Miracle-dz/UniFAR-FTUs huggingface dataset:
RNA Helicase MUT-14-Dependent Gene Silencing Triggered in C. elegans by Short Antisense RNAs

Posttranscriptional gene silencing in Caenorhabditis elegans results from exposure to double-stranded RNA (dsRNA), a phenomenon designated as RNA interference (RNAi), or from co-suppression, in which transgenic DNA leads to silencing of both the transgene and the endogenous gene. Here we show that single-stranded RNA oligomers of antisense polarity can also be potent inducers of gene silencing. As is the case for co-suppression, antisense RNAs act independently of the RNAi genes rde-1 andrde-4 but require the mutator/RNAi gene mut-7 and a putative DEAD box RNA helicase, mut-14. Our data favor the hypothesis that gene silencing is accomplished by RNA primer extension using the mRNA as template, leading to dsRNA that is subsequently degraded.
Muscle performance after the menopause

The timing of the menopause transition has remained fairly constant throughout history. It represents a milestone in female health and, after passing through it, women experience increased musculoskeletal and cardiovascular morbidity. Muscle performance is an important determinant of functional capacity and quality of life among the elderly and is also involved in the maintenance of balance. Therefore, good muscle strength can prevent fragility fractures and lessen the burden of osteoporosis. Muscle strength begins to decline during the perimenopausal years and this phenomenon seems to be partly estrogen dependent. Randomized controlled trials have indicated that hormone replacement therapy may prevent a decline in muscle performance, although the exact mechanism of estrogen-dependent sarcopenia remains to be clarified. Exercises have been shown to improve postmenopausal muscle performance and hormone replacement therapy may also potentiate these beneficial effects. Improvement or maintenance of muscle strength alone, however, may not be considered as a primary indication for long-term hormone replacement therapy in view of current knowledge of its risks and benefits. Work history and educational background may be associated with postmenopausal muscle performance, which itself has unique associations with skeletal and cardiovascular diseases.
The Generalized TTL Security Mechanism (GTSM)

The use of a packet's Time to Live (TTL) (IPv4) or Hop Limit (IPv6) to protect a protocol stack from CPU-utilization based attacks has been proposed in many settings (see for example, RFC 2461). This document generalizes these techniques for use by other protocols such as BGP (RFC 1771), Multicast Source Discovery Protocol (MSDP), Bidirectional Forwarding Detection, and Label Distribution Protocol (LDP) (RFC 3036). While the Generalized TTL Security Mechanism (GTSM) is most effective in protecting directly connected protocol peers, it can also provide a lower level of protection to multi-hop sessions. GTSM is not directly applicable to protocols employing flooding mechanisms (e.g., multicast), and use of multi-hop GTSM should be considered on a case-by-case basis.
Quantification of diverse subcellular immunohistochemical markers with clinicobiological relevancies: validation of a new computer‐assisted image analysis procedure

Tissue microarray technology and immunohistochemical techniques have become a routine and indispensable tool for current anatomical pathology diagnosis. However, manual quantification by eye is relatively slow and subjective, and the use of digital image analysis software to extract information of immunostained specimens is an area of ongoing research, especially when the immunohistochemical signals have different localization in the cells (nuclear, membrane, cytoplasm). To minimize critical aspects of manual quantitative data acquisition, we generated semi‐automated image‐processing steps for the quantification of individual stained cells with immunohistochemical staining of different subcellular location. The precision of these macros was evaluated in 196 digital colour images of different Hodgkin lymphoma biopsies stained for different nuclear (Ki67, p53), cytoplasmic (TIA‐1, CD68) and membrane markers (CD4, CD8, CD56, HLA‐Dr). Semi‐automated counts were compared to those obtained manually by three separate observers. Paired t‐tests demonstrated significant differences between intra‐ and inter‐observer measurements, with more substantial variability when the cellular density of the digital images was > 100 positive cells/image. Overall, variability was more pronounced for intra‐observer than for inter‐observer comparisons, especially for cytoplasmic and membrane staining patterns (P < 0.0001 and P = 0.050). The comparison between the semi‐automated and manual microscopic measurement methods indicates significantly lower variability in the results yielded by the former method. Our semi‐automated computerized method eliminates the major causes of observer variability and may be considered a valid alternative to manual microscopic quantification for diagnostic, prognostic and therapeutic purposes.
The effects of motivating interventions on rehabilitation outcomes in children and youth with acquired brain injuries: A systematic review

Abstract Primary objective: To systematically review the evidence of the effects of motivating rehabilitation interventions on outcomes in children with acquired brain injury (ABI). Methods: A literature search of six databases was conducted to identify intervention studies published until July 2013. The American Academy for Cerebral Palsy and Developmental Medicine (AACPDM) systematic review methodology was used as a framework. Two reviewers independently extracted data and assessed level of evidence and quality of studies. Results: Of 891 records initially retrieved, 166 were screened by abstract and 31 by full text; 10 studies comprised of five randomized controlled trials, two case series and three single subject research design studies met the inclusion criteria. Studies fell into three intervention categories: (1) token economy based interventions; (2) virtual reality (VR); and (3) memory and attention interventions. Conclusions: A paucity of evidence has examined the effects of rehabilitation interventions with a motivational component. Token economies can significantly enhance memory and response inhibition performance in children with ABI. VR systems are motivating, yet findings are limited by the lack of use and availability of psychometrically evaluated measures of motivation. Findings point to the need for further research to evaluate the effects of motivation-based interventions.
Psoriasis Vulgaris with or without Arthritis and Independent of Disease Severity or Duration Is a Risk Factor for Hypercholesterolemia

Background: Psoriasis (Ps) has been associated with an increased incidence of cardiovascular disease. Interesting epidemiological evidence suggests associations between Ps and dyslipidemia (DL), a well-established risk factor for cardiovascular disease. Objective: This study aimed to investigate the association between Ps and multiple measurements of DL, which include levels of triglycerides (TGs), low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol and total cholesterol (TCh). We also studied the relationship between DL and disease duration. Methods: A prospective hospital-based study was conducted. A total of 661 Caucasian patients with chronic plaque Ps and 661 sex- and age-matched controls were enrolled. Results: Multivariate analysis showed that in psoriatic patients the odds ratio (OR) of TCh >200 mg/dl was 1.406 (95% confidence interval 1.115-1.173), the OR of LDL cholesterol >130 mg/dl was 1.375 (95% confidence interval 1.088-1.738), the OR of HDL cholesterol <40 mg/dl was 0.881 (95% confidence interval 0.599-1.297), and the OR of TGs >150 mg/dl was 1.041 (95% confidence interval 0.783-1.385). We did not find a relationship between lipid levels and disease duration. Conclusion: Based on our population Ps is associated with alterations in TCh and LDL cholesterol, but not in TGs and HDL cholesterol, when ATP III panel levels are used. These alterations are not related to disease duration.
CARACTERIZACIÓN DEL CONSUMIDOR DE TORTILLA EN EL ESTADO DE MÉXICO

La tortilla es considerada el alimento principal de los mexicanos, provee energia por su contenido alto de carbohidratos y aporta calcio, potasio, fosforo, fibra, proteinas y algunas vitaminas. El objetivo del presente estudio fue caracterizar a los consumidores de tortilla del Estado de Mexico para identificar el tipo y las caracteristicas del producto que demandan y cuantificar la correlacion de estos aspectos con los niveles de ingreso y consumo. La metodologia consistio del algoritmo CHAID (Chi-squared Automatic Interaction Detection) y pruebas de asociacion mediante la distribucion c2 y la estimacion de un modelo de regresion ordinal. La informacion se obtuvo mediante una encuesta semi-estructurada aplicada a 269 individuos. Para analizar la informacion se usaron tablas de contingencia y frecuencias relativas, y los coeficientes que resultaron significativos para el modelo estimado. El analisis mostro que el ingreso y consumo medios estan correlacionados positiva y significativamente (74.7 %) con el consumo de tortilla elaborada con maiz nixtamalizado y con la preferencia por la de maiz blanco (81.85 %), y el ingreso alto con consumo medio esta correlacionado significativamente (66.7o%) con la compra en tortilleria de barrio.
Architecture and Function of the Human Endonucleases RNase P and RNase MRP

In the past decade, important advances have been made in our knowledge of the composition of human RNase MRP and RNase P complexes. Both ribonucleoprotein particles function as endonucleases and contain RNA components that are structurally related. RNase MRP has been suggested to be involved in the processing of precursor rRNA; RNase P, in the maturation of tRNA. Here we give an overview of current data on the structure and function of human RNase MRP and RNase P particles, with emphasis on their molecular composition. At present, seven protein subunits, probably all associated with both ribonucleoprotein particles, have been isolated and their corresponding cDNAs cloned. Although no known structural motifs can be identified in the amino acid sequences of these proteins, the majority is clearly rich in basic residues. For two protein subunits, a cluster of basic amino acids have been shown to be involved in nucleolar accumulation, whereas another protein, which lacks such a region, probably enters the nucleolus by way of a piggyback mechanism. The binding regions for several of the protein subunits on the RNA have been identified, and the data have been used to create a putative structural model for the RNase MRP particle. The rather obscure situation concerning the association of the autoantigenic Th‐40 protein and its possible relationship with one of the subunits, Rpp38, is discussed.
Purification and Crystallization Reveal Two Types of Interactions of the Fusion Protein Homotrimer of Semliki Forest Virus

ABSTRACT The fusion proteins of the alphaviruses and flaviviruses have a similar native structure and convert to a highly stable homotrimer conformation during the fusion of the viral and target membranes. The properties of the alpha- and flavivirus fusion proteins distinguish them from the class I viral fusion proteins, such as influenza virus hemagglutinin, and establish them as the first members of the class II fusion proteins. Understanding how this new class carries out membrane fusion will require analysis of the structural basis for both the interaction of the protein subunits within the homotrimer and their interaction with the viral and target membranes. To this end we report a purification method for the E1 ectodomain homotrimer from the alphavirus Semliki Forest virus. The purified protein is trimeric, detergent soluble, retains the characteristic stability of the starting homotrimer, and is free of lipid and other contaminants. In contrast to the postfusion structures that have been determined for the class I proteins, the E1 homotrimer contains the fusion peptide region responsible for interaction with target membranes. This E1 trimer preparation is an excellent candidate for structural studies of the class II viral fusion proteins, and we report conditions that generate three-dimensional crystals suitable for analysis by X-ray diffraction. Determination of the structure will provide our first high-resolution views of both the low-pH-induced trimeric conformation and the target membrane-interacting region of the alphavirus fusion protein.
Yeast Ull1/Siz1 Is a Novel SUMO1/Smt3 Ligase for Septin Components and Functions as an Adaptor between Conjugating Enzyme and Substrates*

SUMO1/Smt3, a ubiquitin-like protein modifier, is known to conjugate to other proteins and modulate their functions in various important processes. Similar to the ubiquitin conjugation system, SUMO/Smt3 is transferred to substrate lysine residues through the thioester cascade of E1 (activating enzyme) and E2 (conjugating enzyme). In our previous report (Takahashi, Y., Toh-e, A., and Kikuchi, Y. (2001) Gene 275, 223–231), we showed that Siz1/Ull1 (YDR409w) of budding yeast, a member of the human PIAS family containing a RING-like domain, is a strong candidate for SUMO1/Smt3 ligase because the SUMO1/Smt3 modification of septin components was abolished in the ull1 mutant and Ull1 associated with E2 (Ubc9) and the substrates (septin components) in immunoprecipitation experiments. Here we have developed an in vitro Smt3 conjugation system for a septin component (Cdc3) using purified recombinant proteins. In this system, Ull1 is additionally required as well as E1 (Sua1·Uba2 complex), E2 (Ubc9), and ATP. A cysteine residue of the RING-like domain was essential for the conjugation both in vivo and in vitro. Furthermore, a region containing the RING-like domain directly interacted with Ubc9 and Cdc3. Thus, this SUMO/Smt3 ligase functions as an adaptor between E2 and the target proteins.
An Innovative World Language Centre : Challenges for the Use of Language Technology

The Vigdis International Centre of Multilingualism and Intercultural Understanding at the University of Iceland will work under the auspices of UNESCO. The main objective of the Centre is to promote linguistic diversity and to raise awareness of the importance of multilingualism. The focus will be on research on translations, foreign language learning, language policy and language planning. The centre will also serve as a platform for promoting collaborative activities on languages and cultures, in particular, organizing exhibitions and other events aimed at both the academic community and the general public. The Centre will work in close collaboration with the national and international research community. The Centre aims to create state-of-the-art infrastructure, using Language Technology resources in research and academic studies, in particular in translations and language learning (Computer-Assisted Language Learning). In addition, the centre will provide scholars with a means to conduct corpus-based research for synchronic investigations and for comparative studies. The Centre will also function as a repository for language data corpora. Facilities will be provided so that these corpora can be used by the research community on site and online. Computer technology resources will also be exploited in creating tools and exhibitions for the general audience.
Effect of stage 0 sporulation mutations on subtilisin expression

Subtilisin expression as a function of growth and sporulation was determined using a presubtilisin-beta-galactosidase gene fusion. An approximately 500-base-pair region upstream of the subtilisin gene and including the first eight codons of the presubtilisin protein was fused at the eighth codon of beta-galactosidase in the integrative vector pJF751. This gene fusion does not carry a signal sequence, and therefore its synthesis is uncoupled from maturation of presubtilisin. The fusion protein gene was integrated into a variety of recipient strains to test for the effect of various mutations on the initial rate of presubtilisin-beta-galactosidase synthesis. Among the spo0 mutations tested, the spo0A mutations showed a strong, 10-fold decrease in the rate of beta-galactosidase synthesis. This effect of the spo0A mutations was not evident when the presubtilisin-beta-galactosidase fusion was present on a multicopy plasmid. The sacU mutation, which was known to increase the extracellular level of levansucrase and proteases, was found to increase the synthesis of the presubtilisin-beta-galactosidase gene fusions 7-fold, and the hpr mutations were shown to increase the rate of presubtilisin-beta-galactosidase gene fusions 17-fold, indicating that these mutations influence either transcription or translation of the presubtilisin gene. However, the effect of these mutations was only observed in the stationary phase of growth, indicating they did not render synthesis constitutive. By using multicopy plasmids and an integrated gene fusion, it was shown that there is likely to be a titratable repressor controlling subtilisin synthesis.
A Comparative Approach To Web Evaluation And Website Evaluation Methods

There is still a lack of an engineering approach for building Web systems, and the field of measuring the Web is not yet mature. In particular, there is an uncertainty in the selection of evaluation methods, and there are risks of standardizing inadequate evaluation practices. It is important to know whether we are evaluating the Web or specific website(s). We need a new categorization system, a different focus on evaluation methods, and an in-depth analysis that reveals the strengths and weaknesses of each method. As a contribution to the field of Web evaluation, this study proposes a novel approach to view and select evaluation methods based on the purpose and platforms of the evaluation . It has been shown that the choice of the appropriate evaluation method (s) depends greatly on the purpose of the evaluation .
Molecular epidemiology of Escherichia coli O157:H7 strains by bacteriophage lambda restriction fragment length polymorphism analysis: application to a multistate foodborne outbreak and a day-care center cluster

Genomic DNAs prepared from 168 isolates of Escherichia coli O157:H7 were analyzed for restriction fragment length polymorphisms on Southern blots probed with bacteriophage lambda DNA. The isolates analyzed included strains from a recent large multistate outbreak of E. coli O157:H7 infection associated with consumption of poorly cooked beef in restaurants, a day-care center cluster, and temporally and geographically unrelated isolates. E. coli O157:H7 isolates recovered from the incriminated meat and from 61 (96.8%) of 63 patients from Washington and Nevada possessed identical lambda restriction fragment length patterns. The lambda restriction fragment length polymorphisms observed in 11 (91.7%) of 12 day-care center patients were identical, but they differed from that of the strain associated with the multistate outbreak. E. coli O157:H7 from 42 patients temporally or geographically unrelated to either cluster of infection possessed unique and different lambda restriction fragment length patterns, except for paired isolates from three separate clusters of infection. These data demonstrate that the hybridization of DNA digests of E. coli O157:H7 with radiolabelled bacteriophage lambda DNA can be a useful, stable, and discriminatory epidemiologic tool for analyzing the linkage between strains of E. coli O157:H7.
Paediatric patients with a tracheostomy: a multicentre epidemiological study

Changes in the indications for tracheostomy in children have led to the progressively greater involvement of the paediatric pulmonologist in the care of these patients. The aim of this study was to review the current profile of tracheostomised children in Spain. We undertook a longitudinal, multicentre study over 2 yrs (2008 and 2009) of all patients aged between 1 day and 18 yrs who had a tracheostomy. The study, involving 18 Spanish hospitals, included 249 patients, of whom 150 (60.2%) were <1 yr of age. The main indications for the procedure were prolonged ventilation (n=156, 62.6%), acquired subglottic stenosis (n=34, 13.6%), congenital or acquired craniofacial anomalies (n=25, 10%) and congenital airway anomalies (n=24, 9.6%). The most frequent underlying disorders were neurological diseases (n=126, 50.6%) and respiratory diseases (n=98, 39.3%). Over the 2-yr study period, 92 (36.9%) children required ventilatory support, and decannulation was achieved in 59 (23.7%). Complications arose in 117 patients (46.9%). Mortality attributed to the underlying condition was 12.5% and that related directly to the tracheostomy was 3.2%. Respiratory complexity of tracheostomised children necessitates prolonged, multidisciplinary follow-up, which can often extend to adulthood.
The environmental dependence of neutral hydrogen in the GIMIC simulations

We use the Galaxies-Intergalactic Medium Interaction Calculation (GIMIC) cosmological hydrodynamic simulation at z = 0 to study the distribution and environmental dependence of neutral hydrogen (H I) gas in the outskirts of simulated galaxies. This gas can currently be probed directly in, for example, Lyα absorption via the observation of background quasars. Radio facilities, such as the Square Kilometre Array, will provide a complementary probe of the diffuse H I in emission and will constrain the physics underpinning the complex interplay between accretion and feedback mechanisms which affect the intergalactic medium. We extract a sample of 488 galaxies from a resimulation of the average cosmic density GIMIC region. We estimate the neutral hydrogen content of these galaxies and the surrounding intergalactic medium within which they reside. We investigate the average H I radial profiles by stacking the individual profiles according to both mass and environment. We find high H I column densities at large impact parameters in group environments and markedly lower H I densities for non-group galaxies. We suggest that these results likely arise from the combined effects of ram pressure stripping and tidal interactions present in group environments.
Purification and characterization of a 1-deoxy-D-xylulose 5-phosphate synthase from Cymbopogon flexuosus

Here we report purification and characterization of the enzyme 1-deoxy-D-xylulose 5-phosphate synthase (DXS) of the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway from lemongrass (Cymbopogon flexuosus) leaves. The DXS catalyzes the condensation of pyruvate and glyceraldehyde 3-phosphate (G3P) to produce 1-deoxy-D-xylulose 5-phosphate (DOXP), which is the first and rate-limiting step of the MEP pathway. It is the main flux-controlling step and an attractive target to manipulate the formation of the MEP-derived products. The DXS was extracted from immature (15 days old) leaves of lemongrass cv. Suvarna and purified to homogenity using ion exchange DEAE column and gel filtration (Sephadex G-150) chromatography. The purified DXS was referred as CfDXS. The CfDXS had specific activity 8.56 U/mg. The Km values for the two substrates, pyruvate and G3P were 4.4 and 8.8 μM, respectively and for the cofactor TPP 62 μM. The Vmax of the CfDXS was 20 μmol/min. The optimum pH and temperature of the CfDXS were 7.5 and 40 °C, respectively. The CfDXS activity enhanced significantly in the presence of Mg2+ (1 mM), whereas affected moderately by Mn2+ and Zn2+ (1 mM each). The enzyme was purified upto 11.64 fold with an yield of 32.34%. Its molecular weight was 130 kDa. The DXS was quite stable and retaining more than 80% of the initial activity upon storage at 4 °C in 100 mM Tris-HCl buffer (pH 8) for one month.