Miracle-dz/UniFAR-FTUs huggingface dataset:
Gr upSM Anxiety Disorder as an Important Determinant of Quality of Life in Systemic Sclerosis Patients

Systemic Sclerosis (SSc) is an autoimmune connective tissue disease, characterised by fibrosis of internal organs and skin that leads to visible disfigurements to various body parts, including face, mouth and hands. The changes in these socially relevant body parts are associated with greater body image dissatisfaction, increased depressive symptoms, and social anxiety and avoidance behaviours. The HRQol, usually evaluated in rheumatic conditions by the Medical Outcomes Study 36Item Short Form Health Survey (SF-36), is considered an important outcome in SSc, useful in monitoring the disease. The few data available on the prevalence of anxiety in patients with systemic sclerosis revealed severe anxiety disorders in 19-46.6%, although only a limited number of researches assessed anxiety impact on HRQoL.
Assessment of reactive power pricing by controlling generators' voltage under deregulation

This paper presents the assessment schemes of reactive power pricing through generators' voltage control under the assumption that a reactive power market is decomposed into a real power market. Applying the concept of economic dispatch to minimize the total cost of real power, the algorithm for implementing a reactive power pricing is proposed to determine the generators' optimum voltage profiles. It consists of the reactive power-voltage equation, the objective function which minimizes the total cost of reactive power, and linear analysis of inequality constraints in relation to the voltages at the loads. From this algorithm, the total cost of the reactive power can be yielded to the minimum value within network constraints. It may provide the fair and reasonable price information for reactive power in deregulated electricity market. The proposed algorithm has been tested on the IEEE 14-bus system using MATLAB.
INCOG Guidelines for Cognitive Rehabilitation Following Traumatic Brain Injury: Methods and Overview

Introduction:Traumatic brain injury results in complex cognitive sequelae. However, clinicians have difficulty implementing the available evidence. An international group of researchers and clinicians (known as INCOG) convened to develop clinical practice guidelines for cognitive rehabilitation posttraumatic brain injury. Methods:The Guidelines Adaptation and Development cycle was used to derive the recommendations. Previously published cognitive rehabilitation recommendations were identified and tabulated. An expert panel met to select appropriate recommendations. Afterward, the team enhanced the recommendations by reviewing available literature. To address shortfalls of previous guidelines, the team developed decision algorithms incorporating the recommendations based on inclusion and exclusion criteria of published trials and expert opinion. The team then prioritized the recommendations for implementation and developed audit criteria to evaluate adherence to best practice. Results:The team recommends that individuals have detailed assessments of cognition after resolution of posttraumatic amnesia. Cognitive assessment and rehabilitation should be tailored to the patient's neuropsychological profile, premorbid cognitive characteristics, and goals for life activities and participation. Clinical algorithms and audit tools to evaluate current practice are provided. Conclusion:Cognitive rehabilitation should be offered to select individuals with traumatic brain injury. These guidelines provide assistance to clinicians who want to provide evidence-based care.
The Role of Epidermal Growth Factor Receptor in Cancer Metastasis and Microenvironment

Despite significant improvements in diagnosis, surgical techniques, and advancements in general patient care, the majority of deaths from cancer are caused by the metastases. There is an urgent need for an improved understanding of the cellular and molecular factors that promote cancer metastasis. The process of cancer metastasis depends on multiple interactions between cancer cells and host cells. Studies investigating the TGFα-EGFR signaling pathways that promote the growth and spread of cancer cells. Moreover, the signaling activates not only tumor cells, but also tumor-associated endothelial cells. TGFα-EGFR signaling in colon cancer cells creates a microenvironment that is conducive for metastasis, providing a rationale for efforts to inhibit EGFR signaling in TGFα-positive cancers. In this review, we describe the recent advances in our understanding of the molecular basis of cancer metastasis.
Depends on What the French Say

We present a syntactic annotation scheme for spoken French that is currently used in the Rhapsodie project. This annotation is depend-ency-based and includes coordination and dis-fluency as analogously encoded types of paradigmatic phenomena. Furthermore, we attempt a thorough definition of the discourse units re-quired by the systematic annotation of other phenomena beyond usual sentence boundaries, which are typical for spoken language. This includes so called “macrosyntactic” phenomena such as dislocation, parataxis, insertions, grafts, and epexegesis.
The association between changes in skin echogenicity and the fibroblast production of biglycan and versican in systemic sclerosis.

OBJECTIVE To investigate a possible association between the longitudinal changes in skin involvement and the fibroblast production of proteoglycans in vitro, among patients with early and untreated systemic sclerosis (SSc). METHODS In 11 patients, 6 with diffuse cutaneous systemic sclerosis (dSSc) and 5 with limited cutaneous systemic sclerosis (ISSc), and in 6 controls skin thickness and skin echogenicity of the forearm was measured by high frequency (20 MHz) ultrasound. A skin biopsy was taken from the area of the ultrasound measurements, and from cultivated fibroblasts the production of the proteoglycans versican, perlecan, biglycan and decorin were measured. To investigate longitudinal changes in skin involvement, the ultrasound examination was repeated after 1-3 years. RESULTS Compared to controls, SSc patients had increased skin thickness at the first evaluation. Patients with dSSc had lower skin echogenicity than both patients with lSSc and the controls. Patients with greater changes in skin thickness and skin echogenicity produced more versican, whereas the production of biglycan and decorin was higher only in patients with greater changes in skin echogenicity. There was a negative correlation between fibroblast production of biglycan and disease duration. CONCLUSION High fibroblast synthesis of the proteoglycans versican and biglycan is associated with changes in skin echogenicity and may predict more progressive skin sclerosis in SSc.
Noninvasive In vivo high-resolution magnetic resonance imaging of atherosclerotic lesions in genetically engineered mice.

BACKGROUND The pathogenesis of atherosclerosis is currently being investigated in genetically engineered small animals. Methods to follow the time course of the developing pathology and/or the responses to therapy in vivo are limited. METHODS AND RESULTS To address this problem, we developed a noninvasive MR microscopy technique to study in vivo atherosclerotic lesions (without a priori knowledge of the lesion location or lesion type) in live apolipoprotein E knockout (apoE-KO) mice. The spatial resolution was 0.0012 to 0.005 mm3. The lumen and wall of the abdominal aorta and iliac arteries were identified on all images in apoE-KO (n=8) and wild-type (n=5) mice on chow diet. Images obtained with MR were compared with corresponding cross-sectional histopathology (n=58). MR accurately determined wall area in comparison to histopathology (slope=1.0, r=0.86). In addition, atherosclerotic lesions were characterized in terms of lesion shape and type. Lesion type was graded by MR according to morphological appearance/severity and by histopathology according to the AHA classification. There was excellent agreement between MR and histopathology in grading of lesion shape and type (slope=0.97, r=0.91 for lesion shape; slope=0. 64, r=0.90 for lesion type). CONCLUSIONS The combination of high-resolution MR microscopy and genetically engineered animals is a powerful tool to investigate serially and noninvasively the progression and regression of atherosclerotic lesions in an intact animal model and should greatly enhance basic studies of atherosclerotic disease.
Amino acid residue doublet propensity in the protein–RNA interface and its application to RNA interface prediction

Protein–RNA interactions play essential roles in a number of regulatory mechanisms for gene expression such as RNA splicing, transport, translation and post-transcriptional control. As the number of available protein–RNA complex 3D structures has increased, it is now possible to statistically examine protein–RNA interactions based on 3D structures. We performed computational analyses of 86 representative protein–RNA complexes retrieved from the Protein Data Bank. Interface residue propensity, a measure of the relative importance of different amino acid residues in the RNA interface, was calculated for each amino acid residue type (residue singlet interface propensity). In addition to the residue singlet propensity, we introduce a new residue-based propensity, which gives a measure of residue pairing preferences in the RNA interface of a protein (residue doublet interface propensity). The residue doublet interface propensity contains much more information than the sum of two singlet propensities alone. The prediction of the RNA interface using the two types of propensities plus a position-specific multiple sequence profile can achieve a specificity of about 80%. The prediction method was then applied to the 3D structure of two mRNA export factors, TAP (Mex67) and UAP56 (Sub2). The prediction enables us to point out candidate RNA interfaces, part of which are consistent with previous experimental studies and may contribute to elucidation of atomic mechanisms of mRNA export.
Full-duplex spectrum sensing and access in cognitive radio networks with unknown primary user activities

In this paper, we consider the problem of optimal opportunistic spectrum access using full-duplex (FD) radios in presence of uncertain primary user (PU) channel statistics and propose a Sensing-and-Selectively-Transmit protocol (SaST). To optimize its throughput, the SU sensing period has to be carefully tuned. However, in absence of the exact knowledge of PU activity statistics, under SaST, the PU's performance may be adversely affected. A learning strategy is devised to update the estimated statistics based on spectrum sensing observations. Simulation studies demonstrate that the resulting robust solution provides a good trade-off between optimizing the SU's throughput and protecting the PU.
Port-hamiltonian control of power electronic converters to achieve passivity

In this paper, a control framework is proposed to render a power electronic converter passive by using the port-Hamiltonian (PH) theory. As a result, the stability of the system is guaranteed if the rest of the system that the power electronic converter connects to is passive. The controller consists of two control loops, which form a passive port-Hamiltonian (PH) system, and one lossless block, which interconnects the passive block with the plant. In order to facilitate the implementation of the framework, a new word quorte is coined to represent the quantity that is dual to the torque. Simulation results are presented to demonstrate the effectiveness of the control framework in both grid-connected and islanded modes.
Keyword Auction Protocol for Dynamically Adjusting the Number of Advertisements

Search engines including Yahoo! and Google utilize a keyword auction for ranking the advertisements displayed around the search results. In existing keyword auctions called the GSP, the number of displayed advertisements (slots) is determined in advance. Therefore, we consider adjusting the number of advertisements dynamically based on bids in order to improve both social surplus and seller's revenue. For example, we allow a bidder to display her advertisement exclusively when she is willing to pay a premium. We propose a new keyword auction protocol called the GSP-ExR in which the number of slots can be either 1 or K. The GSP-ExR pricing scheme is relatively simple and the seller's revenue is at least as good as with the GSP. If the highest ranked bidder's bid is large enough, she can exclusively display her advertisement by paying a premium.Otherwise, the GSP-ExR is identical to the GSP.
FDG PET/CT in Patients With Head and Neck Squamous Cell Carcinoma After Primary Surgical Resection With or Without Chemoradiation Therapy.

OBJECTIVE The purpose of this study was to assess the value of posttreatment FDG PET/CT in patients with squamous cell carcinoma of the head and neck (HNSCC) treated with primary surgical resection with or without adjuvant concurrent chemoradiotherapy. MATERIALS AND METHODS A total of 98 HNSCC patients were treated with primary surgical resection and had undergone PET/CT within 6 months of treatment completion. The accuracy of the scans and the added value to clinical assessment and impact on management were established based on the clinical information before and after each scan. Overall survival of patients was estimated with Kaplan-Meier curves. RESULTS Of the total 98 scans, 25 (25.5%) were interpreted as positive and 73 (74.5%) as negative. The sensitivity of posttreatment PET/CT was 80.0%; specificity, 89.5%; positive predictive value, 66.7%; negative predictive value, 94.4%; and accuracy, 87.5%. These scans were helpful in excluding tumor in 31.8% of patients with clinical suspicion of residual disease and identifying suspected residual disease in 13.2% of patients with no prior clinical suspicion. Multivariate regression analysis showed that tumor size, grade (p = 0.041), scan type (p = 0.002), and scan result (p = 0.005) were independent covariates associated with overall survival. Kaplan-Meier analysis showed a significant difference and association in overall survival between patients with a positive versus a negative posttherapy PET/CT scan result (hazard ratio, 5.65; 95% CI, 2.48-12.83; log rank Mantel-Cox p < 0.001). CONCLUSION Posttreatment FDG PET/CT results had a high negative predictive value, added value to clinical assessment of 35% of patients, influenced subsequent management, and were associated with survival outcome of HNSCC patients treated with primary surgical resection.
A Region-Based Motion-Compensated Frame Interpolation Method Using a Variance-Distortion Curve

This brief proposes a new motion-compensated frame interpolation (MCFI) method, and it generates new intermediate frames from existing original frames. The proposed method partitions the original frames into arbitrary-shaped regions and estimates motions for the regions. The region shapes were initially determined by pixel intensity and iteratively refined on the basis of a variance-distortion curve. The experimental results show that the proposed method more accurately interpolates frames than previous MCFI methods.
“Pure” hereditary spastic paraplegias

Spasticity is such a common and nonspecific neurologic finding that its inclusion in the description of many genetic disorders of the nervous system is not surprising. Often, arbitrary decisions have been made in the past as to which syndrome names would contain the term “spastic. ” A group of pure, or uncomplicated, hereditary spastic paraplegias (HSP) were said to share the clinical hallmarks of almost exclusive progressive spasticity and weakness of the lower limbs, with occasional involvement of the dorsal columns or bladder symptoms. HSP are categorized by inheritance: autosomal dominant, autosomal recessive, or X-linked1,2 (table). This issue of Neurology characterizes two new loci. Hedera et al.3 present clinical features of a large chromosome 8q23-24–linked autosomal dominant HSP kindred, and Murillo et al.4 report linkage to a third locus—15q13-q15—for autosomal recessive HSP. The molecular characterization of HSP over the last 6 years has already shed light on the cause of two X-linked and one autosomal recessive HSP (table); the gene products associated with the remaining loci are likely to be identified soon. However, it is already possible to begin to characterize the phenotype of each disorder. View this table: Table 1. Classification of hereditary spastic paraplegias The chromosome 8q–linked5 autosomal dominant HSP kindred described in Hedera et al. includes 15 affected subjects (8 men and 7 women) whose symptoms include lower extremity spasticity and weakness, hyperreflexia, ankle …
SNP Discovery in the Transcriptome of White Pacific Shrimp Litopenaeus vannamei by Next Generation Sequencing

The application of next generation sequencing technology has greatly facilitated high throughput single nucleotide polymorphism (SNP) discovery and genotyping in genetic research. In the present study, SNPs were discovered based on two transcriptomes of Litopenaeus vannamei (L. vannamei) generated from Illumina sequencing platform HiSeq 2000. One transcriptome of L. vannamei was obtained through sequencing on the RNA from larvae at mysis stage and its reference sequence was de novo assembled. The data from another transcriptome were downloaded from NCBI and the reads of the two transcriptomes were mapped separately to the assembled reference by BWA. SNP calling was performed using SAMtools. A total of 58,717 and 36,277 SNPs with high quality were predicted from the two transcriptomes, respectively. SNP calling was also performed using the reads of two transcriptomes together, and a total of 96,040 SNPs with high quality were predicted. Among these 96,040 SNPs, 5,242 and 29,129 were predicted as non-synonymous and synonymous SNPs respectively. Characterization analysis of the predicted SNPs in L. vannamei showed that the estimated SNP frequency was 0.21% (one SNP per 476 bp) and the estimated ratio for transition to transversion was 2.0. Fifty SNPs were randomly selected for validation by Sanger sequencing after PCR amplification and 76% of SNPs were confirmed, which indicated that the SNPs predicted in this study were reliable. These SNPs will be very useful for genetic study in L. vannamei, especially for the high density linkage map construction and genome-wide association studies.
Web ontology reasoning with logic databases

This dissertation addresses the problem of reasoning with Web ontologies in logic databases. The main contribution is the enabling of Web ontology reasoning with logic databases for the Web ontology language (OWL), an international standard that has been recently proposed by the World Wide Web Consortium (W3C). On the theoretical side, we show which fragment of OWL can be correctly supported by logic databases. On the practical side, we show that logic databases allow to overcome the predominant limitation of current approaches to ABox reasoning with Description Logics (DL) such as OWL. Our work specifically addresses the following questions: • Which fragment of OWL can be implemented in logic databases ? We invent a strategy to identify the fragment, which is based on the translation of DL axioms into first-order logic, followed by a transformation into a conjunction of Horn formulae. These formulae can be translated into the different Logic Programming languages which are supported by logic databases. • What are the theoretical properties of the fragment ? We define Description Logic Programs (DLP) as a family of new ontology languages Li, which precisely contains the fragment. We utilize DLP to study the theoretical properties of the fragment. In particular, we show that we can solve ABox related reasoning problems, independent of the TBox, with a low polynomial complexity O(|ADLP i≤2 |)4 in the size of the DLP ABox ADLP . • How can DL reasoning be reduced to operations on logic databases ? We show which and how DL reasoning problems can be reduced to operations on logic databases and identify the limitations of the reduction. • How useful is the related fragment as a practical Web ontology language ? We answer this question by showing two separate hypotheses. Hypothesis 1: The fragment is sufficient to express most available Web ontologies. We analyze the largest currently available collection of Web ontologies and check which fragment of those ontologies can be expressed in DLP. We quantify most in two respects. Firstly, we show that the different DLP languages
Career fit and burnout among academic faculty.

BACKGROUND Extensive literature documents personal distress among physicians and a decrease in their satisfaction with the practice of medicine over recent years. We hypothesized that physicians who spent more of their time in the aspect of work that they found most meaningful would have a lower risk of burnout. METHODS Faculty physicians in the Department of Internal Medicine at a large academic medical center were surveyed in the fall of 2007. The survey evaluated demographic variables, work characteristics, and career satisfaction. Burnout was measured using the Maslach Burnout Inventory. Additional questions evaluated which professional activity (eg, research, education, patient care, or administration) was most personally meaningful and the percentage of effort that was devoted to each activity. RESULTS Of 556 physicians sampled, 465 (84%) returned surveys. A majority (68%) reported that patient care was the aspect of work that they found most meaningful, with smaller percentages reporting research (19%), education (9%), or administration (3%) as being most meaningful. Overall, 34% of faculty members met the criteria for burnout. The amount of time spent working on the most meaningful activity was strongly related to the risk of burnout. Those spending less than 20% of their time (approximately 1 d/wk) on the activity that is most meaningful to them had higher rates of burnout (53.8% vs 29.9%; P<.001). Time spent on the most meaningful activity was the largest predictor of burnout on multivariate analysis (odds ratio, 2.75; P = .001). CONCLUSIONS The extent to which faculty physicians are able to focus on the aspect of work that is most meaningful to them has a strong inverse relationship to their risk of burnout. Efforts to optimize career fit may promote physician satisfaction and help to reduce attrition among academic faculty physicians.
Effect of pseudouridylation on the structure and activity of the catalytically essential P6.1 hairpin in human telomerase RNA

Telomerase extends the 3′-ends of linear chromosomes by adding conserved telomeric DNA repeats and is essential for cell proliferation and genomic stability. Telomerases from all organisms contain a telomerase reverse transcriptase and a telomerase RNA (TER), which together provide the minimal functional elements for catalytic activity in vitro. The RNA component of many functional ribonucleoproteins contains modified nucleotides, including conserved pseudouridines (Ψs) that can have subtle effects on structure and activity. We have identified potential Ψ modification sites in human TER. Two of the predicted Ψs are located in the loop of the essential P6.1 hairpin from the CR4-CR5 domain that is critical for telomerase catalytic activity. We investigated the effect of P6.1 pseudouridylation on its solution NMR structure, thermodynamic stability of folding and telomerase activation in vitro. The pseudouridylated P6.1 has a significantly different loop structure and increase in stability compared to the unmodified P6.1. The extent of loop nucleotide interaction with adjacent residues more closely parallels the extent of loop nucleotide evolutionary sequence conservation in the Ψ-modified P6.1 structure. Pseudouridine-modification of P6.1 slightly attenuates telomerase activity but slightly increases processivity in vitro. Our results suggest that Ψs could have a subtle influence on human telomerase activity via impact on TER–TERT or TER–TER interactions.