Miracle-dz/UniFAR-FTUs huggingface dataset:
Natural Interferon-a Versus Its Combination With 6-MethylPrednisolone in the Therapy of Type I 1 Mixed Cryoglobulinemia : A Long-Term , Randomized , Controlled Study

Type II mixed cryoglobulinemia (MC) is an often progressive vasculitis characterized by circulating cold-precipitable proteins that usually consists of polyclonal IgG and monoclonal lgMK with rheumatoid factor (RF) activity. Its etiology is unknown, although recent evidence strongly suggests that hepatitis C virus (HCV) plays a major role. Plasmapheresis, corticosteroids, and cytotoxic drugs have been used in the therapy of MC patients. Recently, favorable results with recombinant interferon-alpha (rlFNa) have been reported. To further assess its effectiveness, we studied the effects of natural human interferon-a (nlFNa), alone and in combination with 6-methyl-prednisolone (PDN), in a prospective, randomized, controlled trial in patients with symptomatic MC. Sixty-five patients were enrolled onto the trial, 52 (80%) of whom presented serum anti-HCV antibodies and specific genomic RNA sequences. Fifteen patients received nlFNa (3 MU) intramuscularly (IM) three times weekly, whereas 17 patients also received 16 mg/d of PDN orally on non-IFN days. Moreover, 18 patients received 16 mg/d of PDN only, and 15 were untreated. Treatment was discontinued after 1 year and patients were monitored for 8 to 17 months (mean, 13). A complete response was achieved in eight of 15 patients (53.3%) treated with nlFNa and nine of 17 (52.9%) treated with nlFNa plus PDN, as compared with three of 18 patients (16.7%) who received PDN only (P < .05) and one of 15 (6.7%) untreated controls (P < .01). Partial response
Developmental switching in Physarum polycephalum: Petri net analysis of single cell trajectories of gene expression indicates responsiveness and genetic plasticity of the Waddington quasipotential landscape

The developmental switch to sporulation in Physarum polycephalum is a phytochrome-mediated far-red light-induced cell fate decision that synchronously encompasses the entire multinucleate plasmodial cell and is associated with extensive reprogramming of the transcriptome. By repeatedly taking samples of single cells after delivery of a light stimulus pulse, we analysed differential gene expression in two mutant strains and in a heterokaryon of the two strains all of which display a different propensity for making the cell fate decision. Multidimensional scaling of the gene expression data revealed individually different single cell trajectories eventually leading to sporulation. Characterization of the trajectories as walks through states of gene expression discretized by hierarchical clustering allowed the reconstruction of Petri nets that model and predict the observed behavior. Structural analyses of the Petri nets indicated stimulus- and genotype-dependence of both, single cell trajectories and of the quasipotential landscape through which these trajectories are taken. The Petri net-based approach to the analysis and decomposition of complex cellular responses and of complex mutant phenotypes may provide a scaffold for the data-driven reconstruction of causal molecular mechanisms that shape the topology of the quasipotential landscape.
Design and baseline findings of a large-scale rapid response to an HIV outbreak in people who inject drugs in Athens, Greece: the ARISTOTLE programme.

AIMS To (i) describe an intervention implemented in response to the HIV-1 outbreak among people who inject drugs (PWIDs) in Greece (ARISTOTLE programme), (ii) assess its success in identifying and testing this population and (iii) describe socio-demographic characteristics, risk behaviours and access to treatment/prevention, estimate HIV prevalence and identify risk factors, as assessed at the first participation of PWIDs. DESIGN A 'seek, test, treat, retain' intervention employing five rounds of respondent-driven sampling. SETTING Athens, Greece (2012-13). PARTICIPANTS A total of 3320 individuals who had injected drugs in the past 12 months. INTERVENTION ARISTOTLE is an intervention that involves reaching out to high-risk, hard-to-reach PWIDs ('seek'), engaging them in HIV testing and providing information and materials to prevent HIV ('test') and initiating and maintaining anti-retroviral and opioid substitution treatment for those testing positive ('treat' and 'retain'). MEASUREMENTS Blood samples were collected for HIV testing and personal interviews were conducted. FINDINGS ARISTOTLE recruited 3320 PWIDs during the course of 13.5 months. More than half (54%) participated in multiple rounds, resulting in 7113 visits. HIV prevalence was 15.1%. At their first contact with the programme, 12.5% were on opioid substitution treatment programmes and the median number of free syringes they had received in the preceding month was 0. In the multivariable analysis, apart from injection-related variables, homelessness was a risk factor for HIV infection in male PWIDs [odds ratio (OR) yes versus no = 1.89, 95% confidence interval (CI) = 1.41, 2.52] while, in female PWIDS, the number of sexual partners (OR for > 5 versus one partner in the past year = 4.12, 95% CI = 1.93, 8.77) and history of imprisonment (OR yes versus no = 2.76, 95% CI = 1.43, 5.31) were associated with HIV. CONCLUSIONS In Athens, Greece, the ARISTOTLE intervention for identifying HIV-positive people among people who inject drugs (PWID) facilitated rapid identification of a hidden population experiencing an outbreak and provided HIV testing, counselling and linkage to care. According to ARISTOTLE data, the 2011 HIV outbreak in Athens resulted in 15% HIV infection among PWID. Risk factors for HIV among PWID included homelessness in men and history of imprisonment and number of sexual partners in women.
Influenza A ( H 1 N 1 )-associated pneumonia * , * * Pneumonia associada a influenza A ( H 1 N 1 )

Objective: To describe the characteristics of patients with influenza A (H1N1)-associated pneumonia treated at two hospitals in the region of Liguria, Italy, as well as to describe their treatment and outcomes. Methods: This was a prospective observational study including all patients older than 16 years of age with a confirmed diagnosis of influenza A (H1N1) who were admitted to Villa Scassi Hospital, in the city of Genoa, Italy, or to the Sestri Levante General Hospital, in the city of Sestri Levante, Italy, between September of 2009 and January of 2010. The primary outcome measure was mortality within 60 days after diagnosis. Secondary outcome measures were the need for mechanical ventilation and the length of hospital stay. Results: Of the 40 patients with a confirmed diagnosis of influenza A (H1N1), 27 presented pneumonia during the study period. The mean age of the 27 patients was 42.8 ± 14.8 years, and the mean length of hospital stay was 11.6 ± 8.2 days. Of the 27 patients, 20 had respiratory failure, 4 underwent invasive mechanical ventilation, and 5 underwent noninvasive ventilation. One patient had comorbidities, developed multiple organ failure, and died. Conclusions: During the influenza A (H1N1) pandemic, the associated mortality rate was lower in Italy than in other countries, and cases reported in the country typically had a milder course than did those reported elsewhere. Nevertheless, 9 of our cases (33%) rapidly evolved to respiratory failure, requiring mechanical ventilation.
Design and implementation of a highly efficient DBD ozonizer using the single switch resonant converter with piezoelectric transformer

This paper describes the design and construction of a dielectric barrier discharge (DBD) ozonizer using the single switch resonant converter (SSRC), in conjunction with a piezoelectric transformer (PT). The main advantages of the proposed topology are minimum parts count, small footprint the high efficiency. Furthermore, the chamber uses dielectric made from muscovite mica, which is easy to construct and allows for a low initiation voltage. An experimental prototype of the ozonizer is built; it is found that the ozonizer draws very little power, i.e. less than 4 W with an almost constant efficiency at 90%. The maximum achievable ozone yield is 3.6 g/kWh.
DP: A Paradigm for Anonymous Remote Computation and Communication for Cluster Computing

This paper explores the transparent programmability of communicating parallel tasks in a Network of, Workstations (NOW). Programs which are tied up with specific machines will not be resilient to the changing conditions of a NOW. The Distributed Pipes (DP) model enables location independent intertask communication among processes' across machines. This approach enables migration of communicating parallel tasks according to runtime conditions. A transparent programming model for a parallel solution to Iterative Grid Computations using DP is also proposed. Programs written using the model are resilient to the heterogeneity of nodes and changing conditions in the NOW. They are also devoid of any network related code. The design of runtime support and function library support are presented. An engineering problem, namely, the Steady State Equilibrium Problem, is studied over the model. The performance analysis shows the speedup due to parallel execution and scaled down memory requirements. We present a case where the effect of communication overhead can be nullified to achieve a linear to super-linear speedup. The analysis discusses performance resilience of Iterative Grid Computations and characterizes synchronization delay among subtasks and the effect of network overhead and load fluctuations on performance. The performance saturation characteristics of such applications are also studied.
Evaluation of a Commercialized In Situ Hybridization Assay for Detecting Human Papillomavirus DNA in Tissue Specimens from Patients with Cervical Intraepithelial Neoplasia and Cervical Carcinoma

ABSTRACT To evaluate a commercialized in situ hybridization (ISH) assay for detecting human papillomavirus (HPV) DNA, we compared the ability of a new ISH probe, Inform HPV III (Ventana Medical Systems, Tucson, AZ), to that of PCR assays to detect HPV DNA in cervical tissue specimens with normal cervix (20 cases), cervical intraepithelial neoplasia (CIN; CIN 1, 27 cases; CIN 2, 28 cases; and CIN 3, 33 cases), and cervical carcinoma (29 cases). General HPV DNA was detected using consensus primer-mediated PCR assays. HPV genotyping was performed by using EasyChip HPV blot (King Car Yuan Shan Institute, I-Lan, Taiwan). HPV16 integration status (E2/E6 ratio) was determined by using quantitative real-time PCR. Our findings showed that the ISH and PCR had fair to good agreements in detecting HPV DNA across all CIN categories without significant differences (Kappa coefficient, 0.34 to 0.63; P = 0.13 to 1.0). However, ISH detected significantly fewer HPV-positive cases in carcinoma than PCR did (Kappa coefficient, 0.2; P = 0.03). Eleven cases with ISH− PCR+ results had HPV types that can be detected by Inform HPV III. Five carcinoma cases with ISH− PCR+ results showed a significantly higher level of integrated HPV16 (P = 0.008) than did the ISH+ cases. As a consequence, lower copy numbers of episomal HPV16 in carcinoma might be the cause for the false-negative ISH results. Although the punctate signal pattern of HPV significantly increased with the severity of disease (P trend = 0.01), no significant difference in the HPV16 integration status was observed between the cases with a punctate signal only and the cases with mixed punctate and diffuse signals (P = 0.4). In conclusion, ISH using the Inform HPV III probe seems comparable to PCR for detecting HPV DNA in cervical tissue with CINs. False-negative ISH results appear to be associated with the lower copy numbers of the episomal HPV16 but not with the ability of the Inform HPV III probe to detect specific HPV types. In addition, signal patterns, especially a mixed punctate and diffuse pattern of HPV, cannot be reliably used to predict viral integration status.
Phosphorylation‐dependent regulation of skeletogenesis in sea urchin micromere‐derived cells and embryos

Sea urchin embryo micromeres when isolated and cultured in vitro differentiate to produce spicules. Although several authors have used this model, almost nothing is known about the signalling pathways responsible for initiating skeletogenesis. In order to investigate the potential involvement of phosphorylation events in spiculogenesis, the effect of inhibitors of protein kinases and phosphatases on skeleton formation was studied. Results obtained using both cultured micromeres and embryos revealed that protein tyrosine kinase and phosphatase inhibitors blocked skeleton formation, but not serine/threonine phosphatase inhibitors. The inhibitors showed a dose‐dependent effect and when removed from micromere or embryo culture, spicule formation resumed. Inhibition of tyrosine phosphatases resulted in an increase in the tyrosine phosphorylation level of two major proteins and a modest decrease in the expression of the mRNA coding for type I fibrillar collagen. These findings strongly suggest that tyrosine phosphorylation and dephosphorylation is required for micromere differentiation and for normal skeletogenesis during sea urchin embryo development.
MIPS: a database for protein sequences, homology data and yeast genome information

The MIPS group (Martinsried Institute for Protein Sequences) at the Max-Planck-Institute for Biochemistry, Martinsried near Munich, Germany, collects, processes and distributes protein sequence data within the framework of the tripartite association of the PIR-International Protein Sequence Database (,). MIPS contributes nearly 50% of the data input to the PIR-International Protein Sequence Database. The database is distributed on CD-ROM together with PATCHX, an exhaustive supplement of unique, unverified protein sequences from external sources compiled by MIPS. Through its WWW server (http://www.mips.biochem.mpg.de/ ) MIPS permits internet access to sequence databases, homology data and to yeast genome information. (i) Sequence similarity results from the FASTA program () are stored in the FASTA database for all proteins from PIR-International and PATCHX. The database is dynamically maintained and permits instant access to FASTA results. (ii) Starting with FASTA database queries, proteins have been classified into families and superfamilies (PROT-FAM). (iii) The HPT (hashed position tree) data structure () developed at MIPS is a new approach for rapid sequence and pattern searching. (iv) MIPS provides access to the sequence and annotation of the complete yeast genome (), the functional classification of yeast genes (FunCat) and its graphical display, the 'Genome Browser' (). A CD-ROM based on the JAVA programming language providing dynamic interactive access to the yeast genome and the related protein sequences has been compiled and is available on request.
HLA-DR 15 is associated with female sex and younger age at diagnosis in multiple sclerosis

Background: The association between multiple sclerosis and class II alleles of the major histocompatibiliy complex, in particular the DRB1*1501-DQB1*0602 haplotype, is well established but their role in determining specific features of this clinically heterogeneous disease is unknown as few studies involving large sample sizes have been performed. Method: 729 patients with multiple sclerosis were typed for the HLA DR15 phenotype. All patients underwent clinical assessment and a detailed evaluation of their clinical records was undertaken. Results: The presence of DR15 was associated with younger age at diagnosis and female sex but there was no association with disease course (relapsing-remitting or secondary progressive v primary progressive type), disease outcome, specific clinical features (opticospinal v disseminated form), diagnostic certainty (clinically and laboratory supported definite v clinically probable multiple sclerosis), and paraclinical investigations including the presence of oligoclonal bands in the CSF or characteristic abnormalities on MRI imaging of the central nervous system. Conclusion:Even though DR15 carriers are more likely to be female and prone to an earlier disease onset, the results indicate that there is no association with other specific clinical outcomes or laboratory indices examined here. This suggests that DR15 exerts a susceptibility rather than disease modifying effect in multiple sclerosis.
The effect of syntactic simplification on reading EST texts as L1 and L2

There has been a considerable suggestion in the literature that syntactic adaptation of a text would simplify it. This empirical study determined that the complexity of the syntax does not significantly affect the level of reading comprehension. While a complete conceptual and lexical analysis may be necessary for reading comprehension, a thorough syntactic analysis is not. This should be true for both expert and novice readers in a particular professional field, herein computer science. Using American (L1 or E1, English as a native language) and Dutch (L2 or E2, English as a second, nonnative language) computer science and humanities majors reading in EST (English for Science and Technology), it was found that there were no significant differences between subgroups reading an authentic (in original, unadapted form) computer science text and those reading a syntactically adapted text either in comprehension or in time across the four groups of subjects. These results indicate that syntactic simplification of an EST text is not a real simplification. Hence, technical writers and EST teachers might give priority to other more conceptual ways of rewriting texts.
Using Multi-agent Systems to Study Paracrinienne Cells Interaction

An apparatus for mass-analyzing ions contained in plasma. A first vacuum chamber is maintained in a relatively low vacuum state and has a first aperture disposed adjacent to a plasma source for admitting therethrough the plasma into the first vacuum chamber. A second vacuum chamber is maintained in a relatively medium vacuum state and has a second aperture communicating between the first and second vacuum chambers. An ion extracting electrode is disposed in the second vacuum chamber for extracting ions contained in the plasma through the second aperture to form an ion stream composed of the extracted ions. A third vacuum chamber is maintained in a relatively high vacuum state and has a third aperture communicating between the second and third vacuum chambers. An ion focusing electrode is disposed in the third vacuum chamber for focusing the ion stream passing through the third aperture, and a mass spectrometer is disposed in the third vacuum chamber to receive the focused ion stream for analyzing the ions in the focused ion stream.
DESIGN AND EVALUATION OF A VISUALIZATION INTERFACE FOR QUERYING LARGE UNSTRUCTURED SOUND DATABASES

Search is an underestimated problem that plays a big role in any application dealing with large databases. The more extensive and heterogeneous our data is, the harder is to find exactly what we are looking for. This idea resembles the data availability paradox stated by Woods [45]: "more and more data is available, but our ability to interpret what is available has not increased". Then the question arises: is it really useful to collect a big dataset even if we do not have the ability to successfully navigate among it? According to Morville and Callender [27], search is a grand challenge that can be succeeded with courage and vision. A good searching tool completely improves the exploitation we can do of our information resources. As a consequence, commonly used search methods must evolve. Search goal is more than finding, search should become a conversation process where answers change the questions. Having stated all that, it seems clear that extensive effort should be invested on the research and design of appropriate tools for finding our needles in the haystack. However, search is a problem that does not have a general solution. It must be adapted to the context of the information we are dealing with, in the case of the presnet document, unstructured sound databases. The aim of this thesis is the design of a visualization interface that let users graphically define queries for the Freesound Project database (http://www.freesound.org) and retrieve suitable results for a musical context. Music Information Retrieval (MIR) techniques are used to analyze all the files in the database and automatically extract audio features concerning four different aspects of sound perception: temporal envelope, timbre, tonal information and pitch. Users perform queries by graphically specifying a target for each one of these perceptual aspects, that is to say, queries are specified by defining the physical properties of the sound itself rather than indicating its source (as is usually done in common text-based search engines). Similarity search is performed among the whole database to find the most similar sound files, and returned results are represented as points in a two-dimensional space that users can explore.
Superpixels by Bilateral Geodesic Distance

We present a novel superpixel generation algorithm based on a new definition of geodesic distance, called bilateral geodesic distance. In contrast to the traditional geodesic distance, the new bilateral geodesic distance of two pixels considers the distance between their positions as well as their color difference. Superpixel generation is essentially a problem of clustering image pixels with respect to a set of properly selected seeds. We first use an adaptive hexagonal subdivision method to determine the initial seed-based image gradient. Then, we use the bilateral geodesic distance to measure the similarity between the pixels and the seeds. We apply an improved fast marching method to generate superpixels’ contour regions with the expansion velocities dependent on a new gradient formulation that depends on the seeds’ properties. The experimental results indicate that our algorithm is not only much faster than the structure-based method, which uses conventional geodesic distance, but also outperforms the existing methods in terms of region compactness and region boundary regularity.
Stage of the estrous cycle at the time of pregnant mare's serum gonadotropin injection affects the quality of ovulated oocytes in the mouse

The present study aims to analyze the effect of the stage of the estrous cycle at the time of pregnant mare's serum gonadotropin (PMSG) injection on number and quality of mouse oocytes retrieved from oviducts after exogenous ovarian stimulation. Cellular and morphological traits of ovulated oocytes from hybrid (C57Bl/6JIco female X CBA/JIco male) female mice of 12, 40–42, 50–52 or 57–62 weeks of age were analyzed. Superovulation was induced by a priming injection of PMSG at different stages of the estrous cycle followed after a 48‐hr interval by human chrorionic gonadotropin. Injection of PMSG at diestrus‐1 was associated with: (1) increased percentage of cumulus‐free oocytes; (2) raised total percentage of oocytes without polar body; (3) increased total percentage of oocytes with intracytoplasmic mitochondrial aggregates; (4) decreased percentage of oocytes with a normal distribution of chromosomes in the metaphase II plate; and (5) raised percentage of oocytes with chromosome scattering when compared to injection at estrus, diestrus‐2, and proestrus stage. On the contrary, estrus females displayed the highest percentage of oocytes with a normal distribution of chromosomes in the metaphase II plate and the lowest percentage of oocytes denuded of cumulus cells, without polar body, with intracytoplasmic mitochondrial aggregates and/or with chromosome scattering. These data suggest that administration of gonadotropins in mice should be synchronized with the innate estrous cycle of females to optimize the quality of oocytes collected from oviducts.Mol. Reprod. Dev. 61: 398–405, 2002. © 2002 Wiley‐Liss, Inc.