Miracle-dz/UniFAR-FTUs huggingface dataset:
Feasibility study of software reengineering towards role-based access control

Role-Based Access Control (RBAC) is accepted as the most commonly used access control policy; however, it is mainly used during the development of new software systems. In this paper, an approach to reengineering RBAC into legacy systems by applying program transformation is proposed. Wide Spectrum Language (WSL) and MetaWSL are extended. Transformation rules, algorithm and operations for further authorisation management are defined to support access control reorganisation. A case study is demonstrated on a prototype tool FermaT-based Access Control Reorganisation (F-ACR). The result shows that it is a feasible and promising approach to enforcing RBAC in legacy systems.
Genetic polymorphisms of glutathione S-transferase ( GSTM 1 , GSTT 1 and GSTP 1 ) with esophageal cancer risk : a meta-analysis

Glutathione S-transferases (GSTs) are important phase II enzymes and play a crucial role in the elimination of electrophilic carcinogens. Numerous studies have investigated the association between GSTs gene variations with esophageal carcinoma risk, but a final conclusion has not been made. Then we searched PubMed, Web of Knowledge and China National Knowledge Infrastructure (CNKI) for relevant articles until June, 2015. We totally extracted and analyzed the pooled data form 43 published articles about GSTM1 null genotype, GSTT1 null genotype and GSTP1 Ile105Val polymorphism (rs1695) with esophageal carcinoma risk. GSTM1 null genotype and GSTT1 null genotype could significantly increase esophageal cancer risk (OR=1.27, 95% CI=1.11-1.44; OR=1.12, 95% CI=1.05-1.39 respectively). The subgroup analysis showed that the two mutations most likely contribute to esophageal squamous cell carcinoma susceptibility. And Asians carrying the homozygous null genotype were at higher esophageal cancer risk than Caucasians. While GSTP1 Ile105Val variants showed no significant effect to esophageal cancer risk. This meta-analysis provides evidence to support that GSTM1 and GSTT1 null genotypes could increase esophageal cancer risk, which would benefit the diagnosis and prevention of esophageal cancer.
Reliability of RF MEMS Capacitive Switches and Distributed MEMS Phase Shifters using AlN Dielectric

The reliability and charging/discharging dynamics of wideband (1.5-14GHz) phase shifters made of MEMS capacitive switches using Aluminum Nitride (AlN) as dielectric are originally reported. Phase shifter lifetimes exceeding 109 cycles are achieved in hot-cycling (+5dBm RF power). Dynamic tests were done for the first time under ambient conditions (50% humidity) over 2×109 cycles with no major degradation of individual switches performances. It is demonstrated that the phase shifter is very robust (no permanent failure or stiction) and can withstand environmental effects as well as high temperature variations, without the need of expensive hermetical packaging. The excellent reliability is attributed to the slow dielectric charging (a square-root time law) and fast discharging mechanism of AlN (an exponential time law proposed and validated in our work). We extend the validity of charging and discharging models from single device to arrays of parallel MEMS capacitors.
Analytical studies on degradation mechanism of herbicide 4-chlorophenoxyacetic acid in water by gamma/H2O2 and gamma/ozone processes

ABSTRACT Radiolytic degradation of 4-chlorophenoxyacetic acid was followed in the presence of hydrogen peroxide and ozone. The synergic effect of ozone is found to be relatively high since the amounts of detected aromatic intermediates are lower as well as the amounts of small aliphatic acids are higher. Chloride ions are one of the most important mineralization products and splitted with a yield of more than 80%. The amounts of small aliphatic acids formed in the last step before mineralization (oxalic, acetic and formic acid) were followed and their formation from 4-chlorophenoxyacetic acid was confirmed. Dissolved oxygen was consumed to form reactive radicals during irradiation. Product analysis and confirmation are followed by gas chromatography/mass spectrometry and ion chromatography. The degradation path of 4-chlorophenoxyacetic acid was suggested with determined intermediates.
Liver‐Specific Gene Expression in Cultured Human Hematopoietic Stem Cells

Hematopoietic and hepatic stem cells share characteristic markers such as CD34, c‐kit, and Thy1. Based on the recent observations that hepatocytes may originate from bone marrow, we investigated the potential of CD34+ bone marrow cells to differentiate into hepatocytic cells in vitro. CD34+ and CD34− human bone marrow cells were separated by magnetic cell sorting. Cells were cultured on a collagen matrix in a defined medium containing hepatocyte growth factor. Cell count and size were measured by flow cytometry, and reverse transcription polymerase chain reaction was carried out for the liver‐specific markers CK‐19 and albumin. During cell culture, CD34+ cells showed an increasing cell number and proliferative activity as assessed by Ki‐67 staining. Under the specified culture conditions, CD34+ cells expressed albumin RNA and CK‐19 RNA after 28 days, whereas CD34− cells did not show liver‐specific gene expression. The results indicate that CD34+ adult human bone marrow stem cells can differentiate into hepatocytic cells in vitro.
Different Contributions of the Three CXXC Motifs of Human Protein-disulfide Isomerase-related Protein to Isomerase Activity and Oxidative Refolding*

Human protein-disulfide isomerase (hPDI)-related protein (hPDIR), which we previously cloned from a human placental cDNA library (Hayano, T., and Kikuchi, M. (1995) FEBS Lett. 372, 210-214), and its mutants were expressed in the Escherichia coli pET system and purified by sequential nickel affinity resin chromatography. Three thioredoxin motifs (CXXC) of purified hPDIR were found to contribute to its isomerase activity with a rank order of CGHC > CPHC > CSMC, although both the isomerase and chaperone activities of this protein were lower than those of hPDI. Screening for hPDIR-binding proteins using a T7 phage display system revealed that α1-antitrypsin binds to hPDIR. Surface plasmon resonance experiments demonstrated that α1-antitrypsin interacts with hPDIR, but not with hPDI or human P5 (hP5). Interestingly, the rate of oxidative refolding of α1-antitrypsin with hPDIR was much higher than with hPDI or hP5. Thus, the substrate specificity of hPDIR differed from that associated with isomerase activity, and the contribution of the CSMC motif to the oxidative refolding of α1-antitrypsin was the most definite of the three (CSMC, CGHC, CPHC). Substitution of SM and PH in the CXXC motifs with GH increased isomerase activity and decreased oxidative refolding. In contrast, substitution of GH and PH with SM decreased isomerase activity and increased oxidative refolding. Because CXXC motif mutants lacking isomerase activity retain chaperone activity for the substrate rhodanese, it is clear that, similar to PDI and hP5, the isomerase and chaperone activities of hPDIR are independent. These results suggest that the central dipeptide of the CXXC motif is critical for both redox activity and substrate specificity.
Appearance Stylization of Manhattan World Buildings

We propose a method that generates stylized building models from examples (Figure ). Our method only requires minimal user input to capture the appearance of a Manhattan world (MW) building, and can automatically retarget the captured ‘look and feel’ to new models. The key contribution is a novel representation, namely the ‘style sheet’, that is captured independently from a building's structure. It summarizes characteristic shape and texture patterns on the building. In the retargeting stage, a style sheet is used to decorate new buildings of potentially different structures. Consistent face groups are proposed to capture complex texture patterns from the example model and to preserve the patterns in the retarget models. We will demonstrate how to learn such style sheets from different MW buildings and the results of using them to generate novel models.
A Comparison of Actuarial Financial Scenario Generators by

The actuarial profession is encouraging significant work in the area of asset returns to support Risk Based Capital analysis, Dynamic Financial Analysis, pricing embedded options, solvency testing and other financial applications. One recent study is the CAS-SOA research project on Modeling of Economic Series Coordinated with Interest Rate Scenarios. The American Academy of Actuaries also recently released a set of 10,000 prepackaged scenarios for common asset classes in support of the C-3 Phase 2 RBC for Variable Annuities. Both data sets provide practitioners with a large number of iterations for key financial values, including short and long term interest rates and equity returns. This research provides a comparison of the underlying models and the output of these studies to facilitate the understanding and use of the alternative sets of output.
Structural and functional domains of the myb oncogene: requirements for nuclear transport, myeloid transformation, and colony formation

The v-myb oncogene of avian myeloblastosis virus causes acute myelomonocytic leukemia in vivo and transforms only myeloid cells in vitro. Its product, p48v-myb, is a nuclear protein of unknown function. To determine structure-function relationships for this protein, we constructed a series of deletion mutants of v-myb, expressed them in retroviral vectors, and studied their biochemical and biological properties. We used these mutants to identify two separate domains of p48v-myb which had distinct roles in its accumulation in the cell nucleus. We showed that the viral sequences which normally encode both termini of p48v-myb were dispensible for transformation. In contrast, both copies of the highly conserved v-myb amino-terminal repeat were required for transformation. We also identified a carboxyl-terminal domain of p48v-myb which was required for the growth of v-myb-transformed myeloblasts in soft agar but not for morphological transformation.
The Danish Register of Causes of Death

Introduction: Cause-specific mortality statistics is a valuable source for the identification of risk factors for poor public health. Content: Since 1875, the National Board of Health has maintained the register covering all deaths among citizens dying in Denmark, and since 1970 has computerised individual records. Validity and coverage: Classification of cause(s) of deaths is done in accordance to WHO’s rules, since 1994 by ICD-10 codes. A change in coding practices and a low autopsy rate might influence the continuity and validity in cause-specific mortality. Conclusion: The longstanding national registration of causes of death is essential for much research. The quality of the register on causes of death relies mainly upon the correctness of the physicians’ notification and the coding in the National Board of Health.
Modeling and Rendering of the Atmosphere Using Mie‐Scattering

This paper presents a method for rendering of the atmosphere by means of Mie‐scattering. The method is based on a concentric atmospheric model, which is divided into four submodels: for clear air, aerosol, ozone, and rain. In order to simulate and visualize the various atmospheric effects, each of these submodels can be parameterized by the user as desired. The process of rendering an outdoor scene requires an enormous amount of computing power. In order to make this method suitable for efficient implementation, some simplifications and approximations are discussed. In addition, a selection of the rendering results are presented, and our further activities in the field of atmospheric rendering are discussed.
Co-registration of radiographic and pathologic infarct territory in a non-human primate model of stroke

Abstract Objectives: Infarct volume correlation using magnetic resonance imaging (MRI) and pathology specimens enables exact tissue localization of cerebral injury following experimental stroke. We describe a protocol that enables co-registration of radiographic signal change and histologic ischemia in a non-human primate model of stroke. Methods: One male baboon underwent left middle cerebral artery territory occlusion/reperfusion. MRI [5 mm axial T2 weighted (T2W) slices] was carried out 9 days post-ischemia after which the animal was killed. Immediately post-mortem, the whole brain was perfused and fixed in paraformaldehyde and sliced into 5 mm axial sections that corresponded to those demonstrated on MRI. Slices (40 μm) were obtained from each section and were then stained using Luxol hematoxylin and eosin. Results: The relative area of hyperintensity demonstrated on T2W MRI approximates, in size and location, the region of infarct on gross pathology. This was confirmed microscopically. Discussion: With the use of advanced imaging modalities, this co-registration technique affords the capacity to differentiate ischemic core, penumbra, and uninjured cortex following experimental stroke. Such a precise delineation enables immunohistochemical analysis of a wide variety of substrates in each of the aforementioned regions.
Evaluation of the IDI-MRSA Assay for Detection of Methicillin-Resistant Staphylococcus aureus from Nasal and Rectal Specimens Pooled in a Selective Broth

ABSTRACT Rapid detection of methicillin-resistant Staphylococcus aureus (MRSA) by PCR can be performed directly from nasal specimens with the IDI-MRSA assay. To improve the efficiency of screening, we evaluated the performance of the IDI-MRSA assay for the detection of MRSA from pooled and unpooled specimens cultured in a selective broth. Of the 287 specimens evaluated, 71 were culture and PCR positive, 203 were culture and PCR negative, 3 were culture positive and PCR negative, 8 were culture negative and PCR positive, and 2 remained inhibited. A methicillin-susceptible Staphylococcus aureus isolate was recovered from five of the eight specimens with false-positive PCR results. Compared to the results of culture, the sensitivity, specificity, and negative and positive predictive values of the IDI-MRSA assay for detection of MRSA from broth were 96%, 96%, 90%, and 98%, respectively. Following implementation of the IDI-MRSA assay, PCR-positive broths were subcultured for evaluation of assay performance. Of the 298 IDI-MRSA assay-positive broths, the results for 103 could not be confirmed by culture. A methicillin-susceptible S. aureus (MSSA) isolate was recovered from 77 of these 103 broths. Repeat testing by the IDI-MRSA assay directly with the MSSA isolates confirmed the original positive PCR result. The positive predictive value of the IDI-MRSA assay fell from 90% during the evaluation phase to 65% postimplementation. The IDI-MRSA assay performed well for the detection of MRSA from a selective broth compared to the performance of the detection of MRSA from culture. However, because of the burden associated with implementation of infection control precautions, cultures remain essential in confirming positive IDI-MRSA results.
Blood-gene expression reveals reduced circadian rhythmicity in individuals resistant to sleep deprivation.

STUDY OBJECTIVES To address whether changes in gene expression in blood cells with sleep loss are different in individuals resistant and sensitive to sleep deprivation. DESIGN Blood draws every 4 h during a 3-day study: 24-h normal baseline, 38 h of continuous wakefulness and subsequent recovery sleep, for a total of 19 time-points per subject, with every 2-h psychomotor vigilance task (PVT) assessment when awake. SETTING Sleep laboratory. PARTICIPANTS Fourteen subjects who were previously identified as behaviorally resistant (n = 7) or sensitive (n = 7) to sleep deprivation by PVT. INTERVENTION Thirty-eight hours of continuous wakefulness. MEASUREMENTS AND RESULTS We found 4,481 unique genes with a significant 24-h diurnal rhythm during a normal sleep-wake cycle in blood (false discovery rate [FDR] < 5%). Biological pathways were enriched for biosynthetic processes during sleep. After accounting for circadian effects, two genes (SREBF1 and CPT1A, both involved in lipid metabolism) exhibited small, but significant, linear changes in expression with the duration of sleep deprivation (FDR < 5%). The main change with sleep deprivation was a reduction in the amplitude of the diurnal rhythm of expression of normally cycling probe sets. This reduction was noticeably higher in behaviorally resistant subjects than sensitive subjects, at any given P value. Furthermore, blood cell type enrichment analysis showed that the expression pattern difference between sensitive and resistant subjects is mainly found in cells of myeloid origin, such as monocytes. CONCLUSION Individual differences in behavioral effects of sleep deprivation are associated with differences in diurnal amplitude of gene expression for genes that show circadian rhythmicity.
Intra-class Correlation in Random-effects Models for Binary Data

We review the concept of intra-class correlation in random-effects models for binary outcomes as estimated by Stata's xtprobit, xtlogit, and xtclog. We consider the usual measures of correlation based on a latent variable formulation of these models and note corrections to the last two procedures. We also discuss alternative measures of association based on manifest variables or actual outcomes and introduce a new command xtrho for computing these measures for all three types of models.
Conformai integrated multi-layer thin-film antenna by novel LITA technologies for smartwatch wearable device applications

This article presents a conformai integrated multi-layer thin-film antenna design implemented by novel LITA (Laser-Induced Integrated Thin-Film Antenna) technologies for smartwatch device applications. Through the proposed LITA technology which is jointly developed by ITRI and ACON in Taiwan, metal layouts of antennas can be formed on the internal surface of a smartwatch casing successfully with conform al, thin-film type, multi-layer and highly integrating characteristics. It is demonstrated that by designing a compact two-layer thin-film feeding capacitor by LITA, a much smaller PIFA antenna size (5×10 mm2 only) can be achieved successfully compared to the PIFA with a co-planar capacitive feeding structure and the prior PIFA with a direct feed. The constructed antenna prototype analyzed with presence of a user's right hand is discussed in this paper.
Expression and Mutational Status of c-kit in Thymic Epithelial Tumors

Background: Overexpression of c-kit, a tyrosine kinase receptor protein encoded by the protooncogene kit, has been previously reported in thymic epithelial tumors and in other neoplasms such as gastrointestinal stromal tumors, myeloproliferative disorders, melanoma, and seminoma. Mutations in the kit gene have been related to response to imatinib in gastrointestinal stromal tumor and one case report of thymic carcinoma. We studied expression of c-kit in a large retrospective series of thymic epithelial malignancies and sequenced the whole gene in a subset of patients. Methods: Thymic epithelial tumors from 120 patients (13 thymic carcinomas and 107 thymomas) were examined. Immunohistochemical staining with an antic-kit polyclonal antibody was performed on a tissue microarray. Mutation analyses of exons 1 to 20 were conducted by direct DNA sequencing of polymerase chain reaction products in eight thymic carcinomas, five thymomas, and one thymic carcinoma cell line. Results: The percentage of c-kit positive cells was significantly higher in thymic carcinoma (46%) than in thymoma (4%). Decreased disease-related survival and progression-free survival were observed in c-kit positive tumors. No mutations were detected. Conclusion: c-kit expression is strongly but not exclusively related to thymic carcinoma histotype, and it is of prognostic value. Mutations are very rare.
Genetic Diversity of Populations of Akhal-Teke Horses from the Czech Republic, Russia, Estonia and Switzerland

JISKROVA IVA, VRTKOVA IRENA, PRAUSOVA MICHAELA. 2016. Genetic Diversity of Populations of Akhal-Teke Horses from the Czech Republic, Russia, Estonia and Switzerland. Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis, 64(2): 461–466. Our research objective was to evaluate the genetic parameters in the populations of Akhal-Teke horses in 4 countries: Czech Republic, Russia, Estonia and Switzerland. The experiment involved a total of 325 Akhal-Teke horses; 121 horses came from the Czech Republic, 152 were from Russia, 28 were from Estonia and 24 horses came from Switzerland. For the divided database of micro satellites we evaluated the following parameters: eff ective number of alleles, frequency of alleles for the groups of horses; the observed heterozygosity (HO); the expected heterozygosity (HE); the inbreeding coeffi cient (Fis); and the genetic distance. The researched population is polymorphous. The population in the Czech Republic diff ers from the other three countries in the numbers of alleles per locus. The Czech population also includes Akhal-Teke horses which are not purebred Akhal-Teke horses. A confi rmation of this fact is the eff ective number of alleles. The population in the Czech Republic exhibits the highest mean number of eff ective alleles. The Akhal-Teke population in Estonia exhibits the highest mean observed heterozygosity. By contrast, the population in the Czech Republic exhibits the lowest mean observed heterozygosity. In the Czech Republic the mean Fis value is a positive number indicating a reduced number of heterozygotes in the Czech Akhal-Teke population. The genetic distance is the highest between populations of horses bred in Russia and Estonia. The genetic distance is the lowest between populations of Akhal-Teke horses bred in Russia and in the Czech Republic.
Basal phosphorylation of the PEST domain in the I(kappa)B(beta) regulates its functional interaction with the c-rel proto-oncogene product

The product of the c-rel proto-oncogene (c-Rel) belongs to the NF-kappaB/Rel family of polypeptides and has been implicated in the transcriptional control of cell proliferation and immune function. In human T lymphocytes, c-Rel is sequestered in the cytoplasmic compartment by constitutively phosphorylated inhibitors, including I(kappa)B(alpha) and I(kappa)B(beta). Studies with bacterially expressed forms of these inhibitory proteins revealed that unphosphorylated I(kappa)B(alpha) but not I(kappa)B(beta) assembles with c-Rel and inhibits its DNA binding activity. Furthermore, latent I(kappa)B(beta)-c-Rel complexes derived from mammalian cells were sensitive to phosphatase treatment, whereas I(kappa)B(alpha)-c-Rel complexes were resistant. We have identified a constitutive protein kinase in unstimulated T cells that associates with and phosphorylates I(kappa)B(beta) in vitro. The substrate specificity, electrophoretic mobility, and antigenic properties of this I(kappa)B(beta)-associated kinase (BAK) suggest identity with casein kinase II (CKII), an enzyme known to mediate basal phosphorylation of I(kappa)B(alpha). Phosphorylation of recombinant I(kappa)B(beta) by either BAK or CKII restored the capacity of this inhibitor to antagonize the DNA binding activity of c-Rel. Peptide mapping and mutational analyses localized the bulk of the basal phosphorylation sites in I(kappa)B(beta) to the C-terminal PEST domain, which contains two potential acceptors for CKII-mediated phosphoryl group transfer (Ser-313 and Ser-315). Point mutations introduced into the full-length inhibitor at Ser-313 and Ser-315 led to a significant reduction in the phosphorylation of I(kappa)B(beta) and severely impaired its c-Rel inhibitory function in vivo. Taken together, these findings strongly suggest that basal phosphorylation of the PEST domain of I(kappa)B(beta) at consensus CKII sites is required for the efficient formation of latent I(kappa)B(beta)-c-Rel complexes.