Miracle-dz/UniFAR-FTUs huggingface dataset:
Duration of remission after halving of the etanercept dose in patients with ankylosing spondylitis: a randomized, prospective, long-term, follow-up study

Background The aim of this study was to evaluate the proportion of patients with ankylosing spondylitis maintaining clinical remission after reduction of their subcutaneous etanercept dose to 50 mg every other week compared with that in patients receiving etanercept 50 mg weekly. Methods In the first phase of this randomized, prospective, follow-up study, all biologic-naïve patients identified between January 2005 and December 2009 as satisfying the modified New York clinical criteria for ankylosing spondylitis treated with etanercept 50 mg weekly were evaluated for disease remission in January 2010. In the second phase, patients meeting the criteria for remission were randomized to receive subcutaneous etanercept as either 50 mg weekly or 50 mg every other week. The randomization allocation was 1:1. Remission was defined as Bath Ankylosing Spondylitis Disease Activity Index < 4, no extra-axial manifestations of peripheral arthritis, dactylitis, tenosynovitis, or iridocyclitis, and normal acute-phase reactants. The patients were assessed at baseline, at weeks 4 and 12, and every 12 weeks thereafter. The last visit constituted the end of the follow-up. Results During the first phase, 78 patients with ankylosing spondylitis (57 males and 21 females, median age 38 years, median disease duration 12 years) were recruited. In January 2010, after a mean follow-up of 25 ± 11 months, 43 (55.1%) patients achieving clinical remission were randomized to one of the two treatment arms. Twenty-two patients received etanercept 50 mg every other week (group 1) and 21 received etanercept 50 mg weekly (group 2). At the end of follow-up, 19 of 22 (86.3%) subjects in group 1 and 19 of 21 (90.4%) in group 2 were still in remission, with no significant difference between the two groups. The mean follow-up duration in group 1 and group 2 was 22 ± 1 months and 21 ± 1.6 months, respectively. Conclusion Remission of ankylosing spondylitis is possible in at least 50% of patients treated with etanercept 50 mg weekly. After halving of the etanercept dose, remission is maintained in a high percentage of patients during long-term follow-up, with important economic implications.
Evidence for Dust Grain Growth in Young Circumstellar Disks

Hundreds of circumstellar disks in the Orion nebula are being rapidly destroyed by the intense ultraviolet radiation produced by nearby bright stars. These young, million-year-old disks may not survive long enough to form planetary systems. Nevertheless, the first stage of planet formation—the growth of dust grains into larger particles—may have begun in these systems. Observational evidence for these large particles in Orion's disks is presented. A model of grain evolution in externally irradiated protoplanetary disks is developed and predicts rapid particle size evolution and sharp outer disk boundaries. We discuss implications for the formation rates of planetary systems.
Molecular Differentiation at Nuclear Loci in French Host Races of the European Corn Borer (Ostrinia nubilalis)

French populations of the European corn borer consist of two sympatric and genetically differentiated host races. As such, they are well suited to study processes that could be involved in sympatric speciation, but the initial conditions of host-race divergence need to be elucidated. Gene genealogies can provide insight into the processes involved in speciation. We used DNA sequences of four nuclear genes to (1) document the genetic structure of the two French host races previously delineated with allozyme markers, (2) find genes directly or indirectly involved in reproductive isolation between host races, and (3) estimate the time since divergence of the two taxa and see whether this estimate is compatible with this divergence being the result of a host shift onto maize after its introduction into Europe ∼500 years ago. Gene genealogies revealed extensive shared polymorphism, but confirmed the previously observed genetic differentiation between the two host races. Significant departures from the predictions of neutral molecular evolution models were detected at three loci but were apparently unrelated to reproductive isolation between host races. Estimates of time since divergence between French host races varied from ∼75,000 to ∼150,000 years, suggesting that the two taxa diverged recently but probably long before the introduction of maize into Europe.
Control design of an overhead crane system from the perspective of stabilizing undesired oscillations

The feedback stabilization of a generalized model describing an overhead crane with a flexible cable is considered. The cable displacements are presented by a hyperbolic partial differential equation (PDE) in which destabilizing terms are generated. The pursued method gives a systematic technic to convert the concerned model into a well-known one using an integral transformation with a kernel satisfying an appropriate PDE. A feedback controller that asymptotically stabilizes the cable displacements is explicitly constructed in terms of the solution of the kernel PDE.
Functional assessment of the elderly with the use of EASY-Care Standard 2010 and Comprehensive Geriatric Assessment.

BACKGROUND The wide variation in performance among the elderly leads to the search for a suitable instrument to identify the necessary support. The aim of this study was to examine the scope of independent functioning of the elderly and to indicate the necessary support using basic instruments, Comprehensive Geriatric Assessment (CGA) and EASY-Care Standard 2010. METHODS For statistical analysis were qualified 101 questionnaires of patients from oncological surgery clinic. RESULTS The study group was dominated by women (79.2%). The average age for the entire group was 74.7 ± 7.5 years. In terms of basic life activities (Barthel Index), 75.2% of the elderly performed most of their activities independently. The Lawton IADL (Instrumental Activity of Daily Living Scale) median was 25 points. Moderate depression (Geriatric Depression Scale) reported 37.6% of the group. The influence of age, education, mode of movement and efficiency in basic and instrumental life activities and depression (Geriatric Depression Scale) was demonstrated in the results in three scales of the EASY-Care Standard 2010 questionnaire: Independence score, Risk of break down in care and Risk of falls. There was no difference in terms of gender and the nature of the residence. CONCLUSION The study group of the elderly was characterised by a good level of efficiency in basic and instrumental activities of daily living. Questionnaire EASY-Care Standard 2010 enables to identify functional limitations of the elderly that may form the basis for planning individual support.
Metalights: Improved Interleaved Shading

We present metalights, a novel Virtual Point Light (VPL) encapsulating structure which enhances classic interleaved shading by improving VPL sampling, based on few initial screen space samples to estimate VPL contribution to current view. Our method leads to important noise variance reduction in the final picture by only adding a small fraction of computation. The implementation is straight‐forward and well adapted to both CPU and GPU‐based engines. We also present different image‐space assignment schemes for the VPL subsets to break the regularity of the noise pattern or to adapt it to simple antialiasing.
Incremental Dictionary Learning for Unsupervised Domain Adaptation

Domain adaptation (DA) methods attempt to solve the domain mismatch problem between source and target data. In this paper, we propose an incremental dictionary learning method where some target data called supportive samples are selected to assist adaptation. Supportive samples are close to the source domain and have two properties: first, their predicted class labels are reliable and can be used for building more discriminative classification models; second, they act as a bridge to connect the two domains and reduce the domain mismatch. Theoretical analysis shows that both properties are important for adaptation, enabling the idea of adding supportive samples to the source domain. A stopping criterion is designed to guarantee that the domain mismatch decreases monotonically during adaptation. Experimental results on several widely used visual datasets show that the proposed approach performs better than many state-of-the-art methods.
Matrix theory of dissipative antenna arrays

A theory of a phased antenna array with lossy radiating elements is elaborated. The theory is based on representation of a radiating system as the equivalent multi-port linking amplitudes of traveling waves in transmission lines with amplitudes of spherical waves in free space. Relations for calculation of blocks of a scattering matrix, that defines parameters of this multiport, are obtained under assumption that initial parameters of the radiating system the impedance matrix and partial radiation patterns (RP) - are known. A procedure for calculation of these parameters is described. It is based on the solution, with the moments method, of the electromagnetic boundary problem of the antenna array excitation at the alternating excitation of its inputs. The given relations allow effectively calculating parameters of transmitting and receiving phased antenna arrays.
Predictive Value of Methicillin-Resistant Staphylococcus aureus (MRSA) Nasal Swab PCR Assay for MRSA Pneumonia

ABSTRACT Pneumonia due to methicillin-resistant Staphylococcus aureus (MRSA) is associated with poor outcomes and frequently merits empirical antibiotic consideration despite its relatively low incidence. Nasal colonization with MRSA is associated with clinical MRSA infection and can be reliably detected using the nasal swab PCR assay. In this study, we evaluated the performance of the nasal swab MRSA PCR in predicting MRSA pneumonia. A retrospective cohort study was performed in a tertiary care center from January 2009 to July 2011. All patients with confirmed pneumonia who had both a nasal swab MRSA PCR test and a bacterial culture within predefined time intervals were included in the study. These data were used to calculate sensitivity, specificity, positive predictive value, and negative predictive value for clinically confirmed MRSA pneumonia. Four hundred thirty-five patients met inclusion criteria. The majority of cases were classified as either health care-associated (HCAP) (54.7%) or community-acquired (CAP) (34%) pneumonia. MRSA nasal PCR was positive in 62 (14.3%) cases. MRSA pneumonia was confirmed by culture in 25 (5.7%) cases. The MRSA PCR assay demonstrated 88.0% sensitivity and 90.1% specificity, with a positive predictive value of 35.4% and a negative predictive value of 99.2%. In patients with pneumonia, the MRSA PCR nasal swab has a poor positive predictive value but an excellent negative predictive value for MRSA pneumonia in populations with low MRSA pneumonia incidence. In cases of culture-negative pneumonia where initial empirical antibiotics include an MRSA-active agent, a negative MRSA PCR swab can be reasonably used to guide antibiotic de-escalation.
Dispersion of changes in cloned and non-cloned code

Currently, the impacts of clones in software maintenance activities are being investigated by different researchers in different ways. Comparative stability analysis of cloned and non-cloned regions of a subject system is a well-known way of measuring the impacts where the hypothesis is that, the more a region is stable the less it is harmful for maintenance. Each of the existing stability measurement methods lacks to address one important characteristic, dispersion, of the changes happening in the cloned and non-cloned regions of software systems. Change dispersion of a particular region quantifies the extent to which the changes are scattered over that region. The intuition is that, more dispersed changes require more efforts to be spent in the maintenance phase. Measurement of Dispersion requires the extraction of method genealogies. In this paper, we have measured the dispersions of changes in cloned and non-cloned regions of several subject systems using a concurrent and robust framework for method genealogy extraction. We implemented the framework on Actor Architecture platform which facilitates coarse grained parallellism with asynchronous message passing capabilities. Our experimental results on 12 open-source subject systems written in three different programming languages (Java, C and C#) using two clone detection tools suggest that, the changes in cloned regions are more dispersed than the changes in non-cloned regions. Also, Type-3 clones exhibit more dispersion as compared to the Type-1 and Type-2 clones. The subject systems written in Java and C show higher dispersions as well as increased maintenance efforts as compared to the subject systems written in C#.
Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli

An essential part of gene expression is the coordination of RNA synthesis and degradation, which occurs in the same cellular compartment in bacteria. Here, we report a genome‐wide RNA degradation study in Escherichia coli using RNA‐seq, and present evidence that the stereotypical exponential RNA decay curve obtained using initiation inhibitor, rifampicin, consists of two phases: residual RNA synthesis, a delay in the interruption of steady state that is dependent on distance relative to the mRNA's 5′ end, and the exponential decay. This gives a more accurate RNA lifetime and RNA polymerase elongation rate simultaneously genome‐wide. Transcripts typically have a single RNA decay constant along all positions, which is distinct between different operons, indicating that RNA stability is unlikely determined by local sequences. These measurements allowed us to establish a model for RNA processing involving co‐transcriptional degradation, providing quantitative description of the macromolecular coordination in gene expression in bacteria on a system‐wide level.
Linguistic symbiosis between actors and threads

We describe a linguistic symbiosis between AmbientTalk, a flexible, domain-specific language for writing distributed programs and Java, a conventional object-oriented language. This symbiosis allows concerns related to distribution (service discovery, asynchronous communication, failure handling) to be handled in the domain-specific language, while still enabling the reuse of existing software components written in a conventional language. The symbiosis is novel in the sense that a mapping is defined between the concurrency models of both languages. AmbientTalk employs an inherently event-driven model based on actors, while conventional object-oriented languages employ a concurrency model based on threads. The contribution of this paper is a linguistic symbiosis which ensures that the invariants of the event-driven concurrency model are not violated by engaging in symbiosis with multi-threaded programs.
The Impact of Feedback-driven Outflows on Bar Formation

We investigate the coupling between the temporal variation from galaxy-formation feedback and the bar instability. We show that fluctuations from mass outflow on star-formation time scales affect the radial motion of disk orbits. The resulting incoherence in orbital phase leads to the disruption of the bar-forming dynamics. Bar formation is suppressed in starburst galaxies that have fluctuation time scales within the range 10 Myr to 200 Myr with repeated events with wind mass 15% of the disk within 0.5 scale lengths or 1.4% of the total disk mass. The work done by feedback is capable of reducing the amplitude or, with enough amplitude, destroying an existing bar. AGN feedback with similar amplitude and timescales would have similar behavior. To model the dynamics of the coupling and interpret the results of the full N-body simulations, we introduce a generalization of the Hamiltonian mean-field (HMF) model, drawing inspiration from the Lynden-Bell (1979) mechanism for bar growth. Our non-linear 'BarHMF' model is designed to reproduce linear perturbation theory in the low-amplitude limit. Notably, without star-formation feedback, this model exhibits exponential growth whose rate depends on disk mass and reproduces the expected saturation of bar growth observed in N-body simulations. We describe several promising applications of the BarHMF model beyond this study.
Extracting models from IDE ’ s ∗

Systems must co-evolve with their context. Reverse engineering tools are a great help in this process of required adaption. In order for these tools to be flexible, they work with models, abstract representations of the source code. The extraction of such information from source code can be done using a parser. However, it is fairly tedious to build new parsers. And this is made worse by the fact that it has to be done over and over again for every language we want to analyze. In this paper we propose a novel approach which minimizes the knowledge required of a certain language for the extraction of models implemented in that language by reflecting on the implementation of preparsed ASTs provided by an IDE. In a second phase we use a technique referred to as Model Mapping by Example to map platform dependent models onto domain specific model.
Railway subsidence monitoring by high resolution INSAR time series analysis in Tianjin

Large-scale man-made linear features has played more and more important role in modern life and the development of urban are seriously affected by the subsidence of them. Permanent Scatterers (PS) technology was developed as a powerful tool for subsidence monitoring. High resolution of 1m data can be provided by TerraSAR X-band (TSX) with a short revisit period of 11 days. More detail and sensitive subsidence information can be expected to be detected by X-band. In this paper, we exploited the potential of TSX for railway subsidence monitoring. A case study was conducted in Tianjin. A total of 37 TSX images acquired from 2009/4/29 to 2010/11/11 were used in PS analysis. The average deformation map and geocoded Permanent Scatterer were generated by SARPROZ.
Real-time quantification of microRNAs by stem–loop RT–PCR

A novel microRNA (miRNA) quantification method has been developed using stem–loop RT followed by TaqMan PCR analysis. Stem–loop RT primers are better than conventional ones in terms of RT efficiency and specificity. TaqMan miRNA assays are specific for mature miRNAs and discriminate among related miRNAs that differ by as little as one nucleotide. Furthermore, they are not affected by genomic DNA contamination. Precise quantification is achieved routinely with as little as 25 pg of total RNA for most miRNAs. In fact, the high sensitivity, specificity and precision of this method allows for direct analysis of a single cell without nucleic acid purification. Like standard TaqMan gene expression assays, TaqMan miRNA assays exhibit a dynamic range of seven orders of magnitude. Quantification of five miRNAs in seven mouse tissues showed variation from less than 10 to more than 30 000 copies per cell. This method enables fast, accurate and sensitive miRNA expression profiling and can identify and monitor potential biomarkers specific to tissues or diseases. Stem–loop RT–PCR can be used for the quantification of other small RNA molecules such as short interfering RNAs (siRNAs). Furthermore, the concept of stem–loop RT primer design could be applied in small RNA cloning and multiplex assays for better specificity and efficiency.
Mathematics Growth in Early Elementary School: The Roles of Beginning Knowledge, Student Engagement, and Instruction

We used the Early Childhood Longitudinal Study—Kindergarten Cohort (ECLS‐K) data to examine how important mathematics readiness levels are to subsequent achievement growth and the efficacy of instruction and engagement in producing such growth. The ECLS‐K selected a nationally representative sample of kindergartners in fall 1998 and is following these children through the end of eighth grade. We employed the standardized mathematics assessments that were administered to the students by ECLS‐K staff. Separately for students who began kindergarten with low, medium‐low, medium‐high, and high mathematics skill, we examined achievement growth through third grade and the effects of teacher‐reported time on mathematics instruction and student engagement (as perceived by the teacher) on such growth. We found that students who began with the lowest achievement also showed the least growth over this period. Students in the two highest skills groups had similar growth, and the highest levels of growth. Students in the lowest group received the most time on instruction but had the lowest engagement with instruction. Time on instruction increased achievement for all students equally, but the effect of engagement was strongest among the lowest‐performing group. The lower engagement of the lowest‐performing group explained more than half of their lower achievement growth in grades K–3. If inequality in mathematics achievement is to be reduced, teachers must make greater efforts to improve the beginning knowledge and academic engagement of this group.
Evaluation of Blue Gene/Q hardware support for transactional memories

This paper describes an end-to-end system implementation of the transactional memory (TM) programming model on top of the hardware transactional memory (HTM) of the Blue Gene/Q (BG/Q) machine. The TM programming model supports most C/C++ programming constructs on top of a best-effort HTM with the help of a complete software stack including the compiler, the kernel, and the TM runtime. An extensive evaluation of the STAMP benchmarks on BG/Q is the first of its kind in understanding characteristics of running coarse-grained TM workloads on HTMs. The study reveals several interesting insights on the overhead and the scalability of BG/Q HTM with respect to sequential execution, coarse-grain locking, and software TM.
Papillary necrosis with invasive fungal infections: a case series of 29 patients

Background Renal papillary necrosis (RPN) is associated with a number of comorbid conditions. However, it has been rarely reported in patients with fungal infections of the kidney. Methods We analyzed medical records of our hospital for the last two decades and identified 29 patients with fungal infections and RPN. Results Among the 29 patients, there were 24 men and 5 women. The median (range) age at presentation was 31.2 years (2 days–73 years). Three patients (10%) were kidney transplant recipients. The remaining had varied co-existing medical conditions that included diabetes mellitus in 16 (55%) and septicemia in 4 (14%). Clinical features at presentation were fever and oliguric kidney failure in 17 patients and loin pain accompanied by passage of fleshy material per urethra in 11 (38%). Diagnosis was made ante-mortem in 17 (59%) patients. Twenty patients (69%) had infection limited to the kidneys, while in the rest, it was disseminated. Kidney involvement was bilateral in 17 patients (59%). Urinalysis showed pyuria in 23 (79%) and microhematuria in 8 (28%) patients. Fungal infections included candidiasis (69%), aspergillosis (21%) and zygomycosis (10%). Of the 17 patients in whom the diagnoses was made ante-mortem, 12 survived and 5 died. Overall mortality was observed in 48% of cases. Conclusions We herein report a series of patients with RPN associated with fungal infections of the kidney. Presentation varies from asymptomatic urinary tract infection to severe kidney failure with poor outcome. High index of suspicion is necessary to reduce the associated high mortality in these patients.