Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluating Hive and Spark SQL with BigBench

The objective of this work was to utilize BigBench [1] as a Big Data benchmark and evaluate and compare two processing engines: MapReduce [2] and Spark [3]. MapReduce is the established engine for processing data on Hadoop. Spark is a popular alternative engine that promises faster processing times than the established MapReduce engine. BigBench was chosen for this comparison because it is the first end-to-end analytics Big Data benchmark and it is currently under public review as TPCx-BB [4]. One of our goals was to evaluate the benchmark by performing various scalability tests and validate that it is able to stress test the processing engines. First, we analyzed the steps necessary to execute the available MapReduce implementation of BigBench [1] on Spark. Then, all the 30 BigBench queries were executed on MapReduce/Hive with different scale factors in order to see how the performance changes with the increase of the data size. Next, the group of HiveQL queries were executed on Spark SQL and compared with their respective Hive runtimes. This report gives a detailed overview on how to setup an experimental Hadoop cluster and execute BigBench on both Hive and Spark SQL. It provides the absolute times for all experiments preformed for different scale factors as well as query results which can be used to validate correct benchmark execution. Additionally, multiple issues and workarounds were encountered and solved during our work. An evaluation of the resource utilization (CPU, memory, disk and network usage) of a subset of representative BigBench queries is presented to illustrate the behavior of the different query groups on both processing engines. Last but not least it is important to mention that larger parts of this report are taken from the master thesis of Max-Georg Beer, entitled "Evaluation of BigBench on Apache Spark Compared to MapReduce" [5].
PNPLA3 rs738409 Polymorphism Associated with Hepatic Steatosis and Advanced Fibrosis in Patients with Chronic Hepatitis C Virus: A Meta-Analysis

Background/Aims The recognition of a correlation between patatin-like phospholipase domain containing-protein 3 (PNPLA3) rs738409 (C>G) and the severity of liver steatosis or fibrosis in chronic hepatitis C (CHC) has not reached a consensus. This meta-analysis sought to investigate with accuracy the association between the PNPLA3 rs738409 (C>G) polymorphism and liver steatosis and advanced fibrosis in CHC patients. Methods We performed a comprehensive literature search from the PubMed, Embase, Web of Science, and Google Scholar databases up to December 31, 2014. Crude odds ratios (ORs) with 95% confidence intervals (CIs) were calculated. Statistical analyses were performed using Stata 12.0 software. Results The meta-analysis revealed the severity of liver fibrosis was significantly higher in CHC patients with PNPLA3 rs738409 GG in Caucasians (versus CC+CG: OR, 2.29; 95% CI, 1.57 to 3.35; p<0.05) but not Asian populations. In Caucasians, liver steatosis was also more severe in CHC patients with rs738409 GG (versus CC+CG; OR, 4.33; 95% CI, 2.59 to 7.22; p<0.05). The sensitivity analysis indicated the results of this meta-analysis were stable and no publication bias was detected. Conclusions PNPLA3 rs738409 (C>G) was associated with the risk of both advanced liver fibrosis and steatosis in patients with CHC, especially among Caucasian populations.
Analysis of a penalty method for pricing a guaranteed minimum withdrawal benefit (GMWB)

5 The no arbitrage pricing of Guaranteed Minimum Withdrawal Benefits (GMWB) contracts 6 results in a singular stochastic control problem which can be formulated as a Hamilton Jacobi 7 Bellman (HJB) Variational Inequality (VI). Recently, a penalty method has been suggested for 8 solution of this HJB variational inequality (Dai et al., 2008). This method is very simple to 9 implement. In this article, we present a rigorous proof of convergence of the penalty method 10 to the viscosity solution of the HJB VI. Numerical tests of the penalty method are presented 11 which show the experimental rates of convergence, and a discussion of the choice of the penalty 12 parameter is also included. 13
Regeneration in free grafts of normal and denervated muscles in the rat: Morphology and histochemistry

Intact soleus and extensor digitorum longus muscles in the rat were freely grafted to the contralateral leg after either no preliminary tretment or 14 days prior denervation. Normal muscle grafts during the first week were characterized by a central zone of degenerating original muscle fibers (disappearing by 7–9 days) and a peripheral zone, containing regenerating muscle as well as small numbers of surviving original muscle fibers. A radial gradient of regeneration was established, with more mature muscle at the periphery and less mature muscle toward the center. Denervated grafts were characterized by rapid degeneration (within 2–3 days ) of original muscle fibers in the central area, rapid appearance of regenerating muscle fibers (e.g., cross striations by 5 days) with uniform levels of differentiation throughout the graft and larger numbers of surviving original muscle fibers at the periphery. During the first week, stages of muscle differentiation in denervated grafts were attained 1–2 days earlier than comparable stages in normal grafts. Later stages of muscle differentiation were similar in both types of grafts. Histochemical studies revealed a loss of enzyme activity (phosphorylase, ATPase and SDH) in the center of early (2–4‐day) normal and denervated grafts. Denervated grafts, however, possessed a thicker peripheral rim of enzymatically active surviving muscle fibers than normal grafts. In both types of grafts the old muscle fibers in the center were replaced by enzymatically active regenerating muscle fibers which stained uniformly (ATPase) until 30 days. By 60 days a mixed fiber pattern had developed. Muscle spindles were found within the grafts.
Efficient Production of HIV-1 Virus-Like Particles from a Mammalian Expression Vector Requires the N-Terminal Capsid Domain

It is now well accepted that the structural protein Pr55Gag is sufficient by itself to produce HIV-1 virus-like particles (VLPs). This polyprotein precursor contains different domains including matrix, capsid, SP1, nucleocapsid, SP2 and p6. In the present study, we wanted to determine by mutagenesis which region(s) is essential to the production of VLPs when Pr55Gag is inserted in a mammalian expression vector, which allows studying the protein of interest in the absence of other viral proteins. To do so, we first studied a minimal Pr55Gag sequence called Gag min that was used previously. We found that Gag min fails to produce VLPs when expressed in an expression vector instead of within a molecular clone. This failure occurs early in the cell at the assembly of viral proteins. We then generated a series of deletion and substitution mutants, and examined their ability to produce VLPs by combining biochemical and microscopic approaches. We demonstrate that the matrix region is not necessary, but that the efficiency of VLP production depends strongly on the presence of its basic region. Moreover, the presence of the N-terminal domain of capsid is required for VLP production when Gag is expressed alone. These findings, combined with previous observations indicating that HIV-1 Pr55Gag-derived VLPs act as potent stimulators of innate and acquired immunity, make the use of this strategy worth considering for vaccine development.
Competing orders and quantum criticality in doped antiferromagnets

We use a number of large-N limits to explore the competition between ground states of square lattice doped antiferromagnets which break electromagnetic $U(1),$ time-reversal, or square lattice space-group symmetries. Among the states we find are d-, ${(s}^{*}+id)\ensuremath{-},$ and ${(d}_{{x}^{2}\ensuremath{-}{y}^{2}}{+id}_{\mathrm{xy}})$-wave superconductors, Wigner crystals, Wigner crystals of hole pairs, orbital antiferromagnets (or staggered-flux states), and states with spin-Peierls and bond-centered charge stripe order. In the vicinity of second-order quantum phase transitions between the states, we go beyond the large-N limit by identifying the universal quantum field theories for the critical points, and computing the finite temperature, quantum critical damping of fermion spectral functions. We identify candidate critical points for the recently observed quantum critical behavior in photoemission experiments on ${\mathrm{Bi}}_{2}{\mathrm{Sr}}_{2}{\mathrm{Ca}\mathrm{}\mathrm{Cu}}_{2}{\mathrm{O}}_{8+\ensuremath{\delta}}$ by Valla et al. [Science 285, 2110 (1999)]. These involve onset of a charge-density wave, or of broken time-reversal symmetry with ${d}_{{x}^{2}\ensuremath{-}{y}^{2}}{+id}_{\mathrm{xy}}$ or ${s}^{*}+id$ pairing, in a d-wave superconductor. It is not required (although it is allowed) that the stable state in the doped cuprates be anything other than the d-wave superconductor\char22{}the other states need only be stable nearby in parameter space. At finite temperatures, fluctuations associated with these nearby states lead to the observed fermion damping in the vicinity of the nodal points in the Brillouin zone. The cases with broken time-reversal symmetry are appealing because the order parameter is not required to satisfy any special commensurability conditions. The observed absence of inelastic damping of quasiparticles with momenta $(\ensuremath{\pi},k),$ $(k,\ensuremath{\pi})$ (with $0l~kl~\ensuremath{\pi})$ also appears very naturally for the case of fluctuations to ${d}_{{x}^{2}\ensuremath{-}{y}^{2}}{+id}_{\mathrm{xy}}$ order.
The Effect of an Example-Based Dynamic Program Visualization Environment on Students' Programming Skills

The purpose of this study was to investigate and compare the effect of the two computer-assisted learning systems named the Example-Based Dynamic Program Visualization Environment (EDPVE) and the ExampleBased Static Program Visualization Environment (ESPVE) on undergraduate students’ programming skills in an introductory programming course. The study was conducted using a quasi-experimental, non-equivalent control group design with 81 pre-service teachers in a Turkish university. Two classes were randomly assigned to use EDPVE(experimental group) and ESPVE(control group) system. The results of the experiments showed that: (1) there were a significant difference between EDPVE and ESPVE groups in favour of the EDPVE group; and (2) there were no significant difference between male and female students in EDPVE and ESPVE groups respectively. The findings of this study suggest that teaching and learning programming can be improved through the use of dynamic program visualization techniques.
Concise analysis of wave propagation using the spectral element method and identification of delamination in CF/EP composite beams

This paper presents a two-dimensional spectral element method for characterizing wave propagation in composite beam structures for the purpose of damage detection. The interaction of Lamb waves with delamination in an 8-ply carbon fiber/epoxy (CF/EP) laminate is investigated, and some unique mechanisms of interaction between Lamb wave modes and delamination are revealed in detail. It is demonstrated that the reflection at the far end of the delamination is much stronger in magnitude than that from the near end, and when the delamination length is comparable to the wavelength of the wave mode, the reflections from both ends of the delamination merge into one. The fundamental antisymmetric (A0) mode is more suitable for identification of delamination in multilayered composite structures than the fundamental symmetric (S0) mode, especially when the delamination is in the symmetric plane. The curves of the reflection coefficient and transmission coefficient are analyzed, showing an undulating shape, and the values of reflection or transmission coefficient are dependent on the ratio of the delamination length to the wavelength of the Lamb wave. A quantitative identification method for delamination in composite beam structures is proposed and validated using an experimental study.
Association of Genetic Polymorphisms in the LncRNAs with Gastric Cancer Risk in a Chinese Population

Background: Genome-wide association studies have identified that polymorphisms in 8q24 confer susceptibility to gastric cancer. Polymorphisms in the lncRNA PRNCR1, PCAT1, and CCAT2 transcribed from the 8q24 locus have a potential risk for gastric cancer. Methods: To evaluate whether there is such an association in Chinese population, a case-control study enrolled 494 patients and 494 healthy controls was carried out. Sequenom MassARRAY platform was used for genotyping. Results: This study showed that rs16901946 G allele was associated with increased risk of gastric cancer (AG: adjusted OR = 1.33, 95% CI =1.02-1.73, p=0.033; GG: adjusted OR = 2.07; 95% CI = 1.11-3.86, p=0.023, AG/GG: adjusted OR = 1.39, 95% CI = 1.08-1.1.79, p=0.011; additive model: adjusted OR = 1.37; 95% CI = 1.10-1.70, p=0.004). Stratified analysis revealed that the increased risk was more evident in the cohort of younger subjects (adjusted OR = 1.84, 95% CI = 1.18-2.87, p=0.007), males (adjusted OR = 1.55, 95% CI = 1.15-2.08, p=0.004), positive Helicobacter pylori infection (adjusted OR = 1.44, 95% CI = 1.02-2.03, p=0.041), gastric cardia adenocarcinoma (adjusted OR = 1.61, 95% CI = 1.10-2.35, p=0.014), and tumor stage T1-T2 (adjusted OR = 1.58, 95% CI = 1.10-2.28, p=0.013). Conclusions: Our study suggested that rs16901946 G allele carriers have an increased risk of gastric cancer, and the risk could be enhanced by the interactions between the polymorphism and age, sex, Helicobacter pylori infection.
Hidden Markov Model} Induction by Bayesian Model Merging

This paper describes a technique for learning both the number of states and the topology of Hidden Markov Models from examples. The induction process starts with the most specific model consistent with the training data and generalizes by successively merging states. Both the choice of states to merge and the stopping criterion are guided by the Bayesian posterior probability. We compare our algorithm with the Baum-Welch method of estimating fixed-size models, and find that it can induce minimal HMMs from data in cases where fixed estimation does not converge or requires redundant parameters to converge.
AGING INVESTIGATION OF POLYMERIC INSULATORS

Traditional insulators made of glass and porcelain (ceramic insulators) used in power transmission and distribution systems ruled the market till the introduction of polymeric insulators which have potential to replace the ceramic insulators because of lightweight, aesthetic, hydrophobic properties, and superior anti-contamination performance. However, the field experience of polymeric insulators is relatively short which demands that further studies on the performance of these insulators under actual and simulated environmental conditions be carried out before their full scale application on real power systems. This study contains the pioneer work carried out on polymeric insulators in Pakistan. The prime objective of this investigation is to determine how feasible polymeric insulators are for use in Pakistani environment so as to offer suitable recommendation to the national electric utility company (WAPDA) about the possible use of polymeric insulators on real system. Towards that end, polymeric insulators were exposed to lab and field aging representing Pakistani environmental conditions. The laboratory study addressed aging under environmental parameters individually as well as collectively. Moreover, weather cycles, simulating Pakistani conditions were designed and corresponding aging performance was investigated. The environmental stresses used in the study included UV radiation, temperature, electric stress, low pressure and humidity. For field aging the samples were installed at two typical locations representing a clean environment as well as a heavily polluted industrial area of Hatta Industrial Estate. The aged samples were periodically analyzed using advance techniques such as FTIR and SEM. Hydrophobicity characteristics were also studied and samples were critically checked for any obvious surface degradation. The investigation revealed that the polymeric insulators follow a periodic degradation and self-restoration cycle and no irreversible degradation such as tracking or erosion was observed. In multi-stress aging, the samples were exposed to accelerated aging to represent an actual exposure of 12.67 years in the field. The insulators retained their characteristics throughout this period. Based on very promising I results of this pioneering investigation which simulated environmental conditions prevalent in Pakistan, it appears that polymeric insulators made of silicone rubber have 1 bright future for application on real transmission and distribution systems of Pakistan W APDA. The matter will accordingly be taken up with decision makers to build some new distribution lines equipped with polymeric insulators to convert the benefits of polymeric insulators into a practical reality.
Preeclampsia: What Could Happen in a Subsequent Pregnancy?

Importance Preeclampsia is the most common type of the hypertensive disorders of pregnancy, affecting nearly 5% of pregnant women. The risk of recurrence influences the choices of parents regarding subsequent pregnancies and necessitates the counseling of obstetricians. Objective To review the risk of recurrence of hypertensive disorders in a subsequent pregnancy. Evidence Acquisition Women with a history of preeclampsia are at an increased risk of preeclampsia and other adverse pregnancy outcomes in subsequent pregnancies. The magnitude of this risk is dependent on gestational age at the time of disease onset, severity of disease, and presence or absence of preexisting medical disorders. Results For preeclamptic women with severe features in an initial pregnancy, recurrence rates for any type of preeclampsia are very high, approaching 50% in some studies. Significant maternal and fetal complications are more common in recurrent preeclampsia compared with an initial episode. Because women with previous preeclampsia are at an increased risk for adverse pregnancy outcomes (preterm delivery, fetal growth restriction, abruptio placentae, and fetal death) in subsequent pregnancies, we recommend more frequent monitoring for signs and symptoms of severe hypertension or preeclampsia than that recommended for normal pregnancy. Conclusions The best option is to review the existing literature with patients, allow them to make informed decisions, and provide them the best available prenatal care. Target Audience Obstetricians and gynecologists, family physicians Learning Objectives After completing this CME activity, physicians should be better able to assess the overall risk of preeclampsia recurrence in a subsequent pregnancy, evaluate the personal risk factors for recurrence of preeclampsia, explain the obstetric risk factors for recurrence of preeclampsia, and assist patients in decision for a future pregnancy.
Effects of 1-(2-trifluoromethylphenyl)-imidazole (TRIM) on receptor-independent and -dependent contractile responses in rat aorta.

BACKGROUND/AIM This study investigates whether 1-(2-trifluoromethylphenyl)-imidazole (TRIM), originally proposed as a nitric oxide synthase inhibitor and also suggested to be an inhibitor of store-operated calcium entry in mouse anococcygeal muscle, inhibits receptor-independent and -dependent responses in rat thoracic aorta. MATERIALS AND METHODS Cyclopiazonic acid- and serotonin-induced vascular responses were investigated in aortic segments isolated from male Sprague Dawley rats using isolated tissue experiments. Changes in intracellular calcium levels were also monitored via front surface fluorescence measurements in fura-2-loaded embryonic rat vascular smooth muscle cell line A7r5. RESULTS TRIM inhibited serotonin-mediated vascular contractions without affecting cyclopiazonic acid-induced responses. In addition, TRIM caused a nonlinear rightward shift in the serotonin concentration-response curve, possibly via serotonin receptor modulation. CONCLUSION TRIM may have an impact on investigation of tissue-specific receptor-independent and -dependent vascular responses. It may also be used as a lead compound in the development of selective serotonin receptor modulators.
Temperature and humidity variation of specific resistance of carbon fiber reinforced cement

Carbon fiber reinforced cement (CFRC), which mainly composed of hardened cement and short cut carbon fibers, possesses piezoresistive effect, and could be used to produce new type of compressive stress sensors. As having character of low cost, good compatibility with concrete and high durability, CFRC sensor extraordinary adapt to be used in the field of long time health monitoring of concrete structures. Based on large quantity of duplicate tests, the influence of temperature and humidity on electrical specific resistance of CFRC was studied. The function of volume content of carbon fiber or silica fume on above influence is also discussed. Results show that specific resistance of CFRC will decrease with increase of temperature or relative humidity, and above changing have no relationship with carbon fiber or silica fume volume content.
Lipid balance in HepG2 cells: active synthesis and impaired mobilization.

The human hepatoma cell line HepG2 in culture medium synthesized fatty acids de novo (144 +/- 9 nmol fatty acid/mg protein per 24 h) at a rate similar to that observed in freshly prepared rat hepatocytes (192 +/- 8 nmol/mg per 24 h) and in primary cultures of rat hepatocytes (165.4 +/- 29.3 nmol/mg per 24 h). In HepG2 cells, fatty acid synthesis was inhibited by extracellular oleate (0.75 mM), and, to a lesser extent, by glucagon (10(-7) M). Insulin (7.8 x 10(-8) M) had a mild stimulatory effect. Fatty acid synthesis was not influenced by lipogenic precursors (lactate plus pyruvate), substances which, in rat hepatocytes, had pronounced stimulatory effects. Fatty acid synthesis rates were also unchanged in the presence of prostaglandin E2 (PGE2). In general, compared to rat hepatocytes, fatty acid synthesis in HepG2 cells was less sensitive to manipulation of the culture medium in vitro. HepG2 cells had a high capacity for triacylglycerol synthesis from extracellular oleate (469 +/- 43 nmol triacylglycerol/mg protein per 24 h) but phospholipid synthesis was relatively low (15.8 +/- 0.4% of total glycerolipids). Very little of the above newly synthesized triacylglycerol was secreted as lipoprotein (4.62 +/- 0.88 nmol triacylglycerol/mg protein per 24 h) resulting in a large intracellular accumulation of triacylglycerol. This was exacerbated by the absence of any detectable ketogenesis. The secretion of triacylglycerol produced from de novo synthesized fatty acids was also very low in HepG2 compared to that observed in primary cultures of rat hapatocytes. (ABSTRACT TRUNCATED AT 250 WORDS)
Preliminary studies of berberine and its semi-synthetic derivatives as a promising class of multi-target anti-parkinson agents

Abstract Parkinson’s disease (PD) is a neurodegenerative disorder bearing motor and nonmotor symptoms. The treatment today is symptomatical rather than preventive or curative and this leaves the field open for the search of both novel molecular targets and drug candidates. Interference with α-synuclein fibrillation, monoamine oxidase (MAO) inhibition, modulation of adenosine receptors and the inhibition of specific phosphodiesterase (PDE) isoforms are some of the currently pursued strategies. We synthesised and studied some semi-synthetic berberine derivatives using a set of in silico tools. We evaluated their drug-likeness and tested the compounds against a set of target proteins involved in the onset or progression of PD, with a particular attention to MAO-B. Preliminary in vitro assay on MAO-B confirmed our in silico predictions.