Miracle-dz/UniFAR-FTUs huggingface dataset:
Severe Acute Respiratory Syndrome Coronavirus Infection in Vaccinated Ferrets

Abstract Background. Development of vaccines to prevent severe acute respiratory syndrome (SARS) is limited by the lack of well-characterized animal models. Previous vaccine reports have noted robust neutralizing antibody and inflammatory responses in ferrets, resulting in enhanced hepatitis. Methods. We evaluated the humoral immune response and pathological end points in ferrets challenged with the Urbani strain of SARS-associated coronavirus (SARS-CoV) after having received formalin-inactivated whole-virus vaccine or mock vaccine. Results. Humoral responses were observed in ferrets that received an inactivated virus vaccine. Histopathological findings in lungs showed that infection of ferrets produced residual lung lesions not seen in both mock and vaccinated ferrets. SARS-CoV infection demonstrated bronchial and bronchiolar hyperplasia and perivascular cuffing in ferret lung tissue, as seen previously in infected mice. No evidence of enhanced disease was observed in any of the ferrets. All of the ferrets cleared the virus by day 14, 1 week earlier if vaccinated. Conclusions. The vaccine provided mild immune protection to the ferrets after challenge; however, there was no evidence of enhanced liver or lung disease induced by the inactivated whole-virus vaccine. The ferret may provide another useful model for evaluating SARS vaccine safety and efficacy.
Homotopic curves on surfaces

In the following, a surface is always a compact, orientable, twodimensional manifold with or without boundary, a closed surface is one without boundary, and a simple, closed curve on a surface is a closed, connected, one-dimensional submanifold. For simplicity in referring to curves, no notational distinction is made between the embedding of the circle and the image under the embedding-the context will make it clear which is intended. If W is a surface whose boundary consists of n disjoint, simple, closed curves, the genus of W, g(W), is defined to be the genus of a surface without boundary obtained by attaching a 2-cell to each of the boundary curves. The relation between the genus of W and its inner Euler characteristic, x(W) is:
Observation of Permeability Dependence on Flow Rate and Implications for Liquid Composite Molding

The variation of permeability with the flow rate has been investigated. This variation is demonstrated by conducting specially designed experiments. The results show that permeability increases significantly as the flow rate increases. The implication of this observation is that the permeability measured under some given conditions is not always applicable to the actual molding situation. Furthermore, the permeability is not constant over both the space and time domains during the filling process. In order to take such dependence into account, a permeability model and an estimation technique for determining the coefficients of the model are proposed.
The Limits of Price Discrimination the Limits of Price Discrimination

We analyze the welfare consequences of a monopolist having additional information about consumers'tastes, beyond the prior distribution; the additional information can be used to charge di¤erent prices to di¤erent segments of the market, i.e., carry out "third degree price discrimination". We show that the segmentation and pricing induced by the additional information can achieve every combination of consumer and producer surplus such that: (i) consumer surplus is non-negative, (ii) producer surplus is at least as high as pro…ts under the uniform monopoly price, and (iii) total surplus does not exceed the e¢ cient gains from trade. As well as characterizing the welfare impact of price discrimination, we examine the limits of how prices and quantities can change under price discrimination. We also examine the limits of price discrimination in richer environments with quantity discrimination and limited ability to segment the market. We gratefully acknowledge …nancial support from NSF SES 0851200 and ICES 1215808. We would like to thank Nemanja Antic, Omer Reingold, Juha Tolvanen, and Ricky Vohra for informative discussions. We have also bene…tted from comments by seminar participants at NYU and CalTech. Lastly, thanks to Alex Smolin for excellent research assistance.
DOTA: A Double Truthful Auction for spectrum allocation in dynamic spectrum access

Spectrum auctions have been proposed as an effective approach to fairly and efficiently trade the scarce spectrum resource among wireless users. The most significant challenge of the auction design to provide economic robustness, particularly truthfulness, under the local-dependent interference constraints. However, existing designs either do not consider spectrum reuse or are based on the impractical assumption that each user requests at most one channel. In this paper, we address this problem by proposing DOTA, a DOuble Truthful Auction for dynamic spectrum access. DOTA is economic-robust in terms of truthfulness, individual rationality, and no-deficit. It achieves improved utilization by exploiting spectrum reuse as well as dealing with the interference constraints. Moreover, DOTA minimizes the network transaction overhead and provides flexible channel bidding including range bidding and strict bidding.
Subset Seed Extension to Protein BLAST

The seeding technique became central in the theory of sequence alignment and there are several efficient tools applying seeds to DNA homology search. Recently, a concept of subset seeds has been proposed for similarity search in protein sequences. We experimentally evaluate the applicability of subset seeds to protein homology search. We advocate the use of multiple subset seeds derived from a hierarchical tree of amino acid residues. Our method computes, by an evolutionary algorithm, seeds that are specifically designed for a given protein family. The representation of seeds by deterministic finite automata (DFAs) is developed and built into the NCBI-BLAST software. This extended tool, named SeedBLAST, is compared to the original NCBI-BLAST and PSI-BLAST on several protein families. Our results demonstrate a superiority of SeedBLAST in terms of efficiency, especially in the case of twilight zone hits. SeedBLAST is an open source software freely available http://bioputer.mimuw. edu.pl/papers/sblast . Supplementary material and user manual are also provided.
Molecular Expression of a Cysteine Proteinase of Clonorchis sinensis and Its Application to an Enzyme-Linked Immunosorbent Assay for Immunodiagnosis of Clonorchiasis

ABSTRACT We produced a recombinant cysteine proteinase of Clonorchis sinensis and tested its value as an antigen for serologic diagnosis of C. sinensis infections. The predicted amino acid sequence of the cysteine proteinase of C. sinensis was 58, 48, and 40% identical to those of cathepsin L cysteine proteinases from Paragonimus westermani, Schistosoma japonicum, and Fasciola hepatica, respectively. Western blotting analysis showed that sera from patients infected with C. sinensis strongly reacted with the recombinant protein and that sera from patients infected with S. japonicum weakly reacted with the recombinant protein. Antibody against the recombinant protein stained proteins migrating at about 37 and 28 kDa in C. sinensis adult worm crude extracts. Immunostaining revealed that the cysteine proteinase of C. sinensis was located in the intestinal epithelial cells of the adult parasite and in intrauterine eggs. The specificity and sensitivity of the recombinant antigen or C. sinensis adult worm crude extracts were assessed by an enzyme-linked immunosorbent assay (ELISA) using serum samples from humans infected with different parasites, including 50 patients with clonorchiasis, and negative controls. The sensitivities of the ELISA with the recombinant antigen and C. sinensis adult worm crude extracts were 96 and 88%, respectively. The specificities of the ELISA with the recombinant antigen and C. sinensis adult worm crude extracts were 96.2 and 100%, respectively. The results suggested that the recombinant cysteine proteinase-based ELISA could provide a highly sensitive and specific assay for diagnosis of clonorchiasis.
Fatigue in multiple sclerosis compared with chronic fatigue syndrome

Fatigue, a common complaint among patients with multiple sclerosis (MS), is poorly characterized. We developed a computerized method that quantitatively measures fatigue, and defined a fatigue index (FI), which is the ratio between the integral of muscle strength decay over time and maximal voluntary contraction. Thirty patients (mean age, 37.4 +/- 10.3 years) were examined - 20 patients with pyramidal tract involvement and 10 patients with involvement of other neurological systems. We evaluated 10 patients during relapse and 3 months afterwards, and compared their results with those of four patients with chronic fatigue syndrome (CFS) and 13 age-matched health subjects. The FI was significantly higher in the MS patients as compared with the CFS patients and normal controls: 34.2 +/- 6.4% versus 27.5 +/- 1.0% and 23.6 +/- 6.8%, p < 0.05. Within the MS group, the FI correlated with the presence of pyramidal signs- 43.5% compared with 33% in patients without pyramidal signs, p < 0.01. In MS patients, fatigue worsened during a relapse affecting the pyramidal tract, but not during a relapse in other systems. These results demonstrate that fatigue can be quantitatively measured in MS patients, and that pyramidal dysfunction leads to increased fatigability.
Association between depression, parameters of adiposity and genetic polymorphisms of pro-inflammatory cytokines: IL-1α, IL-1β, IL-2 and IL-6 in subjects over 55 years old.

BACKGROUND During the last few decades, adiposity has become a relatively common phenomenon worldwide. The available data on the effects of pro-inflammatory factors in both depression and adiposity has been attracting great attention. AIM We sought to assess the prevalence of -889C>T IL-1α, -31T>C and -511C>T IL-1β, -330T>G IL-2 and -174G>C IL-6 genes and their association with adiposity and depression in Polish subjects. METHODS A cohort study was conducted in 2013/2014, covering a sample of 297 individuals (217 female and 80 male). Anthropometric data was handled using the BIA analysis method, while for genotyping PCR-RFLP techniques were used. RESULTS A positive correlation between depression and anthropometric parameters: adipose tissue (in kg) and adipose tissue (in %) (R=0.135 and p=0.02, R=0.114 and p<0.05, respectively) was found. No association between studied polymorphisms and depression was observed. CONCLUSION Although it was not possible to demonstrate any influence of the studied polymorphisms as the genetic modulator of depression, authors believe that the presented data are noticeable and may provide the basis for future studies on larger groups.
Role of Endogenous Cortistatin in the Regulation of Ghrelin System Expression at Pancreatic Level under Normal and Obese Conditions

Ghrelin-system components [native ghrelin, In1-ghrelin, Ghrelin-O-acyltransferase enzyme (GOAT) and receptors (GHS-Rs)] are expressed in a wide variety of tissues, including the pancreas, where they exert different biological actions including regulation of neuroendocrine secretions, food intake and pancreatic function. The expression of ghrelin system is regulated by metabolic conditions (fasting/obesity) and is associated with the progression of obesity and insulin resistance. Cortistatin (CORT), a neuropeptide able to activate GHS-R, has emerged as an additional link in gut-brain interplay. Indeed, we recently reported that male CORT deficient mice (cort−/−) are insulin-resistant and present a clear dysregulation in the stomach ghrelin-system. The present work was focused at analyzing the expression pattern of ghrelin-system components at pancreas level in cort−/− mice and their control littermates (cort +/+) under low- or high-fat diet. Our data reveal that all the ghrelin-system components are expressed at the mouse pancreatic level, where, interestingly, In1-ghrelin was expressed at higher levels than native-ghrelin. Thus, GOAT mRNA levels were significantly lower in cort−/− mice compared with controls while native ghrelin, In1-ghrelin and GHS-R transcript levels remained unaltered under normal metabolic conditions. Moreover, under obese condition, a significant increase in pancreatic expression of native-ghrelin, In1-ghrelin and GHS-R was observed in obese cort+/+ but not in cort−/− mice. Interestingly, insulin expression and release was elevated in obese cort+/+, while these changes were not observed in obese cort−/− mice. Altogether, our results indicate that the ghrelin-system expression is clearly regulated in the pancreas of cort+/+ and cort −/− under normal and/or obesity conditions suggesting that this system may play relevant roles in the endocrine pancreas. Most importantly, our data demonstrate, for the first time, that endogenous CORT is essential for the obesity-induced changes in insulin expression/secretion observed in mice, suggesting that CORT is a key regulatory component of the pancreatic function.
Multilocus Characterization Scheme for Shiga Toxin-Encoding Bacteriophages

ABSTRACT Shiga toxin-producing Escherichia coli (STEC) strains are food-borne pathogens whose ability to produce Shiga toxin (Stx) is due to integration of Stx-encoding lambdoid bacteriophages. These Stx phages are both genetically and morphologically heterogeneous, and here we report the design and validation of a PCR-based multilocus typing scheme. PCR primer sets were designed for database variants of a range of key lambdoid bacteriophage genes and applied to control phages and 70 stx+ phage preparations induced from a collection of STEC isolates. The genetic diversity residing within these populations could be described, and observations were made on the heterogeneity of individual gene targets, including the unexpected predominance of short-tailed phages with a highly conserved tail spike protein gene. Purified Stx phages can be profiled using this scheme, and the lambdoid phage-borne genes in induced STEC preparations can be identified as well as those residing in the noninducible prophage complement. The ultimate goal is to enable robust and realistically applicable epidemiological studies of Stx phages and their traits. The impact of Stx phage on STEC epidemiology is currently unknown.
The Microstructure of the Foreign-Exchange Market: A Selective Survey of the Literature

though the Section sponsors the Studies, the authors are free to develop their topics as they wish. The Section welcomes the submission of manuscripts for publication in this and its other series. Please see the Notice to Contributors at the back of this Study. The microstructure of the foreign-exchange market: a selective survey of the literature All rights reserved. Except for brief quotations embodied in critical articles and reviews, no part of this publication may be reproduced in any form or by any means, including photocopy, without written permission from the publisher.
Feedback Linearization Of Direct-Drive Synchronous Wind-Turbines Via a Sliding Mode Approach

As the grid code specifies, wind turbines have to remain connected to the grid at voltage levels far below the nominal values. The improvement of wind turbine performance under such conditions has become a problem of general concern. However, this performance usually relies on conventional linear controllers that operate at network faults far off the nominal point for which they were designed. As a consequence, wind turbines should operate with increasing converter currents, which may result in converter damage. This paper proposes a nonlinear controller for converter-based wind turbines that ensures that the currents are maintained within the design limits. The controller is based on feedback linearization theory and is applied to the system through a sliding mode approach. This controller is robust against system perturbations and uncertainties, and overcomes the usually complex implementation that is associated with feedback linearization controllers.
Set Systems with Restricted Intersections modulo Prime Powers

We study set systems satisfying Frankl? Wilson-type conditions modulo prime powers. We prove that the size of such set systems is polynomially bounded, in contrast with V. Grolmusz's recent result that for non-prime-power moduli, no polynomial bound exists. More precisely we prove the following result. Theorem.Let p be a prime and q=pk. Let ? 1, ? , ? sbe distinct integers, 0? i? q? 1. Let X be a set of n elements and let A1, A2, ? , Ambe subsets of X with the following properties: ? |Ai|? (modq) for alli, ? , 1? i? m, 1? s. For alli, j (1? i
The emerging role of CD40 ligand in HIV infection

CD40 ligand (also called CD40L, CD154, or TNFSF5) is a membrane protein expressed mainly by activated CD4+ T cells, which interacts with its receptor, CD40, on a variety of cells. The crucial importance of the CD40L‐CD40 system for many immune responses has been extensively described. This review focuses on the multiple roles that this system may play in HIV infection. In early HIV infection, CD40L expression contributes to the immunological control of viral replication by inducing HIV‐suppressive chemokines and supporting the production of anti‐HIV antibodies and cytotoxic T cells. However, by activating antigen‐presenting cells, such as dendritic cells and macrophages, CD40L can also lead to increased CD4+ T cell activation, which promotes the replication of HIV in these lymphocytes. Later, with the development of AIDS, CD40L‐expressing CD4+ T cells become selectively depleted, perhaps as a result of a gp120‐induced signal through CD4 that down‐regulates CD40L expression. This acquired CD40L deficiency may explain the similarity between the types of opportunistic infections that occur in AIDS and in congenital CD40L deficiency. Vaccines or other strategies that promote the growth of CD4+ T cells capable of expressing CD40L may help to sustain host immunity against HIV and prevent AIDS‐defining opportunistic infections.
Codebook-Based Opportunistic Interference Alignment

For the multiple-input multiple-output interfering multiple-access channels (IMACs), opportunistic interference alignment (OIA) using the singular value decomposition (SVD)-based beamforming at each user fundamentally reduces the user scaling condition required to achieve any target DoF, compared to that for the single-input multiple-output IMAC. In this paper, we tackle two practical challenges of the existing SVD-based OIA: 1) the need of full feedforward of the selected users' beamforming weight vectors and 2) a low rate achieved based on the exiting zero-forcing receiver. We first propose a codebook-based OIA, in which the weight vectors are chosen from a predefined codebook with a finite size so that information of the weight vectors can be sent to the belonging BS with limited feedforward. We derive the codebook size required to achieve the same user scaling condition as the SVD-based OIA case for both Grassmannian and random codebooks. Surprisingly, it is shown that the derived codebook size is the same for the two codebook methods. Second, we introduce an enhanced receiver at the base stations (BSs) in pursuit of further improving the achievable rate. Assuming no collaboration between the BSs, the interfering links between a BS and the selected users in neighboring cells are difficult to be acquired at the belonging BS. We propose the use of a simple minimum Euclidean distance receiver operating with no information of the interfering links. With the help of the OIA, we show that this new receiver asymptotically achieves the channel capacity as the number of users increases.
Impaired alveolar macrophage response to Haemophilus antigens in chronic obstructive lung disease.

RATIONALE Interactions of nontypeable Haemophilus influenzae (NTHI) with macrophages are implicated in the pathogenesis of chronic obstructive pulmonary disease (COPD). However, the immunologic mechanisms that mediate NTHI-macrophage inflammation are poorly understood. Outer membrane protein (OMP) P6 and lipooligosaccharide (LOS) of NTHI are potent immunomodulators. We theorized that alveolar macrophages in COPD possess fundamental immune defects that permit NTHI to evade host responses. OBJECTIVE To test this hypothesis, we obtained human alveolar and blood macrophages from exsmokers with COPD, exsmokers without COPD, and nonsmokers. METHODS Alveolar and blood macrophages from each donor were incubated with purified LOS and OMP P6 and with OMP P2 and the total outer membrane preparation (0.1-1 microg/ml). MEASUREMENTS Supernatants (24 h) were assayed for IL-1beta, TNF-alpha, IL-10, IL-12, and IL-8 by multianalyte multiplexed flow cytometry. RESULTS Comparative induction of COPD and non-COPD alveolar macrophages by LOS and OMP P6 revealed diminished IL-8, TNF-alpha, and IL-1beta responses of COPD alveolar macrophages (p < or = 0.03 for each). COPD alveolar macrophages also had diminished responses to total outer membrane (p < or = 0.03 for each). In contrast, COPD blood macrophages had no significant differences among donor groups in IL-8, TNF-alpha, or IL-1beta responsiveness to NTHI antigens. Diminished IL-12 responses of COPD blood macrophages to NTHI antigens, compared with nonsmokers, could not be independently dissociated from group differences in age and pack-years. CONCLUSIONS These findings support a paradigm of defective immune responsiveness of alveolar macrophages, but not blood macrophages, in COPD.
Self-Adaptive Evolution Toward New Parameter Free Image Registration Methods

Image registration (IR) is a challenging topic in both the computer vision and pattern recognition fields; its main aim is to find the optimal transformation to provide the best overlay or fitting between two or more images. Usually, the success of well-known algorithms, such as iterative closest point, highly depends on several assumptions, e.g., the user should provide an initial near-optimal pose of the images to be registered. In the last decade, a new family of registration algorithms based on evolutionary principles has been contributed in order to overcome the latter drawbacks. However, their performance highly depends on carefully tuning (usually by hand) the control parameters of the algorithm, which is an error-prone and a time-consuming task. In this paper, we propose a new self-adaptive evolution model to deal with IR problems. To our knowledge, this is the first time a self-adaptive approach has been used for tuning the control parameters of evolutionary algorithms tackling computer vision tasks. Specifically, we introduce a novel design of the proposed self-adaptive approach facing pair-wise range IR problem instances, which is a challenging real-world optimization problem. In addition, several classical approaches, as well as state-of-the-art evolutionary IR methods, have been considered for numerical comparison.
Speech Emotion Recognition using an Enhanced Co-Training Algorithm

In previous systems of speech emotion recognition, supervised learning are frequently employed to train classifiers on lots of labeled examples. However, the labeling of abundant data requires much time and many human efforts. This paper presents an enhanced co-training algorithm to utilize a large amount of unlabeled speech utterances for building a semi-supervised learning system. It uses two conditionally independent attribute views(i.e. temporal features and statistic features) of unlabeled examples to augment a much smaller set of labeled examples. Our experimental results demonstrate that compared with the method based on the supervised training, the proposed system makes 9.0% absolute improvement on female model and 7.4% on male model in terms of average accuracy. Moreover, the enhanced co-training algorithm achieves comparable performance to the co-training prototype, while it can reduce the classification noise which is produced by error labeling in the process of semi-supervised learning.