Miracle-dz/UniFAR-FTUs huggingface dataset:
Glutathione S-Transferase Polymorphism Interactions with Smoking Status and HPV Infection in Cervical Cancer Risk: An Evidence-Based Meta-Analysis

Background Human papillomavirus (HPV) infection is considered the major cause of cervical cancer (CC), but a number of infected women do not develop invasive lesions, suggesting the role of genetic susceptibility and environmental co-factors for cancer outbreak. Glutathione S- transferases (GSTs) are multifunctional enzymes that play a key role in the detoxification of varieties of both endogenous products of oxidative stress and exogenous carcinogens. Methods MEDLINE, EMBASE, and Cochrane databases were searched. All studies evaluating the association between GSTM1 polymorphisms and cervical cancer were included. Pooled odds ratio (OR) and 95% confidence interval (CI) were calculated using fixed-or random-effects model. Results A total of 23 case-control studies were included in the meta-analysis. The overall result showed that the association between GSTM1 null genotype and risk for cervical cancer was statistically significant (OR = 1.56; 95%CI, 1.39–1.75). Subgroup analyses were performed based on ethnicity, smoking and HPV infection. Our results showed that smokers with null GSTM1 genotype had higher risk of cervical cancer (OR = 2.27, 95%CI, 1.46–3.54). For the ethnicity stratification, significant increased risk of null GSTM1 genotype was found in Chinese and Indian population, but no increased risk in other population was found. Conclusions this meta-analysis provided strong evidence that the GSTM1 genotype is associated with CC development, especially in Chinese and Indian populations. Smoking and HPV infection modified the association between the null GSTM1 genotype and CC.
Profile guided code positioning

This paper presents the results of our investigation of code positioning techniques using execution profile data as input into the compilation process. The primary objective of the positioning is to reduce the overhead of the instruction memory hierarchy.After initial investigation in the literature, we decided to implement two prototypes for the Hewlett-Packard Precision Architecture (PA-RISC). The first, built on top of the linker, positions code based on whole procedures. This prototype has the ability to move procedures into an order that is determined by a "closest is best" strategy.The second prototype, built on top of an existing optimizer package, positions code based on basic blocks within procedures. Groups of basic blocks that would be better as straight-line sequences are identified as chains. These chains are then ordered according to branch heuristics. Code that is never executed during the data collection runs can be physically separated from the primary code of a procedure by a technique we devised called procedure splitting.The algorithms we implemented are described through examples in this paper. The performance improvements from our work are also summarized in various tables and charts.
Implementation analysis of NoC: a MPSoC trace-driven approach

This paper proposes to tackle Networks-on-chip design for MPSoC on the assumption that area and power overhead control is the primary goal. Analysis of topologies and routing strategies is performed by comparing two approaches, the wormhole and hot potato, both theoretically and using real synthesized data in 0. 13μm technology. It is shown that the hot potato solution is competitive and possibly better for both occupation and dissipation, while its performance, measured by simulation on real multiprocessor traces, is not worse than the wormhole case.
Dislocation Mean Free Paths and Strain Hardening of Crystals

Predicting the strain hardening properties of crystals constitutes a long-standing challenge for dislocation theory. The main difficulty resides in the integration of dislocation processes through a wide range of time and length scales, up to macroscopic dimensions. In the present multiscale approach, dislocation dynamics simulations are used to establish a dislocation-based continuum model incorporating discrete and intermittent aspects of plastic flow. This is performed through the modeling of a key quantity, the mean free path of dislocations. The model is then integrated at the scale of bulk crystals, which allows for the detailed reproduction of the complex deformation curves of face-centered cubic crystals. Because of its predictive ability, the proposed framework has a large potential for further applications.
Correction: Characterization of Tunga penetrans Antigens in Selected Epidemic Areas in Murang'a County in Kenya

Tunga penetrans are fleas that cause tungiasis, a condition characterized by high transmission rate due to poor housing conditions, social neglect and inadequate health care in economically disadvantaged communities in developing countries. This study therefore aimed at characterizing jiggers antigens to identify immunodominant ones to help understand immunological behavior of the parasite that would otherwise be important in future control of the parasite. Samples were gravid fleas and blood samples from infested individuals in Kahuro and Murang’a East district in Murang’a County. Freeze and thaw was used to extract soluble proteins from the fleas. Ouchterlony Double immunodiffusion was used to assess antigen-antibody reactions between extracted soluble protein and the serum from immunized rats, Rattus norvegicus prior to analysis of human sera. These results were comparable to results of immunoelectrphoresis. Jigger protein isolates were analyzed in Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis technique (SDS—PAGE), against Pharmacia standard protein markers. Further analysis of jigger antigens against pooled human sera from infested victims in Western blot revealed three immunodominant antigens. Using simple regression analysis molecular weights of the three immunodominant antigens were estimated as 51.795, 23.395 and 15.38 kDa respectively. These results are important since they would help understand immunological behavior of the parasites. This would help to create basis for designing and improving approaches against jiggers such as development of immune prophylaxis to complement social science approaches that is mainly concerned with maintenance of high standards of hygiene.
On the Development and Evaluation of Spatial-Domain Green’s Functions for Multilayered Structures With Conductive Sheets

This work focuses on Green's functions (GFs) of planar multilayered structures that may include an arbitrary number of conductive sheets. The spectral-domain GFs are derived through an automatized strategy based on the propagator matrix technique, while the spatial-domain counterparts are evaluated using a novel, efficient, and error controlled numerical method. All of the procedures remain general in order to accommodate for the tensorial nature of the surface conductivity of the sheets. Numerical examples of GFs for the mixed potential integral equation method are provided, validating the proposed algorithms.
The Influence of Coping on Vision-Related Quality of Life in Patients With Low Vision: A Prospective Longitudinal Study.

PURPOSE To determine the longitudinal impact of specific coping strategies on vision-related quality of life (VRQoL) in patients with low vision. METHODS This was a single-group, longitudinal study utilizing telephone-administered interviews conducted at baseline and at 3 and 6 months with patients (visual acuity < 6/12 in the better eye) recruited from low vision services. The Coping Strategy Indicator (CSI) assessed three strategies used specifically in relation to vision-related problems: avoidant coping, problem-solving coping, and seeking social support. Vision-related quality of life was assessed using the Impact of Vision Impairment (IVI) questionnaire, which comprises two domains: vision-related functioning and vision-related emotional well-being. We used multivariable mixed linear regression including time as an independent variable to assess change in VRQoL. RESULTS The study comprised 162 patients (mean age = 69.8 years, 66% female), most with age-related macular degeneration (42%) and moderate vision impairment (41%; <6/18-6/60). Multivariable mixed linear regression showed that avoidant coping was a significant determinant of decline in vision-related functioning (β = -0.11, 95% confidence interval [CI] -0.22 to -0.01, P = 0.036) and emotional well-being (β = -0.29, 95% CI -0.45 to -0.13, P < 0.001) over a 6-month period. CONCLUSIONS Our findings showed that avoidant coping has a detrimental impact on VRQoL over time. Low vision specialists should be aware of their patients' coping strategies and encourage them to engage in active rather than avoidant coping to deal with the impact of their vision impairment.
Bank Vole Prion Protein As an Apparently Universal Substrate for RT-QuIC-Based Detection and Discrimination of Prion Strains

Prions propagate as multiple strains in a wide variety of mammalian species. The detection of all such strains by a single ultrasensitive assay such as Real Time Quaking-induced Conversion (RT-QuIC) would facilitate prion disease diagnosis, surveillance and research. Previous studies have shown that bank voles, and transgenic mice expressing bank vole prion protein, are susceptible to most, if not all, types of prions. Here we show that bacterially expressed recombinant bank vole prion protein (residues 23-230) is an effective substrate for the sensitive RT-QuIC detection of all of the different prion types that we have tested so far – a total of 28 from humans, cattle, sheep, cervids and rodents, including several that have previously been undetectable by RT-QuIC or Protein Misfolding Cyclic Amplification. Furthermore, comparison of the relative abilities of different prions to seed positive RT-QuIC reactions with bank vole and not other recombinant prion proteins allowed discrimination of prion strains such as classical and atypical L-type bovine spongiform encephalopathy, classical and atypical Nor98 scrapie in sheep, and sporadic and variant Creutzfeldt-Jakob disease in humans. Comparison of protease-resistant RT-QuIC conversion products also aided strain discrimination and suggested the existence of several distinct classes of prion templates among the many strains tested.
Overexpression of Glycine-Extended Gastrin Inhibits Parietal Cell Loss and Atrophy in the Mouse Stomach

Recently we have reported synergistic effects between glycine-extended gastrin (G-gly) and amidated gastrin-17 on acid secretion in short-term infusion studies. In the present study, we examined the long-term effect of G-gly on the atrophy-promoting effects of amidated gastrin in the mouse stomach with or without Helicobacter infection. Transgenic mice overexpressing amidated gastrin (INS-GAS mice), G-gly (MTI/G-gly mice), and both peptides (INS-GAS/G-gly mice) were used for assessment of acid secretion and ulcer susceptibility and histologic examination and scoring of preneoplastic lesions in response to the 3 and 6 months Helicobacter felis (H. felis) infection. We found that MTI/G-gly mice had normal gastric histology and acid secretion. Double transgenic (INS-GAS/G-gly) mice showed 2-fold increases in acid secretion compared with INS-GAS mice. Acute peptic ulcers after pyloric ligation were noted in 50% of the INS-GAS/G-gly mice but in none of the INS-GAS mice at 6 months of age. Whereas male INS-GAS mice had a >50% decrease in the numbers of parietal cell and enterochromaffin-like cell at 6 months of age, the male double transgenic mice had no such decrease. Overexpression of G-gly reduced the scores of preneoplasia in the stomach; however, it did not prevent the development of amidated gastrin-dependent gastric cancer in both H. felis-infected mice and uninfected mice. We conclude that G-gly synergizes with amidated gastrin to stimulate acid secretion and inhibits parietal cell loss in INS-GAS/G-gly mice. The overexpression of G-gly seems to increase the susceptibility to peptic ulcer disease and delay the development of Helicobacter-mediated gastric preneoplasia in this model.
A systematic review of the validity and reliability of apathy scales in neurodegenerative conditions

ABSTRACT Background: There are several scales used to detect apathy in disease populations. Since apathy is a prevalent symptom in many neurodegenerative diseases, this is an especially important context in which to identify and compare scales. Aims: To provide an overview of apathy scales validated in generic and specific neurodegenerative disease populations, compare validation studies’ methodological quality and the psychometric properties of the validated apathy scales. Methods: A systematic review of literature was conducted of articles published between 1980 and 2013. The final articles selected for review were rated on methodological quality and the psychometric properties of the scales used were interpreted. Results: Sixteen articles validating apathy scales were included in the review, five in a generic neurodegenerative sample and eleven in specific neurodegenerative samples. The methodological quality of specific studies varied from poor to excellent. The highest quality, which had psychometrically favorable scales, were the dementia apathy interview and rating (DAIR) and the apathy evaluation scale-clinical version (AES-C) in Alzheimer's disease and the Lille apathy rating scale (LARS) in Parkinson's disease. Generic neurodegenerative disease validation studies were of average methodological quality and yielded inconsistent psychometric properties. Conclusions: Several instruments can be recommended for use in some specific neurodegenerative diseases. Other instruments should either be validated or developed to assess apathy in more generic populations.
Case‐control data analysis for randomly pooled biomarkers

Pooled study designs, where individual biospecimens are combined prior to measurement via a laboratory assay, can reduce lab costs while maintaining statistical efficiency. Analysis of the resulting pooled measurements, however, often requires specialized techniques. Existing methods can effectively estimate the relation between a binary outcome and a continuous pooled exposure when pools are matched on disease status. When pools are of mixed disease status, however, the existing methods may not be applicable. By exploiting characteristics of the gamma distribution, we propose a flexible method for estimating odds ratios from pooled measurements of mixed and matched status. We use simulation studies to compare consistency and efficiency of risk effect estimates from our proposed methods to existing methods. We then demonstrate the efficacy of our method applied to an analysis of pregnancy outcomes and pooled cytokine concentrations. Our proposed approach contributes to the toolkit of available methods for analyzing odds ratios of a pooled exposure, without restricting pools to be matched on a specific outcome.
An efficient solution to the five-point relative pose problem

An efficient algorithmic solution to the classical five-point relative pose problem is presented. The problem is to find the possible solutions for relative camera motion between two calibrated views given five corresponding points. The algorithm consists of computing the coefficients of a tenth degree polynomial and subsequently finding its roots. It is the first algorithm well suited for numerical implementation that also corresponds to the inherent complexity of the problem. The algorithm is used in a robust hypothesis-and-test framework to estimate structure and motion in real-time.
RN / 14 / 09 Seeing is Slicing : Observation Based Slicing of Picture Description Languages June 26 , 2014

Spectra-Based Fault Localisation (SBFL) aims to assist debugging by applying risk evaluation formulæ (sometimes called suspiciousness metrics) to program spectra and ranking statements according to the predicted risk. Designing a risk evaluation formula is often an intuitive process done by human software engineer. This paper presents a Genetic Programming approach for evolving risk assessment formulæ. The empirical evaluation using 92 faults from four Unix utilities produces promising results. GP-evolved equations can consistently outperform many of the human-designed formulæ, such as Tarantula, Ochiai, Jaccard, Ample, and Wong1/2, up to 5.9 times. More importantly, they can perform equally as well as Op2, which was recently proved to be optimal against If-Then-Else-2 (ITE2) structure, or even outperform it against other program structures. 1 The program spectra data used in the paper, as well as the complete empirical results, are available from: http://www.cs. ucl.ac. uk/staff/s.yoo/evolving-sbfl.html. UCL DEPARTMENT OF COMPUTER SCIENCE Research Note RN/14/09 Seeing is Slicing: Observation Based Slicing of Picture Description Languages
Fast Point-to-Point Shortest Path Computations with Arc-Flags

We present a number of improvements of the basic variant of the arc-flag acceleration (Lauther, 1997, 2004) for point-to-point (P2P) shortest path computations on large graphs. Arc-flags are a modification to the standard Dijkstra algorithm and are used to avoid exploring unnecessary paths during shortest path computation. We assume that for the same input graph the shortest path problem has to be solved repeatedly for different node pairs. Thus, precomputing the arc-flags is possible. We show that the improved arc-flag acceleration achieves speedups of P2P shortest path queries of more than 1,470 on a subnetwork of the German road network with 1M node and 2.5M arcs using 450 bits of additional information per arc. The acceleration factors increase with the size of the input graph. Finally, we present an improved preprocessing version which allows precomputing arc-flags for European and North-American road networks within hours.
Mixer 6

Linguistic Data Consortiums Human Subjects Data Collection lab conducts multi-modal speech collections to develop corpora for use in speech, speaker and language research and evaluations. The Mixer collections have evolved over the years to best accommodate the ever changing needs of the research community and to hopefully keep one step ahead by providing increasingly challenging data. Over the years Mixer collections have grown to include socio-linguistic interviews, a wide variety of telephone conditions and multiple languages, recording conditions, channels and speech acts. Mixer 6 was the most recent collection. This paper describes the Mixer 6 Phase 1 project. Mixer 6 Phase 1 was a study supporting linguistic research, technology development and education. The object of this study was to record speech in a variety of situations that vary formality and model multiple naturally occurring interactions as well as a variety of channel conditions
A directional total variation

Total variation (TV) is an isotropic image prior that penalizes the abrupt changes in the images in all directions. In this paper, we modify TV so as to make it more suitable for images with a dominant direction. Specifically, we describe the implementation of a directional TV, and we demonstrate its utility for image denoising. We show that image denoising with the directional TV prior can be more effective compared to the regular (isotropic) TV for images with a dominant direction.
Global routing with crosstalk constraints

Due to the scaling down of device geometry and increasing frequency in deep sub-micron designs, crosstalk between interconnection wires has become an important issue in VLSI layout design. In this paper, we consider crosstalk avoidance during global routing. We present a global routing algorithm based on a new Steiner tree formulation and the Lagrangian relaxation technique. We also give theoretical results on the complexity of the problem.
Characterization of Trichome-Expressed BAHD Acyltransferases in Petunia axillaris Reveals Distinct Acylsugar Assembly Mechanisms within the Solanaceae1[OPEN]

The assembly of plant defense-related acylsugars in Petunia axillaris trichomes requires four acyltransferase activities that are distinct from those catalyzing acylsugar biosynthesis in tomato. Acylsugars are synthesized in the glandular trichomes of the Solanaceae family and are implicated in protection against abiotic and biotic stress. Acylsugars are composed of either sucrose or glucose esterified with varying numbers of acyl chains of differing length. In tomato (Solanum lycopersicum), acylsugar assembly requires four acylsugar acyltransferases (ASATs) of the BAHD superfamily. Tomato ASATs catalyze the sequential esterification of acyl-coenzyme A thioesters to the R4, R3, R3ʹ, and R2 positions of sucrose, yielding a tetra-acylsucrose. Petunia spp. synthesize acylsugars that are structurally distinct from those of tomato. To explore the mechanisms underlying this chemical diversity, a Petunia axillaris transcriptome was mined for trichome preferentially expressed BAHDs. A combination of phylogenetic analyses, gene silencing, and biochemical analyses coupled with structural elucidation of metabolites revealed that acylsugar assembly is not conserved between tomato and petunia. In P. axillaris, tetra-acylsucrose assembly occurs through the action of four ASATs, which catalyze sequential addition of acyl groups to the R2, R4, R3, and R6 positions. Notably, in P. axillaris, PaxASAT1 and PaxASAT4 catalyze the acylation of the R2 and R6 positions of sucrose, respectively, and no clear orthologs exist in tomato. Similarly, petunia acylsugars lack an acyl group at the R3ʹ position, and congruently, an ortholog of SlASAT3, which catalyzes acylation at the R3ʹ position in tomato, is absent in P. axillaris. Furthermore, where putative orthologous relationships of ASATs are predicted between tomato and petunia, these are not supported by biochemical assays. Overall, these data demonstrate the considerable evolutionary plasticity of acylsugar biosynthesis.
An adaptive sliding mode observer for induction motor sensorless speed control

An adaptive sliding mode flux observer is proposed for speed sensorless vector control of induction motors. Two sliding mode current observers are used in the method to make flux and speed estimation robust to parameter variation. Adaptive speed estimation is derived from the stability theory. The stability of adaptive flux observer is guaranteed by Lyapunov stability theory. The system is first simulated by MATLAB and HIL (hardware-in-the-loop). Then it is implemented based on TMS320F2812, a 32-bit fixed-point DSP controller. Simulation and experimental results are presented to demonstrate the potentials and practicality of the approach.
Recovery of bisulfite-converted genomic sequences in the methylation-sensitive QPCR

Many methods for the detection of genomic DNA methylation states have appeared. Currently, nearly all such methods employ bisulfite-mediated deamination of denatured DNA. While this treatment effectively deaminates cytosines to uracils, leaving most 5-methylcytosines intact, it also introduces abasic sites that generate a significant number of single-strand breaks in DNA. We have investigated the interplay of these two processes in order to determine their relative effects on the methylation-sensitive QPCR method. The extent of cleavage of the input DNA is significant and appears to be an increasing function of DNA concentration. Even so, the results suggest that only ∼10% of a 62-nt target will be lost due to degradation and targets up to 131 nt will suffer only a 20% loss. More significant losses were found to occur during the subsequent removal of bisulfite and desulfonation steps that appear to be the result of size selectivity associated with matrix binding and elution required prior to QPCR in the most commonly used protocols. For biospecimens yielding <1 μg of DNA, these findings suggest that bisulfite treatment, in current implementations of MS-QPCR, result in low recoveries that preclude reliable analysis of DNA methylation patterns regardless of target size.