Miracle-dz/UniFAR-FTUs huggingface dataset:
Aspirin versus warfarin in atrial fibrillation: decision analysis may help patients' choice.

BACKGROUND the primary prevention of ischaemic stroke in chronic non-valvular atrial fibrillation (AF) typically involves consideration of aspirin or warfarin. CHA(2)DS(2)-VASc estimates annual stroke rates for untreated AF patients, which are reduced by 60% with warfarin and by 20% with aspirin. HAS-BLED estimates annual rates of major bleeding on warfarin. The latter risk with aspirin is 0.5-1.2% per year. HYPOTHESIS given a 'warfarin, aspirin or no therapy' choice, AF patients will prefer the option that maximises the annual probability of not having a stroke and not having a major bleed. METHODS decision tree applied to the 60 possible combinations of CHA(2)DS(2)-VASc and HAS-BLED scores. RESULTS according to the pre-specified hypothesis, when CHA(2)DS(2)-VASc is <2, the balance of risk and benefit would advise no treatment; when CHA(2)DS(2)-VASc is 2 or 3, warfarin would be best when HAS-BLED <2, otherwise no treatment would be advised; for CHA(2)DS(2)-VASc =4, warfarin would be best when HAS-BLED <3, otherwise no treatment would be advised and for CHA(2)DS(2)-VASc ≥5, warfarin would be the preferred option if HAS-BLED <4, otherwise aspirin would be advised. CONCLUSION this theoretical exercise illustrates the potential benefit of decision analysis in an area where high complexity and uncertainty still remain.
Pregnancy outcome following first trimester exposure to sumatriptan

We prospectively compared pregnancy outcome after exposure to sumatriptan with that of disease-matched controls and nonteratogen controls. There were no differences in the rates of live births, spontaneous abortions, therapeutic abortions, or major birth defects among the three groups. This first prospective report suggests that the use of sumatriptan during organogenesis is not associated with an apparent increased risk of major birth defects.
Fabrication and properties of arrays of superconducting nanowires

We report on the fabrication and structural characterization of arrays of superconducting nanowires by electroplating lead into the nanopores of track-etched polymer membranes. The diameters of the lead nanowires range from 400 down to 70 nm, whereas their length is about 20 μ m. Large enhancement of the critical field has been observed in good agreement with the Ginsburg–Landau–Silin theory. By comparing the predicted critical field enhancement for thin cylinders with experimental results, we have extracted the effective penetration depth. The dependence of the effective penetration depth and electron mean free path on the wire diameter is also discussed.
Assessment of Evolution of Pandemic Vibrio parahaemolyticus by Multilocus Sequence Typing

ABSTRACT The genetic relatedness of 81 isolates of Vibrio parahaemolyticus was assessed by multilocus sequence typing. The strain with serotype O3:K6 emerged as a pandemic pathogen in 1996, with subsequent expansion to include strains having serotypes O1:KUT, O4:K68, and O1:K25. Sequence data from gyrB, recA, dnaE, and gnd revealed that 16 distinct serogroups isolated prior to the pandemic were highly variable and only isolates of serogroup O3:K6 shared two alleles with the pandemic strains. The pandemic strains regardless of serotype were clonal, with 51 of 54 isolates having the identical allelic profile (AP). Serotype alone did not adequately define a pandemic strain: among O1:KUT strains tested, seven strains with the identical pandemic AP carried previously described pandemic markers, while five nonpandemic strains had five distinct APs. Our sequence data provide strong molecular support for the clonal origin of pandemic V. parahaemolyticus O3:K6 and suggest that strains within such a clonal group may acquire previously identified serotypes.
Application and evaluation of automated methods to extract neuroanatomical connectivity statements from free text

Motivation: Automated annotation of neuroanatomical connectivity statements from the neuroscience literature would enable accessible and large-scale connectivity resources. Unfortunately, the connectivity findings are not formally encoded and occur as natural language text. This hinders aggregation, indexing, searching and integration of the reports. We annotated a set of 1377 abstracts for connectivity relations to facilitate automated extraction of connectivity relationships from neuroscience literature. We tested several baseline measures based on co-occurrence and lexical rules. We compare results from seven machine learning methods adapted from the protein interaction extraction domain that employ part-of-speech, dependency and syntax features. Results: Co-occurrence based methods provided high recall with weak precision. The shallow linguistic kernel recalled 70.1% of the sentence-level connectivity statements at 50.3% precision. Owing to its speed and simplicity, we applied the shallow linguistic kernel to a large set of new abstracts. To evaluate the results, we compared 2688 extracted connections with the Brain Architecture Management System (an existing database of rat connectivity). The extracted connections were connected in the Brain Architecture Management System at a rate of 63.5%, compared with 51.1% for co-occurring brain region pairs. We found that precision increases with the recency and frequency of the extracted relationships. Availability and implementation: The source code, evaluations, documentation and other supplementary materials are available at http://www.chibi.ubc.ca/WhiteText. Contact: paul@chibi.ubc.ca Supplementary information: Supplementary data are available at Bioinformatics Online.
Prediction of protein structural class from the amino acid sequence

The multidimensional statistical technique of discriminant analysis is used to allocate amino acid sequences to one of four secondary structural classes: high α content, high β content, mixed α and β, low content of ordered structure. Discrimination is based on four attributes: estimates of percentages of α and β structures, and regular variations in the hydrophobic values of residues along the sequence, occurring with periods of 2 and 3.6 residues. The reliability of the method, estimated by classifying 138 sequences from the Brookhaven Protein Data Bank, is 80%, with no misallocations between α‐rich and β‐rich classes. The reliability can be increased to 84% by making no allocation for proteins classified with odds close to 1. Classification using previously developed secondary structural prediction methods is considerably less reliable, the best result being 64% obtained using predictions based on the Delphi method.
Genetic Diversity and Virulence Profiles of Escherichia coli Isolates Causing Spontaneous Bacterial Peritonitis and Bacteremia in Patients with Cirrhosis

ABSTRACT Among patients with cirrhosis, infections caused by Escherichia coli organisms that translocate from the gut are a frequent and severe complication. One hundred ten E. coli isolates from 110 cirrhotic patients with spontaneous bacterial peritonitis and/or spontaneous bacteremia were characterized for their phylogenetic group and virulence genotype (34 extraintestinal virulence factor genes). Genetic relatedness was investigated by enterobacterial repetitive intergenic consensus sequence type 2 (ERIC-2) PCR typing and multilocus sequence typing. Phylogenetic groups A, B1, B2, and D accounted for 24%, 4%, 48%, and 24% of the population, respectively. Overall, 68 distinct ERIC-2 profiles were encountered. Eleven clonal groups, represented by multiple isolates (2 to 11) from the same sequence type (ST) or sequence type complex, were identified. These clonal groups accounted for 54 (49%) isolates overall. Membership in one of these clonal groups was more frequent among B2 isolates than non-B2 isolates (67% versus 32%, P < 0.001). The most frequent sequence types were ST95 (n = 13) and ST73 (n = 8), followed by the ST14 and ST10 complexes (n = 7). ST131 and ST69 were represented by three isolates each. Clonal group-associated isolates exhibited a greater prevalence of 11 virulence genes, including pap elements, than the other isolates. However, no association between clonal groups and host factors, type of infection, or mortality was observed. In conclusion, E. coli isolates causing spontaneous bacterial peritonitis and bacteremia in cirrhotic patients are genetically diverse. However, approximately half of the isolates belong to familiar clonal groups and exhibit extensive virulence profiles that may be associated with greater invasive potential.
An application level video gateway

The current model for multicast transmission of video over the Internet assumes that a ﬁxed average bandwidth is uniformly present throughout the network. Consequently, sources limit their transmission rates to accommodate the lowest bandwidth links, even though high-bandwidth connectivity might be available to many of the participants. We propose an architecture where a video transmission can be decomposed into multiple sessions with different bandwidth requirements using an application-level gateway. Our video gateway transparently connects pairs of sessions into a single logical conference by manipulating the data and control information of the video streams. In particular, the gate-way performs bandwidth adaptation through transcoding and rate-control. We describe an efﬁcient algorithm for transcoding Motion-JPEG to H.261 that runs in real-time on standard workstations. By making the Real-time Transport Protocol (RTP) an integral component of our architecture, the video gateway interoperates with the current Internet video tools in a transparent fashion. We have built a prototype of the video gateway and used it to redistribute multi-megabit JPEG video seminars from the Bay Area Gigabit Network as 128 kb/s H.261 MBone sessions.
Deriving the Boyer-Moore-Horspool algorithm

The keyword pattern matching problem has been frequently studied, and many different algorithms for solving it have been suggested. Watson and Zwaan in the early 1990s derived a set of well-known solutions from a common starting point, leading to a taxonomy of such algorithms. Their taxonomy did not include a variant of the Boyer-Moore algorithm developed by Horspool. In this paper, I present the Boyer-Moore-Horspool algorithm in the context of the taxonomy.
YAP3: improved detection of similarities in computer program and other texts

In spite of years of effort, plagiarism in student assignment submissions still causes considerable difficulties for course designers; if students' work is not their own, how can anyone be certain they have learnt anything? YAP is a system for detecting suspected plagiarism in computer programs and other texts submitted by students. The paper reviews YAP3, the third version of YAP, focusing on its novel underlying algorithm - Running-Karp-Rabin Greedy-String-Tiling (or RKS-GST), whose development arose from the observation with YAP and other systems that students shuffle independent code segments. YAP3 is able to detect transposed subsequences, and is less perturbed by spurious additional statements. The paper concludes with a discussion of recent extension of YAP to English texts, further illustrating the flexibility of the YAP approach.
SHAPE MEMORY EFFECT BEHAVIOR OF NITI TORQUE TUBES IN TORSION

In order to simulate the torsional behavior of NiTi torque tubes, two different 3D thermo-mechanical constitut ive models are utilized. Firstly, an available incremental con stitutive model is used in which a return mapping algorithm is impl emented to numerically calculate the strains for any applied s tresses. Secondly, Microplane theory is employed based on which 1D constitutive laws are considered for associated str ess and strain components on any arbitrary plane passing through a material point followed by a homogenization process to gener alize the 1D equations to a 3D macroscopic model. Both of the constitutive models are implemented in ABAQUS by developing UMAT. In order to compare the two approaches, torque-angle of rotation and shear stress-shear str ain responses for torsion of thin-walled Nitinol torque tubes wit h different thicknesses are studied. The numerical results of t hese two approaches show to be in a good agreement indicating the capability of Microplane theory in constitutive mod eling of shape memory alloys. This theory provides explicit relationships to calculate strains in terms of stre sses, and this makes it very beneficial in obtaining the SMA respo nses in a fast and easy manner.
In vivo modulation of nonphotochemical exciton quenching (NPQ) by regulation of the chloroplast ATP synthase

Nonphotochemical quenching (NPQ) of excitation energy, which protects higher plant photosynthetic machinery from photodamage, is triggered by acidification of the thylakoid lumen as a result of light-induced proton pumping, which also drives the synthesis of ATP. It is clear that the sensitivity of NPQ is modulated in response to changing physiological conditions, but the mechanism for this modulation has remained unclear. Evidence is presented that, in intact tobacco or Arabidopsis leaves, NPQ modulation in response to changing CO2 levels occurs predominantly by alterations in the conductivity of the CFO-CF1 ATP synthase to protons (g\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{H}^{+}}}\end{equation*}\end{document}). At a given proton flux, decreasing g\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{H}^{+}}}\end{equation*}\end{document} will increase transthylakoid proton motive force (pmf), thus lowering lumen pH and contributing to the activation of NPQ. It was found that an ≈5-fold decrease in g\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{H}^{+}}}\end{equation*}\end{document} could account for the majority of NPQ modulation as atmospheric CO2 was decreased from 2,000 ppm to 0 ppm. Data are presented that g\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{H}^{+}}}\end{equation*}\end{document} is kinetically controlled, rather than imposed thermodynamically by buildup of ΔGATP. Further results suggest that the redox state of the ATP synthase γ-subunit thiols is not responsible for altering g\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{H}^{+}}}\end{equation*}\end{document}. A working model is proposed wherein g\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{H}^{+}}}\end{equation*}\end{document} is modulated by stromal metabolite levels, possibly by inorganic phosphate.
Multicast Mobility in Mobile IP Version 6 (MIPv6): Problem Statement and Brief Survey

This document discusses current mobility extensions to IP layer multicast. It describes problems arising from mobile group communication in general, the case of multicast listener mobility, and for mobile senders using Any Source Multicast and Source Specific Multicast. Characteristic aspects of multicast routing and deployment issues for fixed IPv6 networks are summarized. Specific properties and interplays with the underlying network access are surveyed with respect to the relevant technologies in the wireless domain. It outlines the principal approaches to multicast mobility, together with a comprehensive exploration of the mobile multicast problem and solution space. This document concludes with a conceptual roadmap for initial steps in standardization for use by future mobile multicast protocol designers. This document is a product of the IP Mobility Optimizations (MobOpts) Research Group.
Color Stability of Composites After Short-term Oral Simulation: An in vitro Study

Background: Although most of the studies investigated color stability of different restorative materials, evaluation of color stability of composites after immersion in multiple beverages in the same day by an in vitro oral simulation study is unclear. Objective: To assess color change of different restorative materials at the end of days 1, 14, and 30 of immersion in multiple liquid types to mimic the oral environment in vitro. Method: Ten disc-shaped specimens were made from each of four different resin composites (Filtek Z250, Voco x-tra base, Beautifil Flow Plus, Beautifil II). Baseline color value of each sample was measured using a spectrophotometer. Each composite was respectively immersed in coffee, an orange/pomegranate juice mixture, black tea, and a mouth rinse on the same day to mimic daily liquid consumption of individuals. Color measurements were taken after 1, 14, and 30 days by spectrophotometer and color change values were calculated. Statistical analyses were executed by one-way ANOVA/Tukey HSD and repeated-measures ANOVA. Results: All materials showed significant color change after 1, 14, and 30 days (P < 0.01) of immersion in liquids, with the lowest color alteration observed at the 1st day and the highest observed after the 30th day. Among the materials tested, at each time point (1, 14, and 30 days), the lowest color alteration was detected in Filtek Z250 and the highest color alteration was detected in Beautifil II. Conclusion: Color alteration of composite resins is affected by composite type and storage time. With the exception of 1 day of storage, color changes of all materials were substantial and clinically unacceptable.
Intracochlear Bleeding Enhances Cochlear Fibrosis and Ossification: An Animal Study

The aim of this study was to investigate the effects of intracochlear bleeding during cochleostomy on cochlear inflammatory response and residual hearing in a guinea pig animal model. Auditory brainstem response threshold shifts were greater in blood injected ears (p<0.05). Interleukin-1β, interleukin-10, tumor necrosis factor-α and nitric oxide synthase 2, cytokines that are related to early stage inflammation, were significantly increased in blood injected ears compared to normal and cochleostomy only ears at 1 day after surgery; with the increased IL-1β being sustained until 3 days after the surgery (p<0.05). Hair cells were more severely damaged in blood injected ears than in cochleostomy only ears. Histopathologic examination revealed more extensive fibrosis and ossification in blood injected ears than cochleostomy only ears. These results show that intracochlear bleeding enhanced cochlear inflammation resulting in increased fibrosis and ossification in an experimental animal model.
Immunoglobulin Kappa C Predicts Overall Survival in Node-Negative Breast Cancer

Background Biomarkers of the immune system are currently not used as prognostic factors in breast cancer. We analyzed the association of the B cell/plasma cell marker immunoglobulin kappa C (IGKC) and survival of untreated node-negative breast cancer patients. Material and Methods IGKC expression was evaluated by immunostaining in a cohort of 335 node-negative breast cancer patients with a median follow-up of 152 months. The prognostic significance of IGKC for disease-free survival (DFS) and breast cancer-specific overall survival (OS) was evaluated with Kaplan-Meier survival analysis as well as univariate and multivariate Cox analysis adjusted for age at diagnosis, pT stage, histological grade, estrogen receptor (ER) status, progesterone receptor (PR) status, Ki-67 and human epidermal growth factor receptor 2 (HER-2) status. Results 160 patients (47.7%) showed strong expression of IGKC. Univariate analysis showed that IGKC was significantly associated with DFS (P = 0.017, hazard ratio [HR] = 0.570, 95% confidence interval [CI] = 0.360–0.903) and OS (P = 0.011, HR = 0.438, 95% CI = 0.233–0.822) in the entire cohort. The significance of IGKC was especially strong in ER negative and in luminal B carcinomas. In multivariate analysis IGKC retained its significance independent of established clinical factors for DFS (P = 0.004, HR = 0.504, 95% CI = 0.315–0.804) as well as for OS (P = 0.002, HR = 0.371, 95% CI = 0.196–0.705). Conclusion Expression of IGKC has an independent protective impact on DFS and OS in node-negative breast cancer.
Effect of Static Stretching of the Biceps Brachii on Torque, Electromyography, and Mechanomyography During Concentric Isokinetic Muscle Actions

The purpose of this study was to determine the effect of an acute static stretching bout of the biceps brachii on torque, electromyography (EMG), and mechanomyography (MMG) during concentric isokinetic muscle actions. Eighteen (men, n = 10; women, n = 8) adult subjects (M ± SD age = 22.7 ± 2.8 years; weight = 78.0 ± 17.0 kg; height = 177.9 ± 11.0 cm) performed maximal isokinetic (30 and 270°·s−1) forearm flexion strength testing on 2 occasions while EMG and MMG were recorded. Subjects were randomly assigned to stretching (STR) or nonstretching (NSTR) protocols before strength testing. Two-way ANOVAs with repeated measures revealed significantly (p ≤ 0.05) greater torque for NSTR (M ± SEM = 36.9 ± 3.3 N·m) vs. STR (35.2 ± 3.3 N·m), significantly greater MMG amplitude for STR vs. NSTR for 30°·s−1 (STR = 93.5 ± 14.4 mV; NSTR = 63.1 ± 10.6 mV) and 270°·s−1 (STR = 207.6 ± 35.6 mV; NSTR = 136.4 ± 31.7 mV), and no difference in EMG amplitude. These results indicate that a greater ability to produce torque without prior stretching is related to the musculotendinous stiffness of the muscle rather than the number of motor units activated. This suggests that performing activities that reduce muscle stiffness (such as stretching), may be detrimental to performance.
On Information Rates for Mismatched Decoders

Reliable transmission over a discrete-time memoryless channel with a decoding metric that is not necessarily matched to the channel (mismatched decoding) is considered. It is assumed that the encoder knows both the true channel and the decoding metric. The lower bound on the highest achievable rate found by Csiszar and Korner (1981) and by Hui (1983) for DMC's, hereafter denoted C/sub LM/, is shown to bear some interesting information-theoretic meanings. The bound C/sub LM/ turns out to be the highest achievable rate in the random coding sense, namely, the random coding capacity for mismatched decoding. It is also demonstrated that the /spl epsiv/-capacity associated with mismatched decoding cannot exceed C/sub LM/. New bounds and some properties of C/sub LM/ are established and used to find relations to the generalized mutual information and to the generalized cutoff rate. The expression for C/sub LM/ is extended to a certain class of memoryless channels with continuous input and output alphabets, and is used to calculate C/sub LM/ explicitly for several examples of theoretical and practical interest. Finally, it is demonstrated that in contrast to the classical matched decoding case, here, under the mismatched decoding regime, the highest achievable rate depends on whether the performance criterion is the bit error rate or the message error probability and whether the coding strategy is deterministic or randomized. >