Miracle-dz/UniFAR-FTUs huggingface dataset:
Partial overlap of anti-mycobacterial, and anti-Saccharomyces cerevisiae mannan antibodies in Crohn's disease.

AIM To test whether humoral immune reaction against mycobacteria may play a role in anti-Saccharomyces cerevisiae antibodies (ASCA) generation in Crohn's disease (CD) and/or whether it correlates with clinical subtypes. METHODS The dominant ASCA epitope was detected by Galanthus nivalis lectin (GNL)-binding assay. ASCA and IgG against mycobacterial lysates (M avium, M smegmatis, M chelonae, M bovis BCG, M avium ssp. paratuberculosis (MAP)] or purified lipoarabinomannans (LAM) were detected by ELISA. ASCA and anti-mycobacterial antibodies were affinity purified to assess cross-reactivities. Anti-mycobacterial IgG were induced by BCG-infection of mice. RESULTS GNL bound to different extents to mycobacterial lysates, abundantly to purified mannose-capped (Man) LAM from M tuberculosis, but not to uncapped LAM from M smegmatis. Fifteen to 45% of CD patients but only 0%-6% of controls were seropositive against different mycobacterial antigens. Anti-mycobacterial IgG correlated with ASCA (r = 0.37-0.64; P = 0.003-P < 0.001). ASCA-positivity and deficiency for mannan-binding lectin synergistically associated with anti-mycobacterial IgG. In some patients, anti-mycobacterial antibodies represent cross-reactive ASCA. Vice-versa, the predominant fraction of ASCA did not cross-react with mycobacteria. Finally, fistulizing disease associated with antibodies against M avium, M smegmatis and MAP (P = 0.024, 0.004 and 0.045, respectively). CONCLUSION Similar to ASCA, seroreactivity against mycobacteria may define CD patients with complicated disease and a predisposition for immune responses against ubiquitous antigens. While in some patients anti-mycobacterial antibodies strongly cross-react with yeast mannan; these cross-reactive antibodies only represent a minor fraction of total ASCA. Thus, mycobacterial infection unlikely plays a role in ASCA induction.
Stuctured Queries for Legal Search

This paper reports the experiments of using Indri for the main and routing (relevance feedback) tasks in the TREC 2007 Legal Track. For the main task, we analyze ranking algorithms using diﬀerent ﬁelds, boolean constraints and structured operators. Evaluation results show that structured queries outperform bag-of-words ones. Boolean constraints improve both precision and recall. For the routing task, we train a linear SVM classiﬁer for each topic. Terms with the largest weights are selected to form new queries. Both keywords and simple structured features (term.ﬁeld) have been investigated. Named-Entity tags, LingPipe sentence breaker and metadata ﬁelds of the original documents are used to generate the ﬁeld information. Results show that structured features and weighted queries improves retrieval, but only marginally. We also show which structures are more useful. It turns out metadata ﬁelds are not as important as we thought.
Contributions of the interdomain loop, amino terminus, and subunit interface to the ligand‐facilitated dimerization of neurophysin: Crystal structures and mutation studies of bovine neurophysin‐I

Current evidence indicates that the ligand‐facilitated dimerization of neurophysin is mediated in part by dimerization‐induced changes at the hormone binding site of the unliganded state that increase ligand affinity. To elucidate other contributory factors, we investigated the potential role of neurophysin's short interdomain loop (residues 55–59), particularly the effects of loop residue mutation and of deleting amino‐terminal residues 1–6, which interact with the loop and adjacent residues 53–54. The neurophysin studied was bovine neurophysin‐I, necessitating determination of the crystal structures of des 1–6 bovine neurophysin‐I in unliganded and liganded dimeric states, as well as the structure of its liganded Q58V mutant, in which peptide was bound with unexpectedly increased affinity. Increases in dimerization constant associated with selected loop residue mutations and with deletion of residues 1–6, together with structural data, provided evidence that dimerization of unliganded neurophysin‐I is constrained by hydrogen bonding of the side chains of Gln58, Ser56, and Gln55 and by amino terminus interactions, loss or alteration of these hydrogen bonds, and probable loss of amino terminus interactions, contributing to the increased dimerization of the liganded state. An additional intersubunit hydrogen bond from residue 81, present only in the liganded state, was demonstrated as the largest single effect of ligand binding directly on the subunit interface. Comparison of bovine neurophysins I and II indicates broadly similar mechanisms for both, with the exception in neurophysin II of the absence of Gln55 side chain hydrogen bonds in the unliganded state and a more firmly established loss of amino terminus interactions in the liganded state. Evidence is presented that loop status modulates dimerization via long‐range effects on neurophysin conformation involving neighboring Phe22 as a key intermediary.
Cache size allocation in backhaul limited wireless networks

Caching popular content at base stations is a powerful supplement to existing limited backhaul links for accommodating the exponentially increasing mobile data traffic. Given the limited cache budget, we investigate the cache size allocation problem in cellular networks to maximize the user success probability (USP), taking wireless channel statistics, backhaul capacities and file popularity distributions into consideration. The USP is defined as the probability that one user can successfully download its requested file either from the local cache or via the backhaul link. We first consider a single-cell scenario and derive a closed-form expression for the USP, which helps reveal the impacts of various parameters, such as the file popularity distribution. More specifically, for a highly concentrated file popularity distribution, the required cache size is independent of the total number of files, while for a less concentrated file popularity distribution, the required cache size is in linear relation to the total number of files. Furthermore, we study the multi-cell scenario, and provide a bisection search algorithm to find the optimal cache size allocation. The optimal cache size allocation is verified by simulations, and it is shown to play a more significant role when the file popularity distribution is less concentrated.
Molecular Modelling Study of the 3D Structure of the Bovine Viral Diarrhea Virus (BVDV) Helicase

Bovine viral diarrhea virus (BVDV) is a member of the Flaviviridae family of viruses and constitutes a very important pathogen for livestock around the world. The viral helicase is an enzyme essential for the proliferation and transmission of the virus. In this work a 3D-model of the BVDV helicase was produced using homology modelling techniques and the known 3D-structure of the hepatitis C helicase of the Flaviviridae family as template, in an attempt to provide the means for structure-based design of novel anti-BVDV agents.
A probabilistic framework to monitor a multi-mode outdoor robot

This paper presents an approach to autonomously monitor the behavior of a robot endowed with several navigation and locomotion modes, adapted to the terrain to traverse. The mode selection process is done in two steps: the best suited mode is firstly selected on the basis of initial information or a qualitative map built on-line by the robot. Then, the motions of the robot are monitored by various processes that update mode transition probabilities in a Markov system. The paper focuses on this latter selection process: the overall approach is depicted, and preliminary experimental results are presented.
Mutant Isolation of the Escherichia coli Quinoprotein Glucose Dehydrogenase and Analysis of Crucial Residues Asp-730 and His-775 for Its Function*

Several mutants of quinoprotein glucose dehydrogenase (GDH) in Escherichia coli were obtained and characterized. Of these, significant mutants were further characterized by kinetic analysis after purification or by site-directed mutagenesis to introduce different amino acid substitutions. H775R and H775A showed a pronounced reduction of affinity for a prosthetic group, pyrroloquinoline quinone (PQQ), suggesting that His-775 may directly interact with PQQ. D730N and D730A showed low glucose oxidase activity without influence on the affinity for PQQ, Mg2+, or substrate, but D730R showed reduced affinity for PQQ. The spectrum of tryptophan fluorescence revealed that the local structure surrounding PQQ was not changed by D730N mutation. Based on these data, we assume that Asp-730 may occur close to PQQ and function as a proton (and also electron) donor to PQQ or acceptor from PQQH2. Substitutions of Gly-689, that are located at the end of a unique segment of GDH among homologous quinoprotein dehydrogenases, directed reduction of the affinity for PQQ or GDH activity. Therefore, the unique segment and Asp-730 may play a specific role for GDH, which might be related to the intramolecular electron transfer from PQQ to ubiquinone.
Efficient linking and transfer of multiple genes by a multigene assembly and transformation vector system

Introduction and expression of multiple transgenes is frequently required for basic and applied studies. However, at present, multigene transformation is very difficult due to technical limitations of existing methods. Here, we describe a vector system for efficient multigene assembly and transformation. The system consists of a transformation-competent artificial chromosome (TAC)-based acceptor vector together with two donor vectors. By exploiting the Cre/loxP recombination system and homing endonucleases, multiple rounds of gene assembly cycling were carried out with alternate use of the donor vectors, and multiple genes were sequentially delivered into the TAC vector. With this system, we created constructs containing as many as 10 foreign DNA fragments. Multiple genes, including six resistant genes stacked in a construct, were transferred into rice genome by Agrobacterium-mediated transformation. This system extends the repertoire of molecular genetic studies and biotechnological endeavors by enabling simultaneous manipulation of multiple genes.
Report of the Expert Group on Diversity Index: A Comment

‘Unity in diversity’ is an oft-repeated characterization of India as well as a muchcherished aspiration. But ‘diversity’ explicitly as a policy objective is a new and loaded ideal path, and needs to be trodden with care to avoid any negative fallout. This note, essentially focused on issues arising out of the Report of the Expert Group on the Diversity Index (hereafter the Report or REG) (GoI, 2008a), is divided into six sections. The first section refers to the immediate context and the source of contemplation towards a conscious promotion of diversity as a policy, which necessitates monitoring the progress with the help of a simple and transparent measure like the Diversity Index (DI). The second section refers to the terms of reference (ToR) of the Expert Group and its approach. The third section addresses the issues arising out of the core part of the Report, viz. the proposed DI. The fourth part reflects on the areas of application proposed by the Expert Group. The fifth and the last part refers to what may turn out to be the more controversial organizational aspects proposed by the Expert Group. Since the discussion aims to help in arriving at some consensus on all these issues, this note does not make any conclusive statements.
Low complexity image matching using color based SIFT

Image matching and search is gaining significant commercial importance nowadays due to various applications it enables such as augmented reality, image-queries for internet search, etc. Many researchers have effectively used color information in an image to improve its matching accuracy. These techniques, however, cannot be directly used for large scale mobile visual search applications that pose strict constraints on the size of the extracted features, computational resources and the system accuracy. To overcome this limitation, we propose a new and effective technique to incorporate color information that can use the SIFT extraction technique. We conduct our experiments on a large dataset containing around 33, 000 images that is currently being investigated in the MPEG-Compact Descriptors for Visual Search Standard and show substantial improvement compared to baseline.
Stability Analysis of Networked Control Systems With Aperiodic Sampling and Time-Varying Delay

This paper addresses the stability of networked control systems with aperiodic sampling and time-varying network-induced delay. The sampling intervals are assumed to vary within a known interval. The transmission delay is assumed to belong to a given interval. The closed-loop system is first converted to a discrete-time system with multiple time-varying delays and norm-bounded uncertainties resulting from the variation of the sampling intervals. And then, it is transformed into a delay-free system being form of an interconnection of two subsystems. By utilizing scaled small gain theorem, an asymptotic stability criterion for the closed-loop system is proposed in terms of linear matrix inequality. Finally, numerical examples demonstrate the effectiveness of the proposed method and its advantages over existing methods.
Underwater localization with time-synchronization and propagation speed uncertainties

Underwater localization is a key element in most underwater communication applications. Since GPS signals highly attenuate in water, accurate ranging based techniques for localization need to be developed. In this paper we describe a sequential algorithm for time-synchronization and localization in the underwater acoustic channel. We consider the realistic case where nodes are not time-synchronized and the sound speed in water is unknown, and formalize the localization problem as a sequence of two linear estimation problems. Simulation results demonstrate that our algorithm compensates for time-synchronization and signal propagation speed uncertainties, and achieves good localization accuracy using only two anchor nodes.
Unique Epitope of Bovine Immunodeficiency Virus Gag Protein Spans the Cleavage Site between p16MA and p2L

ABSTRACT Bovine immunodeficiency virus (BIV) and Jembrana disease virus (JDV) are closely related bovine lentiviruses that are difficult to distinguish by presently available diagnostic methods. Recently, in our laboratory, a monoclonal antibody (MAb; MAb 10H1) against the BIV Gag protein identified a differential epitope, located at the 6.4-kDa N terminus of a 29-kDa Gag capsid protein, which was absent in JDV. To define the essential amino acids of the epitope, a series of primers within the 163 bp of DNA corresponding to the 6.4-kDa protein were designed. The full-length 163-bp DNA fragment and the smaller DNA fragments with deletions were amplified by PCR and then cloned into pQE32 vectors for protein expression studies. The expressed proteins were analyzed with MAb 10H1 by Western blotting. The differential epitope has been narrowed to a 26-amino-acid region (R121 to R146), which includes 6 residues of p16MA (where MA represents the matrix protein) and 20 residues of p2L. A synthetic peptide corresponding to the putative 26-amino-acid epitope blocked MAb 10H1 binding to the expressed peptide. These experiments revealed that the epitope spans the cleavage site between p16MA and p2L and presumably will be valuable in distinguishing the two viruses.
Ovarian cancer risk in Ashkenazi Jewish carriers of BRCA1 and BRCA2 mutations.

PURPOSE Several studies to date have reported ovarian cancer risk due to inherited BRCA1 and BRCA2 mutations using familial data or population-based series of probands. Familial aggregation associated with both of these methods may result in a substantial ascertainment bias. To address this, we have used a case-control design that does not involve familial aggregation to estimate the lifetime penetrance of ovarian cancer due to BRCA1 and BRCA2 mutations. EXPERIMENTAL DESIGN A total of 382 ovarian cancer cases self-identified as being Jewish with no prior diagnosis of breast cancer were derived from two hospital-based series. In the first series, all 197 invasive epithelial ovarian cancer cases self-identified as Jewish and without a prior history of breast cancer, diagnosed and treated at Memorial Sloan-Kettering Cancer Center between 1986 and 2000, were identified. In the second series, 185 Jewish invasive epithelial ovarian cancer patients without prior breast cancer were identified in a study conducted at 11 centers in North America and Israel from 1995 to 1996. Controls were 3434 Jewish women without any prior history of breast or ovarian cancer from a large study of genotyped volunteers of Jewish origin in the Washington, D. C. area recruited by investigators at the National Cancer Institute. The cases and controls were genotyped for three Ashkenazi Jewish founder mutations, namely 185delAG and 5382insC in BRCA1 and 6174delT in BRCA2. The lifetime penetrances were estimated using the odds ratios, mutation prevalence in the controls, and ovarian cancer incidence rates in the general American population obtained from the Surveillance, Epidemiology and End Results database adjusted for the incidence of ovarian cancer following breast cancer. RESULTS Mutations were identified in 147 cases and 62 controls. The estimated penetrances at age 70 years were 37% (95% confidence interval, 25-71%) for a BRCA1 mutation and 21% (95% CI, 13-41%) for a BRCA2 mutation. CONCLUSIONS The lifetime penetrances of BRCA1 mutations are lower than estimates obtained using familial data with multiple affected members but larger than estimates from some population-based proband series. The lifetime penetrance estimate of a BRCA2 mutation is in the range reported by some of the studies based on familial data. These results could have implications for clinical counseling, surgical interventions, and screening recommendations in women carrying these founder mutations.
Time-Varying Autoregressive Process for Ultra-Wideband Indoor Channel Model

Subsequently a time-variant AR model is proposed in order to model the radio channel. This method is useful for a channel model that cannot be assumed to be stationary. The basis function, having the invariant basis coefficients approach, is used for estimating the time-variant AR parameters. Moreover, a path loss model is addressed in this work. In the end, the accuracy of the methods are analyzed by comparing the channel characteristics and the cumulative distribution functions of the RMS delay spread with that of the measurement results, the modified version of the IEEE 802.15. 3a channel model and the conventional AR model. The results show that a fifth order time-varying autoregressive model is sufficient to represent the statistical characteristics of the channel where each pole identifies the arrival of a cluster of paths and is more accurate than the conventional AR model.
Characterizing web content, user interests, and search behavior by reading level and topic

A user's expertise or ability to understand a document on a given topic is an important aspect of that document's relevance. However, this aspect has not been well-explored in information retrieval systems, especially those at Web scale where the great diversity of content, users, and tasks presents an especially challenging search problem. To help improve our modeling and understanding of this diversity, we apply automatic text classifiers, based on reading difficulty and topic prediction, to estimate a novel type of profile for important entities in Web search -- users, websites, and queries. These profiles capture topic and reading level distributions, which we then use in conjunction with search log data to characterize and compare different entities. We find that reading level and topic distributions provide an important new representation of Web content and user interests, and that using both together is more effective than using either one separately. In particular we find that: 1) the reading level of Web content and the diversity of visitors to a website can vary greatly by topic; 2) the degree to which a user's profile matches with a site's profile is closely correlated with the user's preference of the website in search results, and 3) site or URL profiles can be used to predict 'expertness' whether a given site or URL is oriented toward expert vs. non-expert users. Our findings provide strong evidence in favor of jointly incorporating reading level and topic distribution metadata into a variety of critical tasks in Web information systems.
COASTAL FLOODING: DAMAGE CLASSIFICATION AND CASE STUDIES IN CALABRIA, ITALY

Coastal flooding is a topic of particular interest both in scientific research and for public administration. In fact, effective management of both coastal erosion and coastal flood risk requires a mapping of flooding areas by current European legislation (Directive 2007/60/EC). Regarding Italy, coastal erosion is widely studied and mapped, but coastal flooding has not been uniformly examined across all regions. This paper analyses the main factors that influence coastal flooding, being mainly tidal excursion and run-up, and a new methodology is proposed for the classification of storm damage based on the effects produced by the coastal wave action. In fact, six classes of damage have been defined, sorted by increasing severity, namely: traffic interruption, infrastructure damage, maritime works damage, erosion of beaches and dunes, flooding to homes, and a combination of these various factors. The new classification was applied to two case studies, both in Calabria (Italy): Scilla on the Tyrrhenian coast, and Monasterace on the Ionian coast. The two locations were chosen because in Scilla the coastal morphology makes it particularly subject to storms that overreach the beach and reach local houses, even those located upstream of the seafront. In Monasterace, on the other hand, there is an important archaeological site on a coastal dune that, over the years, has often been damaged by sea storms. The analysis of the events was conducted starting with data present in the A.Si. Cal. (Historically flooded areas in Calabria) of the CNR-IRPI of Cosenza, which containing data relating to events of hydrogeological instability, including sea storms which have occurred in Calabria over the last few centuries, and from the MeteoCean group of the University of Genoa, which contains wave data for the period 1979–2017, which is reconstructed from the Climate Forecast System Reanalysis (CFSR) data.
PAWS - A Deployed Game-Theoretic Application to Combat Poaching

Poaching is considered a major driver for the population drop of key species such as tigers, elephants, and rhinos, which can be detrimental to whole ecosystems. While conducting foot patrols is the most commonly used approach in many countries to prevent poaching, such patrols often do not make the best use of the limited patrolling resources.