Miracle-dz/UniFAR-FTUs huggingface dataset:
Homocysteine and ischaemic stroke in men: the Caerphilly study

OBJECTIVE To assess the risk of ischaemic stroke associated with total serum homocyst(e)ine (tHcy) concentration. DESIGN Cohort study. SETTING Caerphilly, South Wales PARTICIPANTS 2254 men age 50 to 64 years recruited between 1984 and 1988. RESULTS 107 men developed ischaemic stroke and mean follow up time was 10.2 years. There was no significant difference in mean serum total homocyst(e)ine levels between stroke cases (12.2 μmol 95% CI 11.6 to 13.1) and non-cases (11.7 μmol 95% CI 11.5 to 11.9) (p=0.14). There was no significant risk for a standard deviation increase in homocyst(e)ine (adjusted hazard ratio = 1.1, 95% CI 0.9 to 1.4). An interaction was observed between homocyst(e)ine and age at entry (p=0.003). The adjusted odds ratio comparing the top quintile of homocyst(e)ine with the rest was 2.5 (95% CI 1.0 to 6.2) for strokes occurring under 65 years and 0.5 (95% CI 0.2 to 1.3) at 65 years or older (p value for interaction =0.02). Risk also differed by blood pressure status. The adjusted hazard ratio for a standard deviation increase in homocyst(e)ine was 0.8, (95% CI 0.6 to 1.2) for normotensive men and 1.3 (95% CI 1.1 to 1.7) for hypertensive men (p value for interaction =0.01). CONCLUSIONS Overall, there is no significant relation between homocyst(e)ine and ischaemic stroke in this cohort. However, its aetiological importance may be greater for premature ischaemic strokes (<65 years) and in hypertensive men.
Morphology of Verticillium dahliae and V. tricorpus on semi-selective media used for the detection of V. dahliae in soil.

The morphology of two soil-borne Verticillium species, V. dahliae and V. tricorpus, was studied on two semi-selective agar media, in the absence and presence of soil. Morphology of the fungi differed considerably between the media, with respect to presence and shape of microsclerotia, dark hyphae (i.e. short melanised hyphae attached to the microsclerotia) and dark mycelium (i.e. melanised mycelium throughout the colony). On modified soil extract agar (MSEA), a pectate based agar, V. dahliae always had globose to elongate microsclerotia, without dark hyphae or dark mycelium, whereas V. tricorpus always had dark hyphae or dark mycelium, and microsclerotia, whenever present, were globose to irregular in shape. On ethanol agar (EA), V. dahliae had large microsclerotia and abundant dark hyphae, whereas V. tricorpus did not form microsclerotia, but always abundant dark mycelium. For the first time we observed the formation of dark hyphae by V. dahliae to a great extent. In the presence of soil, most characteristics were less pronounced, and V. dahliae microsclerotia were smaller, but V. tricorpus produced large microsclerotia, even when they were absent in pure culture. Morphological characteristics suitable for discrimination between the two species on MSEA plates in the presence of soil were selected and tested with fresh isolates from agricultural fields. The two fungi could be distinguished using qualitative characteristics and microsclerotial size. Molecular analysis and morphology on potato dextrose agar confirmed all identifications made on soil dilution plates.
UNIVERSITY OF SOUTHERN CALIFORNIA Center for Applied Financial Economics (CAFE) On the Network Topology of Variance Decompositions: Measuring the Connectedness of Financial Firms

We propose several connectedness measures built from pieces of variance decompositions, and we argue that they provide natural and insightful measures of connectedness among financial asset returns and volatilities. We also show that variance decompositions define weighted, directed networks, so that our connectedness measures are intimately-related to key measures of connectedness used in the network literature. Building on these insights, we track both average and daily time-varying connectedness of major U.S. financial institutions’ stock return volatilities in recent years, including during the financial crisis of 2007-2008.
Design and Implementation of a Laser-Based Ammonia Breath Sensor for Medical Applications

Design and Implementation of a Laser-Based Ammonia Breath Sensor for Medical Applications Kyle G. Owen Laser-based sensors can be used as non-invasive monitoring tools to measure parts per billion (ppb) levels of trace gases. Ammonia sensors are useful for applications in environmental pollutant monitoring, atmospheric and combustion kinetic studies, and medical diagnostics. This sensor was specifically designed to measure ammonia in exhaled breath to be used as a medical diagnostic and monitoring tool, however, it can also be extended for use in other applications. Although ammonia is a naturally occurring species in exhaled breath, abnormally elevated levels can be an indication of adverse medical conditions. Laser-based breath diagnostics have many benefits since they are cost effective, non-invasive, painless, real time monitors. They have the potential to improve the quality of medical care by replacing currently used blood tests and providing immediate feedback to physicians. This sensor utilizes a Quantum Cascade Laser and Wavelength Modulation Spectroscopy with second harmonic normalized by first harmonic detection in a 76 m multi-pass absorption cell to measure ppb levels of ammonia with improved sensitivity over previous sensors. Initial measurements to determine the ammonia absorption
Discourse-aware Statistical Machine Translation as a Context-sensitive Spell Checker

Real-word errors or context sensitive spelling errors, are misspelled words that have been wrongly converted into another word of vocabulary. One way to detect and correct real-word errors is using Statistical Machine Translation (SMT), which translates a text containing some real-word errors into a correct text of the same language. In this paper, we improve the results of mentioned SMT system by employing some discourseaware features into a log-linear reranking method. Our experiments on a real-world test data in Persian show an improvement of about 9.5% and 8.5% in the recall of detection and correction respectively. Other experiments on standard English test sets also show considerable improvement of real-word checking results.
A Concept for ab initio Prediction of cis-regulatory Modules

An important concern in the attempt of understanding the functional code of eukaryotic genes is to elucidate the control structures for regulating gene activation and suppression. One objective in the attempt to understand mechanisms of gene regulation is the elucidation of the regulatory network structure. A preliminary step of a detailed network analysis is identifying the transcription factor binding sites of a regulatory network. Known as cis-regulatory module (CRM), it is understood as part of the genome that comprises a set of short length binding sites. Gene regulatory systems are known to be quite stable during evolution, as compared to relatively frequent replication processes of genes and mutations of the coding sequences. This conservation property of regulatory code can advantageously be used for identifying cis-regulatory modules of potentially co-regulated genes. As the degree of similarity is expected to depend on the phylogenetic distance of homologs or orthologs, we favor an approach that is based on a comparison paradigm. The paper introduces a novel concept for measuring the similarity ofcis-regulatory modules which can then be used in an algorithm for comparing regulatory regions. The proposed algorithm searches for pairs of similar modules, and a prototype implementation is applied to human and mouse liver sequences. The results are compared to that of random sequences, and it is shown that a clear decision about co-regulation is possible at this level.
Use of Depth Measure for Multivariate Functional Data in Disease Prediction: An Application to Electrocardiograph Signals

Abstract In this paper we develop statistical methods to compare two independent samples of multivariate functional data that differ in terms of covariance operators. In particular we generalize the concept of depth measure to this kind of data, exploiting the role of the covariance operators in weighting the components that define the depth. Two simulation studies are carried out to validate the robustness of the proposed methods and to test their effectiveness in some settings of interest. We present an application to Electrocardiographic (ECG) signals aimed at comparing physiological subjects and patients affected by Left Bundle Branch Block. The proposed depth measures computed on data are then used to perform a nonparametric comparison test among these two populations. They are also introduced into a generalized regression model aimed at classifying the ECG signals.
Generalized Linear Mixing Rule for Classical Coulomb Mixtures

It is shown that the Coulomb energy U of fully ionized ionic mixture can be written as a sum over partial contributions of ion species j: U = T Σj Nju (Γj, yj) (generalized linear mixing rule). In contrast to the traditional linear mixing rule ULM = T Σj NjuOCP(Γj), applicable for strong coupling, the partial contribution function u depends not only on Γj, but on an additional parameter yj = (rD/rDOCP)2 also. Here rD and rDOCP are Debye radiuses in the mixture and in the one component plasma at coupling parameter Γj, correspondingly. The parameter yj does not depend on a specific composition of the mixture, but on the Debye radius rD only, making function u (Γj, yj) universal. The generalized linear mixing rule can be applied at any coupling parameter, if ionic mixture is not crystallized. It reproduces results of the Debye‐Hückel theory at weak coupling and traditional linear mixing rule at strong coupling. It can be easily applied to the complicated mixtures, composed of a large number of ion species. Since yj is temperature independent, the Coulomb contribution to Helmholtz free energy of the mixture can also be presented in a form of generalized linear mixing rule (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Type-of-Service Routing in Datagram Delivery Systems

The Internet is expected to support various services, including best-effort services and guaranteed services. For best-effort services, we propose a new approach to achieving type-of-service (TOS) classes with adaptive next-hop routing. We consider two TOS classes, namely, delay-sensitive and throughput-sensitive. As in routing protocols such as OSPF and integrated IS-IS, each node has a different next-hop for each destination and TOS class. Traditionally, a node has a single FCFS queue for each outgoing link, and the next-hops are computed using link measurements. In our approach, we attempt to isolate the two traffic classes by using for each outgoing link a separate FCFS queue for each TOS class; the link is shared cyclicly between its TOS queues. The next-hops for the delay-sensitive traffic adapts to link delays of that traffic. The next-hops for the throughput-sensitive traffic adapts to overall link utilizations. We compare our approach with the traditional approach using discrete-event simulation and Lyapunov analysis (for stability of routes). Our approach offers lower end-to-end delay to the delay-sensitive traffic. A related property is that the routes for the delay-sensitive traffic are more stable, i.e., less oscillations. An unexpected property is that the overall end-to-end delay is lower, because the throughput-sensitive traffic moves away to under-utilized routes. >
The complete mitochondrial DNA of white shark (Carcharodon carcharias) from Isla Guadalupe, Mexico

Abstract The Isla Guadalupe white shark mitochondrial structure is similar to the one previously reported for a white shark individual from Taiwan with a total length of 16,745 and 16,742 bp respectively; the base composition of the genomes was as follow A (30.60%), T (28.67%), C (26.86%) and G (13.87%), contains 13 protein-coding genes and 24 tRNA genes and the non-coding control region. The tRNA genes range from 70–72 bp. Gene order is the same as in other vertebrates and teleosts.
Near-Optimal Distributed Maximum Flow: Extended Abstract

We present a near-optimal distributed algorithm for (1+o(1))-approximation of single-commodity maximum flow in undirected weighted networks that runs in (D+ √n)⋅ no(1) communication rounds in the Congest model. Here, n and D denote the number of nodes and the network diameter, respectively. This is the first improvement over the trivial O(m) time bound, and it nearly matches the Ω(D+√n) round complexity lower bound. The algorithm contains two sub-algorithms of independent interest, both with running time (D+√n)⋅ no(1): Distributed construction of a spanning tree of average stretch no(1). Distributed construction of an no(1)-congestion approximator consisting of the cuts induced by O(log n) virtual trees. The distributed representation of the cut approximator allows for evaluation in (D+√n)⋅ no(1) rounds. All our algorithms make use of randomization and succeed with high probability.
Identifying Inhibitors of the Hsp90-Aha1 Protein Complex, a Potential Target to Drug Cystic Fibrosis, by Alpha Technology

Deletion of a single phenylalanine residue at position 508 of the protein CFTR (cystic fibrosis transmembrane conductance regulator), a chloride channel in lung epithelium, is the most common cause for cystic fibrosis. As a consequence, folding of the CFTRΔF508 protein and delivery to the cell surface are compromised, resulting in degradation of the polypeptide. Accordingly, decreased surface presence of CFTRΔF508 causes impaired chloride ion conductivity and is associated with mucus accumulation, a hallmark of cystic fibrosis. Molecular chaperones such as Hsp90 and its co-chaperone partner Aha1 are thought to play a key role in targeting folding-deficient CFTRΔF508 for degradation. Thus, pharmacologic manipulation to inhibit Hsp90-Aha1 chaperone complex formation appears beneficial to inhibit proteolysis of CFTRΔF508 and rescue its residual chloride channel activity. Therefore, we have screened a collection of 14,400 druglike chemical compounds for inhibitors of the Hsp90-Aha1 complex by amplified luminescence proximity homogeneous assay (Alpha). We identified two druglike molecules that showed promising results when we tested their ability to restore chloride channel activity in culture cells expressing the mutant CFTRΔF508 protein. The two molecules were most effective in combination with the corrector VX-809 and may therefore serve as a lead compound that can be further developed into a drug to treat cystic fibrosis patients.
Research on Applied Technology of Palmprint Recognition Based on Fisher Linear Discriminant and Improved PCA Algorithm

The information applied technology of palmprint recognition is a biometric technology, it’s based on the effective information on the palm (such as: palmprint) to identifies people. The palmprint is unique and characteristic, these are the identification of critical conditions. The feature extraction of palmprint image is a prerequisite for recognition, feature extraction algorithm depends on the quality of the recognition rate and efficiency. This paper presents a method of palmprint recognition algorithm based on Fisher linear discriminant analysis and improved PCA algorithm. The experimental results show that, the recognition rate is improved.
Supplemental Data Fpr 3 and Zip 3 Ensure that Initiation of Meiotic Recombination Precedes Chromosome Synapsis in Budding Yeast

Strains We replaced the ZIP1 ORF using pEJW1, a ZIP1-GFP integrating plasmid marked with URA3 [1], and then selected for colonies resistant to 5-FOA to isolate a uracil-requiring strain carrying a single copy of ZIP1-GFP. Sporulation-competent haploid strains were constructed by using pB211 to integrate MATa at THR1 in a MATα haploid. fpr3::KAN and dmc1::KAN deletion alleles were constructed using dominant marker gene replacement [2]. The following gene disruptions were previously described: CTF19 tagged with 13-myc [3], zip3::URA3 [4], zip2::LEU2 and ZIP2-GFP:URA3 [5], and spo11::ADE2 [6]. Strains used to measure meiotic gene conversion carried heteroalleles at both HIS4 (his4-260/his4-Hpa) and ARG4 (arg4Nsp/arg4-Bgl).
Rendering localized spatial audio in a virtual auditory space

High-quality virtual audio scene rendering is required for emerging virtual and augmented reality applications, perceptual user interfaces, and sonification of data. We describe algorithms for creation of virtual auditory spaces by rendering cues that arise from anatomical scattering, environmental scattering, and dynamical effects. We use a novel way of personalizing the head related transfer functions (HRTFs) from a database, based on anatomical measurements. Details of algorithms for HRTF interpolation, room impulse response creation, HRTF selection from a database, and audio scene presentation are presented. Our system runs in real time on an office PC without specialized DSP hardware.
HPHA effect on reversible resistive switching of Pt/Nb-doped SrTiO3 Schottky junction for nonvolatile memory application

We investigated the effect of high-pressure hydrogen annealing (HPHA) on a Pt/Nb-doped SrTiO 3 Schottky junction for nonvolatile memory applications. Hysteretic current-voltage (I-V) characteristic curves reveal that the HPHA-treated Schottky junction interface has a higher resistance ratio than the control sample in dc bias sweep. The HPHA sample also exhibits switching behavior by pulsed voltage stress with excellent electrical characteristics including voltage pulse duration as short as 1 μs, endurance cycles of up to 10 6 times, and retention time as long as 10 5 s. These indicate that HPHA improved resistance switching characteristics of the Schottky junction.
Evolutionary Accessibility of Mutational Pathways

Functional effects of different mutations are known to combine to the total effect in highly nontrivial ways. For the trait under evolutionary selection (‘fitness’), measured values over all possible combinations of a set of mutations yield a fitness landscape that determines which mutational states can be reached from a given initial genotype. Understanding the accessibility properties of fitness landscapes is conceptually important in answering questions about the predictability and repeatability of evolutionary adaptation. Here we theoretically investigate accessibility of the globally optimal state on a wide variety of model landscapes, including landscapes with tunable ruggedness as well as neutral ‘holey’ landscapes. We define a mutational pathway to be accessible if it contains the minimal number of mutations required to reach the target genotype, and if fitness increases in each mutational step. Under this definition accessibility is high, in the sense that at least one accessible pathway exists with a substantial probability that approaches unity as the dimensionality of the fitness landscape (set by the number of mutational loci) becomes large. At the same time the number of alternative accessible pathways grows without bounds. We test the model predictions against an empirical 8-locus fitness landscape obtained for the filamentous fungus Aspergillus niger. By analyzing subgraphs of the full landscape containing different subsets of mutations, we are able to probe the mutational distance scale in the empirical data. The predicted effect of high accessibility is supported by the empirical data and is very robust, which we argue reflects the generic topology of sequence spaces. Together with the restrictive assumptions that lie in our definition of accessibility, this implies that the globally optimal configuration should be accessible to genome wide evolution, but the repeatability of evolutionary trajectories is limited owing to the presence of a large number of alternative mutational pathways.
Building bilingual lexicon to create Dialect Tunisian corpora and adapt language model

Since the Tunisian revolution, Tunisian Dialect (TD) used in daily life, has became progressively used and represented in interviews, news and debate programs instead of Modern Standard Arabic (MSA). This situation has important negative consequences for natural language processing (NLP): since the spoken dialects are not officially written and do not have standard orthography, it is very costly to obtain adequate corpora to use for training NLP tools. Furthermore, there are almost no parallel corpora involving TD and MSA. In this paper, we describe the creation of Tunisian dialect text corpus as well as a method for building a bilingual dictionary, in order to create language model for speech recognition system for the Tunisian Broadcast News. So, we use explicit knowledge about the relation between TD and MSA.
Completeness of birth and death registration in a rural area of South Africa: the Agincourt health and demographic surveillance, 1992–2014

Background Completeness of vital registration remains very low in sub-Saharan Africa, especially in rural areas. Objectives To investigate trends and factors in completeness of birth and death registration in Agincourt, a rural area of South Africa covering a population of about 110,000 persons, under demographic surveillance since 1992. The population belongs to the Shangaan ethnic group and hosts a sizeable community of Mozambican refugees. Design Statistical analysis of birth and death registration over time in a 22-year perspective (1992–2014). Over this period, major efforts were made by the government of South Africa to improve vital registration. Factors associated with completeness of registration were investigated using univariate and multivariate analysis. Results Birth registration was very incomplete at onset (7.8% in 1992) and reached high values at end point (90.5% in 2014). Likewise, death registration was low at onset (51.4% in 1992), also reaching high values at end point (97.1% in 2014). For births, the main factors were mother's age (much lower completeness among births to adolescent mothers), refugee status, and household wealth. For deaths, the major factors were age at death (lower completeness among under-five children), refugee status, and household wealth. Completeness increased for all demographic and socioeconomic categories studied and is likely to approach 100% in the future if trends continue at this speed. Conclusion Reaching high values in the completeness of birth and death registration was achieved by excellent organization of the civil registration and vital statistics, a variety of financial incentives, strong involvement of health personnel, and wide-scale information and advocacy campaigns by the South African government.