Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of Genetic Linkage Data for Mendelian Traits

This unit describes linkage analysis, an invaluable tool in mapping human disease genes. Linkage analysis is one of several methods used to map genes. Specifically, in linkage analysis, cosegregation of two or more genes (traits) is examined in a family unit to determine if they segregate independently of each other according to Mendel's laws or if they do not segregate independently because of their close physical proximity. The procedures outlined in this unit are not always straightforward, and a number of caveats are presented in the commentary regarding possible complications and confounding factors that may arise. Specific examples are given, but it is not possible to cover all possible scenarios or variables. The intention is to enable the reader to master basic principles used in the linkage approach, and thus be in a position to undertake, with proper consultation, a linkage‐analysis study. This unit deals specifically with lod score analysis in Mendelian disorders. Curr. Protoc. Hum. Genet. 83:1.4. 1‐1.4. 31. © 2014 by John Wiley & Sons, Inc.
Serum ferritin concentration predicts mortality in patients awaiting liver transplantation

Additional markers are required to identify patients on the orthotopic liver transplant (OLT) waiting list at increased risk of death and adverse clinical events. Serum ferritin concentration is a marker of varied pathophysiological events and is elevated with increased liver iron concentration, hepatic necroinflammation, and systemic illness, all of which may cause a deterioration in liver function and clinical status. The aim of this study was to determine whether serum ferritin concentration is an independent prognostic factor in subjects awaiting OLT. This is a dual‐center retrospective study. The study cohort consisted of 191 consecutive adults with cirrhosis accepted by the Queensland (Australia) Liver Transplant Service between January 2000 and June 2006 and a validation cohort of 131 patients from University of California Los Angeles (UCLA) Transplant Center. In the study cohort, baseline serum ferritin greater than 200 μg/L was an independent factor predicting increased 180‐day and 1‐year waiting list mortality. This effect was independent of model for end‐stage liver disease (MELD), hepatocellular carcinoma, age, and sex. Subjects with higher serum ferritin had increased frequency of liver‐related clinical events. The relationship between serum ferritin and waiting list mortality was confirmed in the UCLA cohort; all deceased patients had serum ferritin greater than 400 μg/L. Serum ferritin greater than 500 μg/L and MELD were independent risk factors for death. Conclusion: Serum ferritin concentration is an independent predictor of mortality‐related and liver‐related clinical events. Baseline serum ferritin identifies a group of “higher‐risk” patients awaiting OLT and should be investigated as an adjunct to MELD in organ allocation. (HEPATOLOGY 2010)
Integrating nonmarket and market resources, strategy and performance in Chinese enterprises: a review of the field and a resource-based empirical study

Abstract The resource-based view (RBV) regards strategy as deploying resources to obtain a competitive advantage. This article adopts such a RBV, by a simultaneous consideration of nonmarket and market factors, and then an empirical analysis of the relationships between such nonmarket and market resources, strategies and performance, focusing specifically on Chinese enterprises. The results test hypotheses related to the integrated strategy and RBV of the firm on linkages of nonmarket and market components. Combining those two views, this study reveals that there is a high and positive correlation between nonmarket and market strategies, while nonmarket strategy has a positive indirect effect on market performance via nonmarket performance. These findings suggest that the RBV is an appropriate theory for addressing the shortcomings in integrated strategy research.
Movement based biometric authentication with smartphones

The widespread use of small, mobile computing devices such as smartphones increases the need to protect these devices and the sensitive data they contain against unauthorized use. Authentication solutions based on biometrics are a promising way to replace common mechanisms relying on personal identification numbers or passwords, which are often perceived as inconvenient by users. Fingerprint based authentication schemes have been introduced to the latest generations of smartphones. Fingerprints are easy to record and they show low intra-class variation. However, fingerprints or fingerprint templates must be safely stored on the phone and not transmitted to other data bases. Since fingerprints are linked to users for life, the damage caused by compromised fingerprint data is likely to be very significant and potentially permanent for users. Here we present a proof-of-principle demonstration for movement based biometrics with built-in smartphone motion sensors. Such dynamic biometric approaches have a lower potential for misuse than fingerprints while being fast and user friendly. Using an approach based on the implementation of a dynamic time warping algorithm we find that in a feasible application scenario a 0.02% false acceptance rate at a 10% false rejection rate can be achieved (equal error rate about 3%). We also investigate the threat posed by skilled forgeries, where access to a detailed video recording of the original user movement is provided. Furthermore, forgers were asked to practice the movement until they feel comfortable executing it. This lead to an increase in the equal error rate to 9%. A similarly detailed video recording of a user entering a password would likely result in a nearly 100% equal error rate. These proof-of-principle results demonstrate that movement based authentication with smartphones holds significant potential but must be improved further to serve as a stand-alone authentication method.
Improved Computation of Attenuated Light with Application in Scenes with Many Light Sources

This paper presents and investigates methods for fast and accurate illumination of scenes containing many light sources that have limited spatial influence, e.g. point light sources. For speeding up the computation, current graphics applications use an assumption that the light sources range can be limited using bounding spheres due to their limited spatial influence and illumination is computed only if a surface lies within the sphere. Therefore, we explore the differences in illumination between scenes illuminated with spatially limited light sources and physically more correct computation where the light radius is infinite. We show that the difference can be small if we add appropriate ambient lighting. The contribution of the paper is the method for fast estimation of ambient lighting in scenes illuminated by numerous light sources. We also propose a method for elimination of color discontinuities at the edges of the bounding spheres. Our solution is tested on two different scenes: a procedurally generated city and the Sibenik cathedral. Our approach allows for correct lighting computation in scenes with numerous light sources without any modification of the scene graph or other data structures or rendering procedures. It thus can be applied in various systems without any structural modifications.
Suppression of Eye-Blink Associated Artifact Using Single Channel EEG Data by Combining Cross-Correlation With Empirical Mode Decomposition

Eye-blink signals are the major sources of artifacts in the electroencephalogram (EEG). Conventionally, the wavelet-based approach is used for analysis and suppression of these artifacts from single channel EEG data by applying the threshold in the decomposition of the signal in terms of a set of predefined basis functions. Here, we report a novel approach for effective suppression of these artifacts by combining the data-driven technique called empirical mode decomposition (EMD) with cross-correlation. The contaminated EEG signal is decomposed into a series of intrinsic mode functions (IMFs) using EMD; in this decomposition, some of the IMFs capture features corresponding to the eye-blink signals and are termed as noisy IMFs. The artifact suppression proposed in this paper relies on the elimination of noisy IMFs based on cross-correlation with a suitable template extracted from the contaminated segment of EEG. We illustrate the method by applying it for suppressing artifacts corresponding to eye blinks during the measurement of visual evoked EEG response and compare it with conventionally used single channel wavelet technique.
High-throughput thermal stability assessment of DNA hairpins based on high resolution melting

On the basis of high-resolution melting, a high-throughput approach to measure melting temperatures (Tms) of short DNA hairpins was developed. With this method, Tms of thousands of triloop, tetraloop, and pentaloop hairpins involving various loop sequences and various closing base pairs (cbp) were obtained in hours. The stability of triloop hairpins decreased with the change of cbp (5′–3′) in the order of c-g > g-c > t-a ≥ a-t, showing that the cbp of 5′-Pyr-Pur-3′ (Pyr = pyrimidine, Pur = purine) contributed more stability than 5′-Pur-Pyr-3′. For tetraloop hairpins, GNNA, GNAB, and CNNG (N = A, G, C, or T; B = G, C, or T) were found to be highly stable irrespective of the cbp type. TNNA was also stable in both g-c and a-t families, while CGNA only in the c-g family. Pentaloop hairpins of cTGNAGg, cGNYNAg (Y = T or C) and cCGNNAg were exceptionally stable motifs. In most cases, pyrimidine-rich loops were more favorable to stabilize the whole structure than purine-rich ones. The present approach showed a good performance in assessing the thermal stability of large amounts of DNA hairpins comprehensively. These data are useful to understand the sequence dependence of the stability of DNA secondary structures and promising to improve the structure simulation by consummating basic databases.
Urokinase-type plasminogen activator receptor promotes proliferation and invasion with reduced cisplatin sensitivity in malignant mesothelioma

Malignant mesothelioma (MM) is a rare neoplasm associated with asbestos exposure. The prognosis of MM is poor because it is aggressive and highly resistant to chemotherapy. Using a rat model of asbestos-induced MM, we found elevated urokinase-type plasminogen activator receptor (uPAR; Plaur) expression in rat tissues, which was associated with poor prognosis. The proliferation, migration and invasion of MM cells were suppressed by uPAR knockdown and increased by overexpression experiments, irrespective of urokinase-type plasminogen activator (uPA; Plau) levels. More importantly, we found that uPAR expression is associated with sensitivity to cisplatin in MM through the PI3K/AKT pathway, which was demonstrated with specific inhibitors, LY294002 and Akti-1/2. uPAR knockdown significantly increased sensitivity to cisplatin whereas its overexpression significantly decreased cisplatin sensitivity. Furthermore, sera and tissues from MM patients showed significantly high uPAR levels, which suggested the pathogenic role of uPAR in the tumor biology of human MM. In conclusion, our findings indicate that uPAR levels are associated with malignant characteristics and cisplatin sensitivity of MM. In addition to the potential use of uPAR as a prognostic marker, the combination of uPAR abrogation and cisplatin may reveal a promising therapeutic approach for MM.
Optimal control theory and application in the optimal fiscal policies in Iran

This paper analyzes the design of macroeconomic policies for Iran during the forth five year development plan (2005-2009). For this purpose, we develop and use a macroeconomic model for Iran. We use Applied Mathematics in Optimal Control Theory methods and determine optimal fiscal policies as solutions of optimum control problems with a quadratic objective function, Least Square Method, and the macro-econometric model as a constraint. The results show that, the optimal values of current and capital government expenditures (except for the first year of government current expenditures) are greater than those proposed in forth development plan whereas the tax revenues is less than the proposed one. The comparison between the effects of the optimal fiscal policies on goal variables, show that using the optimal fiscal policies will improve the economic growth rate.
A Pragmatic Cognitive System Engineering Approach to Model Dynamic Human Decision-Making Activities in Intelligent and Automated Systems

Abstract : Defence Research and Development Canada, Valcartier, has undertaken Research and Development (R&D) work to provide Canadian warships with a revolutionary decision support capability explicitly designed to make the automation transparent and provide warfighters with effective and trusted decision support. This effort uses cognitive system engineering (CSE) as the essential design framework. CSE approaches are well suited to deal with decision support issues, but in practice are very expensive to conduct, time consuming, and inefficient from a design process perspective. With the latter limitations in mind, a pragmatic CSE approach, known as Applied Cognitive Work Analysis (ACWA), was developed to bridge - in a structured, efficient, and converging way - the gap between cognitive analysis and design. As a result, the cost to conduct CSE analyses using the ACWA approach is reduced and analysis-design efficiency is significantly improved. This makes it easier to identify decision-aiding concepts suited to provide effective decision support. This paper presents a brief overview of CSE analysis methods and their benefits, particularly ACWA. It also presents some lessons learned when using ACWA for a specific project. Specifically, the first three steps of the ACWA approach were used during the initial phase of the ATAC (Advanced Threat Assessment Capability) project for the Canadian Navy. One important requirement for that project was to use a formal modeling and design approach that allowed one to trace back the origin of a specific algorithm development. The ACWA approach in concert with a systematic documentation methodology (FAH and its artifacts) was found to be very useful in the ATAC project, as it provided the means to meet that traceability requirement. (2 tables, 17 refs.)
Effects of chronic alcohol dependence and chronic cigarette smoking on cerebral perfusion: a preliminary magnetic resonance study.

BACKGROUND Although approximately 80% of individuals with alcohol use disorders are chronic smokers and despite reported associations between chronic cigarette smoking and lower cerebral perfusion in nonalcoholics, previous brain perfusion studies with alcoholics did not account for the potential effects of concurrent chronic cigarette smoking. METHODS One-week-abstinent alcohol-dependent individuals in treatment (ALC) [19 smokers (sALC) and 10 nonsmokers (nsALC)] and 19 healthy light drinking, nonsmoking control participants (nsLD) were scanned with a pulsed arterial spin labeling method to measure cerebral perfusion without an exogenous contrast agent. Studies were performed with 2 different postlabeling delay times (time from labeling pulse to the excitation pulse; PLD=1,500 ms and PLD=1,200 ms) to assess the potential effect of arterial blood transit time on the perfusion. Average gray matter (GM) and white matter (WM) perfusion for the frontal and parietal lobes were calculated for each hemisphere from voxels containing at least 90% GM and 100% WM. RESULTS At PLD=1,500 ms, multivariate analyses compared ALC (combined sALC and nsALC) with nsLD (p=0.04) and contrasted sALC, nsALC, and nsLD (p=0.006). ALC, as a group, showed 13% lower frontal GM perfusion (p=0.005) and 8% lower parietal GM perfusion than nsLD (p=0.03). With ALC separated into smokers and nonsmokers, sALC showed 19% lower frontal GM perfusion (p=0.001) and 12% lower parietal GM perfusion than nsLD (p=0.004). In sALC, a higher number of cigarettes smoked per day was associated with lower perfusion. Overall, regional perfusion did not differ significantly between nsALC and nsLD. Results obtained with PLD=1,200 ms generally confirmed the 1,500 ms findings. CONCLUSIONS This study provides preliminary evidence that chronic cigarette smoking adversely affects cerebral perfusion in frontal and parietal GM of 1-week-abstinent alcohol-dependent individuals. These results are in line with our spectroscopic and structural magnetic resonance studies that suggest chronic cigarette smoking compounds the detrimental effects of alcohol dependence on brain neurobiology.
Tissue-Specific Profiling Reveals Transcriptome Alterations in Arabidopsis Mutants Lacking Morphological Phenotypes[C][W]

Most loss-of-function single mutants show no visible phenotype differences compared with the wild type. This work shows that mutations in duplicate transcription factor genes of the root epidermis elicit dramatic changes in transcript profiles despite the lack of a morphological defect, illustrating the importance of in-depth phenotypic analyses and the complexity of duplicate gene diversification. Traditional genetic analysis relies on mutants with observable phenotypes. Mutants lacking visible abnormalities may nevertheless exhibit molecular differences useful for defining gene function. To examine this, we analyzed tissue-specific transcript profiles from Arabidopsis thaliana transcription factor gene mutants with known roles in root epidermis development, but lacking a single-gene mutant phenotype due to genetic redundancy. We discovered substantial transcriptional changes in each mutant, preferentially affecting root epidermal genes in a manner consistent with the known double mutant effects. Furthermore, comparing transcript profiles of single and double mutants, we observed remarkable variation in the sensitivity of target genes to the loss of one or both paralogous genes, including preferential effects on specific branches of the epidermal gene network, likely reflecting the pathways of paralog subfunctionalization during evolution. In addition, we analyzed the root epidermal transcriptome of the transparent testa glabra2 mutant to clarify its role in the network. These findings provide insight into the molecular basis of genetic redundancy and duplicate gene diversification at the level of a specific gene regulatory network, and they demonstrate the usefulness of tissue-specific transcript profiling to define gene function in mutants lacking informative visible changes in phenotype.
Automatic documents summarization using ontology based methodologies

When humans summarize a document they usually read the text first, understand it then attempt to write a summary. In essence, these processes require at least some basic level of background knowledge by the reader. The least of which would be the Natural Language the text is written in. In this thesis, an attempt is made to bridge the gap of machines understanding by proposing a framework backed with knowledge repositories constructed by humans and containing real human concepts. I use WordNet, a hierarchically-structured repository that was created by linguistic experts and is rich in its explicitly defined lexical relations. With WordNet, algorithms for computing the semantic similarity between terms were proposed and implemented. These algorithms were especially useful when applied to the application of Automatic Documents Summarization as shown with the obtained evaluation results. I also use Wikipedia, the largest encyclopedia to date. Because of its openness and structure, three problems had to be handled in this thesis: Extracting knowledge and features from Wikipedia, enriching the representation of text documents with the extracted features, and using them in the application of Automatic Summarization. When applying the features extractor to a summarization system, competitive evaluation results were obtained.
Globicatella sanguinis Is an Etiological Agent of Ventriculoperitoneal Shunt-Associated Meningitis

ABSTRACT Globicatella sanguinis is a very rare isolate in clinical samples. We present a case of meningitis in a 69-year-old female patient after implantation of an external left ventricular drainage due to a hydrocephalus. She recovered after antibiotic treatment with ceftriaxone.
Optimal Transport on Discrete Domains

Inspired by the matching of supply to demand in logistical problems, the optimal transportation (or Monge-Kantorovich) problem involves the matching of probability distributions defined over a geometric domain such as a surface or manifold. After discretization, optimal transportation becomes a large-scale linear program, which typically is infeasible to solve efficiently on triangle meshes, graphs, point clouds, and other domains encountered in graphics and machine learning. Recent breakthroughs in numerical optimal transportation enable scalability to orders-of-magnitude larger problems, solvable in a fraction of a second. In these lecture notes, we discuss advances in numerical optimal transport that leverage understanding of both discrete and smooth aspects of the problem. State-of-the-art techniques in discrete optimal transportation combine insight from partial differential equations (PDE) with convex analysis to reformulate, discretize, and optimize transportation problems. The end result is a set of theoretically-justified models suitable for domains with thousands or millions of vertices. Since numerical optimal transport is a relatively new discipline, special emphasis is placed on identifying and explaining open problems in need of mathematical insight and additional research.
Effects of the NQO 1 609 C > T Polymorphism on Leukemia Susceptibility : Evidence from a Meta-analysis

NQO1 (NAD(P)H dehydrogenase, quinone 1) is a member of the NAD(P)H dehydrogenase family and encodes a cytoplasmic 2-electron reductase. This FADbinding protein forms homodimers and reduces quinones to hydroquinones (Snyder et al., 1996; North et al., 2011). In organism, NQO1 functions as a gatekeeper of the 20S proteasomes (Asher et al., 2005), it binds to a subset of short-lived proteins (such as p53, p73 and ornithine decarboxilase) and protects them from 20S proteasomal degradation. The NQO1 609C>T polymorphism is characterized by a single proline-to-serine amino acid substitution, that decreases the half time of NQO1 from 18 h (wild-type) to only 1.2 h via ubiquitination and proteasome pathways. Moreover, other research demonstrated that cell lines and tissues genotyped as homozygous for the NQO1 609C>T polymorphism are deficient in NQO1 activity (Siegel et al., 2001). NQO1 protein prevents one electron reduction of quinones that results in the production of radical species. Mutations in this gene have been associated with tardive dyskinesia (TD) (Pae et al., 2004; Pae, 2008), an increased risk of hematotoxicity after exposure to benzene (Iskander et al., 2005; Ross, 2005), increased risk of childhood asthma (David et al., 2003; Li et al., 2009), susceptibility to various forms of cancer (Sameer et al., 2010; Pandith et