Miracle-dz/UniFAR-FTUs huggingface dataset:
A fast CUDA implementation of agrep algorithm for approximate nucleotide sequence matching

The availability of huge amounts of nucleotide sequences catalyzes the development of fast algorithms for approximate DNA and RNA string matching. However, most existing online algorithms can only handle small scale problems. When querying large genomes, their performance becomes unacceptable. Offline algorithms such as Bowtie and BWA require building indexes, and their memory requirement is high. We have developed a fast CUDA implementation of agrep algorithm for approximate nucleotide sequence matching by exploiting the huge computational power of modern GPU hardware. Our CUDA program is capable of searching large genomes for patterns of length up to 64 with edit distance up to 9. For example, it is able to search the entire human genome (3.10 Gbp in 24 chromosomes) for patterns of lengths of 30 and 60 with edit distances of 3 and 6 within 371 and 1,188 milliseconds respectively on one NVIDIA GeForce GTX285 graphics card, achieving 70-fold and 36-fold speedups over multithreaded QuadCore CPU counterpart. Our program employs online approach and does not require building indexes of any kind, it thus can be applied in real time. Using two-bits-for-one-character binary representation, its memory requirement is merely one fourth of the original genome size. Therefore it is possible to load multiple genomes simultaneously. The x86 and x64 executables for Linux and Windows, C++ source code, documentations, user manual, and an AJAX MVC website for online real time searching are available at http://agrep.cse. cuhk.edu. hk. Users can also send emails to CUDAagrepGmail.com to queue up for a job.
Thioredoxin and NADPH-Dependent Thioredoxin Reductase C Regulation of Tetrapyrrole Biosynthesis1[OPEN]

TRX and NTRC coordinate the stability and activity of Mg-protoporphyrin IX methyltransferase. In chloroplasts, thioredoxin (TRX) isoforms and NADPH-dependent thioredoxin reductase C (NTRC) act as redox regulatory factors involved in multiple plastid biogenesis and metabolic processes. To date, less is known about the functional coordination between TRXs and NTRC in chlorophyll biosynthesis. In this study, we aimed to explore the potential functions of TRX m and NTRC in the regulation of the tetrapyrrole biosynthesis (TBS) pathway. Silencing of three genes, TRX m1, TRX m2, and TRX m4 (TRX ms), led to pale-green leaves, a significantly reduced 5-aminolevulinic acid (ALA)-synthesizing capacity, and reduced accumulation of chlorophyll and its metabolic intermediates in Arabidopsis (Arabidopsis thaliana). The contents of ALA dehydratase, protoporphyrinogen IX oxidase, the I subunit of Mg-chelatase, Mg-protoporphyrin IX methyltransferase (CHLM), and NADPH-protochlorophyllide oxidoreductase were decreased in triple TRX m-silenced seedlings compared with the wild type, although the transcript levels of the corresponding genes were not altered significantly. Protein-protein interaction analyses revealed a physical interaction between the TRX m isoforms and CHLM. 4-Acetoamido-4-maleimidylstilbene-2,2-disulfonate labeling showed the regulatory impact of TRX ms on the CHLM redox status. Since CHLM also is regulated by NTRC (Richter et al., 2013), we assessed the concurrent functions of TRX m and NTRC in the control of CHLM. Combined deficiencies of three TRX m isoforms and NTRC led to a cumulative decrease in leaf pigmentation, TBS intermediate contents, ALA synthesis rate, and CHLM activity. We discuss the coordinated roles of TRX m and NTRC in the redox control of CHLM stability with its corollary activity in the TBS pathway.
Hydrolytically degradable poly(ethylene glycol) hydrogel scaffolds as a cell delivery vehicle: Characterization of PC12 cell response

The central nervous system (CNS) has a low intrinsic potential for regeneration following injury and disease, yet neural stem/progenitor cell (NPC) transplants show promise to provide a dynamic therapeutic in this complex tissue environment. Moreover, biomaterial scaffolds may improve the success of NPC‐based therapeutics by promoting cell viability and guiding cell response. We hypothesized that a hydrogel scaffold could provide a temporary neurogenic environment that supports cell survival during encapsulation, and degrades completely in a temporally controlled manner to allow progression of dynamic cellular processes such as neurite extension. We utilized PC12 cells as a model cell line with an inducible neuronal phenotype to define key properties of hydrolytically degradable poly(ethylene glycol) hydrogel scaffolds that impact cell viability and differentiation following release from the degraded hydrogel. Adhesive peptide ligands (RGDS, IKVAV, or YIGSR), were required to maintain cell viability during encapsulation; as compared to YIGSR, the RGDS, and IKVAV ligands were associated with a higher percentage of PC12 cells that differentiated to the neuronal phenotype following release from the hydrogel. Moreover, among the hydrogel properties examined (e.g., ligand type, concentration), total polymer density within the hydrogel had the most prominent effect on cell viability, with densities above 15% w/v leading to decreased cell viability likely due to a higher shear modulus. Thus, by identifying key properties of degradable hydrogels that affect cell viability and differentiation following release from the hydrogel, we lay the foundation for application of this system towards future applications of the scaffold as a neural cell delivery vehicle. © 2013 American Institute of Chemical Engineers Biotechnol. Prog. , 29:1255–1264, 2013
Protein structure and phenotypic analysis of pathogenic and population missense variants in STXBP1

Syntaxin‐binding protein 1, encoded by STXBP1, is highly expressed in the brain and involved in fusing synaptic vesicles with the plasma membrane. Studies have shown that pathogenic loss‐of‐function variants in this gene result in various types of epilepsies, mostly beginning early in life. We were interested to model pathogenic missense variants on the protein structure to investigate the mechanism of pathogenicity and genotype–phenotype correlations.
The Effect of RANTES Chemokine Genetic Variants on Early HIV-1 Plasma RNA Among African American Injection Drug Users

HIV-1 plasma RNA is a prognostic indicator of HIV-1, and increased levels of HIV-1 plasma RNA are associated with rapid progression to AIDS. Because chemokines and chemokine receptors are involved in the binding and entry of HIV-1, possible effects of host genetics on viral RNA levels should be visible in early infection. HIV-1 plasma RNA was measured within 2 years of seroconversion in 198 seroincident injection drug users followed in the AIDS Link to Intravenous Experience cohort. Genetic variants were identified in the chemokine receptors (CCR2, CCR5, and CCR5 promoter) and the chemokine RANTES using TaqMan and restriction fragment length polymorphism assays. Linear regression of RANTES haplotypes on early HIV-1 plasma RNA identified individuals homozygous for the RANTES R1 haplotype as having a lower viral load by almost one-half log10 unit compared with those bearing non-RANTES R1 haplotypes (−0.43, 95% confidence interval: −0.74, −0.12). Genetic variants in RANTES may downregulate RANTES gene expression and increase early HIV-1 plasma RNA. Because RANTES is a critical chemokine and competitively inhibits HIV-1 by binding to its receptor CCR5, treatment to enhance RANTES expression may assist in delaying the progression of AIDS by decreasing the initial viral load.
Meta-Emotion Philosophy Among Asian Indian Immigrant Mothers in the United States

We explored the meta-emotion philosophies of Indian immigrant mothers living in the Midwest region of the United States to expand the scarce literature on emotion socialization in diverse families. A total of 15 mothers of teen and preteen children participated in a meta-emotion interview, in which they were asked about their own and their children’s experiences of anger, sadness, and fear. We analyzed interview responses through an open-ended phenomenological approach and found the following major themes: familial context of emotions, subtle communication of emotions, and an overarching philosophy centering on inevitability of negative emotions and the importance of moving on. Mothers differed in how well they believed that they could move on. Overall, the present findings demonstrate the role culture plays in emotional experiences of immigrant mothers and serve as a reminder that theories based on European American families might have limited applicability to other cultural and ethnic groups.
Motion Parameter Estimation in the SAR System With Low PRF Sampling

A novel approach to motion parameter estimation with low pulse repetition frequency (PRF) sampling based on compressed sensing (CS) theory is introduced. As is known to us, when PRF is less than the Doppler spectrum bandwidth, moving targets suffer both Doppler centroid frequency ambiguity and Doppler spectrum ambiguity. Under this condition, the traditional parameter estimation method in the Doppler domain is out of action. The key of this letter converts motion parameter estimation in the synthetic aperture radar system with low PRF sampling into solving an optimization equation based on CS theory. Because moving targets in the scene can be regarded as sparse signals after clutter cancellation, an optimization algorithm based on CS theory is proposed to reconstruct sparse signals and meanwhile estimate the along-track velocities and azimuth positions of moving targets. Considering the fact that range cell migration of moving targets is not subject to PRF limitations, Radon transform is adopted to obtain unambiguous across-track velocities and range positions. Results on simulation and real data are provided to show the effectiveness of this method.
The Political is Personal: Personalized and Public Movement Frames in Turkey's Gezi Park Protests

This paper investigates the following puzzle: on the one hand, elite political discourse is increasingly personalized at the expense of the public sphere while social movement politics are increasingly making use of personalized action frames. The former is said to be depoliticizing the the public sphere while the latter is said to be politicizing the personal sphere. We examine the role of personal and public discourses in the organization of the Gezi Park protests in Turkey in 2013. The data analysis draws upon a survey of protest participants and the analysis of 3.6 million tweets collected over 10 days. The findings show that personalized discourse is more likely to give rise to the formation of political community and that, conversely, public discourse is less likely to do the same.
Mammal Hip Morphology and Function: Coxa Recta and Coxa Rotunda

Using 15 parameters, we provide a systematic description of mammal proximal femoral morphology. We established two types of proximal femoral morphology, termed coxa recta and coxa rotunda, characterized by low versus high concavity of the head–neck junction. Concavity is a measure of the sphericity of the femoral head as it meets the femoral neck that can be quantified by angular measurements. We asked whether the parameter of concavity corresponds with the classification of mammal proximal femoral morphology based on coalesced versus separate ossification patterns and locomotor patterns. Statistical analysis demonstrated a distinction between coxa recta and coxa rotunda with significant differences between the two groups in all but 3 of the 15 parameters examined. We found the most discriminating measurement between mammal hips to be the concavity of the posterior head–neck junction (beta angle). Coxa recta (small concavity) and coxa rotunda (large concavity) relate to the ossification pattern seen in proximal femoral development, and species‐specific patterns of locomotion. We interpret the two hip types to reflect optimization for strength (recta) versus mobility (rotunda). Conceptually, both hip types can be recognized in humans, where coxa recta can be related to the development of osteoarthritis. Anat Rec, 2013. © 2012 Wiley Periodicals, Inc.
Transdermal Fentanyl for Cancer Pain Repeated Dose Pharmacokinetics

BackgroundThe transdermal therapeutic system (fentanyl), or TTS(fentanyl), continuously delivers fentanyl for up to 72 h. The transdermal therapeutic system (fentanyl)-lOO delivers approximately 100 μg/h. The repeated dose pharmacokinetics of this drug using the recommended dosing interval have not been evaluated previously and were determined in the present study. MethodsBlood samples were obtained from ten opioid-tolerant cancer patients who received five applications of TTS(fentanyl) at 72-h intervals. A sample of venous blood was taken before each dose; multiple samples were taken during and after the fifth application. A gas chromatographic/mass spectrometry method was used to assay fentanyl (limit of detection 0.2 ng/ml). ResultsFor the fifth dose, the mean (SD) maximum concentration was 2.6 (1.3) ng/ml and the mean (SD) area under the serum fentanyl concentration-time curve (0–72 h) was 116.9 (59.9). Following removal of the system, the mean (SD) apparent half-life was 21.9 (8.9) h. There were no differences among the serum fentanyl concentrations measured before the second through fifth doses. Fentanyl absorption was 47% complete at 24 h, 88% complete at 48 h, and 94% complete at 72 h. The mean (SD) dose delivered during the 72-h period was 4.3 (1.1) mg. A first-dose trough concentration predicted from fifth-dose kinetics and the actual first-dose trough concentration were very similar. Adverse effects ascribed to the transdermal system were minimal. ConclusionsThese results suggest that steady-state serum concentrations are approached by the second dose of TTS(fentanyl) and that the kinetics are stable with repeated dosing. The apparent half-life following system removal is relatively long, indicating ongoing absorption from a subcutaneous depot.
The Three In-frame ATG, Clustered in the Translation Initiation Sequence of Human Factor IX Gene, Are Required for an Optimal Protein Production

Summary Three in-frame potential methionine codons have been identified in human factor IX gene and are clustered at amino acids -46, -41 and -39. In view of initiating a gene therapy approach, human factor IX production has been evaluated after modifications of these first three in-frame translation start sites. To characterize the most efficient translation initiation context, five factor IX cDNA expression vectors directed by CMV promoter-enhancer were generated. These vectors contained different starting site combinations including one, two or three ATG. A quantitative analysis of factor IX production in stably transfected CHO cells and in a rabbit reticulocyte lysate cell free system revealed the ability of all single site to generate fully active factor IX. However, the factor IX production level increased with the ATG number and the wild type (WT) cDNA bearing the 3 ATG induced the highest protein production. A truncated intron I of factor IX, previously suggested of having an expression-augmenting activity, was also placed in the WT factor IX cDNA. In stably transfected CHO cells, a 8-fold increase in protein production was measured. These results show that at least in vitro, the presence of the three ATG seems to be crucial for a maximal factor IX production. The data also suggest that both the three ATG and the truncated intron I are required for an optimal factor IX production in a perspective of a human gene therapy of haemophilia.
A new stochastic computing multiplier with application to deep convolutional neural networks

Stochastic computing (SC) allows for extremely low cost and low power implementations of common arithmetic operations. However inherent random fluctuation error and long latency of SC lead to the degradation of accuracy and energy efficiency when applied to convolutional neural networks (CNNs). In this paper we address the two critical problems of SC-based CNNs, by proposing a novel SC multiply algorithm and its vector extension, SC-MVM (Matrix-Vector Multiplier), under which one SC multiply takes just a few cycles, generates much more accurate results, and can be realized with significantly less cost, as compared to the conventional SC method. Our experimental results using CNNs designed for MNIST and CIFAR-10 datasets demonstrate that not only is our SC-based CNN more accurate and 40×∼490× more energy-efficient in computation than the conventional SC-based ones, but ours can also achieve lower area-delay product and lower energy compared with bitwidth-optimized fixed-point implementations of the same accuracy.
Egypt and the Euro‐Mediterranean partnership: Strategic choice or adaptive mechanism?

After the end of the cold war, Egypt began to pursue an active Euro‐Mediterranean policy. This policy was designed to minimize the risk of marginalization in view of Europe's growing emphasis on interests in eastern Europe and the Maghreb. Egypt's Euro‐Med policy was reflected in active campaigning for the establishment of a Mediterranean Forum and in negotiations with the European Union aimed at signing a Euro‐Egyptian Partnership agreement. Whereas the Mediterranean Forum has proved to be a useful mechanism to secure Egypt's continued involvement in Mediterranean affairs, the Euro‐Egyptian Partnership negotiations have been more difficult. The major stumbling block, in the Egyptian view, has been the EU determination to exclude the agricultural sector from the projected Euro‐Mediterranean free trade area. Most likely, Egypt will sign a partnership agreement with the European Union. However, the future course of the Euro‐Egyptian partnership will depend upon Egypt's ability to finalize the processes of e.
Heterogeneity and Limited Stock Market Participation

We derive the equilibrium interest rate and risk premiums using recursive utility with heterogeneity in a continuous time model. We solve the associated sup-convolution problem, and obtain explicit closed form solutions. The heterogeneous two-agent model is calibrated to the data of Mehra and Prescott (1985) assuming the market portfolio is not a proxy of the wealth portfolio. This results in plausible values for the preference parameters of the two agents under various assumptions for the wealth portfolio.
Rubella-specific IgM reactivity in sera from cases of infectious mononucleosis

SUMMARY Eight sera from 125 cases of infectious mononucleosis (IM) were reactive for rubella-specific IgM in an M-antibody capture radioimmunoassay. The reactivity of individual sera varied depending upon the source of the rubella antigen used in the assay. One serum gave strongly positive results with some rubella haemagglutinating antigens but negative results with others and may have contained an IgM antibody which was capable of distinguishing between strains of rubella virus. If the diagnosis of rubella is based solely on detection in solid-phase immunoassay of rubella-specific IgM, IM should be excluded.
A simple way to detect disease‐associated cellular molecular alterations from mixed‐cell blood samples

&NA; Blood is a promising surrogate for solid tissue to investigate disease‐associated molecular biomarkers. However, proportion changes of the constituent cells in the often‐used peripheral whole blood (PWB) or peripheral blood mononuclear cell (PBMC) samples may influence the detection of cell‐specific alterations under disease states. We propose a simple method, Ref‐REO, to detect molecular alterations in leukocytes using the mixed‐cell blood samples. The method is based on the predetermined within‐sample relative expression orderings (REOs) of genes in purified leukocytes of healthy people. Both the simulated and real mixed‐cell blood gene expression profiles were used to evaluate the method. Approximately 99% of the differentially expressed genes (DEGs) detected by Ref‐REO in the simulated mixed‐cell data are owing to the transcriptional alterations in leukocytes rather than the proportion changes of leukocytes. For the real mixed‐cell data, the DEGs detected by Ref‐REO in the PBMCs expression data for systemic lupus erythematosus (SLE) patients overlap significantly with the DEGs detected in the expression data of SLE CD4 + T cells and B cells and they are mainly enriched with mRNA editing and interferon‐associated genes. The detected DEGs in the PWB data for lung carcinoma patients are significantly enriched with coagulation‐associated functional categories that are closely associated with cancer progression. In conclusion, the proposed method is capable of detecting the disease‐associated leukocyte‐specific molecular alterations, using mixed‐cell blood samples, which provides simple, transferable and easy‐to‐use candidates for disease biomarkers.
Cricopharyngeal achalasia in children: indications for treatment and management options

Purpose of reviewCricopharyngeal achalasia (CPA) is an infrequently encountered but important diagnosis in pediatric dysphagia. This disorder is characterized by difficulty in feeding, regurgitation of feeds, and recurrent aspiration episodes. In this review, we discuss the current understanding of the pathophysiology of the disease and the recent developments in the diagnosis and therapeutic management of CPA. Recent findingsBecause of the rarity of the disease, the literature reporting the treatment of CPA is limited to small case series. Although open surgical treatments including cricopharyngeal myotomy have been reported in the past, recent studies advocate less-invasive endoscopic approaches, including balloon dilation, endoscopic cricopharyngeal myotomy, and botulinum toxin injections. SummaryWhen CPA is suspected as a cause of dysphagia in a child, the diagnosis can be confirmed with videofluoroscopic swallow studies that demonstrate narrowing at the region of the cricopharyngeus muscle. Treatment should be initiated for children who are unable to feed orally. Current options for treatment include botulinum toxin injections, endoscopic balloon dilation, and open or endoscopic cricopharyngeal myotomy. All techniques have shown success in the treatment of the disease. Further studies comparing treatment modalities are needed before a clear recommendation can be made.
[Cardiovascular risk of SCORE compared to Framingham. Consequences of the change proposed by the European Societies].

BACKGROUND AND OBJECTIVE The European Societies in their last update introduce substantial changes to calculate the cardiovascular risk without thinking about the practical consequences. The objective was to evaluate the agreement between the charts of cardiovascular risk of second and the third recommendations of the European Societies to classify the patients of high risk and to analyze its differences. PATIENTS AND METHOD Patients (1,227) belonging to 3 primary care centres. Risk calculated to the 10 years by means of the equation of Framingham and SCORE for countries lowers risk. A risk of Framingham > or = 20% or SCORE > or = 5% defined the high risk. RESULTS The patients of high risk were 8.4% according to Framingham and 5.5% according to SCORE and the coefficient Kappa 0.718. 41.7% of the patients of high risk disagreed: high risk Framingham and SCORE not (40 patients, 88.9%) and high SCORE and Framingham not (5 patients, 11.1%). The group high risk Framingham and SCORE not 1 is constituted by 95% of males, age 60 years, cholesterol 246.2 mg/dl and 37.5% smokers. CONCLUSIONS The chart SCORE and Framingham have an acceptable agreement, but classify from high risk different percentage of population and with different characteristics. The use of the chart of the SCORE would exclude an important group of patients with Framingham high risk.