Miracle-dz/UniFAR-FTUs huggingface dataset:
A NOVEL AND EFFICIENT ALGORITHM FOR DE NOVO DISCOVERY OF MUTATED DRIVER PATHWAYS IN CANCER

Next-generation sequencing studies on cancer somatic mutations have discovered that driver mutations tend to appear in most tumor samples, but they barely overlap in any single tumor sample, presumably because a single driver mutation can perturb the whole pathway. Based on the corresponding new concepts of coverage and mutual exclusivity, new methods can be designed for de novo discovery of mutated driver pathways in cancer. Since the computational problem is a combinatorial optimization with an objective function involving a discontinuous indicator function in high dimension, many existing optimization algorithms, such as a brute force enumeration, gradient descent and Newton's methods, are practically infeasible or directly inapplicable. We develop a new algorithm based on a novel formulation of the problem as non-convex programming and nonconvex regularization. The method is computationally more efficient, effective and scalable than existing Monte Carlo searching and several other algorithms, which have been applied to The Cancer Genome Atlas (TCGA) project. We also extend the new method for integrative analysis of both mutation and gene expression data. We demonstrate the promising performance of the new methods with applications to three cancer datasets to discover de novo mutated driver pathways.
Simultaneous determination of guanidinoacetate, creatine and creatinine in urine and plasma by un-derivatized liquid chromatography-tandem mass spectrometry

Background Creatine plays an important role in the storage and transmission of phosphate-bound energy. The cerebral creatine deficiency syndromes (CCDS) comprise three inherited defects in creatine biosynthesis and transport. They are characterized by mental retardation, speech and language delay and epilepsy. All three disorders cause low-creatine signal on brain magnetic resonance spectroscopy (MRS); however, MRS may not be readily available and even when it is, biochemical tests are required to determine the underlying disorder. Methods Analysis was performed by liquid chromatography-tandem mass spectrometry in positive ionization mode. Samples were analysed underivatized using a rapid ‘dilute and shoot’ approach. Chromatographic separation of the three compounds was achieved. Stable isotope internal standards were used for quantification. Results Creatine, creatinine and guanidinoacetate were measured with a 2.5 minute run time. For guanidinoacetate, the standard curve was linear to at least 5000 μmol/L and for creatine and creatinine it was linear to at least 25 mmol/L. The lower limit of quantitation was 0.4 μmol/L for creatine and guanidinoacetate and 0.8 μmol/L for creatinine. Recoveries ranged from 86% to 106% for the three analytes. Intra- and inter-assay variation for each analyte was <10% in both urine and plasma. Conclusion A tandem mass spectrometric method has been developed and validated for the underivatized determination of guanidinoacetate, creatine and creatinine in human urine and plasma. Minimal sample preparation coupled with a rapid run time make the method applicable to the routine screening of patients with suspected CCDS.
Applicability of Fenton and photo-Fenton Processes to Combined Industrial and Domestic Wastewater

The applicability of Fenton and photo-Fenton processes as a pretreatment stage to combined wastewater was investigated. The wastewater was obtained from the inlet of the aeration tank in 42 Evler industrial and domestic wastewater treatment plant. The ef- fects of different process variables such as initial Fe 2+ (c o = 8-33 mmol L -1 ) and H 2 O 2 (c o = 65 -165 mmol L -1 ) concentrations, pH (3-7.75) and reaction time (t = 5-180 min) were evaluated. The Fenton process was investigated which under the operating conditions (pH 3, c Fe 2+ = 12 mmol L -1 , c H 2 O 2 = 130 mmol L -1 ) 100 % color and 44 % total organic carbon (TOC) removal were achieved. However, 71 % TOC removal was achieved at pH 7.75 by coagulation but color was poorly removed (c = 20 mmol L -1 Fe 2+ , c = 165 mmol L -1 H 2 O 2 ). In the photo-Fenton process, 84 % TOC and 87 % color removal were achieved in 30 min reaction time (pH 3, c Fe 2+ = 26 mmol L -1 , C H 2 O 2 = 130 mmol L -1 ) .
Efficient Resource Allocation and Sectorization for Fractional Frequency Reuse (FFR) in LTE Femtocell Systems

The Fractional Frequency Reuse (FFR) is a resource allocation technique that can effectively mitigate inter-cell interference (ICI) in LTE based HetNets and it is a promising solution. Various FFR schemes have been suggested to address the challenge of interference in femtocell systems. In this paper, we study the scopes of interference mitigation and capacity improvement. We propose a resource allocation scheme that gradually varies frequency resource share with distance from the eNodeB for both macrocells and femtocells in order to attain better utilization of the resources. This is performed effectively using three layers in the cell. The proposal also employs high number sectors in a cell, low interference and good frequency reuse. Monte-Carlo simulations are performed, which show that the proposed scheme achieves signifi- cantly better throughput compared to the existing FFR schemes.
Acute Effects of a 50% Partial Pancreatectomy on Total Pancreatic and Islet Blood Flow in Rats

Objectives: The aim of the study was to investigate how an acute increase in functional demand for insulin release affected islet blood perfusion in anesthetized rats. Methods: We measured total pancreatic and islet blood flow with differently colored microspheres before and 30 minutes after a 50% partial pancreatectomy. Results: The blood glucose concentrations increased in the animals subjected to partial pancreatectomy. The fact that serum insulin concentrations remained unaffected implies that the islets in fact doubled their output of insulin to maintain the same degree of insulinemia. Still, pancreatic islet blood flow was the same as in the sham-operated animals. Likewise, the number of perfused pancreatic islets and the flow distribution between individual islets were not influenced by the partial pancreatectomy. Conclusions: We conclude that the acute demand for insulin secretion induced by a 50% partial pancreatectomy is not necessarily associated with an acute increase in islet blood perfusion. These findings suggest that basal islet blood flow is high enough to allow for short-term changes in hormone release without simultaneous changes in blood perfusion.
Preparing augmented reality learning content should be easy: UNED ARLE—an authoring tool for augmented reality learning environments

The purpose of this study was to investigate how an augmented reality learning environment system (UNED ARLE) can be used both by teachers and students to add virtual content into educational resources and how can it serve as a tool for acquiring knowledge, motivating and encouraging students. UNED ARLE is used to add contextualized virtual content (3D objects, animated 3D objects, videos, sound files and images) and the accompanying descriptions or narratives into printed material, thereby enriching existing content without any programming skills. This study recruited 44 students of advanced and intermediate cycles of vocational training and two teachers. It analyses UNED ARLE by examining the interaction between teachers and the system and by comparing the results of two groups of students. The study concludes that the students who used UNED ARLE show significantly better learning achievements compared to the traditional system. In regards to the teachers, the study shows that incorporating multimedia resources into augmented reality is directly influenced by their knowledge of this technology, due to the difficulty of developing new virtual objects. © 2015 Wiley Periodicals, Inc. Comput. Appl. Eng. Educ. Comput Appl Eng Educ 23:778–789, 2015; View this article online at wileyonlinelibrary.com/journal/cae; DOI 10.1002/cae.21650
The impact of long-term systemic glucocorticoid use in severe asthma: A UK retrospective cohort analysis

ABSTRACT Objective: Systemic glucocorticoids (SGCs) are a treatment option for severe asthma but are associated with the development of adverse events (AEs). Evidence on the extent of SGC use and the relationship between SGC dose and AE risk in severe asthma is limited. Methods: Patients with severe asthma (Global Initiative for Asthma step 4/5), with no SGC use during the <6–12 months before severe asthma determination (index date) were identified in the UK-based Clinical Practice Research Datalink database (2004–2012). Patients were assessed for SGC exposure and an incident diagnosis of an SGC-related AE (cataracts, diabetes, myocardial infarction [MI], osteoporosis, peptic ulcer or stroke) during the 8-year observation phase. The dose-related risk of an SGC-related AE was determined using AE-specific Cox proportional hazards models. Results: Overall, 75% of 60,418 patients identified with severe asthma received SGC during the 8-year follow-up, with the majority receiving an average of >0–≤2.5 mg/day. The risk of diabetes (hazard ratio [HR]:1.20 [95% confidence interval (CI): 1.11, 1.30]), MI (HR: 1.25 [95% CI: 1.09, 1.43]) and osteoporosis (HR: 1.64 [95% CI: 1.51, 1.78]) was increased at low SGC doses (0–2.5 mg/day), with further risk increases at doses >2.5 mg/day versus no SGC use. Compared with no SGC use, SGC increased the risk of peptic ulcer in a non-dose-dependent manner, but the risk of stroke was unchanged. Conclusions: Most patients with severe asthma are exposed to SGC, which increases SGC-related AE risk. This suggests that SGC exposure should be minimized as recommended by asthma treatment guidelines.
A novel splice variant of human XRN2 gene is mainly expressed in blood leukocyte†

The XRN2 gene (XRN2a) is the human homologue of the Saccharomyces cerevisiae RAT1 gene, which encodes a nuclear 5′→3′ exoribonuclease, and is essential for RNA metabolism and cell viability. Xrn2p/Rat1p, product of XRN2/RAT1 gene, functions in the mRNA degradation and processing of rRNAs and small nucleolar RNAs (snoRNAs) in the nucleus. Here we describe the cloning and characterization of a novel splice variant of the human XRN2 gene (XRN2b). The 3271-bp cDNA encodes a putative protein with 907 amino acid residues, which shares high homology with mouse DHM1 protein. RT-PCR analysis showed that XRN2b was mainly expressed in blood leukocyte tissue, while XRN2a was detected in several human tissues and in human tumor tissues.
Microscopic spectrum of the QCD Dirac operator with finite quark masses

We compute the microscopic spectrum of the QCD Dirac operator in the presence of dynamical fermions in the framework of random-matrix theory for the chiral Gaussian unitary ensemble. We obtain results for the microscopic spectral correlators, the microscopic spectral density, and the distribution of the smallest eigenvalue for an arbitrary number of flavors, arbitrary quark masses, and arbitrary topological charge.
Model-based reasoning in financial domains

Abstract Finance is a challenging yet appropriate domain for model-based reasoning, an area of research otherwise grounded in classical physics. Among the many features that suggest a model-based approach are that firms have formal internal structures, business entities have idealizable behaviours, and there is a history of formal analysis of business problems. This article discusses the motivations and foundations of the model-based approach, and surveys several existing artificial intelligence programs that exploit its advantages. The survey shows that there are ample opportunities for useful systems and significant research in this area. However, accomplishing either of these goals depends crucially upon moving beyond qualitative models based only on accounting information, which tend not to capture the actual complexities of the domain.
Incidence of vertebral fractures in calcium and vitamin D-supplemented postmenopausal Brazilian women with osteopenia or osteoporosis: data from Arzoxifene Generations Trial

ABSTRACT Objective Vertebral fracture is the most common osteoporotic fracture, affecting quality of life and increasing mortality. Epidemiological data on incidence of vertebral fracture are scarce in Brazil and throughout Latin America. Our aim was to determine vertebral fracture incidence and risk factors in a female Brazilian population. Subjects and methods Postmenopausal women with low bone mass were studied from the Brazilian placebo group of Arzoxifene Generations Trial (n = 974), followed for up to 5 years. The primary endpoint was new vertebral fractures, detected by X-Ray. Experimental design defined two strata: A. Osteoporosis or previous vertebral fracture with osteopenia; B. Osteopenia without previous fracture. Previous fracture, T-score, ionized calcium, alkaline phosphatase, creatinine and glucose were analyzed at baseline. Crude and adjusted incidence rates of vertebral fractures were estimated and Poisson regression model was used. Results Incidence rate was 7.7 (95% CI of 5.4 to 10.9) per 1,000 person-years (PY), increasing as a function of age. Women with new vertebral fractures had higher prevalence of previous nonvertebral fracture after menopause, were older and had lower lumbar spine (LS) T-score. Fracture risk increased by 46% for each unit reduction in LS T-score. Variables correlated with new vertebral fracture were age (p = 0.034), LS T-score, stratum A (p = 0.001 for both) and previous nonvertebral fracture after menopause (p = 0.019). In the final model, LS T-score was the strongest predictor. Conclusions Incidence rate of vertebral fracture of 7.7 per 1,000 PY. Age and previous fractures were associated with new vertebral fracture, but LS T-score was the most important predictor.
Spatial locality based supplemental modes for intra prediction of HEVC

The latest generation standard of video coding, High Efficiency Video Coding (HEVC) achieves the goal of requiring 50% bit-rate of the H.264/AVC at the same image quality. It adopts quad-tree based flexible coding unit structure as prediction unit (PU) sizes which are defined from 64×64 to 4×4, and plenty of intra prediction modes whose reference samples are spatially reconstructed neighboring samples which are at the bottom left, left, top left, above, above right. However, such modes may not come off well enough in high resolution video compression. This paper presents a novel prediction algorithm for intra prediction of HEVC. The proposed supplemental modes based on spatial locality can utilize the spatially neighboring referencing samples more efficient. Compared with the original HEVC, the result of coding efficiency increasing is about 8.04%.
Link Clustering for Extracting Collaborative Patterns in a Scientific Co-Authored Network

In this article, we analyse a collaborative network to understand the underlying patterns that structure the co-writing process of scientific articles. Our goal is to identify and understand the collaboration tendencies from authors publishing activities. For this purpose, we adopt a descriptive modelling through a network approach that consists first in generating the collaborative network from data on publications. Nodes of the network are then enriched with a set of individual attributes extracted from the publishing activity of each author. Finally, we search for conceptual views, a recent link clustering approach, which allows to summarize any kind of networks by highlighting the sets of attributes found frequently linked. Results show that it exists strong tendencies that unconsciously structure the collaboration behaviours. In this paper, we present these tendencies and show how they evolve according to different extraction thresholds.
Kinetic determinations of trace element bioaccumulation in the mussel, Mytilus edulis

Laboratory experiments employing radiotracer methodology were conducted to determine the assimilation efficiencies from ingested natural seston, the influx rates from the dissolved phase and the efflux rates of 6 trace elements (Ag, Am, Cd, Co. Se and Zn) in the mussel Mytilus edulis. A kinetic model was then employed to predict trace element concentration in mussel tissues in 2 locations for which mussel and environmental data are well described: South San Francisco Bay (California, USA) and Long Island Sound [New York, USA). Assimilation efficiencies from natural seston ranged from 5 to 18": for Ag, 0.6 to 1% for Am, 8 to 20% for Cd, 12 to 16% for CO, 28 to 34% for Se, and 32 to 41 ':, for Zn. Differences in chlorophyll a concentration in ingested natural seston did not have significant impact on the assimilation of Am, CO, Se and Zn. The influx rate of elements from the dissolved phase increased with the dissolved concentration, conforming to Freundlich adsorption isotherms. The calculated dissolved uptake rate constant was greatest for Ag, followed by Zn > Am -; Cd > CO > Se. The estimated absorption efficiency from the d~ssolved phase was 1.53 % for Ag, 0.34 % for Am, 0.31 X for Cd, 0.11 % for CO, 0.03"' for Se and 0.89% for Zn. Salinity had an inverse effect on the influx rate from the dissolved phase and dissolved organic carbon concentration had no significant effect on trace element uptake. The calculated efflux rate constants for all elements ranged from 1.0 to 3.0% d-' The route of trace element uptake (food vs dissolved) and the duration of exposure to dissolved trace elements (12 h vs 6 d) did not significantly influence trace element efflux rates. A model which used the experimentally determined influx and efflux rates for each of the trace elements, following exposure from ingested food and from water, predicted concentrations of Ag. Cd, Se and Zn in mussels that were directly comparable to actual tissue concentrations independently measured in the 2 reference sites in national monitoring programs. Sensitivity analysis indicated that the total suspended solids load, which can affect mussel feeding activity, assimilation, and trace element concentration in the dissolved and particulate phases, can significantly influence metal bioaccumulation for particlereactive elements such as Ag and Am. For all metals, concentrations in mussels are proportionately related to total metal load in the water column and their assimilation efficiency from ingested particles. Further, the model predicted that over 96% of Se in mussels is obtained from ingested food, under conditions typical of coastal waters. For Ag, Am, Cd, CO and Zn, the relative contribution from the dissolved phase decreases significantly with increasing trace element parhtion coefficients for suspended particles and the assimilation efficiency in mussels of ingested trace elements, values range between 33 and 67% for Ag, 5 and 1 7 % for Am, 47 and 82% for Cd, 4 and 30% for CO, and 17 and 51 ? h for Zn.
Adult reference ranges for serum cystatin C, creatinine and predicted creatinine clearance

Serum cystatin C measurement has been previously shown by ourselves and others to be a better indicator of changes in glomerular filtration rate (GFR) than serum creatinine. However, the available literature on reference values for cystatin C concentration remains surprisingly sparse; we thus set out to determine an adult reference range. Blood was taken from 309 healthy blood donors and creatinine and cystatin C concentrations were measured using commercially available automated methodologies. In addition, predicted creatinine clearances were calculated using the Cockcroft and Gault formula. The 95% reference intervals for creatinine, predicted creatinine clearance and cystatin C for all blood donors, regardless of gender, were 68-118 µmol/L, 58-120 ml/min/1·73 m 2 and 0·51-0·98 mg/L, respectively. For women, the intervals were 68-98 µmol/L, 60-119 ml/min/1·73 m 2 and 0·49-0·94 mg/ L; for men, they were 78-123 µmol/L, 57-122 ml/min/1·73 m 2 and 0·56-0·98 mg/L. The mean 95% reference interval for cystatin C in all donors under 50 years of age was 0·53-0·92 mg/L; for those over 50 years of age it was 0·58-1·02 mg/L. The small difference between male and female ranges meant that a single reference range for cystatin C could be established for all adults under 50 years of age without adjustment for body surface area. Serum cystatin C measurement offers a simpler and more sensitive screening test than serum creatinine for early changes in GFR.
Hepatic Vein Reconstruction for Resection of Hepatic Tumors

Summary Background DataInvolvement of the hepatic veins requiring reconstruction has traditionally been considered a contraindication to resection for advanced tumors of the liver because the surgical risks are high and the long-term prognosis poor. Recent advances in liver surgery gleaned from split and live donor liver transplantation that necessitate hepatic vein reconstruction can be applied to hepatic resection in some cases. MethodsSixteen patients who underwent hepatic resection requiring hepatic vein reconstruction from 1996-2001 were reviewed. The mean age was 43 years (range 2–61). Nine patients were resected for hepatocellular carcinoma (HCC), five patients for colorectal metastases, and one patient each for hepatoblastoma and cholangiocarcinoma. In six patients with HCC and cirrhosis, the right hepatic vein was reconstructed to provide venous outflow to liver segments not adequately drained by a remaining major hepatic vein. Four of these six patients required the use of Gore-Tex (W. L. Gore & Associates, Inc., Newark, DE) interposition grafts. In the 10 other cases the entire venous outflow from the remnant liver was reconstructed or reimplanted into the inferior vena cava primarily (n = 8) or using segments of the portal vein from the resected side of the liver as a graft (n = 2). Ex-vivo procedures with the use of veno-venous bypass were required in two cases and in-situ cold perfusion of the liver was used in one case. ResultsThere were two perioperative deaths (12%). One patient died of liver failure 3 weeks after right trisegmentectomy with reconstruction of the left hepatic vein and one patient died at 3 months after resection due to sepsis from a segment of small bowel that perforated into a diaphragmatic hernia. Four patients had evidence of postoperative liver failure that resolved with supportive management and one patient required temporary dialysis. All vascular reconstructions were patent at last followup. With median followup of 23 months, 3 patients have died of recurrent malignancy at 14, 18 and 30 months, while an additional patient went on to die of progressive liver failure at 22 months. Actuarial 1 and 3 year survival was 88% and 50% respectively. ConclusionHepatic vein involvement by hepatic malignancy does not necessarily preclude resection. Liver resection with reconstruction of the hepatic veins can be performed in selected cases. The increased risk associated with the procedure appears to be balanced by the possible benefits, particularly when the lack of alternative curative approaches is considered.
Five-Factor Measure of Borderline Personality Traits

This study provides psychometric data for a new self-report measure of borderline personality traits from the perspective of the Five-factor model (FFM) of general personality. Subscales were constructed in an undergraduate sample (n = 109) to assess maladaptive variants of 12 FFM traits (e.g., Affective Dysregulation as a maladaptive variant of FFM Vulnerability). On the basis of data from a second undergraduate sample (n = 111), the Five Factor Borderline Inventory (FFBI) subscales were shown to have good internal consistency, convergent, discriminant, and incremental validity. These psychometric results were replicated in a clinical sample of female residents at a substance abuse treatment facility (n = 94).