Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of autoantibody biomarkers for primary Sjögren's syndrome using protein microarrays

Sjögren's syndrome (SS) is a chronic, progressive autoimmune disease primarily affecting women. Diagnosis of SS requires an invasive salivary gland tissue biopsy and a long delay from the start of the symptoms to final diagnosis has been frequently observed. In this study, we aim to identify salivary autoantibody biomarkers for primary SS (pSS) using a protein microarray approach. Immune‐response protoarrays were used to profile saliva autoantibodies from patients with pSS (n=14), patients with systemic lupus erythematosus (SLE, n=13), and healthy control subjects (n=13). We identified 24 potential autoantibody biomarkers that can discriminate patients with pSS from both patients with SLE and healthy individuals. Four saliva autoantibody biomarkers, anti‐transglutaminase, anti‐histone, anti‐SSA, and anti‐SSB, were further tested in independent pSS (n=34), SLE (n=34), and healthy control (n=34) subjects and all were successfully validated with ELISA. This study has demonstrated the potential of a high‐throughput protein microarray approach for the discovery of autoantibody biomarkers. The identified saliva autoantibody biomarkers may lead to a clinical tool for simple, noninvasive detection of pSS at low cost.
Cryptree: A Folder Tree Structure for Cryptographic File Systems

We present Cryptree, a cryptographic tree structure which facilitates access control in file systems operating on untrusted storage. Cryptree leverages the file system's folder hierarchy to achieve efficient and intuitive, yet simple, access control. The highlights are its ability to recursively grant access to a folder and all its subfolders in constant time, the dynamic inheritance of access rights which inherently prevents scattering of access rights, and the possibility to grant someone access to a file or folder without revealing the identities of other accessors. To reason about and to visualize Cryptree, we introduce the notion of cryptographic links. We describe the Cryptrees we have used to enforce read and write access in our own file system. Finally, we measure the performance of the Cryptree and compare it to other approaches
Web-application composition through direct editing of Web documents and multiplexing of information access scenarios

In order to support user information retrieval on the Web, a framework is needed in which a user can define various types of data links as necessary by extracting only the necessary components from a Web application and then create a new compound document. This compound document refers to a document that includes services and tools embedded in it. In this research, the authors propose a framework which allows for clipping the structural elements of a Web application and directly manipulating the data linkages using formulas. As a result, the user can clip these components into cells from different Web applications, and then by linking them, create a unique compound document. Moreover, the authors provide a framework for cloning the clipped cells in order to compare the results of various different searches. Furthermore, in this paper the authors describe a method to use a word processing document or spreadsheet as a destination for embedding the clipped components, and function linking for these documents and the clipped cells. As a result, the created custom complex document can be reused and shared more easily. © 2007 Wiley Periodicals, Inc. Syst Comp Jpn, 38(12): 1–13, 2007; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/scj.20861
A belief theory-based static posture recognition systems for real-time video surveillance applications

This paper presents a system that can automatically recognize four different static human body postures for video surveillance applications. The considered postures are standing, sitting, squatting, and lying. The data come from the persons 2D segmentation and from their face localization. It consists in distance measurements relative to a reference posture (standing, arms stretched horizontally). The recognition is based on data fusion using the belief theory, because this theory allows the modelling of imprecision and uncertainty. The efficiency and the limits of the recognition system are highlighted thanks to the processing of several thousands of frames. A considered application is the monitoring of elder people in hospitals or at home. This system allows real-time processing.
Efficient Encodings for Document Ranking Vectors (Extended Abstract)

A spark gap switching device for high peak currents including a pair of main electrodes with protruding, opposing sub-electrodes, surrounded by high permeability cores typically of ferrite material. Small air gaps separate the sub-electrodes. The switch is activated by an over voltage or the like causing one of the sub-electrodes to breakover producing a flux time rate of change in the core. A voltage is induced in the non conducting sub-electrodes causing aligned pairs to rapidly increase in potential difference until one by one they all conduct.
Reduced kynurenine pathway metabolism and cytokine expression in the prefrontal cortex of depressed individuals.

BACKGROUND Neuroinflammatory processes are increasingly believed to participate in the pathophysiology of a number of major psychiatric diseases, including depression. Immune activation stimulates the conversion of the amino acid tryptophan to kynurenine, leading to the formation of neuroactive metabolites, such as quinolinic acid and kynurenic acid. These compounds affect glutamatergic neurotransmission, which plays a prominent role in depressive pathology. Increased tryptophan degradation along the kynurenine pathway (KP) has been proposed to contribute to disease etiology. METHODS We used postmortem brain tissue from the ventrolateral prefrontal cortex (VLPFC) to assess tissue levels of tryptophan and KP metabolites, the expression of several KP enzymes and a series of cytokines as well as tissue pathology, including microglial activation. Tissue samples came from nonpsychiatric controls (n = 36) and individuals with depressive disorder not otherwise specified (DD-NOS, n = 45) who died of natural causes, homicide, accident, or suicide. RESULTS We found a reduction in the enzymatic conversion of tryptophan to kynurenine, determined using the kynurenine:tryptophan ratio, and reduced messenger RNA expression of the enzymes indoleamine-2,3-dioxygenase 1 and 2 and tryptophan-2,3-dioxygenase in depressed individuals irrespective of the cause of death. These findings correlated with reductions in the expression of several cytokines, including interferon-γ and tumour necrosis factor-α. Notably, quinolinic acid levels were also lower in depressed individuals than controls. LIMITATIONS Information on the use of antidepressants and other psychotropic medications was insufficient for statistical comparisons. CONCLUSION Contrary to expectations, the present results indicate that depression, in the absence of medical illness or an overt inflammatory process, is associated with compromised, rather than increased, KP metabolism in the VLPFC.
Mutations in the Essential Spindle Checkpoint Gene bub1 Cause Chromosome Missegregation and Fail to Block Apoptosis in Drosophila

We have characterized the Drosophila mitotic checkpoint control protein Bub1 and obtained mutations in the bub1 gene. Drosophila Bub1 localizes strongly to the centromere/kinetochore of mitotic and meiotic chromosomes that have not yet reached the metaphase plate. Animals homozygous for P-element–induced, near-null mutations of bub1 die during late larval/pupal stages due to severe mitotic abnormalities indicative of a bypass of checkpoint function. These abnormalities include accelerated exit from metaphase and chromosome missegregation and fragmentation. Chromosome fragmentation possibly leads to the significantly elevated levels of apoptosis seen in mutants. We have also investigated the relationship between Bub1 and other kinetochore components. We show that Bub1 kinase activity is not required for phosphorylation of 3F3/2 epitopes at prophase/prometaphase, but is needed for 3F3/2 dephosphorylation at metaphase. Neither 3F3/2 dephosphorylation nor loss of Bub1 from the kinetochore is a prerequisite for anaphase entry. Bub1's localization to the kinetochore does not depend on the products of the genes zw10, rod, polo, or fizzy, indicating that the kinetochore is constructed from several independent subassemblies.
Insectes Émergeants : Échange Non Contrôlé ou Changement Climatique ? : Comment Prévenir ? = Emerging Insects : Uncontrolled Exchange or Climate Change ? : How to Prevent ?

Avec les échanges de matériel végétal non contrôlé et le commerce international, l’agriculture mondiale et la santé humaine se trouvent confrontées aujourd’hui à l’invasion de nouveaux insectes ravageurs. Nous abordons, ici les principaux facteurs d’émergences de maladies et insectes qui comprennent, la démographie et la concentration urbaine, les pratiques agricoles, la mondialisation des échanges de biens et de marchandises, la progression du transport aérien, le changement climatique et la biodiversité. Dans le cas des nouvelles invasions d’insectes et pour améliorer les chances de survie des cultures, il est essentiel de savoir reconnaître les éléments de dépistage de leur présence et d’avoir une forte volonté politique pour les gérer et intervenir le plus tôt possible pour limiter leur distribution. Ceci implique une prise de conscience des agriculteurs du danger encouru et de l’installation d’une quarantaine interne (intra et extra régionales) stricte. Comment faire face aux ravageurs émergeants? Ne faut-il pas utiliser de nouveaux outils et créer de nouvelles spécialités? Voire favoriser l’établissement de modèles de prévision pour l’analyse du risque, le développement de la génétique des populations et l’utilisation du GIS (Système d’Information Géographique) ? Cette approche nécessite la création d’une base de données pour chaque insecte important économiquement, pour connaître son abondance, son aire de distribution, ses dégâts afin de prédire l’évolution de la colonisation de l’espace et son impact sur les cultures. Les modèles une fois établis permettent aussi de bien choisir et positionner les méthodes de lutte appropriées selon le comportement de l’insecte dans son nouveau milieu. En ce qui concerne les pucerons, nous avons déjà un réseau de piégeage qui permet la détection rapide des nouvelles espèces et l’anticipation des invasions exotiques. Une base de données de 11 années est disponible pour construire un modèle de prédiction des risques. Les pucerons sont aussi des vecteurs de maladies bien évidemment liés aux maladies émergeantes et souches de virus en évolution. L’utilisation de la génétique moléculaire pourrait assurer une meilleure compréhension de la biologie des insectes par l’étude des structures génétiques en fonction des systèmes de reproduction, la paléontologie et l’évolution. Le GIS, permet, également, de suivre la progression de l’insecte grâce à des logiciels de gestion des cartes géographiques et l’évaluation de leur impact sur le rendement.Ce sont toutes ces approches multidisciplinaires dans une équipe de recherche qui pourraient aider l’entomologiste à la prise des décisions et à la réussite de la lutte.
The use of legal knowledge-based systems in public administration: what can go wrong?

In recent years, practical applications of legal knowledge-based systems have become increasingly common. This raises the issue of their functioning in practice and their actual influence on the quality of decisions. In this paper we investigate to what extent incorrect decisions may be caused by factors that cannot be attributed to flaws in the programme’s knowledge base or reasoning. Based on a literature study, five possible causes are identified that pertain to the interaction between a programme and its user. Then it is illustrated how this list of causes may be used to investigate risk factors in practical applications, with a small case study on the use of a knowledgebased system in processing claims for general income support in a Dutch municipality.
Caspase-mediated Cleavage of Focal Adhesion Kinase pp125FAK and Disassembly of Focal Adhesions in Human Endothelial Cell Apoptosis

Normal endothelial and epithelial cells undergo apoptosis when cell adhesion and spreading are prevented, implying a requirement for antiapoptotic signals from the extracellular matrix for cell survival. We investigated some of the molecular changes occurring in focal adhesions during growth factor deprivation–induced apoptosis in confluent monolayers of human umbilical vein endothelial cells. Among the first morphologic changes after initiation of the apoptotic process are membrane blebbing, loss of focal adhesion sites, and retraction from the matrix followed by detachment. We observe a specific proteolytic cleavage of focal adhesion kinase (pp125FAK), an important component of the focal adhesion complex, and identify pp125FAK as a novel substrate for caspase-3 and caspase-3–like apoptotic caspases. The initial cleavage precedes detachment, and coincides with loss of pp125FAK and paxillin from focal adhesion sites and their redistribution into the characteristic membrane blebs of apoptotically dying cells. Cleavage of pp125FAK differentially affects its association with signaling and cytoskeletal components of the focal adhesion complex; binding of paxillin, but not pp130Cas (Cas, Crk-associated substrate) and vinculin, to the COOH terminally truncated pp125FAK is abolished. Therefore, caspase-mediated cleavage of pp125FAK may be participating in the disassembly of the focal adhesion complex and actively interrupting survival signals from the extracellular matrix, thus propagating the cell death program.
Empirical evaluation of data transformations for network infrastructure applications

It is estimated that the amount of data coming out of an optical fibre is doubling every nine months and, thus, the growth rate in network bandwidth by far exceeds that of transistor density stated by Moore's law. This causes excessive strain on network infrastructure nodes such as routers which need to operate at line rate in order to keep up with the external bandwidth requirements. Consequently, manufacturers of network processors have developed a wide range of technologies including highly parallel and specialised architectures to cope with ever increasing processing demands. Software tool support, however, lags behind and most research in compiling for network processors has focused on improved sequential and parallel code generation. In this paper we show that not code, but data organisation is the key obstacle to overcome in order to achieve high performance on network infrastructure applications. We evaluate three specialised data transformations (structure splitting, array regrouping, and software caching) against the industrial Eembc networking benchmarks and real-world data sets. We demonstrate that speedups of up to 2.62 can be achieved, but at the same time no single solution performs equally well across all network traffic scenarios. This clearly indicates that adaptive data transformation schemes are necessary to ensure optimal performance under varying network loads.
Width of a scale-free tree

Consider the random graph model of Barabasi and Albert, where we add a new vertex in every step and connect it to some old vertices with probabilities proportional to their degrees. If we connect it to only one of the old vertices then this will be a tree. These graphs have been shown to have a power-law degree distribution, the same as that observed in some large real-world networks. We are interested in the width of the tree and we show that it is W n ∼ n/√π log n at the nth step; this also holds for a slight generalization of the model with another constant. We then see how this theoretical result can be applied to directory trees.
The design of a high-frequency multiphase voltage regulator with adaptive voltage positioning and all ceramic capacitors

The paper presents a high-frequency multiphase synchronous buck converter design for next generation microprocessors. Only ceramic capacitors are used in the output stage to reduce space and improve reliability. A simplified analysis of the multiphase converter with adaptive voltage positioning is given and used in the voltage loop compensation. Fast transient response is achieved, and the analysis and design are confirmed by test results and simulation
Translating HPSG-Style Outputs of a Robust Parser into Typed Dynamic Logic

The present paper proposes a method by which to translate outputs of a robust HPSG parser into semantic representations of Typed Dynamic Logic (TDL), a dynamic plural semantics defined in typed lambda calculus. With its higher-order representations of contexts, TDL analyzes and describes the inherently inter-sentential nature of quantification and anaphora in a strictly lexicalized and compositional manner. The present study shows that the proposed translation method successfully combines robustness and descriptive adequacy of contemporary semantics. The present implementation achieves high coverage, approximately 90%, for the real text of the Penn Treebank corpus.
Identification of ATP-Binding Regions in the RyR1 Ca2+ Release Channel

ATP is an important modulator of gating in type 1 ryanodine receptor (RyR1), also known as a Ca2+ release channel in skeletal muscle cells. The activating effect of ATP on this channel is achieved by directly binding to one or more sites on the RyR1 protein. However, the number and location of these sites have yet to be determined. To identify the ATP-binding regions within RyR1 we used 2N3ATP-2′,3′-Biotin-LC-Hydrazone (BioATP-HDZ), a photo-reactive ATP analog to covalently label the channel. We found that BioATP-HDZ binds RyR1 specifically with an IC50 = 0.6±0.2 mM, comparable with the reported EC50 for activation of RyR1 with ATP. Controlled proteolysis of labeled RyR1 followed by sequence analysis revealed three fragments with apparent molecular masses of 95, 45 and 70 kDa that were crosslinked by BioATP-HDZ and identified as RyR1 sequences. Our analysis identified four glycine-rich consensus motifs that can potentially constitute ATP-binding sites and are located within the N-terminal 95-kDa fragment. These putative nucleotide-binding sequences include amino acids 699–704, 701–706, 1081–1084 and 1195–1200, which are conserved among the three RyR isoforms. Located next to the N-terminal disease hotspot region in RyR1, these sequences may communicate the effects of ATP-binding to channel function by tuning conformational motions within the neighboring cytoplasmic regulatory domains. Two other labeled fragments lack ATP-binding consensus motifs and may form non-canonical ATP-binding sites. Based on domain topology in the 3D structure of RyR1 it is also conceivable that the identified ATP-binding regions, despite their wide separation in the primary sequence, may actually constitute the same non-contiguous ATP-binding pocket within the channel tetramer.
HIV-Associated Tuberculosis

The intersecting HIV and Tuberculosis epidemics in countries with a high disease burden of both infections pose many challenges and opportunities. For patients infected with HIV in high TB burden countries, the diagnosis of TB, ARV drug choices in treating HIV-TB coinfected patients, when to initiate ARV treatment in relation to TB treatment, managing immune reconstitution, minimising risk of getting infected with TB and/or managing recurrent TB, minimizing airborne transmission, and infection control are key issues. In addition, given the disproportionate burden of HIV in women in these settings, sexual reproductive health issues and particular high mortality rates associated with TB during pregnancy are important. The scaleup and resource allocation to access antiretroviral treatment in these high HIV and TB settings provide a unique opportunity to strengthen both services and impact positively in meeting Millennium Development Goal 6.
RETENTION OF A PRIMORDIAL COLD CLASSICAL KUIPER BELT IN AN INSTABILITY-DRIVEN MODEL OF SOLAR SYSTEM FORMATION

The cold classical population of the Kuiper Belt exhibits a wide variety of unique physical characteristics, which collectively suggest that its dynamical coherence has been maintained throughout the solar system's lifetime. Simultaneously, the retention of the cold population's relatively unexcited orbital state has remained a mystery, especially in the context of a solar system formation model, that is driven by a transient period of instability, where Neptune is temporarily eccentric. Here, we show that the cold belt can survive the instability, and its dynamical structure can be reproduced. We develop a simple analytical model for secular excitation of cold Kuiper Belt objects and show that comparatively fast apsidal precession and nodal recession of Neptune, during the eccentric phase, are essential for preservation of an unexcited state in the cold classical region. Subsequently, we confirm our results with self-consistent N-body simulations. We further show that contamination of the hot classical and scattered populations by objects of similar nature to that of cold classicals has been instrumental in shaping the vast physical diversity inherent to the Kuiper Belt.
Electrospun nanofibrous structure: a novel scaffold for tissue engineering.

The architecture of an engineered tissue substitute plays an important role in modulating tissue growth. A novel poly(D,L-lactide-co-glycolide) (PLGA) structure with a unique architecture produced by an electrospinning process has been developed for tissue-engineering applications. Electrospinning is a process whereby ultra-fine fibers are formed in a high-voltage electrostatic field. The electrospun structure, composed of PLGA fibers ranging from 500 to 800 nm in diameter, features a morphologic similarity to the extracellular matrix (ECM) of natural tissue, which is characterized by a wide range of pore diameter distribution, high porosity, and effective mechanical properties. Such a structure meets the essential design criteria of an ideal engineered scaffold. The favorable cell-matrix interaction within the cellular construct supports the active biocompatibility of the structure. The electrospun nanofibrous structure is capable of supporting cell attachment and proliferation. Cells seeded on this structure tend to maintain phenotypic shape and guided growth according to nanofiber orientation. This novel biodegradable scaffold has potential applications for tissue engineering based upon its unique architecture, which acts to support and guide cell growth.
Risk Assessment for Banking Systems

We propose a new approach to assess systemic financial stability of a banking system using standard tools from modern risk management in combination with a network model of interbank loans. We apply our model to a unique data set of all Austrian banks. We find that correlation in banks' asset portfolios dominates contagion as the main source of systemic risk. Contagion is rare but can nonetheless wipe out a major part of the banking system. Low bankruptcy costs and an efficient crisis resolution policy are crucial to limit the systemwide impact of contagious default events. We compute the “value at risk” for a lender of last resort and find that the funds necessary to prevent contagion are surprisingly small.