Miracle-dz/UniFAR-FTUs huggingface dataset:
Analytical Performance of a Real-time PCR-based Assay for V600 Mutations in the BRAF Gene, Used as the Companion Diagnostic Test for the Novel BRAF Inhibitor Vemurafenib in Metastatic Melanoma

Melanomas frequently harbor BRAFV600 mutations. Vemurafenib (RG7204/PLX4032), a small-molecule inhibitor of mutant BRAF, has shown striking clinical efficacy in BRAFV600 mutant melanoma, creating the need for a well-validated companion diagnostic to select patients for treatment. We describe analytic performance characteristics of the cobas 4800 BRAF V600 Mutation Test, the test used to select patients for the pivotal vemurafenib trials. This real-time polymerase chain reaction assay was designed to detect the V600E (1799T>A) mutation DNA from formalin-fixed paraffin-embedded tissue samples. Sensitivity was assessed using blends of cell lines or tumor DNA, and tumor specimens with low levels of mutant alleles, as determined by 454 sequencing (a quantitative next-generation pyrosequencing method). A >96% hit rate was obtained across all specimen types with 5% mutant alleles at a DNA input of 125 ng, an amount readily obtained from one 5-&mgr;m section. The cobas test showed a higher sensitivity and specificity than direct bidirectional sequencing in a panel of 219 melanoma specimens. Cross reactivity with V600K and V600D was observed. Repeated testing of 5 specimens by 2 operators, using different instruments and reagent lots, yielded correct calls in 158/160 tests (98.8%). A set of 26 highly pigmented samples were identified that gave invalid test results. A simple 1:2 dilution resulted in a valid test result of 76% in such cases. The cobas test is a reproducible assay that detects some non-V600E mutations and is more accurate than direct sequencing in detecting BRAFV600E.
Self-Supervised Learning of Visual Features through Embedding Images into Text Topic Spaces

End-to-end training from scratch of current deep architectures for new computer vision problems would require Imagenet-scale datasets, and this is not always possible. In this paper we present a method that is able to take advantage of freely available multi-modal content to train computer vision algorithms without human supervision. We put forward the idea of performing self-supervised learning of visual features by mining a large scale corpus of multi-modal (text and image) documents. We show that discriminative visual features can be learnt efficiently by training a CNN to predict the semantic context in which a particular image is more probable to appear as an illustration. For this we leverage the hidden semantic structures discovered in the text corpus with a well-known topic modeling technique. Our experiments demonstrate state of the art performance in image classification, object detection, and multi-modal retrieval compared to recent self-supervised or natural-supervised approaches.
Robust stability analysis for uncertain time-delay systems based on polyhedral Lyapunov-Krasovskii functional

This paper introduces some robust stability conditions for a class of time delay systems whose uncertainties are assumed to be time-invariant and belong to convex bounded polytopic domain. Both single polyhedral and double polyhedral Lyapunov functionals are defined according to the form of Lyapunov-Krasovskii functional. And based on these functionals, the new results of robust stability analysis can reduce the conservatism of quadratic stability. All the proposed stability conditions are expressed in terms of linear matrix inequality (LMI). Two numerical examples are given to illustrate the advantages of the stability conditions based on the double polyhedral Lyapunov functional.
Whispering-Gallery-Mode Resonator Technique With Microfluidic Channel for Permittivity Measurement of Liquids

Studies of biochemical liquids require precise determination of their complex permittivity. We developed a microwave characterization technique on the basis of a high-quality whispering-gallery mode (WGM) sapphire resonator with a microfluidic channel filled with the liquid under test. A novel approach allows obtaining the complex permittivity of biochemical liquids of sub-microliter/nanoliter volumes with high accuracy. The method is based on a special procedure of analysis of the interaction of electromagnetic field with liquid in a WGM microfluidic resonator and measurements of both the WGM resonance frequency shift and the change of the inverse quality factor. The approach is successfully applied to obtain the complex permittivity in the Ka-band of glucose, albumin bovine serum, lactalbumin, and cytochrome C aqueous solutions using the developed microwave technique.
Motor unit recruitment and bursts of activity in the surface electromyogram during a sustained contraction

Bursts of activity in the surface electromyogram (EMG) during a sustained contraction have been interpreted as corresponding to the transient recruitment of motor units, but this association has never been confirmed. The current study compared the timing of trains of action potentials discharged by single motor units during a sustained contraction with the bursts of activity detected in the surface EMG signal. The 20 motor units from 6 subjects [recruitment threshold, 35.3 ± 11.3% maximal voluntary contraction (MVC) force] that were detected with fine wire electrodes discharged 2–9 trains of action potentials (7.2 ± 5.6 s in duration) when recruited during a contraction that was sustained at a force below its recruitment threshold (target force, 25.4 ± 10.6% MVC force). High‐pass filtering the bipolar surface EMG signal improved its correlation with the single motor unit signal. An algorithm applied to the surface EMG was able to detect 75% of the trains of motor unit action potentials. The results indicate that bursts of activity in the surface EMG during a constant‐force contraction correspond to the transient recruitment of higher‐threshold motor units in healthy individuals, and these results could assist in the diagnosis and design of treatment in individuals who demonstrate deficits in motor unit activation. Muscle Nerve, 2008
Argumentation-based reasoning in agents with varying degrees of trust

In any group of agents, trust plays an important role. The degree to which agents trust one another will inform what they believe, and, as a result the reasoning that they perform and the conclusions that they come to when that involves information from other agents. In this paper we consider a group of agents with varying degrees of trust of each other, and examine the combinations of trust with the argumentation-based reasoning that they can carry out. The question we seek to answer is "What is the relationship between the trust one agent has in another and the conclusions that it can draw using information from that agent? ", and show that there are a range of answers depending upon the way that the agents deal with trust.
What's the link between household income and going to university?

The association between household income and university entry is a matter of clear academic and policy interest. This paper sheds new light on the matter using the LSYPE, a recent longitudinal survey from England. While those in the top income quintile group are more likely than those in the bottom quintile group to attend university (66% vs. 24%), much of this gap is explained by earlier educational outcomes. The paper also examines admissions decisions in more detail, separating applying from attending. This analysis yields results suggesting most of the difference in participation rates is driven by the application decision. The attendance gap conditional on having applied is much smaller (85% vs. 68%) and closes completely when earlier educational outcomes are taken into account. Finally, the paper considers attendance at high quality Russell Group universities. By contrast with the main analysis, the Russell Group attendance gap persists even among those who attend university. The findings suggest policies aimed at reducing the university participation gap at point of entry face small rewards. More likely successful are policies aimed at closing the application gap, for example encouraging a wider cross-section of the population to apply and ensuring they have the necessary qualifications.
Fault diagnosis aware ATE assisted test response compaction

Recently a new method called ATE assisted compaction for achieving test response compaction has been proposed. The method relies on testers to achieve additional compaction, without compromising fault coverage, beyond what may already be achieved using on-chip response compactors. The method does not add additional logic or modify the circuit under test or require additional tests and thus can be used with any design including legacy designs. In this work, we enhance this method so that the level of diagnostic resolution achieved without it can be maintained. Experimental results on larger ISCAS-89 show that additional test response compaction can be achieved while diagnostic resolution for single and double stuck-at faults is not adversely impacted by the procedure.
A mouse model for monitoring islet cell genesis and developing therapies for diabetes

SUMMARY Transient expression of the transcription factor neurogenin-3 marks progenitor cells in the pancreas as they differentiate into islet cells. We developed a transgenic mouse line in which the surrogate markers secreted alkaline phosphatase (SeAP) and enhanced green florescent protein (EGFP) can be used to monitor neurogenin-3 expression, and thus islet cell genesis. In transgenic embryos, cells expressing EGFP lined the pancreatic ducts. SeAP was readily detectable in embryos, in the media of cultured embryonic pancreases and in the serum of adult animals. Treatment with the γ-secretase inhibitor DAPT, which blocks Notch signaling, enhanced SeAP secretion rates and increased the number of EGFP-expressing cells as assayed by fluorescence-activated cell sorting (FACS) and immunohistochemistry in cultured pancreases from embryos at embryonic day 11.5, but not in pancreases harvested 1 day later. By contrast, treatment with growth differentiation factor 11 (GDF11) reduced SeAP secretion rates. In adult mice, partial pancreatectomy decreased, whereas duct ligation increased, circulating SeAP levels. This model will be useful for studying signals involved in islet cell genesis in vivo and developing therapies that induce this process.
Business Model Shocks and Abnormal Accrual Models

Basic economics challenge the specification of discretionary accrual models. Since rent seeking firms pursue differentiated business strategies, firms in the same industry have heterogeneous accrual generating processes. Moreover, technological innovation, regulatory changes, and entry of new firms force existing firms to revise their extant business models. We present evidence that such business model shocks are widespread, propagate through multiple years of financial statements, reduce accrual models’ goodness of fit, and result in unrealistically large unsigned “abnormal” accruals. Further, there is a spillover effect among firms in the same industry in that one firm’s abnormal accrual is affected by business model shocks experienced by the other firms in the industry. We show that business model shocks not only add noise to abnormal accruals, but can also introduce biases into both unsigned and signed discretionary accruals. Our results suggest that removing observations with business model shocks leads to better specified accrual models, and reduces both Type I and Type II errors in tests of earnings management.
Fuzzy model of control for quantum-controlled mobile robots

In this work we consider a navigation of quantum-controlled mobile robot by the use of fuzzy methods. A fuzzy model of the robot behavior is obtained by transformation of the robot's states (that appear in a form of qubits) into the pairs of membership functions. For a full description of the robot's turns, we define a reverse fuzzy Hadamard operator that completes the known Hannachi, Hatakeyama and Hirota model. The suggested transformations and methods were comparatively studied by field trials using small mobile robots and by numerical simulations that model the robot's behavior in the presence of noise.
Wilson loops and QCD/string scattering amplitudes

We generalize modern ideas about the duality between Wilson loops and scattering amplitudes in N=4 super Yang-Mills theory to large N QCD by deriving a general relation between QCD meson scattering amplitudes and Wilson loops. We then investigate properties of the open-string disk amplitude integrated over reparametrizations. When the Wilson-loop is approximated by the area behavior, we find that the QCD scattering amplitude is a convolution of the standard Koba-Nielsen integrand and a kernel. As usual poles originate from the first factor, whereas no (momentum-dependent) poles can arise from the kernel. We show that the kernel becomes a constant when the number of external particles becomes large. The usual Veneziano amplitude then emerges in the kinematical regime, where the Wilson loop can be reliably approximated by the area behavior. In this case, we obtain a direct duality between Wilson loops and scattering amplitudes when spatial variables and momenta are interchanged, in analogy with the N=4 super Yang-Mills theory case.
Processing Spatial-Keyword (SK) Queries in Geographic Information Retrieval (GIR) Systems

Location-based information contained in publicly available GIS databases is invaluable for many applications such as disaster response, national infrastructure protection, crime analysis, and numerous others. The information entities of such databases have both spatial and textual descriptions. Likewise, queries issued to the databases also contain spatial and textual components, for example, "Find shelters with emergency medical facilities in Orange County," or "Find earthquake-prone zones in Southern California. " We refer to such queries as spatial-keyword queries or SK queries for short. In recent times, a lot of interest has been generated in efficient processing of SK queries for a variety of applications from Web-search to GIS decision support systems. We refer to systems built for enabling such applications as Geographic Information Retrieval (GIR) Systems. An example GIR system that we address in this paper is a search engine built on top of hundreds of thousands of publicly available GIS databases. Building a search engine over such large repositories is a challenge. One of the key aspects of such a search engine is the performance. In this paper, we propose a framework for GIR systems and focus on indexing strategies that can process SK queries efficiently. We show through experiments that our indexing strategies lead to significant improvement in efficiency of answering SK queries over existing techniques.
[Bronchoscopic diagnosis of pneumonia].

INTRODUCTION . CLINICAL ASPECTS. Clinical Indications. Pneumonia in immunosuppressed patients VAP . CAP. Therapeutic Implications. Cost/benefit ratio. Reliability of negative culture results. BfRONCH0.l('AOPIC TFCHNIOI--Procedure. 536 Specimen Types.537 Bronchial washings . 537 Bronchial brushings . 537 PSB. 537 BAL. 538 TBB. 538 Complications.538 VERVIEW OF LABORATORY METHODS. 538
The value of serum biomarkers in prediction models of outcome after mild traumatic brain injury.

BACKGROUND To determine, using a civilian model of mild traumatic brain injury (TBI), the added value of biomarker sampling upon prognostication of outcome at 1 week and 6 weeks postinjury. METHODS The Galveston Orientation and Amnesia test was administered, and blood samples for serum protein S100B and neuron-specific enolase (NSE) were collected from 141 emergency department patients within 4 hours of a suspected mild TBI (mTBI). The Rivermead Post-Concussion Symptoms Questionnaire (RPQ) was administered via telephone 3 days postinjury. Patients were assessed by a physician at 1 week (n = 113; 80%) and 6 weeks (n = 95; 67%) postinjury. Neurocognitive and postural stability measures were also administered at these follow-ups. RESULTS Levels of S100B and NSE were found to be abnormally elevated in 49% and 65% of patients with TBI, respectively. Sixty-eight percent and 38% of the patients were considered impaired at 1 week and 6 weeks postinjury, respectively. Stepwise logistic regression modeling identified admission Galveston Orientation and Amnesia test score, S100B level, and RPQ score at day 3 postinjury to be predictive of poor outcome at 1 week postinjury (c-statistic 0.877); female gender, loss of consciousness, NSE level, and RPQ score at day 3 postinjury were predictive of poor outcome at 6 weeks postinjury (c-statistic 0.895). The discriminative power of the biomarkers alone was limited. CONCLUSIONS Biomarkers, in conjunction with other readily available determinants of outcome assessed in the acute period after injury, add value in the early prognostication of patients with mTBI. Our findings are consistent with the notion that S100B and NSE point to biological mechanisms underlying poor outcome after mTBI.
Low power implementation of MDCT/IMDCT for MP3 audio decoder

The MDCT/IMDCT is the basic processing component for digital audio compression. It is also the most computationally intensive operation in audio compression standards. MP3 is still used in the audio standards for audio compression. This paper presents a new and efficient implementation of 12/36-point MDCT/IMDCT architectures for MP3. The proposed architecture utilize Chartered 90nm CMOS technology and optimized for low power applications. Low power libraries and clock gating technique are used for power reduction. Our experimental results show the effectiveness to implementation of MDCT /IMDCT core for MP3
Dynamics and star formation activity of CG J1720-67.8 unveiled through integral field spectroscopy and radio observations

CG J1720-67.8 is an ultra compact group of several galaxies with a low-velocity dispersion, and displaying the hallmarks of mutual interaction and possible tidal dwarf galaxy formation. In hierarchical models, the system is a possible precursor to a massive elliptical galaxy. In this paper, we use new optical integral field spectroscopic and radio observations to investigate the evolutionary status of the group in more detail: global star formation rates are estimated using Ha and 1.4-GHz radio continuum measurements; H I observations provide an upper limit to the global neutral gas content; optical broadband colours and spectra provide ages and stellar mass estimates for the tidal dwarf candidates; the bi-dimensional Ha velocity field is used to trace the kinematics of the group and its members, which are compared with numerical simulations of galaxy encounters. The observations suggest a model in which multiple interactions have occurred, with the latest strong encounter involving at least two major components within the last 200 Myr. Debris from the encounter fuels ongoing star formation at the global level of ∼20 M ○. yr -1 , with self-gravity within the tidal tail possibly providing a mechanism to enhance the star formation rate of the tidal dwarf candidates, with bursts of star formation in clumps of mass ∼2 x 10 7 M ○. appearing within the last 10 Myr. The amount of time required for final merging of all group components remains uncertain.
Consumer response to dual incentives under multitiered prescription drug formularies.

OBJECTIVE To decompose the overall effect of multitiered formularies on drug utilization and spending into the following 2 observed effects on consumer behavior: first, higher copayments on drug equivalents create an incentive to reduce the number of prescriptions, and, second, wider differential copayments between drug equivalents create an incentive to use a greater proportion of generics. STUDY DESIGN We merged drug claims for 352,760 retired Medicare enrollees having employer-sponsored health insurance with benefit information. Our unit of analysis was the enrollee. We used cross-sectional variation in incentive-based formularies to compare the effects of increased copayment amounts for drug equivalents with those of increased copayment differentials between drug equivalents. The study sample may not be representative of the Medicare population. METHODS Multivariate regression analysis using the 2002 MarketScan Medicare Supplemental and Coordination of Benefits database and Benefit Plan Design database. RESULTS A 10% increase in copayments for drug equivalents was associated with a 1.3% reduction in total drug spending, a 16.0% increase in out-of-pocket expenditures, a 2.0% reduction in the number of prescriptions filled, and a 0.7% reduction in proportion of prescriptions filled with generics. A 10% increase in copayment differentials between drug equivalents was associated with a 1.0% reduction in total drug spending, a 4.1% increase in out-of-pocket expenditures, a 1.0% reduction in the number of prescriptions filled, and a 0.7% increase in proportion of prescriptions filled with generics. CONCLUSION Increasing copayment differentials between drug equivalents is as effective a strategy for reducing total drug spending as increasing copayment amounts for drug equivalents but better maintains access to prescription medications.
Comparison of three different sit and reach tests for measurement of hamstring flexibility in female university students

Background: The sit and reach test is the most common flexibility test used in health related fitness test batteries. Objective: To examine and compare three different sit and reach tests as a measure of hamstring flexibility in 102 female students. Method: The traditional sit and reach test, the chair sit and reach test, the back saver sit and reach test, and passive straight leg raise were administered in three trials to all 102 students (mean (SD) age 22 (1) years) on the same day. Results: A Pearson correlation coefficient analysis was significant (p<0.01) for the traditional sit and reach test with back saver sit and reach test and flexibility of hamstrings (r = 0.45 and 0.65 for left and right legs, and 0.63 and 0.53 for left and right legs respectively). Also, the back saver sit and reach test for the left (p<0.01) and right (p<0.05) leg was significantly associated with hamstring flexibility (r = 0.37 and 0.25 for the left leg and 0.50 and 0.44 for the right leg respectively). Conclusion: The results indicate that the back saver sit and reach test produces reasonably accurate and stable measures of hamstring flexibility. Moreover, it appears that this test is a safe and acceptable alternative to the traditional and chair sit and reach tests as a measure of hamstring flexibility in young women.
Low dose ionizing radiation strongly stimulates insertional mutagenesis in a γH2AX dependent manner

Extrachromosomal DNA can integrate into the genome with no sequence specificity producing an insertional mutation. This process, which is referred to as random integration (RI), requires a double stranded break (DSB) in the genome. Inducing DSBs by various means, including ionizing radiation, increases the frequency of integration. Here we report that non-lethal physiologically relevant doses of ionizing radiation (10-100 mGy), within the range produced by medical imaging equipment, stimulate RI of transfected and viral episomal DNA in human and mouse cells with an extremely high efficiency. Genetic analysis of stimulated RI (S-RI) revealed that it is distinct from the background RI, requires histone H2AX S139 phosphorylation (γH2AX) and is not reduced by DNA polymerase θ (Polq) inactivation. S-RI efficiency was unaffected by the main DSB repair pathway (homologous recombination and non-homologous end joining) disruptions, but double deficiency in MDC1 and 53BP1 phenocopies γH2AX inactivation. The robust responsiveness of S-RI to physiological amounts of DSBs has implications for radiation risk assessment and can be exploited for extremely sensitive, macroscopic and direct detection of DSB-induced mutations.