Miracle-dz/UniFAR-FTUs huggingface dataset:
Message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines

A mixed parallel scheme that combines message passing interface (MPI) and multithreading was implemented in the AutoDock Vina molecular docking program. The resulting program, named VinaLC, was tested on the petascale high performance computing (HPC) machines at Lawrence Livermore National Laboratory. To exploit the typical cluster‐type supercomputers, thousands of docking calculations were dispatched by the master process to run simultaneously on thousands of slave processes, where each docking calculation takes one slave process on one node, and within the node each docking calculation runs via multithreading on multiple CPU cores and shared memory. Input and output of the program and the data handling within the program were carefully designed to deal with large databases and ultimately achieve HPC on a large number of CPU cores. Parallel performance analysis of the VinaLC program shows that the code scales up to more than 15K CPUs with a very low overhead cost of 3.94%. One million flexible compound docking calculations took only 1.4 h to finish on about 15K CPUs. The docking accuracy of VinaLC has been validated against the DUD data set by the re‐docking of X‐ray ligands and an enrichment study, 64.4% of the top scoring poses have RMSD values under 2.0 Å. The program has been demonstrated to have good enrichment performance on 70% of the targets in the DUD data set. An analysis of the enrichment factors calculated at various percentages of the screening database indicates VinaLC has very good early recovery of actives. © 2013 Wiley Periodicals, Inc.
Chronic Cold Exposure Increases Skeletal Muscle Oxidative Structure and Function in Monodelphis domestica, a Marsupial Lacking Brown Adipose Tissue

Monodelphis domestica (Marsupialia: Didelphidae) was used as a model animal to investigate and compare muscle adaptation to exercise training and cold exposure. The experimental treatment consisted of four groups of animals: either warm or cold acclimation temperature and with or without endurance exercise training. Maximal aerobic capacity during a running \( \dot{\mathrm{V}}{\small O}_{2^{\mathrm{max}\,}} \) test in the warm‐exercised or cold‐exposed (with or without exercise) groups was about 130 mL O2/kg/min, significantly higher than the warm‐acclimated controls at 113.5 mL O2/kg/min. Similarly, during an acute cold challenge ( \( \dot{\mathrm{V}}{\small O}_{2^{\mathrm{summit}\,}} \) ), maximal aerobic capacity was higher in these three experimental groups at ∼95 mL O2/kg/min compared with 80.4 mL O2/kg/min in warm‐acclimated controls. Respiratory exchange ratio was significantly lower (0.89–0.68), whereas relative heart mass (0.52%–0.73%) and whole‐body muscle mitochondrial volume density (2.59 to 3.04 cm3) were significantly higher following cold exposure. Chronic cold exposure was a stronger stimulus than endurance exercise training for tissue‐specific adaptations. Although chronic cold exposure and endurance exercise are distinct challenges, physiological adaptations to each overlap such that the capacities for aerobic performance in response to both cold exposure and running are increased by either or both treatments.
The preoperative and postoperative oxidative status of children with chronic adenotonsillar hypertrophy.

AIM This study aimed to evaluate the preoperative and postoperative oxidative status of children with chronic adenotonsillar hypertrophy. MATERIALS AND METHODS The study comprised 25 patients with indications for tonsillectomy and/or adenoidectomy following a diagnosis of chronic adenotonsillar hypertrophy and 25 age-gender matched control patients were included to the study. Blood samples were taken from the patients preoperatively and at four weeks postoperatively. Preoperative and postoperative serum total oxidant (TOS) and total antioxidant (TAS) levels were measured and the oxidative stress index (OSI) was calculated. RESULTS The serum total oxidant level and oxidant stress index values in the preoperative and postoperative periods of the patients were found to be significantly high compared to those of the control group. While the preoperative serum total oxidant level values were found to be significantly high compared to the postoperative values, no statistical significance was found between the total antioxidant and oxidative stress index values. CONCLUSION The development of chronic adenotonsillar hypertrophy plays a role in oxidative status and therefore, to neutralize high levels of oxidants in patients, the use of antioxidants for a period preoperatively and postoperatively is thought to be necessary.
High Affinity Binding of Inositol Phosphates and Phosphoinositides to the Pleckstrin Homology Domain of RAC/Protein Kinase B and Their Influence on Kinase Activity*

The influence of inositol phosphates and phosphoinositides on the α isoform of the RAC-protein kinase B (RAC/PKB) was studied using purified wild type and mutant kinase preparations and a recombinant pleckstrin homology (PH) domain. Binding of inositol phosphates and phosphoinositides to the PH domain was measured as the quenching of intrinsic tryptophan fluorescence. Inositol phosphates and D3-phosphorylated phosphoinositides bound with affinities of 1-10 μM and 0.5 μM, respectively. Similar values were obtained using RAC/PKB expressed and purified from baculovirus-infected Sf9 cells in the fluorescence assay. The influence of synthetic dioctanoyl derivatives of phosphatidylinositol 3,4-bisphosphate and phosphatidylinositol 3,4,5-trisphosphate on the activity of RAC/PKB purified from transfected COS-1 cells was studied. Phosphatidylinositol 3,4,5-trisphosphate was found to inhibit the RAC/PKB kinase activity with half-maximal inhibition at 2.5 μM. In contrast, phosphatidylinositol 3,4-bisphosphate stimulated kinase activity (half-maximal stimulation at 2.5 μM). A mutant RAC/PKB protein lacking the PH domain was not affected by D3-phosphorylated phosphoinositides. These results demonstrate that the PH domain of RAC/PKB binds inositol phosphates and phosphoinositides with high affinity, and suggest that the products of the phosphatidylinositide 3-kinase can act as both a membrane anchor and modulator of RAC/PKB activity. The data also provide further evidence for a link between phosphatidylinositide 3-kinase and RAC/PKB regulation.
Determination of the stability of antibiotics in matrix and reference solutions using a straightforward procedure applying mass spectrometric detection

The stability of an antibiotic is a very important characteristic, especially in the field of antibiotic residue analysis. During method development or validation, the stability of the antibiotic has to be demonstrated no matter if the method is used for screening, confirmation, qualitative or quantitative analysis. A procedure for testing the stability of antibiotics in solutions and food samples using LC-MS/MS is described. The procedure is based on the assumption that the antibiotics are stable when stored at −70°C. Representative solutions or spiked samples containing the antibiotic were stored at the temperature to be tested (−18 or 4°C) and at −70°C. After a selected storing time samples were moved from the chosen storage temperature to −70°C. At the end of the study, all samples – per class of antibiotic – were analysed in one batch. By applying statistical models, it was finally concluded in which circumstances the antibiotic is stable. The stability of 60 antibiotics belonging to the classes of tetracyclines, sulphonamides, quinolones, penicillins, macrolides and aminoglycosides were tested. The stability of solutions containing tetracyclines and penicillins is only guaranteed for 3 months while stored at −18°C. Solutions of all other antibiotics tested are stable for at least 6 or 12 months when stored at 4°C. In muscle tissue stored at −18°C no severe degradation of the tested antibiotics was observed, with the exception of the penicillins. The stability data reported here are useful as a reference for laboratories carrying out validation studies of analytical methods for antibiotic (residue) detection. The data should save the time needed for long-term stability testing of solutions and samples.
Three level DC-DC boost converter for high conversion ratio

This paper present three level DC-DC boost converter topology for high conversion ratio. This topology is a combination of traditional boost topology with voltage multiplier. The Traditional boost converter is unable to provide high gain ratio since it has high voltage stress and high duty cycle, hence the three level DC-DC boost converter is used which gives the reliable high conversion ratio. The main advantage of proposed topology is output voltage can be increased by using the combination of capacitors and diodes at output side of the converter, without altering main circuit. Proposed circuit is used for high power application with severe duty cycle. The proposed three level dc-dc boost converter topology consists of 5 capacitors, 7 diodes, 2 inductors and a switch. The design parameters of proposed topology are input voltage, output voltage and duty cycle which are of the ratings 28V, 167V and 46% respectively. The verification of proposed topology is done by experimental results.
Prognostic Potential of DNA Methylation and Transcript Levels of HIF1A and EPAS1 in Colorectal Cancer

Hypoxic conditions during the formation of colorectal cancer may support the development of more aggressive tumors. Hypoxia-inducible factor (HIF) is a heterodimeric complex, composed of oxygen-induced HIFα and constitutively expressed HIFβ subunits, which mediates the primary transcriptional response to hypoxic stress. Among HIFα isoforms, HIF1α (HIF1A) and endothelial PAS domain–containing protein 1 (EPAS1) are able to robustly activate hypoxia-responsive gene signatures. Although posttranslational regulation of HIFα subunits is well described, less is known about their transcriptional regulation. Here, molecular analysis determined that EPAS1 mRNA was significantly reduced in primary colonic adenocarcinoma specimens compared with histopathologically nonneoplastic tissue from 120 patients. In contrast, no difference in HIF1A mRNA levels was observed between cancerous and noncancerous tissue. Bisulfite DNA sequencing and high-resolution melting analysis identified significant DNA hypermethylation in the EPAS1 regulatory region from cancerous tissue compared with nonneoplastic tissue. Importantly, multivariate Cox regression analysis revealed a high HR for patients with cancer with low EPAS1 transcript levels (HR, 4.91; 95% confidence interval, CI, 0.42–56.15; P = 0.047) and hypermethylated EPAS1 DNA (HR, 33.94; 95% CI, 2.84–405.95; P = 0.0054). Treatment with a DNA methyltransferase inhibitor, 5-Aza-2′-deoxycytidine (5-aza-dC/Decitabine), upregulated EPAS1 expression in hypoxic colorectal cancer cells that were associated with DNA demethylation of the EPAS1 regulatory region. In summary, EPAS1 is transcriptionally regulated by DNA methylation in colorectal cancer. Implications: DNA methylation and mRNA status of EPAS1 have novel prognostic potential for colorectal cancer. Mol Cancer Res; 12(8); 1112–27. ©2014 AACR.
Effects of mood manipulation on subjective and behavioural measures of cigarette craving

Cigarette cravings were evaluated in a sample of moderately heavy smokers, using the Questionnaire on Smoking Urges (QSU), and a progressive-ratio (PR) operant procedure in which responding on a computer keyboard was reinforced by puffs on a cigarette, under a progressively increasing work requirement. Subjects were also exposed to musical mood-induction procedures: the induction and maintenance of depressed and elated mood states was confirmed by visual analogue scales and a mood questionnaire. Smoking did not alter mood state. However, relative to the elated condition, induction of a depressed mood caused increases in both QSU scores and measures of PR performance. The results provide the first experimental confirmation of a causal relationship between depressed mood and cigarette craving.
Complex-bilinear recurrent neural network for equalization of a digital satellite channel

Equalization of satellite communication using complex-bilinear recurrent neural network (C-BLRNN) is proposed. Since the BLRNN is based on the bilinear polynomial, it can be used in modeling highly nonlinear systems with time-series characteristics more effectively than multilayer perceptron type neural networks (MLPNN). The BLRNN is first expanded to its complex value version (C-BLRNN) for dealing with the complex input values in the paper. C-BLRNN is then applied to equalization of a digital satellite communication channel for M-PSK and QAM, which has severe nonlinearity with memory due to traveling wave tube amplifier (TWTA). The proposed C-BLRNN equalizer for a channel model is compared with the currently used Volterra filter equalizer or decision feedback equalizer (DFE), and conventional complex-MLPNN equalizer. The results show that the proposed C-BLRNN equalizer gives very favorable results in both the MSE and BER criteria over Volterra filter equalizer, DFE, and complex-MLPNN equalizer.
A Close Scrutiny of Self-Assessment System and its Impact on the Tax Compliance Level of Taxpayers: The Case of Wolaita Zone

Based on the result, the risk based audits are not satisfactorily implemented in Wolaita zone. and most of the respondents responded that there is no good tax service by the tax collecting authority. The other essential condition of effective self-assessment system; fair and timely dispute resolution of the tax disputes is not fulfilled in Wolaita zone tax administration. To effectively implement the self-assessment tax system, the authors of this research recommend policymakers to create awareness of the tax laws through tax education programs, to simplify the tax laws and tax filing procedures, to create effective tax administration so as to effectively enforce the tax laws, to apply the tax penalties strongly and uniformly, to improve the tax service provided for tax payers and to implement effective risk based audits on the tax documents of the taxpayers regularly. The principal aim of the study was to explore the implementation of self assessment tax system and its impact on the tax compliance level of the taxpayers of Wolaita zone. Based on empirical works of scholars, self assessment system is believed to be effective in promoting voluntary tax compliance of the taxpayers provided that some conditions are met. These conditions are; Tax knowledge of the taxpayers, simplicity of the tax system, effective enforcement of the tax laws and penalties, good service to tax payers, simple filing procedure and risk-based tax audits. To test the implementation of these conditions in Wolaita zone, a set of close-ended questionnaires were administered to sampled taxpayers of the zone. A total of two hundred fifty respondents were selected based on simple random sampling from five purposively selected Woredas and addressed. In addition to this, unstructured interview was conducted for two zonal tax officials and two district collecting officials so as to obtain complementary tax collection information. The data gathered through questionnaires was systematically tabulated and analyzed using percentages, mean and weighted mean whereas the data gathered through interview was directly incorporated in the literature part of the study. According to the survey result; Even though Wolaita zone tried to implement self-assessment tax system, the practice is not good. Most taxpayers use official assessment system though the law required taxpayers to assess their tax liability by themselves. The reason is the lack of essential conditions of self-assessment. The study result shows that, most tax payers lack knowledge of the tax laws and procedures needed to apply self assessment system. The Ethiopian filing procedures are not simple for tax payers which makes it difficult to pay based on self assessment. Furthermore, there are no effective tax collection enforcement and penalty by Wolaita zone tax office.
K-glass: Real-time markerless augmented reality smart glasses platform

Recently, augmented reality (AR) has been actively studied with the proliferation of advanced displays such as a head mounted display (HMD). Nevertheless, it was almost impossible for the conventional HMDs to process the complex AR algorithm in real time, because it requires highly accurate registration and positioning of virtual objects in the real environment. In this paper, we present the world's first markerless AR HMD system equipped with a high-throughput AR processor. Thanks to the dedicated AR processor, it can recognize general objects without any help of markers and give 3D information to the user in real time (30fps). Also, the processor adopts dynamic voltage and frequency scaling as a power managing scheme for low power consumption. As a result, it sustains one-day long real-time AR operation consuming 381mW on average when it performs the full chain of AR processing including object recognition, camera pose estimation, and 3D graphics rendering on a HD (720p) input video stream.
Multiprogram digital control for bilinear object

In works [1-4] the multiprogram stabilization problem (MPS problem) is considered for various classes of continuous control systems. Such systems are described by ordinary differential equations. In the article [5] for the first time this problem has been solved for a linear model of a digital object, i.e. for the linear difference system. Here we consider the bilinear control systems. This is broader class that allows simulating processes in various applications [6-9]. So it is important to extend multiprogram approach to the class of bilinear discrete control systems.
Interactions of hydrogen with the iron and iron carbide interfaces: a ReaxFF molecular dynamics study.

Hydrogen embrittlement (HE) is a well-known material phenomenon that causes significant loss in the mechanical strength of structural iron and often leads to catastrophic failures. In order to provide a detailed atomistic description of HE we have used a reactive bond order potential to adequately describe the diffusion of hydrogen as well as its chemical interaction with other hydrogen atoms, defects, and the host metal. The currently published ReaxFF force field for Fe/C/H systems was originally developed to describe Fischer-Tropsch (FT) catalysis [C. Zou, A. C. T. van Duin and D. C. Sorescu, Top. Catal. , 2012, 55, 391-401], and especially had been trained for surface formation energies, binding energies of small hydrocarbon radicals on different surfaces of iron and the barrier heights of surface reactions. We merged this force field with the latest ReaxFF carbon parameters [S. Goverapet Srinivasan, A. C. T. van Duin and P. Ganesh, J. Phys. Chem. A, 2015, 119, 1089-5639] and used the same training data set to refit the Fe/C interaction parameters. The present work is focused on evaluating the applicability of this reactive force field to describe material characteristics and study the role of defects and impurities in the bulk and at the precipitator interfaces. We study the interactions of hydrogen with pure and defective α-iron (ferrite), Fe3C (cementite), and ferrite-cementite interfaces with a vacancy cluster. We also investigate the growth of nanovoids in α-iron using a grand canonical Monte Carlo (GCMC) scheme. The calculated hydrogen diffusion coefficients for both ferrite and cementite phases predict a decrease in the work of separation with increasing hydrogen concentration at the ferrite-cementite interface, suggesting a hydrogen-induced decohesion behavior. Hydrogen accumulation at the interface was observed during molecular dynamics (MD) simulations, which is consistent with experimental findings. These results demonstrate the ability of the ReaxFF potential to elucidate various aspects of hydrogen embrittlement in α-iron and hydrogen interactions at a more complex metal/metal carbide interface.
Secondhand Smoke Exposure in Public Places in Guatemala: Comparison with other Latin American Countries

Objective: To measure secondhand smoke levels in workplaces in Guatemala and to compare exposure to levels in other Latin American cities. Methods: Exposure was estimated by passive sampling of vapor phase nicotine using a filter badge. Filters were placed in 1 hospital, 1 school, 2 universities, 1 government building, the airport, and 10 restaurants/bars. In total, 103 filters were deployed (plus 7 duplicates and 10 blanks). Nicotine (μg/m3) was measured by gas chromatography. Medians [interquartile ranges (IQR)] of nicotine concentrations were reported and compared with other Latin American cities. A survey about attitudes for smoke-free workplaces was distributed among employees. Results: Nicotine was detected in most (68%) locations surveyed (including workplaces where smoking is banned). The highest levels were found in bars [median, 4.58 μg/m3 (IQR, 1.71-6.44)] and restaurants [median, 0.56 μg/m3 (IQR, 0.46-0.71)]. Nicotine concentrations in bars and restaurants were 710 and 114 times higher, respectively, compared with hospital concentrations after adjustment for smoking ban signs, type of ventilation, and volume of the area. Support for smoke-free environments was high, except in bar/restaurant and airport workers. Airborne nicotine levels in Guatemala were similar to those found in other Latin American cities. Conclusion: In Guatemala, exposure to secondhand smoke is highly prevalent. Workers in bars and restaurants are disproportionately exposed to secondhand smoke compared with other workers. There is an urgent need for complete smoke-free legislation and for educating workers about the benefits of smoke-free workplaces. (Cancer Epidemiol Biomarkers Prev 2007;16(12):2730–5)
16 nm FinFET High-k/Metal-gate 256-kbit 6T SRAM macros with wordline overdriven assist

We demonstrate 16 nm FinFET High-k/Metal-gate SRAM macros with a wordline (WL) overdriven read/write-assist circuit. Test-chip measurements confirm improved minimum operating voltage (Vmin), standby leakage current, and access time compared to planar bulk CMOS. The proposed assist circuit improves Vmin by 50 mV and improves read-access-time by more than 1.5 times in 256-kbit SRAM macros. Read current (Iread) dependence against the fin diffusion length was observed. An extra design guard-band is needed to provide a reliable operation margin.
Economies of Scale and Scope in Urban Public Transport

Local public transport in Germany is characterized by high fragmentation and formative changes in market structure with mergers and competitive tendering. In this paper we estimate cost functions in order to estimate economies of scale and scope. The unbalanced panel data set for the analysis consists of 573 observations of single- and multi-output German bus, tram and light rail companies from 1997 to 2006. This is the first empirical application of such a unique data set to Germany’s local public transport. We apply Stochastic Frontier panel data models to align the estimations at optimal cost curves. The results suggest increasing global, bus-specific as well as tram- and light railway-specific economies of scale favoring mergers and tendering in large output volume. Furthermore we find slight diseconomies of scope in particular for smaller companies accompanying the increased complexity of providing dierent modes of transport. The results are consistent for both a Random and a True Random Eects model (which is used to account for unobserved heterogeneity) which are preferred to a Fixed Eects model.