Miracle-dz/UniFAR-FTUs huggingface dataset:
Interaction between the small GTPase Ran/Gsp1p and Ntf2p is required for nuclear transport

Bidirectional movement of proteins and RNAs across the nuclear envelope requires Ran, a Ras-like GTPase. A genetic screen of the yeast Saccharomyces cerevisiae was performed to isolate conditional alleles of GSP1, a gene that encodes a homolog of Ran. Two temperature-sensitive alleles, gsp1-1 and gsp1-2, were isolated. The mutations in these two alleles map to regions that are structurally conserved between different members of the Ras family. Each mutant strain exhibits various nuclear transport defects. Both biochemical and genetic experiments indicate a decreased interaction between Ntf2p, a factor which is required for protein import, and the mutant GSP1 gene products. Overexpression of NTF2 can suppress the temperature sensitive phenotype of gsp1-1 and gsp1-2 and partially rescue nuclear transport defects. However, overexpression of a mutant allele of NTF2 with decreased binding to Gsp1p cannot rescue the temperature sensitivity of gsp1-1 and gsp1-2. Taken together, these data demonstrate that the interaction between Gsp1p and Ntf2p is critical for nuclear transport.
The relationship between the expression of abscisic acid biosynthesis genes, accumulation of abscisic acid and the promotion of Vitis vinifera L. berry ripening by abscisic acid.

Background and Aims: Grapevines (Vitis vinifera L.) are considered to have non-climacteric fruit, but the trigger initiating ripening (veraison) is poorly understood. This study aimed to further investigate the role of abscisic acid (ABA) during berry ripening. Methods and Results: In field-grown grapes over three seasons, free ABA levels increased at veraison then subsequently declined to low levels. Bound ABA increased as the free ABA level decreased after 10–11 weeks post-flowering (wpf), but ABA must also be degraded and/or exported. The absence of a large pool of bound ABA before veraison makes it unlikely that the increase in free ABA is due to the mobilization of conjugated ABA. The expression pattern of genes crucial for ABA synthesis, zeaxanthin epoxidase and two 9-cis-epoxycartenoid dioxygenases (NCEDs) indicates that berries may have the potential to synthesize ABA in situ. However, the expression profile of these genes did not correlate well with ABA levels indicating that ABA accumulation is under more complex control. The application of (+)-ABA advanced ripening as measured by colour formation, berry size increase and to a lesser extent sugar accumulation and altered the expression of one of the NCED genes. Conclusions: The changes in berry ABA levels around the time of veraison, which influence the timing of ripening, are under complex developmental control. Significance of the Study: The improved understanding of the control of berry ripening is vital to attempts to successfully manipulate this process.
Intensive cognitive rehabilitation therapy for chronic traumatic brain injury: a case study of neural correlates of functional improvement

ABSTRACT Background: Some four million Americans are living with chronic disability related to traumatic brain injury (TBI). Yet, very little research has investigated training-induced neuroplasticity over many hours of treatment well into the chronic stage for the most commonly impaired functions (attention, executive functions (EFs), and prospective memory (PM)). Aims: The purpose of the present study was to investigate whether a 30-h course of intensive evidence-based treatments of attention, EFs, and PM would show behavioural gains and associated brain structural and/or functional changes in an individual well into the chronic phase of recovery from TBI. Methods & Procedures: An A-B single-participant quasi-experimental design with 1 month post-treatment follow-up was employed for cognitive rehabilitation of a 54-year-old man, 7.5 years after severe TBI. After an initial 4-week pre-treatment baseline phase, 30 hours of therapy was provided over 3 weeks, targeting attention, PM, and EFs, with follow-up testing at 1-month post-treatment. Treatments (selected from evidence-based practice guidelines) consisted of attention process training, metacognitive strategy instruction, and PM training. Neuroimaging (auditory oddball paradigm, resting state, and diffusion tensor imaging) was conducted weekly from the end of the A-phase, through the end of the B-phase, and then at 1-month follow-up. Outcomes & Results: Results demonstrated gains to behavioural and quality of life measures for attention and EFs, with evidence of associated structural and functional neuroplasticity. There was no evidence of change to PM skills. Conclusions: Intensive evidence-based treatment of attention and EFs improved functioning and quality of life in an individual well into the chronic phase of TBI, and may be associated with structural and functional neuroplasticity.
Comparison of fault detection and isolation methods: A review

Fault Detection and Isolation (FDI) is important in many industries to provide safe operation of a process. To determine the kind, size, location and time of fault, many Fault detection and Identification (FDI) Techniques are proposed. The Characteristic of FDI techniques include robustness, fast detection and isolation of faults. In this paper a comparison of fault diagnosis system based on Artificial Neural Network (ANN), Observer, Fuzzy, Kalman filter is presented. To achieve fault detection and isolation, a set of residuals need to be determined. Residual indicates the state of the system and provide information about the source of possible faults. A comparison of residual generation methods such as observer based residual generation, parity relation, Kalman filter and structural analysis is also presented in this paper.
Hospital automation RFID-based

RFID is a technology have been adopted in many business fields, especially in medical field. This work has the objective to present a system for automation of a hospital clinical analysis laboratory. This system initially uses contactless smart cards to store patientpsilas data and for authentication of hospital employees in the system. The proposed system also uses RFID tags stuck in each patientpsilas collected samples container for correct identification of the patient who gave away the samples. This work depicts a hospital laboratory workflow, presents the system modeling and deals with security matters related to information stored in the smart cards.
Evaluation of automatic mobile playlist generator

Mobile music consumption is increasing and many of the current mobile phones already offer music listening capabilities. Still, most of the current automatic playlist generation systems do not function in the mobile domain. This paper presents an evaluation of a content-based prototype mobile playlist generator. A user study was conducted to find out the quality and performance of our content-based automatic playlist generation engine from the user's perspective. In addition, possible benefits, usage scenarios, and future improvements are covered in this study, to support further development. There were 30 test subjects taking part in the usability study consisting of individual interviews and a trial. The overall performance of the automatic playlist generator satisfied 90% of the test subjects and they would like to use such system. Still, there are many improvements and new design ideas to take into account in further development to gain even better user acceptance and performance. These development ideas include e.g. getting rid of the most unsuccessful recommendations, providing option to group similar artists on the playlists and adding support for new ways of creating playlists by utilizing multiple seed songs.
Almost-Uniform Sampling of Points on High-Dimensional Algebraic Varieties

We consider the problem of uniform sampling of points on an algebraic variety. Specifically, we develop a randomized algorithm that, given a small set of multivariate polynomials over a sufficiently large finite field, produces a common zero of the polynomials almost uniformly at random. The statistical distance between the output distribution of the algorithm and the uniform distribution on the set of common zeros is polynomially small in the field size, and the running time of the algorithm is polynomial in the description of the polynomials and their degrees provided that the number of the polynomials is a constant.
Tool Support for Unit Testing of Aspect-Oriented Software

In this paper, we present a data ow based unit testing approa h and its tool support for aspe t-oriented software. Our approa h tests two types of units for an aspe t-oriented program, i.e., aspe ts that are modular units of ross utting implementation of the program, and those lasses whose behaviors may be a e ted by one or more aspe ts. We use the ontrol ow graph as a basis to ompute def-use pairs of aspe ts or lasses being tested in an aspe t-oriented program and use su h information to perform dataow testing on the aspe ts and lasses of the program.
5G radio access network and its requirements on mobile optical network

Toward the realization of the 5th generation (5G) mobile communication network that offers super high bit rates and capacity, a further enhancement of the mobile optical network to support 5G radio access technologies is indispensable. At first, this paper briefly summarizes the concept of 5G radio access network based on the Phantom Cell concept in which small cells that offer super high bit rate transmission using higher frequency bands and wider bandwidth are overlapped onto macro cells that support coverage and mobility, and the radio links corresponding to User (U)-plane and (C)-plane are separately supported by small cells and macro cells, respectively. Next, technical issues and requirements on the mobile optical network for supporting 5G radio access technologies are discussed, focusing on massive MIMO and carrier aggregation.
Diffuse Low-Grade Glioma – Changing Concepts in Diagnosis and Management: A Review

Though diffuse low-grade gliomas (dLGGs) represent only 15% of gliomas, they have been receiving increasing attention in the past decade. Significant advances in knowledge of the natural history and clinical diversity have been documented, and an improved pathological classification of gliomas that integrates histological features with molecular markers has been issued by the WHO. Advances in the radiological assessment of dLGG, particularly new magnetic resonance imaging scanning sequences, allow improved diagnostic and prognostic information. The management paradigms are evolving from “wait and watch” of the past to more active interventional therapy to obviate the risk of malignant transformation. New surgical technologies allow more aggressive surgical resections with a reduction of morbidity. Many reports suggest the association of gross total resection with longer overall survival and progression-free survival in addition to better seizure control. The literature also shows the use of chemotherapeutics and radiation therapy as important adjuncts to surgery. The goals of management have has been increasing survival with increasing stress on quality of life. Our review highlights the recent advances in the molecular diagnosis and management of dLGG with trends toward multidisciplinary and multimodality management of dLGG with an aim to surgically resect the primary disease, followed by chemoradiation in cases of progressive or recurrent disease.
Identification of proteomic differences in asthenozoospermic sperm samples.

BACKGROUND Asthenozoospermia is one of the most common findings present in infertile males, but its aetiology remains unknown in most cases. Present proteomic tools now offer the opportunity to identify proteins which are differentially expressed in asthenozoospermic semen samples and potentially involved in infertility. METHODS We compared the expression of 101 sperm protein spots in 20 asthenozoospermic samples to that of 10 semen donor controls using two-dimensional proteomic analysis. RESULTS Seventeen protein spots have been identified at different amounts in the asthenozoospermic samples compared with controls. These are cytoskeletal actin-B, annexin-A5, cytochrome C oxidase-6B, histone H2A, prolactin-inducible protein and precursor, calcium binding protein-S100A9 (2 spots), clusterin precursor, dihydrolipoamide dehydrogenase precursor, fumarate hydratase precursor, heat shock protein-HSPA2, inositol-1 monophosphatase, 3-mercapto-pyruvate sulfurtransferase/dienoyl-CoA isomerase precursor, proteasome subunit-PSMB3, semenogelin 1 precursor and testis expressed sequence 12. The detected amount of these proteins enabled the grouping of asthenozoospermic sperm samples in an unsupervised clustering analysis. CONCLUSIONS We have identified several proteins present at different amount in asthenozoospermic sperm samples. These proteins could be candidates towards the development of diagnostic markers, and open up the opportunity to gain further insight into the pathogenic mechanisms involved in asthenozoospermia.
A prospective, randomized comparison of the metabolic effects of pioglitazone or rosiglitazone in patients with type 2 diabetes who were previously treated with troglitazone.

OBJECTIVE To characterize potential differences in glycemic control, plasma lipid level, and weight in a cohort of patients previously treated with troglitazone (TROG) who were switched to either pioglitazone or rosiglitazone. RESEARCH DESIGN AND METHODS After a 2-week washout from TROG, 186 patients were randomly assigned to receive either pioglitazone (PIO) or rosiglitazone (ROSI). Weight, HbA(1c), and fasting lipid profile were documented before discontinuing TROG and at 4 months after starting either pioglitazone or rosiglitazone. Secondarily, the effect of concurrent medications on study outcomes was assessed. RESULTS A total of 127 patients completed follow-up: 67 individuals in the PIO group (32 women, 35 men) and 60 individuals in the ROSI group (33 women, 27 men). There were no significant differences in gender mix, age, weight, fasting lipid profile, or HbA(1c) between the ROSI and PIO groups. After 4 months of randomized treatment, no change in HbA(1c) from baseline between or within groups was noted. Both groups experienced an equal and significant increase in weight from baseline of approximately 2.0 kg. Thiazolidinedione and HMG-CoA reductase inhibitor therapy had significant and independent effects on lipid profile (P < 0.005). Significant improvements in lipid profile were noted in the PIO group (P < 0.01), whereas none were detected with conversion to ROSI. Specifically, the PIO group experienced an average decrease in total cholesterol of approximately 20 mg/dl. CONCLUSIONS Differing effects on lipid profile were apparent after random conversion from TROG to either PIO or ROSI, despite similar weight increase and glycemic control. The clinical significance of these differences remains to be determined, and further comparative research is warranted.
No 942 July 2009 Trade , Wages and Productivity

We develop a new general equilibrium model of monopolistic competition with heterogeneous firms, variable demand elasticity and multiple asymmetric regions, in which trade integration induces wage and productivity changes. Using Canada-US interregional trade data, we structurally estimate a theory-based gravity equation system featuring endogenous wages and productivity. Given the estimated parameter values, we first decompose border effects into a pure border effect, relative and absolute wage effects, and a selection effect. We then quantify the impacts of removing the trade distortions generated by the Canada-US border on regional market aggregates such as wages, productivity, markups, the mass of varieties produced and consumed, as well as welfare. Last, we extend the counterfactual analysis to the firm level by generating productivity distributions and their changes via simulation.
QuASAR: Quantitative Allele Specific Analysis of Reads

Motivation Expression quantitative trait loci (eQTL) studies have discovered thousands of genetic variants that regulate gene expression, enabling a better understanding of the functional role of non-coding sequences. However, eQTL studies are costly, requiring large sample sizes and genome-wide genotyping of each sample. In contrast, analysis of allele specific expression (ASE) is becoming a popular approach to detect the effect of genetic variation on gene expression, even within a single individual. This is typically achieved by counting the number of RNA-seq reads matching each allele at heterozygous sites and testing the null hypothesis of a 1:1 allelic ratio. In principle, when genotype information is not readily available it could be inferred from the RNA-seq reads directly. However, there are currently no existing methods that jointly infer genotypes and conduct ASE inference, while considering uncertainty in the genotype calls. Results We present QuASAR, Quantitative Allele Specific Analysis of Reads, a novel statistical learning method for jointly detecting heterozygous genotypes and inferring ASE. The proposed ASE inference step takes into consideration the uncertainty in the genotype calls while including parameters that model base-call errors in sequencing and allelic over-dispersion. We validated our method with experimental data for which high quality genotypes are available. Results for an additional dataset with multiple replicates at different sequencing depths demonstrate that QuASAR is a powerful tool for ASE analysis when genotypes are not available. Availability http://github.com/piquelab/QuASAR Contact fluca@wayne.edu; rpique@wayne.edu
Regularized interference alignment for heterogeneous networks

In order to improve the capacity of hierarchical interference alignment (HIA) scheme for heterogeneous networks in the low Signal to Noise Ratio (SNR) regime, a regularized interference alignment (RIA) scheme for heterogeneous networks is proposed in this paper. In the proposed scheme, the equivalent channel matrices in hierarchical interference alignment scheme are used as weighed matrices, and the transmit and receive beam forming matrices are iteratively optimized by weighed Minimum Mean Square Error (W-MMSE) criterion, hence the interferences are eliminated and Signal to Interference plus Noise Ratio (SINR) is optimized. Theoretical analysis and simulation results show that, the proposed scheme can converge by a few iterations, and improve the capacity of heterogeneous networks in the low SNR regime.
The Role of Uterine and Umbilical Arterial Doppler in High-risk Pregnancy: A Prospective Observational Study from India

Aim To study the role of Doppler imaging in prediction of high-risk pregnancies and their outcomes. Methods and Material This prospective study in a setup of tertiary-level care center includes 500 high-risk pregnant women from rural and urban sectors and evaluates the predictive values of various Doppler indices. Results Out of 500 patients, 110 patients had abnormal Doppler among them, 70 patients had abnormal uterine artery Doppler, and 50 patients had abnormal umbilical artery Doppler flow indices. In all, 10 patients had both umbilical artery and uterine artery abnormal Doppler indices. When uterine artery was abnormal (70 patients), 20 patients had preeclampsia, 10 patients had pregnancy-induced hypertension (PIH), and 25 patients had intrauterine growth restriction (IUGR). Systolic/diastolic (S/D) ratio and notch had sensitivity of 60% and positive predictive value of 33.3% and 37.5%, respectively. When umbilical artery was abnormal (50 patients), 10 had preeclampsia, 15 had PIH, and 15 had IUGR. S/D ratio had the highest positive predictive value of 40%; sensitivity is same for all. In uterine artery, combination of parameters had the best sensitivity of 80%, followed by notch and S/D ratio. In umbilical artery, combination of parameters, S/D ratio, and RI (resistance index) had sensitivity of 40%; specificity of all the indices was 91-96%. In all, 20 patients had bilateral notch, and among them 15 developed preeclampsia and 15 developed IUGR. When both uterine and umbilical artery Doppler were abnormal (10 patients), all patients had preeclampsia and IUGR. Conclusion Therefore, Doppler study may be used for the prediction of preeclampsia and IUGR to reduce the maternal and perinatal morbidity and mortality.
A New Proof of a Theorem in Analysis by Generating Integrals and Fractional Calculus

The idea of generating integrals analogous to generating functions is first introduced in this paper. A new proof of the well-known Finite Harmonic Series Theorem in Analysis and Analytical Number Theory is then obtained by the method of Generating Integrals and Fractional Calculus. A generalization of the Riemann zeta function up to non-integer order is derived.
Stimulus Specificity of Brain-Computer Interfaces Based on Code Modulation Visual Evoked Potentials

A brain-computer interface (BCI) based on code modulated visual evoked potentials (c-VEP) is among the fastest BCIs that have ever been reported, but it has not yet been given a thorough study. In this study, a pseudorandom binary M sequence and its time lag sequences are utilized for modulation of different stimuli and template matching is adopted as the method for target recognition. Five experiments were devised to investigate the effect of stimulus specificity on target recognition and we made an effort to find the optimal stimulus parameters for size, color and proximity of the stimuli, length of modulation sequence and its lag between two adjacent stimuli. By changing the values of these parameters and measuring classification accuracy of the c-VEP BCI, an optimal value of each parameter can be attained. Experimental results of ten subjects showed that stimulus size of visual angle 3.8°, white, spatial proximity of visual angle 4.8° center to center apart, modulation sequence of length 63 bits and the lag of 4 bits between adjacent stimuli yield individually superior performance. These findings provide a basis for determining stimulus presentation of a high-performance c-VEP based BCI system.
WIBL: Workbench for Integrative Biological Learning

Summary The construction of integrated datasets from potentially hundreds of sources with bespoke formats, and their subsequent visualization and analysis, is a recurring challenge in systems biology. We present WIBL, a visualization and model development environment initially geared towards logic-based modelling of biological systems using integrated datasets. WIBL combines data integration, visualisation and modelling in a single portalbased workbench providing a comprehensive solution for interdisciplinary systems biology projects.
On Mean-Risk Models Consistent with Stochastic Dominance

Comparing uncertain prospects is one of fundamental interests of the economic decision theory. Two methods are frequently used for modeling the choice among uncertain outcomes: stochastic dominance and mean-risk approaches. The former is based on the axiomatic model of risk-averse preferences but does not provide a convenient computational recipe. It is, in fact, a multiple criteria model with a continuum of criteria. The mean-risk approach quantifies the problem in a lucid form of only two criteria: the mean, representing the expected outcome, and the risk: a scalar measure of the variability of outcomes. The mean-risk model is appealing to decision makers and allows a simple trade-off analysis, analytical or geometrical. On the other hand, for typical dispersion statistics used as risk measures, the mean-risk approach may lead to inferior conclusions. Several risk measures, however, can be combined with the mean itself into the robust optimization criteria thus generating SSD consistent performances (safety) measures. In this paper we introduce general conditions for risk measures sufficient to provide the SSD consistency of the corresponding safety measures.