Miracle-dz/UniFAR-FTUs huggingface dataset:
Sigma B Contributes to PrfA-Mediated Virulence in Listeria monocytogenes

ABSTRACT Transcription of the Listeria monocytogenes positive regulatory factor A protein (PrfA) is initiated from either of two promoters immediately upstream of prfA (prfAp1 and prfAp2) or from the upstream plcA promoter. We demonstrate that prfAp2 is a functional σB-dependent promoter and that a sigB deletion mutation affects the virulence phenotype of L. monocytogenes. Thus, the alternative sigma factor σB contributes to virulence in L. monocytogenes.
A fast approach for edge preserving super-resolution

In this paper we propose a fast approach for edge preserving super-resolution (SR) based on learning of contourlet coefficients. Given a low resolution test image, we first obtain an initial HR estimate i.e., a close approximation to SR image by learning the contourlet coefficients from a training database consisting of low resolution (LR) and high resolution (HR) images. The final SR image is obtained by using a regularization framework in which both the SR and the LR images are modeled as separate homogeneous Markov Random Fields (MRFs). The LR image formation process is modeled as a decimated and noisy version of the SR image and the final cost function is minimized by using a gradient descent method. Novelty of our approach lies in preserving the edges in the final SR image while using a non edge preserving MRF prior. This is definitely advantageous since it avoids the use of discontinuity preserving prior and hence the computationally taxing optimization methods. The edges in the final SR correspond to those learned from the initial HR estimate. The use of MRF on the low resolution image imposes an additional constraint on the final solution and hence we expect a better solution. In addition, we use the initial HR image for estimating the decimation matrix entries as well as for learning the corresponding MRF parameter. We show the effectiveness of the proposed approach by conducting the experiments on images captured using a real camera.
The word-length effect in reading: A review

The finding that visual processing of a word correlates with the number of its letters has an extensive history. In healthy subjects, a variety of methods, including perceptual thresholds, naming and lexical decision times, and ocular motor parameters, show modest effects that interact with high-order effects like frequency. Whether this indicates serial processing of letters under some conditions or indexes low-level visual factors related to word length is unclear. Word-length effects are larger in pure alexia, where they probably reflect a serial letter-by-letter strategy, due to failure of lexical whole-word processing and variable dysfunction in letter encoding. In pure alexia, the word-length effect is systematically related to mean naming latency, with the word-length effect becoming proportionally greater as naming latency becomes more delayed in severe cases. Other conditions may also generate enhanced word-length effects. This occurs in right hemianopia: Computer simulations suggest a criterion of 160 ms/letter to distinguish hemianopic dyslexia from pure alexia. Normal reading development is accompanied by a decrease in word-length effects, whereas persistently elevated word-length effects are characteristic of developmental dyslexia. Little is known about word-length effects in other reading disorders. We conclude that the word-length effect captures the efficiency of the perceptual reading process in development, normal reading, and a number of reading disorders, even if its mechanistic implications are not always clear.
Posttraumatic Stress Disorder's Underlying Dimensions and Their Relation With Impulsivity Facets

Abstract Research indicates a significant relationship between posttraumatic stress disorder (PTSD) and impulsivity (Kotler, Julian, Efront, and Amir, J Nerv Ment Dis 189:162–167, 2001; Ledgerwood and Petry, J Trauma Stress 19:411–416, 2006). The present study assessed relations between PTSD symptom clusters and impulsivity subscales in an effort to assess the specific impulsivity component most related to PTSD's alterations in arousal/reactivity and alterations in mood/cognitions symptoms. In the current study, the PTSD Checklist for Diagnostic and Statistical Manual of Mental Disorders, 5th Edition, and the UPPS Impulsivity Scale were administered to a sample of 412 nonclinical subjects with a trauma history. Results indicated that PTSD's alterations in arousal/reactivity and mood/cognition factors were most related to impulsivity's sensation-seeking tendency compared with other impulsivity components. Results highlight the importance of assessing and addressing (1) sensation-seeking tendencies and (2) urges to act impulsively when experiencing negative affect in trauma treatment. Furthermore, it is possible that sensation-seeking tendencies are primarily driving the comorbidity between PTSD and certain impulsive behaviors.
IGF2R polymorphisms and risk of esophageal and gastric adenocarcinomas

The mannose‐6‐phosphate/insulin‐like growth factor 2 receptor (M6P/IGF2R) encodes a protein that plays a critical role in tumor suppression, in part by modulating bioavailability of a potent mitogen, insulin‐like growth factor‐2 (IGF2). We tested the hypothesis that the common nonsynonymous genetic variants in M6P/IGF2R c.901C > G (Leu > Val) in exon 6 and c.5002G > A (Gly > Arg) in exon 34 are associated with risk of esophageal and gastric cancers. Study participants in this population‐based study comprise 197 controls and 182 cases, including 105 with esophageal‐gastric cardia adenocarcinoma (EGA), 57 with noncardia gastric adenocarcinoma and 20 with esophageal squamous (ES) cell carcinoma. Among white males, odds ratios (ORs) were elevated in relation to carrying at least 1 c.901C > G allele for EGA [OR = 1.9; 95% confidence intervals (CIs) = 1.0–3.6] and noncardia gastric cancer (OR = 2.5; 95% CI = 1.2–5.5), but not ES. Exploratory subgroup analyses suggested that associations between EGA and this variant were stronger among irregular or nonusers of nonsteroidal anti‐inflammatory drugs (NSAIDs) (OR = 2.3; 95% CI = 1.2–4.2) and cigarette smokers (OR = 2.1; 95% CI = 1.0–4.2). An association between carrying the c.5002G > A genotype and EGA was not evident. These findings suggest that nonsynonymous polymorphisms in M6P/IGF2R may contribute to the risks of EGA and noncardia adenocarcinomas. Larger studies are required to confirm these findings. © 2009 UICC
The use of benchmarking to identify top performing critical care units: a preliminary assessment of their policies and practices.

PURPOSE To describe the policies and practices of intensive care units (ICUs) with good patient survival and highly efficient resource use and to identify relevant variables for future investigation. MATERIALS AND METHODS We used clinical data for 359,715 patients from 108 ICUs to compare the ratios of actual with Acute Physiology and Chronic Health Evaluation (APACHE) III predicted hospital mortality, ICU and hospital stay, and the proportion of low-risk monitor patients. The best performing ICUs (top 10%) were defined by a mortality ratio of 1.0 or less, and either the lowest ratio for ICU stay, hospital stay, or percentage of low-risk monitor patients. The medical and nursing directors of top performing ICUs completed a questionnaire to describe their unit's structure policies and practices. RESULTS Among the 108 ICUs, 61 (56%) had a ratio of actual to predicted hospital mortality of 1.0 or less and the best performing units had ICU stay ratios of 0.62 to 0.79, hospital stay ratios of 0.73 to 0.77, and admitted 10% to 38% low-risk monitor patients. ICU structure varied among the best performing ICUs. Units with the shortest ICU and hospital stay had alternatives to intensive care, methods to facilitate patient throughput, used multiple protocols for high-volume diagnoses and care processes, and continuously monitored resource use. Units with the fewest low-risk monitor patients screened potential admissions, had intermediate care areas, extended-stay recovery rooms, and care pathways for high-volume diagnoses. CONCLUSIONS Benchmarking can be used to identify ICUs with good patient survival and highly efficient resource use. The combination of policies and practices used by these units might improve resource use in other ICUs.
Seam Carving for Content Aware VideoCompression

Seam-carving has achieved the most widespread use with the blossom of content-aware resizing methods. This paper proposes the video retargeting method where the aspect ratio and the size of the video are reduced. It deals with the spatial and temporal coherence for the purpose of resizing videos. The proposed algorithm is mainly based on matching-area-based temporal energy adjustment. Each frame is seam carved and the corresponding optimal pixels are removed. In order to track the object it previously carved, the temporal energy adjustment is used. So carving the seam on different objects in two consecutive frames is greatly reduced. The spatially and temporally continuous resized images are obtained after this process. The seam carved frames are enhanced by both global and local process on luminance and chrominance components of the image by using the virtual histogram distribution method. The output video with reduction in both size and memory and also with the better visual quality can be obtained.
Angular aspects of microwave single scattering albedo from tapered vegetation constituents

In microwave radiometry of vegetation canopies, the most important contributor to the emission is the long vegetation constituents such as tree trunks and primary branches. Their scattering pattern depends strongly on both shape and orientation. Since they are a dominant contributor to the emission, their scattering pattern must be taken into account properly when solving radiative transfer (RT) equations. A uniform dielectric cylinder model provides a simple model for a tree trunk and primary branches, which are mostly bent, not straight, and not symmetrical with respect to ground in nature. In this paper, the effect of tapering the trunk and branch diameter with height on the single scattering albedo is investigated with numerical simulations of a vertical cone and a vertical cylinder of the same height and volume. The preliminary results show that the single scattering albedo is not symmetric with respect to 90° of incidence angle for those objects such as tapered vegetation components. Its implications on the zero-order RT solutions such as tau-omega model will be also discussed.
Structure and function of the SWIRM domain, a conserved protein module found in chromatin regulatory complexes

The SWIRM domain is a module found in the Swi3 and Rsc8 subunits of SWI/SNF-family chromatin remodeling complexes, and the Ada2 and BHC110/LSD1 subunits of chromatin modification complexes. Here we report the high-resolution crystal structure of the SWIRM domain from Swi3 and characterize the in vitro and in vivo function of the SWIRM domains from Saccharomyces cerevisiae Swi3 and Rsc8. The Swi3 SWIRM forms a four-helix bundle containing a pseudo 2-fold axis and a helix–turn–helix motif commonly found in DNA-binding proteins. We show that the Swi3 SWIRM binds free DNA and mononucleosomes with high and comparable affinity and that a subset of Swi3 substitution mutants that display growth defects in vivo also show impaired DNA-binding activity in vitro, consistent with a nucleosome targeting function of this domain. Genetic and biochemical studies also reveal that the Rsc8 and Swi3 SWIRM domains are essential for the proper assembly and in vivo functions of their respective complexes. Together, these studies identify the SWIRM domain as an essential multifunctional module for the regulation of gene expression.
El proceso de observación: El caso de la práctica supervisada en inglés en la Sede de Occidente, Universidad de Costa Rica

El siguiente articulo tiene como objetivo primordial compartir con la comunidad academica y aquella relacionada con el desarrollo de actividades que implican la supervision de la labor docente y el proceso de observacion que se realiza a los profesores practicantes2 de la carrera de Bachillerato en la ensenanza del Ingles de la Sede de Occidente, Universidad de Costa Rica, por un periodo de tres a cuatro meses, aproximadamente. Durante este lapso de tiempo, los profesores practicantes3 son ubicados en instituciones de ensenanza secundaria de la Direccion de Educacion de Occidente, para que efectuen la experiencia docente que les ayuda a fortalecer y desarrollar una serie de destrezas, habilidades, actitudes y valores, necesarios para ejercer de forma adecuada la labor docente como futuros profesionales en el campo de la educacion. Durante este periodo, los estudiantes son observados regularmente por el profesor supervisor, quien mediante una escala de calificacion, evalua el trabajo del profesor practicante. Esta escala no solo facilita la evaluacion del trabajo que realiza el profesor practicante, sino que permite a la vez, reflexionar a partir de un dialogo entre el supervisor y el profesor practicante, acerca del accionar general de las lecciones observadas, propiciando el crecimiento profesional de ambas partes por medio de esta dinamica reflexiva. El documento toma como marco de referencia diferentes posiciones de autores y la experiencia personal, de mas de diez anos de trabajo continuo en esta area del quehacer y campo de estudio, de la autora.
Evaluation of contextual descriptors for HMM-based speech synthesis in French

In HTS, a HMM-based speech synthesis system, about fifty contextual factors are introduced to label a segment to synthesize English utterances. Published studies indicate that most of them are used for clustering the prosodic component of speech. Nevertheless, the influence of all these factors on modeling is still unclear for French. The work presented in this paper deals with the analysis of contextual factors on acoustic parameters modeling in the context of a French synthesis purpose. Two objective and one subjective methodologies of evaluation are carried out to conduct this study. The first one relies on a GMM-approach to achieve a global evaluation of the synthetic acoustic space. The second one is based on a pairwise distance determined according to the acoustic parameter evaluated. Finally, a subjective evaluation is conducted to complete this study. Experimental results show that using phonetic context improves the overall spectrum and duration modeling and using syllable informations improves the F0 modeling. However other contextual factors do not significantly improve the quality of the HTS models.
On energy conservation in extended magnetohydrodynamics

A systematic study of energy conservation for extended magnetohydrodynamic (MHD) models that include Hall terms and electron inertia is performed. It is observed that commonly used models do not conserve energy in the ideal limit, i.e., when viscosity and resistivity are neglected. In particular, a term in the momentum equation that is often neglected is seen to be needed for conservation of energy.
The end of the shrink

Andrew Kahng, a professor at the University of California, San Diego, and an expert on high-performance chip design, says the chip industry has made it a priority to keep up the pace of Moore's Law, ensuring that manufacturers can continue to build and release new product families while using a new process every 18 to 24 months. This means there hasn't been time to explore a number of design tricks that could be used to cut down on power or boost performance. “When you're on that kind of schedule, you don't have time to optimize things,” he says. As the value of the simple shrink decreases, he says, chipmakers should then be able to revisit their designs and find chip-improving approaches they may have missed or else left on the cutting-room floor.
Adversarial attacks in the twin-code framework

Ensuring the security and reliability of the stored data in a Distributed Storage System (DSS) is a pivotal issue in a distributed storage network. The storage system must be secured against passive and active types of attacks for efficient protection of the stored data. The aim is achieving satisfactory level of security of the storage system and at the same time maintaining the desired level of reliability, which arises when there are node failures. In our work we apply this concept in a Twin-code framework, in presence of an intruder who can observe and modify the stored data on the networks nodes. We are making a new code construction, which is simultaneously secure against passive and active attacks and at the same time satisfies particular bound for reliability. Moreover, for this construction we are proving the level of security under the above mentioned constraints.
Characterization of an Immunogenic Mutation in a Patient with Metastatic Triple-Negative Breast Cancer

Purpose: The administration of autologous tumor-infiltrating lymphocytes (TILs) can mediate durable tumor regressions in patients with melanoma likely based on the recognition of immunogenic somatic mutations expressed by the cancer. There are limited data regarding the immunogenicity of mutations in breast cancer. We sought to identify immunogenic nonsynonymous mutations in a patient with triple-negative breast cancer (TNBC) to identify and isolate mutation-reactive TILs for possible use in adoptive cell transfer. Experimental Design: A TNBC metastasis was resected for TIL generation and whole-exome sequencing. Tandem minigenes or long 25-mer peptides encoding selected mutations were electroporated or pulsed onto autologous antigen-presenting cells, and reactivity of TIL was screened by upregulation of CD137 and IFNγ ELISPOT. The nature of the T-cell response against a unique nonsynonymous mutation was characterized. Results: We identified 72 nonsynonymous mutations from the tumor of a patient with TNBC. CD4+ and HLA-DRB1*1501–restricted TILs isolated from this tumor recognized a single mutation in RBPJ (recombination signal binding protein for immunoglobulin kappa J region). Analysis of 16 metastatic sites revealed that the mutation was ubiquitously present in all samples. Conclusions: Breast cancers can express naturally processed and presented unique nonsynonymous mutations that are recognized by a patient's immune system. TILs recognizing these immunogenic mutations can be isolated from a patient's tumor, suggesting that adoptive cell transfer of mutation-reactive TILs could be a viable treatment option for patients with breast cancer. Clin Cancer Res; 23(15); 4347–53. ©2017 AACR.
Protein, and dietary fiber-rich new foodstuff from brewer's spent grain increased excretion of feces and jejunum mucosal protein content in rats.

We made a new protein-rich and fibrous foodstuff by milling and sieving brewer's spent grain. This product contained glutamine-rich protein and the dietary fibers cellulose, hemicellulose, and lignin. We called this product germinated barley foodstuff (GBF). GBF had the effect of increasing fecal dry weight and number of feces and of significantly increasing jejunum mucosal protein content in rats over the cellulose group. In GBF, Gln-rich protein is thought to have strong chemical bonds with dietary fiber, an arrangement which would be important in the way these physiological effects arise. As dietary supplements of Gln or dietary fibers (i.e., cellulose, hemicellulose, lignin, and a mixture of these) did not improve defecation and jejunum mucosal protein simultaneously, the effects of GBF are thought to be caused not by the individual ingredients, but by the combination of protein with dietary fiber.
Logically controlled energy management circuit

An effective energy management circuit based on switching mode is presented. Switches are monitored and controlled logically. The energy management circuit offers a direct supply of the application by the energy source. Excess of energy is stored in storage units (two supercapacitors), to be used when no enough energy is generated by the source. The evaluation of the circuit is based on its power consumption showing low electrical needs (lower than 6 μA at 3.50 V). Solar energy represents the energy input of the circuit. However, through simple adjustment, our circuit is adaptable for different energy sources.
Ultrasound‐based transient elastography for the detection of hepatic fibrosis in patients with recurrent hepatitis C virus after liver transplantation: A systematic review and meta‐analysis

Ultrasound‐based transient elastography (TE) is a promising noninvasive alternative to liver biopsy for the detection of hepatic fibrosis due to recurrent hepatitis C virus (HCV) after liver transplantation (LT). However, its overall test performance in various settings remains unknown. The aim of this study was to perform a systematic review and diagnostic accuracy meta‐analysis of studies comparing ultrasound‐based TE to liver biopsy for the detection of hepatic fibrosis due to a recurrent HCV infection after LT. Electronic and manual bibliographic searches (including scientific abstracts) were performed to identify potential studies. A meta‐analysis was conducted to generate pooled estimates of the sensitivity values, specificity values, likelihood ratios, and diagnostic odds ratios of individual studies. The extent of the heterogeneity and the reasons for it were assessed. Six fully published studies were identified for analysis. Five studies that evaluated significant fibrosis were identified. Among these studies, the pooled estimates were 83% for sensitivity [95% confidence interval (CI) = 77%‐88%], 83% for specificity (95% CI = 77%‐88%), 4.95 for the positive likelihood ratio (95% CI = 3.4‐7.2), 0.17 for the negative likelihood ratio (95% CI = 0.09‐0.35), and 30.5 for the diagnostic odds ratio (95% CI = 12.8‐72.4). For the 5 studies that assessed cirrhosis, the pooled estimates were 98% for sensitivity (95% CI = 90%‐100%), 84% for specificity (95% CI = 80%‐88%), 7 for the positive likelihood ratio (95% CI = 2.8‐17.3), 0.06 for the negative likelihood ratio (95% CI = 0.02‐0.19), and 130 for the diagnostic odds ratio (95% CI = 36.5‐462.1). A diagnostic threshold (or cutoff value) bias was identified as an important cause of heterogeneity for the pooled results of both patient groups. In conclusion, ultrasound‐based TE has excellent diagnostic accuracy for identifying cirrhosis due to a recurrent HCV infection after LT. The detection of significant fibrosis is more accurate for these patients versus patients whose native liver is chronically infected with HCV. Liver Transpl 18:323–331, 2012. © 2012 AASLD.