetic mice. Conclusions—These results indicate that hyperglycemia augments cutaneous O2− levels, at least in part, via NADPH oxidase and protein kinase C pathways, resulting in impaired wound healing in type 1 diabetic mice. Gene therapy strategies aimed at restoring cutaneous NO bioavailability may provide an effective means to ameliorate delayed diabetic wound healing.
Development of Tools for the Prediction of Return to Work and the Recovery of Post-Concussion Symptoms After Mild Tramatic Brain Injury (mTBI) Using Initial Clinical & Demographic Variables

Objective: Whilst much is known about the psychopathology of TBI, clinicians have difficulty in deciding which patients require intervention or further care. There is a need to develop simple methods and tools to identify those cases whose recovery will be problematic. The NeuroTrauma Research Group has examined a wide range of brief demographic and clinical measures to develop such tools. Method: A population sample of 450 patients presenting with mTBI at the Department of Emergency Medicine, Royal Hobart Hospital, were followed to examine outcome in terms of return to work/study, and post-concussion symptoms (measured using the Rivermead Post-Concussion Symptom Questionnaire, Rivermead PCS). Data was collected on a wide range of variables, including demographic (years of education, age, sex), psychosocial (anxiety, depression, quality of life), functional (Functional Independence Measure, FIM; Disability Rating Scale, DRS), and clinical (loss of consciousness, post-traumatic amnesia, PTA; post-concussion symptoms, Rivermead PCS). These variables were used to investigate predictors of time to return to work/study, and post-concussion symptoms up to 12 months post-trauma, using multiple regression. Data were collected within 1 week of TBI, and at 14 days, 28 days, 3 months, 6 months, and 12 months post-injury. Results: Variables contributing to the prediction of return to work included initial measures of anxiety, depression, fatigue, pain, and other post-concussion symptoms, as well as age. Pre-morbid quality of life, initial FIM, and PTA were amongst the variables contributing little to outcome prediction. Prediction of post-concussion symptoms at 3 and 6 months post-TBI was related to initial symptomatology, including anxiety and depression. Discussion: Our research to date suggests it is feasible to provide clinicians with a small range of measurement tools which will enable them to identify patients who do/do not require additional care or intervention following mTBI. Presenter Biography. Clive Skilbeck is a clinical neuropsychologist and clinical psychologist currently working as an Associate Professor in the School of Psychology at the University of Tasmania. His primary research interest is the assessment of impairments in cognitive and psychosocial functioning, and the measurement of their recovery, following acquired brain damage.
Journal of Multivariate Analysis

Multivariate dependence of spacings of generalized order statistics is studied. It is shown that spacings of generalized order statistics from DFR (IFR) distributions have the CIS (CDS) property. By restricting the choice of the model parameters and strengthening the assumptionsontheunderlyingdistribution,strongerdependencerelationsareestablished. For instance, if the model parameters are decreasingly ordered and the underlying distribution has a log-convex decreasing (log-concave) hazard rate, then the spacings satisfy the MTP 2 (S-MRR 2 ) property. Some consequences of the results are given. In particular, conditions for non-negativity of the best linear unbiased estimator of the scale parameter in a location-scale family are obtained. By applying a result for dual generalized order statistics, we show that in the particular situation of usual order statistics the assumptions can be weakened.
Teaching Cryptology Course Based on Theory-Algorithm-Practice-Application Mode

The cryptology course is an important curriculum of the major in information security and the interrelated majors. The teaching mode based on theory- algorithm-practice-application in cryptology course is proposed by combining the characteristic of cryptology course, the teaching experience and the scientific research experience in this paper. The practice proved it can improve the student’s ability of analyzing and resolving the engineering problem.
A Self-Configurable Desktop Grid System On-Demand

Desktop Grids have been used intensively to deploy applications at low cost. Applications types are classified into high throughput computing and high throughput data management. Desktop Grids such as Condor, BOINC, XtremWeb and Our Grid provide a wide range of high throughput computing systems. on the other hand, several data management systems such as Bit dew, GatorShare, Stork, Grid FTP, have been developed to handle a huge amount of data. Users are restricted to exploit Desktop Grid resources with a specific computing system and a specific data management system. to address this limitation, we propose in this work an extension of the Bonjour Grid middleware, to support different data management systems by exploiting existing data protocols and middleware. with Bonjour Grid, users of the same infrastructure can select, each one, the desired Desktop Grid middleware among the most popular ones to deploy and execute their applications. Now, users can select in addition to the computing system, the desired data manager protocol in a transparent and decentralized manner. Experimentation, using Bit Dew and Stork, on the Grid'5000 platform, demonstrate that the new release of Bonjour Grid provides with performance and at a low overhead.
Serum lipid changes and insulin resistance in familial Mediterranean fever.

OBJECTIVE Inflammation is known to alter lipid profiles and to induce insulin resistance. This study was planned to test the hypothesis that familial Mediterranean ferver (FMF) patients and their first-degree asymptomatic relatives may have lipid profile changes and/or insulin resistance, similar to other inflammatory diseases. MATERIAL AND METHODS We studied 72 FMF patients, 30 asymptomatic first-degree relatives, and 75 healthy controls. Fasting and 2-hour postprandial glucose, insulin, apolipoprotein (Apo) A1, Apo B, acute phase reactants, and lipid profiles of all subjects were studied. Insulin resistance was determined by the HOMA (Homeostasis Model Assessment) index. RESULTS There was no difference between the groups with regard to sex, mean systolic and diastolic blood pressure, body mass index, smoking status, fasting and postprandial 2-hour glucose, insulin, acute phase reactants, and HOMA index levels. High-density lipoprotein cholesterol (HDL-C) levels were similar between FMF patients and FMF relatives (48.9±12.4 mg/dL vs 49.3±13.8 mg/dL; p=NS), and both were lower than controls (48.9±12.4 mg/dL vs 59.6±15.1 mg/dL; p<0.001 and 49.3±13.8 mg/dL vs 59.8±15.1 mg/dL; p=0.001, respectively). Apo A1 levels in FMF patients and asymptomatic first-degree FMF relatives were both lower than in controls, similar to the HDL-C levels (126.1±25.7 mg/dL vs 151.2±31.4 mg/dL; p<0.001 and 129.5±29.0 mg/dL vs 151.2±31.4 mg/dL; p=0.002, respectively). TG levels were significantly higher in FMF relatives as compared to controls (113.4±53.6 mg/dL vs 97.1± 54.9 mg/dL; p=0.025). CONCLUSION Low HDL-C and low Apo A1 levels are found in FMF patients and their first-degree asymptomatic relatives. Low-grade inflammation caused by MEFV mutations may be responsible for these lipid profile changes.
Reuse of teaching components: a UML-based approach to delivering and managing academic courses

In this paper we present a model for the representation of academic courses based on the organization and semantic relation of reusable teaching components using the unified modeling language. We describe an application of the model to cs101, but we believed that the model can be applied to any subject content of any discipline. Results indicate that by following this model, the knowledge of more experienced teachers can be stored in its representation and the course components are easier to be reused by less experienced teachers.
Pulmonary aspergillosis: clinical presentation, diagnostic tests, management and complications.

PURPOSE OF REVIEW When functioning properly, the immune system recognizes inhaled fungi and controls their growth, while avoiding injurious inflammation and allergy. 'Aspergillosis' represents a spectrum of clinical diseases resulting from impaired or excessive immune responses. Invasive aspergillosis is principally disease of severely immunocompromised patients, whereas allergic forms of aspergillosis result from an excessive inflammatory response to hyphae colonizing the sinopulmonary tract. We will review insights gained in host defense against Aspergillus species and the immunopathogenesis of Aspergillus-related diseases as well as important advances made in fungal diagnostics and antifungal therapy. RECENT FINDINGS Important advances have been made in diagnosis of invasive aspergillosis and in antifungal agents. Voriconazole was superior to amphotericin B deoxycholate as primary therapy for invasive aspergillosis. There is significant interest in combination antifungal therapy for invasive aspergillosis. Fungal genomics offers a powerful opportunity to gain knowledge about fungal virulence factors that can be targets for drug development. In addition, new insights have been gained regarding host defense against Aspergillus species that may be exploited therapeutically. SUMMARY We have gained substantial knowledge regarding how the immune system recognizes inhaled fungi and calibrates the inflammatory response. There has also been substantial progress in tools to diagnose aspergillosis and in antifungal therapeutics. Future progress will likely involve the development of more refined diagnostic tools, new classes of antifungal agents, and greater knowledge of pathogen and host factors that predispose to aspergillosis.
Eating and ageing: A comparison over time of Italy, Ireland, the United Kingdom and France

This research analysed household budget survey data from Ireland, the United Kingdom, France and Italy from 1985/1987 to 2004/2005 to determine how age groups differ in terms of food-related practices, how these patterns are changing and to see if these patterns differ across countries. Descriptive analysis and fractional multinomial logistic regression were used. Food practices seem to be changing over time across all age cohorts in Ireland and the United Kingdom; older people have different food practices now than they would have had a few decades ago. However, in Italy and France, food-related practices seem to be related to age and life course with older people eating out less as they age than they did when they were younger. If these trends continue, older people will continue to prepare their own meals to a greater extent in Italy and France in the future with the retention of home preparation skills, while the home preparation of food will continue to decline in Ireland and the United Kingdom. These trends have implications for the health and well-being of older people in those countries.
Objective-Guided Image Annotation

Automatic image annotation, which is usually formulated as a multi-label classification problem, is one of the major tools used to enhance the semantic understanding of web images. Many multimedia applications (e.g., tag-based image retrieval) can greatly benefit from image annotation. However, the insufficient performance of image annotation methods prevents these applications from being practical. On the other hand, specific measures are usually designed to evaluate how well one annotation method performs for a specific objective or application, but most image annotation methods do not consider optimization of these measures, so that they are inevitably trapped into suboptimal performance of these objective-specific measures. To address this issue, we first summarize a variety of objective-guided performance measures under a unified representation. Our analysis reveals that macro-averaging measures are very sensitive to infrequent keywords, and hamming measure is easily affected by skewed distributions. We then propose a unified multi-label learning framework, which directly optimizes a variety of objective-specific measures of multi-label learning tasks. Specifically, we first present a multilayer hierarchical structure of learning hypotheses for multi-label problems based on which a variety of loss functions with respect to objective-guided measures are defined. And then, we formulate these loss functions as relaxed surrogate functions and optimize them by structural SVMs. According to the analysis of various measures and the high time complexity of optimizing micro-averaging measures, in this paper, we focus on example-based measures that are tailor-made for image annotation tasks but are seldom explored in the literature. Experiments show consistency with the formal analysis on two widely used multi-label datasets, and demonstrate the superior performance of our proposed method over state-of-the-art baseline methods in terms of example-based measures on four image annotation datasets.
Understanding the Relationship Between Social Support and Posttraumatic Stress Disorder/Posttraumatic Growth Among Adolescents After Ya’an Earthquake: The Role of Emotion Regulation

Objective: Posttraumatic distress disorder (PTSD) and posttraumatic growth (PTG) may coexist in trauma survivors, but there are mixed relationships between PTSD and PTG. To elucidate their relationship and constructs, it is necessary to examine simultaneously predictive factors, and to compare their determining factors. The aim of this study was to increasing our understanding the relationship between PTSD and PTG by examining simultaneously the role of social support and emotion regulation in PTSD and PTG among adolescents after the earthquake. Methods: Six months after the Ya’an earthquake, 315 middle school students in Lushan county were assessed using measures of trauma exposure, social support, and emotion regulation, as well as Child PTSD Symptom Scale and Posttraumatic Growth Inventory. Results: Social support had significant direct association with PTG but not with PTSD, but social support had a negative indirect prediction on PTSD and a positive indirect prediction on PTG through cognitive reappraisal. Social support, through expressive suppression, had a significant and indirect prediction on PTSD, but a nonsignificant indirect prediction on PTG. Conclusions: This study indicate that the predictive mechanism of PTSD and PTG were different and further suggest that PTSD and PTG are separate, independent dimensions of psychological experiences following adversity.
Diverse Molecular Targets for Therapeutic Strategies in Alzheimer's Disease

Alzheimer's disease (AD) is the most common form of dementia caused by neurodegenerative process and is tightly related to amyloid β (Aβ) and neurofibrillary tangles. The lack of early diagnostic biomarker and therapeutic remedy hinders the prevention of increasing population of AD patients every year. In spite of accumulated scientific information, numerous clinical trials for candidate drug targets have failed to be preceded into therapeutic development, therefore, AD-related sufferers including patients and caregivers, are desperate to seek the solution. Also, effective AD intervention is desperately needed to reduce AD-related societal threats to public health. In this review, we summarize various drug targets and strategies in recent preclinical studies and clinical trials for AD therapy: Allopathic treatment, immunotherapy, Aβ production/aggregation modulator, tau-targeting therapy and metabolic targeting. Some has already failed in their clinical trials and the others are still in various stages of investigations, both of which give us valuable information for future research in AD therapeutic development.
Realization of mechanical systems from second-order models

Congruent coordinate transformations are used to convert second-order models to a form in which the mass, damping, and stiffness matrices can be interpreted as a passive mechanical system. For those systems which can be constructed from interconnected mass, stiffness, and damping elements, it is shown that the input–output preserving transformations can be parametrized by an orthogonal matrix whose dimension corresponds to the number of internal masses—those masses at which an input is not applied nor an output measured. Only a subset of these transformations results in mechanically realizable models. For models with a small number of internal masses, complete discrete mapping of the transformation space is possible, permitting enumeration of all mechanically realizable models sharing the original model’s input–output behavior. When the number of internal masses is large, a nonlinear search of transformation space can be employed to identify mechanically realizable models. Applications include scale model.
Judgment of Line Orientation in Patients with Unilateral Cerebrovascular Lesions

This study examined the relationship between visual neglect and ability to judge the angular orientation of lines in patients with unilateral cerebrovascualar lesions. Participants were 75 patients with right-hemisphere cerebrovascular lesions (RCVA) and 39 patients with left-hemisphere cerebrovascular lesions (LCVA). All were administered the Judgment of Line Orientation test (JLO). Results revealed that twice as many RCVA patients (56%) exhibited impairment on the JLO as did LCVA patients (26%). In RCVA patients, much lower performance was seen in patients with left visual neglect. Among LCVA patients, no relationship was found between JLO performance and the presence of visual neglect. Correlations between JLO scores and WAIS-R variables suggested that JLO performance may be related in part to general cognitive factors, as well as to other perceptual and spatial abilities.