Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene profiling predicts rheumatoid arthritis responsiveness to IL-1Ra (anakinra).

OBJECTIVES The overall non-response rate to biologics remains 30-40% for patients with RA resistant to MTX. The objective of this study was to predict responsiveness to the anakinra-MTX combination by peripheral blood mononuclear cell gene profiling in order to optimize treatment choice. METHODS Thirty-two patients treated with anakinra (100 mg/day s.c.) and MTX were categorized as responders when their 28-joint DAS (DAS-28) had decreased by ≥1.2 at 3 months. Pre-treatment blood samples had been drawn. RESULTS For seven responders and seven non-responders, 52 microarray-identified mRNAs were expressed as a function of the response to treatment, and unsupervised hierarchical clustering correctly separated responders from non-responders. The levels of seven of these 52 transcripts, as assessed by real-time, quantitative RT-PCR, were able to accurately classify 15 of 18 other patients (8 responders and 10 non-responders), with 87.5% specificity and 77.8% negative-predictive value for responders. Among the 52 genes, 56% were associated with IL-1β. CONCLUSION This predictive gene expression profile was obtained with a non-invasive procedure. After further validation in other cohorts of patients, it could be proposed and used on a large scale to select likely RA responders to combined anakinra-MTX. Trial registration. Clinical Trials; NCT00213538 (http://www.clinicaltrials.gov).
Chronic peer victimization heightens neural sensitivity to risk taking

Abstract Although behavioral and experimental studies have shown links between victimization and antisocial behavior, the neural correlates explaining this link are relatively unknown. In the current study, we recruited adolescent girls from a longitudinal study that tracked youths’ reports of peer victimization experiences annually from the second through eighth grades. Based on these reports, 46 adolescents were recruited: 25 chronically victimized and 21 nonvictimized. During a functional magnetic resonance imaging scan, participants completed a risk-taking task. Chronic peer victimization was associated with greater risk-taking behavior during the task and higher levels of self-reported antisocial behavior in everyday life. At the neural level, chronically victimized girls showed greater activation in regions involved in affective sensitivity, social cognition, and cognitive control, which significantly mediated victimization group differences in self-reported antisocial behavior.
Rapid Simultaneous Determination of Lidocaine, Bupivacaine, and Their Two Main Metabolites Using Capillary Gas‐Liquid Chromatography with Nitrogen Phosphorus Detector

A gas-liquid chromatographic method for the simultaneous measurement in serum of bupivacaine, lidocaine, and their main metabolites, 2,6-pipecolylxylidide (PPX) and monoethylglycine xylidide (MEGX), respectively, is described. The procedure involves a one-step extraction and injection of the extract into a gas chromatograph equipped with a capillary column and nitrogen phosphorus detector under constant temperature conditions. Recovery of all components averaged 94%, with the lowest detection limit of 15 ng/ml for the four drugs. The precision within-series coefficients of variation ranged from 7.7% for bupivacaine, 8.6% for lidocaine, 10.2% for MEGX, and 15.8% for PPX. The interday coefficients ranged from 0.7 to 6.5%. Concomitant use of caffeine and carbamazepine may interfere with MEGX and bupivacaine determination, respectively. For this reason, in patients receiving one of these two drugs (or ingesting foods and beverages containing caffeine), the described method is not recommended.
Simultaneous Fault Detection and Sensor Selection for Condition Monitoring of Wind Turbines

Data collected from the supervisory control and data acquisition (SCADA) system are used widely in wind farms to obtain operation and performance information about wind turbines. The paper presents a three-way model by means of parallel factor analysis (PARAFAC) for wind turbine fault detection and sensor selection, and evaluates the method with SCADA data obtained from an operational farm. The main characteristic of this new approach is that it can be used to simultaneously explore measurement sample profiles and sensors profiles to avoid discarding potentially relevant information for feature extraction. With K-means clustering method, the measurement data indicating normal, fault and alarm conditions of the wind turbines can be identified, and the sensor array can be optimised for effective condition monitoring.
A Back-EMF Threshold Self-Sensing Method to Detect the Commutation Instants in BLDC Drives

By predicting future phase-current commutation instants of brushless dc (BLDC) machines, self-sensing control is achieved. Detection of the back electromotive force (EMF) zero-crossing moments is one of the methods used to predict the phase-current commutation instants. Most of the techniques based on back-EMF zero-crossing detection have the inherit disadvantage of an indirect prediction of commutation instants. This is the result of the commutation instant occurring at the 30° electrical position after zero-crossing of the induced back-EMF in the unexcited phase. Often, the time difference between the zero-crossing of the back-EMF and the current commutation instant is assumed constant. This assumption can be valid for steady-state operation; however, a different time span should be taken into account during transient operation of the BLDC machine. To overcome this problem, an enhancement is proposed here, which improves the performance while keeping the simplicity of the back-EMF zero-crossing detection method.
Family-based analysis of apelin and AGTRL1 gene polymorphisms with hypertension in Han Chinese

Objective Apelin and AGTRL1 (angiotensin receptor-like 1), elements of a newly identified pathway with a role in counter regulating the renin-angiotensin system, have been implicated in blood pressure regulation. This study aims to assess whether the apelin and AGTRL1 genetic polymorphisms might contribute to essential hypertension or its related phenotypes. Methods We recruited 1015 Han Chinese from 248 families with essential hypertension. Each individual was genotyped for 6 single nucleotide polymorphisms (SNPs) in apelin and 6 SNPs in AGTRL1. Data were analyzed using the family-based association test (FBAT) and the haplotype-based association test (HBAT). Results FBAT analysis showed that two SNPs rs3761581 and T-1860C within apelin conferred significant association with hypertension and its related phenotypes even after correcting for age and gender. Three SNPs (rs7119375, rs10501367 and rs9943582) within AGTRL1 were found to be associated with hypertension, BMI and the onset age of hypertension, whereas after correction, only marginal associations were noted. Of the common haplotypes (with frequencies over 3%), haplotypes (A-T) and (C-C) comprising rs3761581 and T-1860C in apelin and haplotype (G-G) comprising rs10501367 and rs7119375 in AGTRL1 were shown to be significantly associated with hypertension, BMI and the onset age of hypertension, even after a permutation correction. Conclusions Our study suggests that genetic variation within apelin and AGTRL1 likely contributes to essential hypertension, BMI and the onset age of hypertension. Future well designed epidemiological or functional studies would be warranted to validate this hypothesis.
The Situational Assessment Method put to the test: Improvements based on case studies

This paper presents an improved Situational Assessment Method (SAM) for Software Product Management (SPM). The improvement is the result of an evaluation process, of which one of the cases is included in this paper. The SAM is tool which allows product managers to evaluate and improve their processes in an incremental manner. It does this by determining which capabilities the organization has currently achieved, and what capabilities should be achieved. A gap analysis can then be performed which results in an advice to implement specific capabilities. This advice includes suggestions for method fragments (best practices) which the organization can use to achieve the capabilities.
Shared Genomics: Accessible High Performance Computing for Genomic Medical Research

The study of the genetic causes of disease is entering a new era. Variations in DNA sequence between individuals at a single position (locus) within the human genome are termed single nucleotide polymorphisms (SNPs), and may lead to a frank disease state or a variation in normal physiology. By comparing and contrasting the genomes of people who have a disease with the genomes of people who don't, we can begin to identify those genetic locii which potentially play a role in the disease. Modern biotechnology allows for the genotyping of individuals at hundreds of thousands of genetic locii. Whilst metrics to quantify the statistical importance of a single locus are essentially of low complexity, for example calculation of a x2 statistic, within a genome-wide association study this process is repeated at every locus. In addition, the entire computational process is often repeated with a number of randomised data sets, necessary for estimation of the statistical significance. The large number of locii, number of randomized data sets, and rapid combinatorial increase when analysing multiple SNPs, naturally dictates that a high performance computing (HPC) solution be developed. On a single core machine analysis of significant numbers of SNP pairs would take many years. Once statistical analysis of the data has been performed results must be annotated with relevant information to aid biological interpretation and hypothesis generation - this is a standard, but not in substantial bioinformatic task.
A fully-dynamic data structure for external substring search

We address the issue of efficiently searching on external dynamic data structures for strings, introducing the External Dynamic Substring Search problem. Consider a set A of (external) text strings kept into secondary storage. The set A can be dynamically changed by inserting or deleting strings, and on-line searched to find all the occurrences of an arbitrary pattern string as a substring of the text strings in A. We introduce the SBTree data structure for A, which is the first fully-dynamic data structure allowing the External Dynamic Substring Search problem to be solved with provably good worst-case and amortized 1/0 bounds. It requires optimal space and makes the on-line search alphabet independent also into main memory. The SB-tree can also be used to solve a natural extension of our problem to parameterized strings (p-strings) within the same bounds.
A Case Study on Teaching Software Engineering Concepts using a Case-Based Learning Environment

Case-based teaching is a well-known teaching methodology consisting of learning by reading, discussing and analyzing real-life cases and scenarios. We present a Case-Oriented Learning Environment (COSEEd) for teaching Software Engineering concepts to undergraduate and graduate students in a first course of Software Engineering. The novelty of the proposed model lies in being a complete learning environment framework, consisting of pedagogy, broad level learning objectives, assessment, resources and management details, all designed specifically for Software Engineering. Learning and teaching is centered around well-designed SE case studies from authentic software development instances. We describe the COSEEd model, a sample case-study and share out insights as well as lessons learnt while applying the proposed model in practice. We implement and evaluate the proposed model in Software Engineering courses at a University in India focused on the core areas of Information Technology. We use empirical studies on student perception and actual performance to determine the effectiveness of COSEEd towards achieving various learning goals of SE.
HANDEDNESS AND BILATERAL FEMORAL BONE DENSITIES IN MEN AND WOMEN

To examine the relation of hand preference to bilateral femoral bone mineral density (BMD), the right and left total and regional (neck, trochanter, intertrochanteric, and Ward's triangle) proximal femur BMDs (g/cm2) were measured using dual-energy X-ray absorbtiometry (DEXA) in 32 right- and 26 left-handed university students. The mean total BMD of the total right-handers and the mean trochanteric BMD of the right- handed males were greater in the left femur than the right femur. Contrarily, the total left-handers had higher mean intertrochanteric BMD in the right side than in the left side. There were negative correlations between R-L BMD differences and Geschwind scores of total, male, and female subjects. The results suggest that femur-BMD may be related to hand preference.
Effects of a protection gradient on carnivore density and survival: an example with leopards in the Luangwa valley, Zambia

Abstract Human activities on the periphery of protected areas can limit carnivore populations, but measurements of the strength of such effects are limited, largely due to difficulties of obtaining precise data on population density and survival. We measured how density and survival rates of a previously unstudied leopard population varied across a gradient of protection and evaluated which anthropogenic activities accounted for observed patterns. Insights into this generalist's response to human encroachment are likely to identify limiting factors for other sympatric carnivore species. Motion‐sensitive cameras were deployed systematically in adjacent, similarly sized, and ecologically similar study areas inside and outside Zambia's South Luangwa National Park (SLNP) from 2012 to 2014. The sites differed primarily in the degree of human impacts: SLNP is strictly protected, but the adjacent area was subject to human encroachment and bushmeat poaching throughout the study, and trophy hunting of leopards prior to 2012. We used photographic capture histories with robust design capture–recapture models to estimate population size and sex‐specific survival rates for the two areas. Leopard density within SLNP was 67% greater than in the adjacent area, but annual survival rates and sex ratios did not detectably differ between the sites. Prior research indicated that wire‐snare occurrence was 5.2 times greater in the areas adjacent to the park. These results suggest that the low density of leopards on the periphery of SLNP is better explained by prey depletion, rather than by direct anthropogenic mortality. Long‐term spatial data from concurrent lion studies suggested that interspecific competition did not produce the observed patterns. Large carnivore populations are often limited by human activities, but science‐based management policies depend on methods to rigorously and quantitatively assess threats to populations of concern. Using noninvasive robust design capture–recapture methods, we systematically assessed leopard density and survival across a protection gradient and identified bushmeat poaching as the likely limiting factor. This approach is of broad value to evaluate the impacts of anthropogenic activities on carnivore populations that are distributed across gradients of protection.
The Corynebacterium glutamicum mycothiol peroxidase is a reactive oxygen species‐scavenging enzyme that shows promiscuity in thiol redox control

Cysteine glutathione peroxidases (CysGPxs) control oxidative stress levels by reducing hydroperoxides at the expense of cysteine thiol (‐SH) oxidation, and the recovery of their peroxidatic activity is generally accomplished by thioredoxin (Trx). Corynebacterium glutamicum mycothiol peroxidase (Mpx) is a member of the CysGPx family. We discovered that its recycling is controlled by both the Trx and the mycothiol (MSH) pathway. After H2O2 reduction, a sulfenic acid (‐SOH) is formed on the peroxidatic cysteine (Cys36), which then reacts with the resolving cysteine (Cys79), forming an intramolecular disulfide (S‐S), which is reduced by Trx. Alternatively, the sulfenic acid reacts with MSH and forms a mixed disulfide. Mycoredoxin 1 (Mrx1) reduces the mixed disulfide, in which Mrx1 acts in combination with MSH and mycothiol disulfide reductase as a biological relevant monothiol reducing system. Remarkably, Trx can also take over the role of Mrx1 and reduce the Mpx‐MSH mixed disulfide using a dithiol mechanism. Furthermore, Mpx is important for cellular survival under H2O2 stress, and its gene expression is clearly induced upon H2O2 challenge. These findings add a new dimension to the redox control and the functioning of CysGPxs in general.
Comparison of Estimation Procedures for Multilevel AR(1) Models

To estimate a time series model for multiple individuals, a multilevel model may be used. In this paper we compare two estimation methods for the autocorrelation in Multilevel AR(1) models, namely Maximum Likelihood Estimation (MLE) and Bayesian Markov Chain Monte Carlo. Furthermore, we examine the difference between modeling fixed and random individual parameters. To this end, we perform a simulation study with a fully crossed design, in which we vary the length of the time series (10 or 25), the number of individuals per sample (10 or 25), the mean of the autocorrelation (−0.6 to 0.6 inclusive, in steps of 0.3) and the standard deviation of the autocorrelation (0.25 or 0.40). We found that the random estimators of the population autocorrelation show less bias and higher power, compared to the fixed estimators. As expected, the random estimators profit strongly from a higher number of individuals, while this effect is small for the fixed estimators. The fixed estimators profit slightly more from a higher number of time points than the random estimators. When possible, random estimation is preferred to fixed estimation. The difference between MLE and Bayesian estimation is nearly negligible. The Bayesian estimation shows a smaller bias, but MLE shows a smaller variability (i.e., standard deviation of the parameter estimates). Finally, better results are found for a higher number of individuals and time points, and for a lower individual variability of the autocorrelation. The effect of the size of the autocorrelation differs between outcome measures.
Immunocytochemical and Morphological Evidence for Intracellular Self-Repair as an Important Contributor to Mammalian Hair Cell Recovery

Although recent studies have provided evidence for hair cell regeneration in mammalian inner ears, the mechanism underlying this regenerative process is still under debate. Here we report immunocytochemical, histological, electron microscopic, and autoradiographic evidence that, in cultured postnatal rat utricles, a substantial number of hair cells can survive gentamicin insult even their stereocilia are lost. These partially damaged hair cells can survive for a prolonged time and regrow the stereocilia. Although the number of stereocilia-bearing hair cells increases over time after gentamicin insult, hair cell and supporting cell numbers remain essentially unchanged. Tritiated thymidine autoradiography and bromodeoxyuridine immunocytochemistry of the cultures demonstrate that cell proliferation in the sensory epithelium is very limited and is far below the number of recovered hair cells. Furthermore, terminal deoxynucleotidyl transferase-mediated biotinylated UTP nick end labeling analysis indicates that gentamicin-induced apoptosis in the sensory epithelium occurs mainly during a 2 d treatment period, and additional cell death is minimal 2–11 d after treatment. Considered together, intracellular repair of partially damaged hair cells can be an important contributor to spontaneous hair cell recovery in mammalian inner ears.
Pensions and quitting: a test among competing explanations

Multiple regression analysis of 402 unionized, public utility employees is used to examine the effects of a final-earnings pension plan and other human resource management programs on the willingness to engage in quit behaviours in response to problems as work. Consistent with expectations, employees facing higher expected losses under the pension plan are found less likely to quit. The willingness to quit is also found to be reduced by other factors that raise the cost of this action to the individual (e.g., compensation premia), where dispute resolution options are perceived to be more effective (e.g., voice) and where the current setting is viewed more favourably (e.g., under conditions of higher affective commitment and job satisfaction). Implications for pension theory and research are discussed.
An adaptive overtaking maneuver assistant system using VANET

One of the most risky maneuvers in suburban roads containing one lane for each direction is overtaking another vehicle which caused a large number of accidents and fatalities. Although, the single overtaking task counts as hazardous action, it becomes more challenging while involving in hybrid scenarios with comprising various factors. This paper presents an intelligent driver assistant system in scenarios performing overtaking maneuver of a long vision obstructing vehicle as a frontrunner with a probability of another vehicle in front with obstacle likelihood on the road. The principal of this system is to reduce the risk of overtaking maneuver in a hybrid scenario cases by using wireless technology based on Vehicular Ad hoc Network (VANET) to optimize driver's behavior in high risk situations with guidance for making proper decision in case of performing safe overtaking action.
On quantum effects and low frequency noise spectroscopy in Si Gate-All-Around Nanowire MOSFETs at cryogenic temperatures

In this work, DC and low frequency noise have been investigated in Gate-All-Around Nanowire MOSFETs at very low temperatures. Static characteristics at 4.2 K exhibit step-like effects that can be associated to energy subbands scattering. The mobility and subthreshold swing are also investigated. Finally the low frequency noise spectroscopy (from 10 K to 70 K) leads to the identification of silicon film traps.
A novel video-based smoke detection method based on color invariants

In this paper, we address the issue of designing a smoke detector robust to illumination variations. Our contribution consists in resorting to color invariants as salient smoke features. More precisely, the proposed detector employs consecutively of an illumination invariant color representation, a photometric gain based background subtraction, a chrominance detection and a smoke identification based on two invariant color descriptors. The experimental results show that the proposed method can effectively detect smoke with robustness to illumination changes and noises, frequently encountered in wildfire video-surveillance environments.