Miracle-dz/UniFAR-FTUs huggingface dataset:
The NFATc2 Gene Is Involved in a Novel Cloned Translocation in a Ewing Sarcoma Variant That Couples Its Function in Immunology to Oncology

Purpose: Ewing sarcoma is an aggressive sarcoma and is the second most common bone sarcoma in childhood. Disease-specific t(11;22) (∼85-90%), t(21;22) (∼5-10%), or rarer variant translocations with the involvement of chromosome 22 (∼5%) are present. At the gene level, the EWSR1 gene fuses with FLI1, ERG, or other ETS transcription factor family members. Thus far, no Ewing sarcoma has been identified with a fusion to transcription factors other than ETS. Experimental Design: Using molecular tools such as multicolor fluorescence in situ hybridization and array comparative genomic hybridization, a ring chromosome containing chromosomes 20 and 22 was identified in four Ewing sarcoma cases. The breakpoint was mapped with (fiber-) fluorescence in situ hybridization and reverse transcription-PCR followed by sequencing of the fusion partners. Results: Molecular karyotyping showed the translocation and amplification of regions of chromosomes 20q13 and 22q12. Cloning of the breakpoint showed an in-frame fusion between the EWSR1 and NFATc2 genes, resulting in loss of the NH2-terminal, calcineurin-dependent control region and an intact active domain of NFATc2 controlled by the transactivation domains of EWSR1. Conclusion: A new translocation involving EWSRI and NFATc2 was cloned. NFATc2 is a transcription factor that is not a member of the ETS family and functions in T-cell differentiation and immune response. Direct involvement of NFATc2 has not yet been observed in oncogenesis. We show that due to the shared sequence recognition of NFATc2 and the ETS family, shared transcriptional control is possible using activating protein complex 1.
Mental Health & Psychosocial Distress Sequelae of Katrina: An Empirical Study of Survivors 1

This study focuses on mental health and psychosocial distress sequelae of Hurricane Katrina cataclysm among survivors. The purpose of this article is to: (1) assess the variation in psychosocial distress among the survivors of Katrina by socio-demographic, structural and situational factors; (2) determine if there are significant racial and gender differences in the extent of psychological stress, especially between Black and White, male and female survivors; and (3) to evaluate the influence of resource loss or financial burden imposed, social support, and perceived victimization on psychosocial distress among survivors. The Gallup/CNN/USA Today survey data collected in 2005 and 2006 from a representative (random) sample of Katrina survivors are used. Among the results, significant racial differences were found in psychological impacts including reported symptoms of sleeplessness, anxiety, depression, and worries about the future. In a series of multivariate analyses including factor analysis and OLS regression models, residency in Orleans parish prior to the storm, older age, female gender, having dependent children, unemployment, extent of property damage, and financial impacts sustained consistently predict psychological distress among the survivors. The theoretical, methodological, and applied policy implications of these findings are discussed.
Expression of herpes simplex virus type 1 glycoprotein I in baculovirus: preliminary biochemical characterization and protection studies

We have constructed a recombinant baculovirus expressing the herpes simplex virus type 1 (HSV-1) glycoprotein I (gI). Sf9 cells infected with this recombinant virus synthesized gI-related polypeptides with apparent molecular sizes of 52 and 56 kDa. The recombinant gI appeared to be glycosylated, since it was susceptible to both tunicamycin and endoglycosidase H, and the expressed gI was transported to the surface of infected cells as judged by indirect immunofluorescence. Antibodies to the recombinant gI raised in mice neutralized HSV-1 infectivity. Finally, we show here for the first time that vaccination with gI can protect mice against HSV-1 challenge.
Obstructive sleep apnoea and its therapy influence high-density lipoprotein cholesterol serum levels

Recent studies suggest an association of obstructive sleep apnoea (OSA) with cardiovascular risk factors, such as dyslipidaemia. The present study analyses the effects of OSA and its therapy on serum lipid concentrations in 470 OSA patients in a single centre study. Multivariate regression showed a significant association between the apnoea–hypopnoea index and high-density lipoprotein cholesterol (HDL-C) serum levels (n = 366), independent of age, sex, body mass index, diabetes and lipid lowering medication. There were no independent associations with total cholesterol, triglyceride and low-density lipoprotein cholesterol serum levels. During follow-up (6 months) with effective bilevel or continuous positive airway pressure therapy in 127 patients (lipoproteins: n = 86) without change in their lipid lowering therapy, the mean HDL-C serum level increased significantly by 5.8% from 46.9±15.8 to 49.6±15.3 mg·dL−1 (mean±SD). An independent relationship was found between the change of apnoea–hypopnoea index and the change of high-density lipoprotein cholesterol or triglycerides, respectively. All patients with abnormal serum lipid/lipoprotein levels improved significantly under bilevel or continuous positive airway pressure therapy. This study demonstrates an influence of obstructive sleep apnoea and its therapy on high-density lipoprotein cholesterol levels.
Modulation of the binding characteristics of a fluorescent nucleotide derivative to the sarcoplasmic reticulum adenosinetriphosphatase.

Trinitrophenyladenosine monophosphate (TNP-AMP) binding to the phosphorylated Ca2+-ATPase of sarcoplasmic reticulum results in manyfold higher fluorescence intensity and longer lifetimes of the nucleotide analogue, as compared to TNP-AMP binding to the nonphosphorylated enzyme. This is observed when the phosphoenzyme intermediate is formed either from ATP or from inorganic phosphate (Pi). An important question is whether the TNP-AMP fluorescence properties can also reflect the kinetically defined interconversions of different phosphoenzyme species during catalysis. We have approached this question by manipulating the phosphorylation conditions in a manner which is known to result in accumulation of different species of the phosphoenzyme, i.e., by variations in pH, substrates, and K+ and Ca2+ concentrations. Decreasing pH or increasing [K+] caused large decreases in fluorescence intensity at a given concentration of TNP-AMP under conditions of phosphorylation with either ATP or Pi. In contrast, low to high intravesicular Ca2+ concentrations had no effect on fluorescence during steady-state turnover. TNP-AMP titrations of the phosphorylated enzyme stabilized in different states revealed that H+ and K+ caused a shift in TNP-AMP binding affinity to the site responsible for high fluorescence enhancement, while maintaining approximately the same maximal fluorescence yield at saturation. The fluorescence lifetimes of TNP-AMP bound to phosphoenzyme did not change with variations in pH, [K+], and substrates. We conclude that the environment of that part of the TNP-AMP binding site which binds the trinitrophenyl moiety undergoes a change upon enzyme phosphorylation resulting in enhanced fluorescence yield; this change is invariant between different phosphoenzyme species. (ABSTRACT TRUNCATED AT 250 WORDS)
Introduction - Background, Goal and Content of the Lecture Series on Polarimetric SAR Interferometry

Abstract : Scientists and engineers already engaged in the fields of radar surveillance, reconnaissance and scattering measurements, for instance, generally gain their specialist knowledge in Polarimetry by working through scientific papers and specialised literature available on the subject. Usually, this is a time consuming exercise, as it is difficult for a newcomer to collate material especially on Polarimetry but also on Interferometry and related subjects. Presently, the treatment of basic Polarimetry concepts, in the currently available literature, lacks a coherent framework of theory, and, moreover, several basic definitions and conventions are not yet unified sufficiently under the light of physical principles. This Lecture Series is an attempt to readdress this problem. The aim of this Lecture Series is to provide a substantial and balanced introduction to the basic theory, scattering concepts, systems and applications typical to polarimetric and interferometric radar reconnaissance and surveillance, and to introduce the cutting-edge technologies, new ideas and methodologies as well. The following topics will be addressed: Basics, advanced concepts and applications of both radar Polarimetry and SAR Interferometry, cross track and along track Interferometry, single and dual pass Interferometry, differential interferometry, Interferometry errors and accuracy, polarimetric SAR processing and image analysis, decomposition theorems, polarimetric interferometry and polarimetric-interferometric SAR image analysis, processing principles, calibration, Polarimetric SAR analysis and applications, Digital Elevation Models, realized and future airborne and space-borne systems as Examples E-SAR, SIR-C/X-SAR, SRTM, ERS-1/2, RadarSAT, ENVISAT/ASAR, TerraSAR-X, Tandem-X, and CARTWHEEL.
Overall C as a measure of discrimination in survival analysis: model specific population value and confidence interval estimation

The assessment of the discrimination ability of a survival analysis model is a problem of considerable theoretical interest and important practical applications. This issue is, however, more complex than evaluating the performance of a linear or logistic regression. Several different measures have been proposed in the biostatistical literature. In this paper we investigate the properties of the overall C index introduced by Harrell as a natural extension of the ROC curve area to survival analysis. We develop the overall C index as a parameter describing the performance of a given model applied to the population under consideration and discuss the statistic used as its sample estimate. We discover a relationship between the overall C and the modified Kendall's τand construct a confidence interval for our measure based on the asymptotic normality of its estimate. Then we investigate via simulations the length and coverage probability of this interval. Finally, we present a real life example evaluating the performance of a Framingham Heart Study model. Copyright © 2004 John Wiley & Sons, Ltd.
Enhancing Branch Monitoring for Security Purposes: From Control Flow Integrity to Malware Analysis and Debugging

Malware and code-reuse attacks are the most significant threats to current systems operation. Solutions developed to countermeasure them have their weaknesses exploited by attackers through sandbox evasion and antidebug crafting. To address such weaknesses, we propose a framework that relies on the modern processors’ branch monitor feature to allow us to analyze malware while reducing evasion effects. The use of hardware assistance aids in increasing stealthiness, a key feature for debuggers, as modern software (malicious or benign) may be antianalysis armored. We achieve stealthier code execution control by using the branch monitor hardware’s inherent interrupt capabilities, keeping the code under execution intact. Previous works on branch monitoring have already addressed the ROP attack problem but require code injection and/or are limited in their capture window size. Therefore, we also propose a ROP detector without these limitations.
Feedback Optimization Schemes for Downlink MISO-OFDMA Systems With Heterogeneous Users

This paper proposes feedback optimization schemes for multiple-input single-output orthogonal frequency-division multiple access (MISO-OFDMA) systems with heterogeneous users. The proposed scheme adjusts the unit and resolution of the feedback to efficiently exploit the long-term channel statistics, including the path loss, delay spread, and mobility. To develop an analytical optimization framework, we first derive the sum-rate of MISO-OFDMA systems when the channel-state information (CSI) at the transmitter is imperfect because of the quantization error, channel variation, and feedback delay. Based on the derived results, we present effective solutions to the sum-rate maximization problem for distributed and centralized scenarios. When the channel statistics of the users are not available at the base station, each user can improve the sum-rate of the system by minimizing the distortion on CSI feedback under a fixed per-user feedback rate. With the channel statistics of the users, the base station can further control the user set and the feedback rate in addition to the feedback granularity. We evaluate the performance of both distributed and centralized schemes over practical wireless environments, where each user has different long-term channel statistics. Simulation results show that both methods significantly improve the performance of MISO-OFDMA systems.
Design of a Disk Resonator Gyroscope With High Mechanical Sensitivity by Optimizing the Ring Thickness Distribution

In this paper, we present the mechanical sensitivity improvement of a disk resonator gyroscope (DRG) by optimizing the thickness distribution of the nested rings. The mechanical sensitivities of the DRGs with uniform, linearly changing, and step changing rings have been simulated. The results suggest that the ring thickness distribution has great influence on the performance of the DRG. Then, the optimized ring thickness distribution was obtained by using the traditional method of moving asymptotes (MMA), which result in a 24% improvement of the mechanical sensitivity. Finally, the bio-inspired particle swarm optimization (PSO) algorithm has also been used. The optimization results of PSO coincide well with that of MMA, and the optimized result is the global optimum. Meanwhile, the optimized distribution rules can be used on the series of DRGs and the optimization methods can be widely used on other microelectromechanical systems (MEMS) devices.
What is the effect of position for VDT dynamic/static displays on users&#146; reading comprehension?

The study investigated the effects of position (upper, below, right-hand, and left-hand side of the screen) for VDT dynamic display and other factors including speed (150, 200, 250, and 300 wpm), display type of dynamic information (leading, flash and RSVP), and polarity combination of dynamic/static (black-on-white/black-on-white, white-on-black/white-on-black, black-on-white/white-on-black, and white-on-black/black-on-white) on subjects' comprehension for reading static and dynamic display information. The result of this research showed that position and type of dynamic information had no significant effect on subjects' comprehension for dynamic and static information. Polarity combination and speed also had no significant effect on subjects' comprehension for static information; however, the two factors had significant effects on subjects' comprehension for dynamic information. When display speed was set at 200 wpm, subjects' comprehension was better than with at speed settings. When the dynamic/static display was set to be the same polarity combination (black-on-white/black-on-white), subjects' performance was better than other polarity combinations
Correction: Root Exudation of Phytochemicals in Arabidopsis Follows Specific Patterns That Are Developmentally Programmed and Correlate with Soil Microbial Functions

Plant roots constantly secrete compounds into the soil to interact with neighboring organisms presumably to gain certain functional advantages at different stages of development. Accordingly, it has been hypothesized that the phytochemical composition present in the root exudates changes over the course of the lifespan of a plant. Here, root exudates of in vitro grown Arabidopsis plants were collected at different developmental stages and analyzed using GC-MS. Principle component analysis revealed that the composition of root exudates varied at each developmental stage. Cumulative secretion levels of sugars and sugar alcohols were higher in early time points and decreased through development. In contrast, the cumulative secretion levels of amino acids and phenolics increased over time. The expression in roots of genes involved in biosynthesis and transportation of compounds represented in the root exudates were consistent with patterns of root exudation. Correlation analyses were performed of the in vitro root exudation patterns with the functional capacity of the rhizosphere microbiome to metabolize these compounds at different developmental stages of Arabidopsis grown in natural soils. Pyrosequencing of rhizosphere mRNA revealed strong correlations (p,0.05) between microbial functional genes involved in the metabolism of carbohydrates, amino acids and secondary metabolites with the corresponding compounds released by the roots at particular stages of plant development. In summary, our results suggest that the root exudation process of phytochemicals follows a developmental pattern that is genetically programmed. This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Selection of Specific Endophytic Bacterial Genotypes by Plants in Response to Soil Contamination

ABSTRACT Plant-bacterial combinations can increase contaminant degradation in the rhizosphere, but the role played by indigenous root-associated bacteria during plant growth in contaminated soils is unclear. The purpose of this study was to determine if plants had the ability to selectively enhance the prevalence of endophytes containing pollutant catabolic genes in unrelated environments contaminated with different pollutants. At petroleum hydrocarbon contaminated sites, two genes encoding hydrocarbon degradation, alkane monooxygenase (alkB) and naphthalene dioxygenase (ndoB), were two and four times more prevalent in bacteria extracted from the root interior (endophytic) than from the bulk soil and sediment, respectively. In field sites contaminated with nitroaromatics, two genes encoding nitrotoluene degradation, 2-nitrotoluene reductase (ntdAa) and nitrotoluene monooxygenase (ntnM), were 7 to 14 times more prevalent in endophytic bacteria. The addition of petroleum to sediment doubled the prevalence ofndoB-positive endophytes in Scirpus pungens, indicating that the numbers of endophytes containing catabolic genotypes were dependent on the presence and concentration of contaminants. Similarly, the numbers of alkB- orndoB-positive endophytes in Festuca arundinaceawere correlated with the concentration of creosote in the soil but not with the numbers of alkB- or ndoB-positive bacteria in the bulk soil. Our results indicate that the enrichment of catabolic genotypes in the root interior is both plant and contaminant dependent.
Electrical and structural properties of nanotetrapod zinc oxide thin films prepared with different deposition temperature

Nanotetrapod zinc oxide (ZnO) thin films have been deposited by thermal chemical vapor deposition (TCVD) technique. The films were deposited at 700°C and 800°C to study the temperature effect of physical properties of the nanotetrapod ZnO thin films. From XRD result shows the highest peak can observed from sample 700°C at (002) orientation. It was found that the size of nanotetrapod increased with increased of deposition temperature. The energy dispersive X-ray spectrometer (EDX) spectrum shows that the grown product contains zinc and oxygen only. At 800°C show the minimum of resistivity for the thin film which is 1.10 ohm. cm. Photoluminescence measurement shows a sharp peak ultraviolet emission at 380 nm and high intensity visible peak at 700°C because of defect due to oxygen vacancy and crystallization of ZnO nanotetrapod.
Correntropy induced metric based graph regularized non-negative matrix factorization

Non-negative matrix factorization (NMF) is an efficient dimension reduction method and plays an important role in many pattern recognition and computer vision tasks. However, conventional NMF methods are not robust since the objective functions are sensitive to outliers and do not consider the geometric structure in datasets. In this paper, we proposed a correntropy graph regularized NMF (CGNMF) to overcome the aforementioned problems. CGNMF maximizes the correntropy between data matrix and its reconstruction to filter out the noises of large magnitudes, and expects the coefficients to preserve the intrinsic geometric structure of data. We also proposed a modified version of our CGNMF which construct the adjacent graph by using sparse representation to enhance its reliability. Experimental results on popular image datasets confirm the effectiveness of CGNMF.
Novel Approach Toward Plasma Enhancement in Trench-Insulated Gate Bipolar Transistors

In this letter, a trench-insulated gate bipolar transistor (IGBT) design with local charge compensating layers featured at the cathode of the device is presented and analyzed. The superjunction or reduced surface effect proves to be very effective in overcoming the inherited ON-state versus breakdown tradeoff appearing in conventional devices, such as the soft punch through plus or field stop plus (FS+) IGBTs. This design enhances the ON-state performance of the FS+IGBT by increasing the plasma concentration at the cathode side without affecting either the switching performance or the breakdown rating.
Adaptation d'Œnococcus œni à l'environnement œnologique : approches génomique comparative, transcriptomique et protéomique

Par ses capacites a tolerer un pH acide, une concentration elevee en ethanol et une multitude d'inhibiteurs non identifies, O. œni est une espece bacterienne particulierement bien adaptee a l'environnement œnologique. Afin de resoudre des problemes recurrents de fermentation, la possibilite d'implantation de levains malolactiques selectionnes represente un grand interet pour le viticulteur. Les nombreuses etudes et observations realisees dans les laboratoires et chez les industriels ont demontre que l'adaptation d'O. œni dependait grandement de la souche. L'objectif de notre travail est de tenter de mettre en evidence les differences entre les deux types de souches : celles qui s'adaptent mieux et les autres. Cette etude, basee sur des techniques de biologie moleculaire telles que la genomique comparative, l'hybridation comparative sur puce a ADN et l'electrophorese bidimensionnelle des proteines, s'appuie sur une collection de souches caracterisees par leurs aptitudes œnologiques.