Miracle-dz/UniFAR-FTUs huggingface dataset:
WaxElephant: A Realistic Hadoop Simulator for Parameters Tuning and Scalability Analysis

MapReduce is becoming the state-of-the-art computation paradigm for processing large-scale datasets on a large cluster with tens or thousands of nodes. Hadoop, an open-source implementation of MapReduce framework, has gained much popularity due to its high scalability and performance. Two challenging issues for a large-scale Hadoop cluster are how to analyze the scalability and identify the optimal parameters configurations. To address these issues, we designed and implemented a Hadoop simulator called Wax Elephant, which provides the following capabilities: (1) loading real MapReduce workloads derived from the historical log of Hadoop clusters, and replaying the job execution history, (2) synthesizing workloads and executing them based on statistical characteristics of workloads, (3) identifying the optimal parameters configurations, and (4) analyzing the scalability of the cluster. Extensive experiments have been conducted to validate the accuracy of the Wax Elephant simulator.
Fractional vortices and lumps

We study what might be called fractional vortices, vortex configurations with the minimum winding from the viewpoint of their topological stability, but which are characterized by various notable substructures in the transverse energy distribution. The fractional vortices occur in diverse Abelian or non-Abelian generalizations of the Higgs model. The global and local features characterizing these are studied, and we identify the two crucial ingredients for their occurrence - the vacuum degeneracy leading to non-trivial vacuum moduli M, and the BPS nature of the vortices. Fractional vortices are further classified into two kinds. The first type of such vortices appear when M has orbifold Z_n singularities; the second type occurs in systems in which the vacuum moduli space M possesses either a deformed geometry or some singularity. These general features are illustrated with several concrete models.
Linear-complexity exponentially-consistent tests for universal outlying sequence detection

We study a universal outlying sequence detection problem, in which there are M sequences of samples out of which a small subset of outliers need to be detected. A sequence is considered as an outlier if the observations therein are generated by a distribution different from those generating the observations in the majority of the sequences. In the universal setting, the goal is to identify all the outliers without any knowledge about the underlying generating distributions. In prior work, this problem was studied as a universal hypothesis testing problem, and a generalized likelihood (GL) test was constructed and its asymptotic performance characterized. In this paper, we propose a different class of tests for this problem based on distribution clustering. Such tests are shown to be exponentially consistent and their time complexity is linear in the total number of sequences, in contrast with the GL test, which has time complexity that is exponential in the number of outliers. Furthermore, our tests based on clustering are applicable to more general scenarios. For example, when both the typical and outlier distributions form clusters, the clustering based test is exponentially consistent, but the GL test is not even applicable.
Pneumococcal Capsular Switching: A Historical Perspective

Background.Changes in serotype prevalence among pneumococcal populations result from both serotype replacement and serotype (capsular) switching. Temporal changes in serotype distributions are well documented, but the contribution of capsular switching to such changes is unknown. Furthermore, it is unclear to what extent vaccine-induced selective pressures drive capsular switching. Methods.Serotype and multilocus sequence typing data for 426 pneumococci dated from 1937 through 2007 were analyzed. Whole-genome sequence data for a subset of isolates were used to investigate capsular switching events. Results.We identified 36 independent capsular switch events, 18 of which were explored in detail with whole-genome sequence data. Recombination fragment lengths were estimated for 11 events and ranged from approximately 19.0 kb to ≥58.2 kb. Two events took place no later than 1960, and the imported DNA included the capsular locus and the nearby penicillin-binding protein genes pbp2x and pbp1a. Conclusions.Capsular switching has been a regular occurrence among pneumococcal populations throughout the past 7 decades. Recombination of large DNA fragments (>30 kb), sometimes including the capsular locus and penicillin-binding protein genes, predated both vaccine introduction and widespread antibiotic use. This type of recombination has likely been an intrinsic feature throughout the history of pneumococcal evolution.
Design and optimization of a long-stroke compliant micropositioning stage driven by voice coil motor

A micro-/nanopositioning system with both large motion range and compact size is highly desired in various precision engineering applications. In this paper, the design of a new compliant micropositioning stage with translational motion is proposed based on flexure mechanisms. The stage parameters are optimized by using the genetic algorithm (GA) to achieve a large natural frequency under the constraints on motion range (i.e., over 10 mm) and compact physical dimension along with a high safety factor for the material. Both analytical calculations and simulations based on finite element analysis are performed to validate the stage performances. A physical prototype system which employs a voice coil motor and a laser displacement sensor for actuation and sensing, respectively, is fabricated for experimental tests. Result confirms the long-stroke performance of the developed micropositioning system.
Pathway Analysis of Metabolic Syndrome Using a Genome-Wide Association Study of Korea Associated Resource (KARE) Cohorts

Metabolic syndrome (MetS) is a complex disorder related to insulin resistance, obesity, and inflammation. Genetic and environmental factors also contribute to the development of MetS, and through genome-wide association studies (GWASs), important susceptibility loci have been identified. However, GWASs focus more on individual single-nucleotide polymorphisms (SNPs), explaining only a small portion of genetic heritability. To overcome this limitation, pathway analyses are being applied to GWAS datasets. The aim of this study is to elucidate the biological pathways involved in the pathogenesis of MetS through pathway analysis. Cohort data from the Korea Associated Resource (KARE) was used for analysis, which include 8,842 individuals (age, 52.2 ± 8.9 years; body mass index, 24.6 ± 3.2 kg/m2). A total of 312,121 autosomal SNPs were obtained after quality control. Pathway analysis was conducted using Meta-analysis Gene-Set Enrichment of Variant Associations (MAGENTA) to discover the biological pathways associated with MetS. In the discovery phase, SNPs from chromosome 12, including rs11066280, rs2074356, and rs12229654, were associated with MetS (p < 5 × 10-6), and rs11066280 satisfied the Bonferroni-corrected cutoff (unadjusted p < 1.38 × 10-7, Bonferroni-adjusted p < 0.05). Through pathway analysis, biological pathways, including electron carrier activity, signaling by platelet-derived growth factor (PDGF), the mitogen-activated protein kinase kinase kinase cascade, PDGF binding, peroxisome proliferator-activated receptor (PPAR) signaling, and DNA repair, were associated with MetS. Through pathway analysis of MetS, pathways related with PDGF, mitogen-activated protein kinase, and PPAR signaling, as well as nucleic acid binding, protein secretion, and DNA repair, were identified. Further studies will be needed to clarify the genetic pathogenesis leading to MetS.
Intracellular ATP Concentration Contributes to the Cytotoxic and Cytoprotective Effects of Adenosine

Extracellular adenosine (Ade) interacts with cells by two pathways: by activating cell surface receptors at nanomolar/micromolar concentrations; and by interfering with the homeostasis of the intracellular nucleotide pool at millimolar concentrations. Ade shows both cytotoxic and cytoprotective effects; however, the underlying mechanisms remain unclear. In the present study, the effects of adenosine-mediated ATP on cell viability were investigated. Adenosine treatment was found to be cytoprotective in the low intracellular ATP state, but cytotoxic under the normal ATP state. Adenosine-mediated cytotoxicity and cytoprotection rely on adenosine-derived ATP formation, but not via the adenosine receptor pathway. Ade enhanced proteasome inhibition-induced cell death mediated by ATP generation. These data provide a new pathway by which adenosine exerts dual biological effects on cell viability, suggesting an important role for adenosine as an ATP precursor besides the adenosine receptor pathway.
Bacteria and bacterial DNA in atherosclerotic plaque and aneurysmal wall biopsies from patients with and without periodontitis

Background Several studies have reported an association between chronic periodontitis (CP) and cardiovascular diseases. Detection of periodontopathogens, including red complex bacteria (RCB), in vascular lesions has suggested these bacteria to be involved in the pathogenesis of atherosclerosis and abdominal aortic aneurysms. Objective In this study, we investigate bacteria and their DNA in vascular biopsies from patients with vascular diseases (VD; i.e. abdominal aortic aneurysms, atherosclerotic carotid, and common femoral arteries), with and without CP. Methods DNA was extracted from vascular biopsies selected from 40 VD patients: 30 with CP and 10 without CP. The V3-V5 region of the 16S rDNA (V3-V5) was polymerase chain reaction (PCR)-amplified, and the amplicons were cloned into Escherichia coli, sequenced, and classified (GenBank and the Human Oral Microbiome database). Species-specific primers were used for the detection of Porphyromonas gingivalis. In addition, 10 randomly selected vascular biopsies from the CP group were subjected to scanning electron microscopy (SEM) for visualization of bacteria. Checkerboard DNA–DNA hybridization was performed to assess the presence of RCB in 10 randomly selected subgingival plaque samples from CP patients. Results A higher load and mean diversity of bacteria were detected in vascular biopsies from VD patients with CP compared to those without CP. Enterobacteriaceae were frequently detected in vascular biopsies together with cultivable, commensal oral, and not-yet-cultured bacterial species. While 70% of the subgingival plaque samples from CP patients showed presence of RCB, only P. gingivalis was detected in one vascular biopsy. Bacterial cells were seen in all 10 vascular biopsies examined by SEM. Conclusions A higher bacterial load and more diverse colonization were detected in VD lesions of CP patients as compared to patients without CP. This indicated that a multitude of bacterial species both from the gut and the oral cavity, rather than exclusively periodontopathogens, may be involved as additional risk factors in the pathogenesis of VD.
Using Evidence for Trust Computation

Trust can have its life-cycle and we can model it and utilize it for establishing secure environment for mobile environments. We assume that entities in the collaborating environment are mobile. It is not possible to perform entity enrollment. There is no globally trusted third party. Usual authentication mechanisms can not be used. We propose use of trust based on principal behaviour observations. The overall model has been devised with the SECURE project. The article makes a brief overview of the model and proposes speciflc approach for computation of trust values from observations. The method to be introduced is based on Dempster-Shafer theory of conflrmation.
Conditional Diagnosability of k-Ary n-Cubes under the PMC Model

Processor fault diagnosis plays an important role in measuring the reliability of multiprocessor systems and the diagnosis of many well-known interconnection networks. The conditional diagnosability, which is more general than the classical diagnosability, is to measure the diagnosability of a multiprocessor system under the assumption that all of the neighbors of any node in the system cannot fail at the same time. This study shows that the conditional diagnosability for <i>k</i>-ary <i>n</i>-cubes under the PMC model is 8<i>n</i> − 7 for <i>k</i> ≥ 4 and <i>n</i> ≥ 4.
Liquid – liquid phase separation and viscosity within secondary organic aerosol generated from diesel fuel vapors

Information on liquid–liquid phase separation (LLPS) and viscosity (or diffusion) within secondary organic aerosol (SOA) is needed to improve predictions of particle size, mass, reactivity, and cloud nucleating properties in the atmosphere. Here we report on LLPS and viscosities within SOA generated by the photooxidation of diesel fuel vapors. Diesel fuel contains a wide range of volatile organic compounds, and SOA generated by the photooxidation of diesel fuel vapors may be a good proxy for SOA from anthropogenic emissions. In our experiments, LLPS occurred over the relative humidity (RH) range of ∼ 70 % to ∼ 100 %, resulting in an organic-rich outer phase and a water-rich inner phase. These results may have implications for predicting the cloud nucleating properties of anthropogenic SOA since the presence of an organic-rich outer phase at high-RH values can lower the supersaturation with respect to water required for cloud droplet formation. At≤ 10 % RH, the viscosity was ≥ 1×108 Pa s, which corresponds to roughly the viscosity of tar pitch. At 38 %–50 % RH, the viscosity was in the range of 1× 108 to 3× 105 Pa s. These measured viscosities are consistent with predictions based on oxygen to carbon elemental ratio (O : C) and molar mass as well as predictions based on the number of carbon, hydrogen, and oxygen atoms. Based on the measured viscosities and the Stokes–Einstein relation, at ≤ 10 % RH diffusion coefficients of organics within diesel fuel SOA is ≤ 5.4× 10−17 cm2 s−1 and the mixing time of organics within 200 nm diesel fuel SOA particles (τmixing) is 50 h. These small diffusion coefficients and large mixing times may be important in laboratory experiments, where SOA is often generated and studied using low-RH conditions and on timescales of minutes to hours. At 38 %–50 % RH, the calculated organic diffusion coefficients are in the range of 5.4× 10−17 to 1.8× 10−13 cm2 s−1 and calculated τmixing values are in the range of ∼ 0.01 h to ∼ 50 h. These values provide important constraints for the physicochemical properties of anthropogenic SOA.
Human papilloma virus infection in head and neck cancer.

BACKGROUND The causal link between cervical cancer and human papilloma virus (HPV) is well known. It is now becoming clear that some types of squamous-cell carcinoma of the head and neck, particularly oropharyngeal carcinoma (OPC), are also linked to HPV infection. The development of vaccines against certain HPV genotypes has changed the management strategy for HPV-associated diseases of the uterine cervix. An analogous approach is now being considered for the prevention of HPV-associated diseases of the head and neck. METHOD We review pertinent articles retrieved by a selective search of the literature for phase II and III trials providing evidence about a possible effect of HPV status on the survival rates of patients with OPC. Seven trials fulfilled our search criteria: four phase III trials with retrospective HPV analysis and three phase II trials with retrospective and prospective HPV analysis. RESULTS Patients with HPV-positive OPC survive significantly longer than those with HPV-negative OPC. Tobacco smoking has been identified as a negative prognostic factor in patients with either HPV-negative or HPV-positive disease. CONCLUSION The established treatment strategy for OPC in patients with and without the traditional risk factors (tobacco and alcohol consumption) is now being reconsidered in the light of what we have learned about the role of HPV infection. Ongoing and projected clinical trials with risk-factor stratification may soon lead to changes in treatment. Further study is needed to answer the question whether HPV infection in the head and neck region is carcinogenic.
Exploiting query term correlation for list caching in web search engines

Caching technologies have been widely employed to boost the performance of Web search engines. Motivated by the correlation between terms in query logs from a commercial search engine, we explore the idea of a caching scheme based on pairs of terms, rather than individual terms (which is the typical approach used by search engines today). We propose an inverted list caching policy, based on the Least Recently Used method, in which the co-occurring correlation between terms in the query stream is accounted for when deciding on which terms to keep in the cache. We consider not only the term co-occurrence within the same query but also the co-occurrence between separate queries. Experimental results show that the proposed approach can improve not only the cache hit ratio but also the overall throughput of the system when compared to existing list caching algorithms.
Sit4p/PP6 regulates ER-to-Golgi traffic by controlling the dephosphorylation of COPII coat subunits

Previous studies show that the COPII coat is phosphorylated. The phosphorylated coat, however, cannot rebind to the ER to initiate a new round of vesicle budding. The present study shows that Sit4p/PP6, a Ser/Thr phosphatase, dephosphorylates the COPII coat. Consistent with a role in coat recycling, Sit4p/PP6 regulates ER-to-Golgi traffic.
Skill Acquisition 1 Production Composition : A Simple Theory of Complex Skill Acquisition

In psychology many of theories of skill acquisition have had great success in addressing the fine details of learning relatively simple tasks, but can they scale up to complex tasks that are more typical of human learning in the real world? In this paper we describe production composition, a theory of skill acquisition that combines aspects of the theories forwarded by Anderson (1982) and Newell and Rosenbloom (1981), that we believe can model the fine details of learning in complex and dynamic tasks. We use production composition to model in detail learning in a simulated air-traffic controller task.
Unitary Query for the  $M\times L\times N$ MIMO Backscatter RFID Channel

A multiple-input multiple-output backscatter radio frequency identification (RFID) system consists of three operational ends: the query end (with M reader transmitting antennas), the tag end (with L tag antennas), and the receiving end (with N reader receiving antennas). Such an M × L × N setting in RFID can bring spatial diversity and has been studied with the use of space-time code (STC) at the tag end. Current research generally has ignored query signaling as a means to improve performance. Here we propose a novel unitary query scheme, which creates time diversity within the channel coherent time and can yield significant performance improvements. To overcome the difficulty of evaluating the performance when unitary query is employed at the query end and STC is employed at the tag end, we derive a new measure based on the ranks of certain carefully constructed matrices to show that unitary query has superior performance. Simulations show that unitary query can bring 5-10 dB gain in mid signal-to-noise ratio regimes. In addition, different from the conventional uniform query case, unitary query can also improve the performance of single-antenna tags significantly, enabling single-antenna tags with low complexity and small size to be used for high performance.
Egg consumption as part of an energy-restricted high-protein diet improves blood lipid and blood glucose profiles in individuals with type 2 diabetes

The role of dietary cholesterol in people with diabetes has been little studied. We investigated the effect of a hypoenergetic high-protein high-cholesterol (HPHchol) diet compared to a similar amount of animal protein (high-protein low-cholesterol, HPLchol) on plasma lipids, glycaemic control and cardiovascular risk markers in individuals with type 2 diabetes. A total of sixty-five participants with type 2 diabetes or impaired glucose tolerance (age 54·4 (sd 8·2) years; BMI 34·1 (sd 4·8) kg/m2; LDL-cholesterol (LDL-C) 2·67 (sd 0·10) mmol/l) were randomised to either HPHchol or HPLchol. Both hypoenergetic dietary interventions (6–7 MJ; 1·4–1·7 Mcal) and total carbohydrate:protein:fat ratio of 40:30:30 % were similar but differed in cholesterol content (HPHchol, 590 mg cholesterol; HPLchol, 213 mg cholesterol). HPHchol participants consumed two eggs per d, whereas HPHchol participants replaced the eggs with 100 g of lean animal protein. After 12 weeks, weight loss was 6·0 (sd 0·4) kg (P < 0·001). LDL-C and homocysteine remained unchanged. All the subjects reduced total cholesterol ( − 0·3 (sd 0·1) mmol/l, P < 0·001), TAG ( − 0·4 (sd 0·1) mmol/l, P < 0·001), non-HDL-cholesterol (HDL-C, − 0·4 (sd 0·1) mmol/l, P < 0·001), apo-B ( − 0·04 (sd 0·02) mmol/l, P < 0·01), HbA1c ( − 0·6 (sd 0·1) %, P < 0·001), fasting blood glucose ( − 0·5 (sd 0·2) mmol/l, P < 0·01), fasting insulin ( − 1·7 (sd 0·7) mIU/l, P < 0·01), systolic blood pressure ( − 7·6 (sd 1·7) mmHg, P < 0·001) and diastolic blood pressure ( − 4·6 (sd 1·0) mmHg; P < 0·001). Significance was not altered by diet, sex, medication or amount of weight loss. HDL-C increased on HPHchol (+0·02 (sd 0·02) mmol/l) and decreased on HPLchol ( − 0·07 (sd 0·03) mmol/l, P < 0·05). Plasma folate and lutein increased more on HPHchol (P < 0·05). These results suggest that a high-protein energy-restricted diet high in cholesterol from eggs improved glycaemic and lipid profiles, blood pressure and apo-B in individuals with type 2 diabetes.
Geração Y e o emprego ideal: percepção dos estudantes de um Centro Universitário

A multiplicidade de comportamentos que são próprias dos seres humanos, quando avaliadas nos contextos organizacionais, oferece a oportunidade de observar como as relações dos grupos geracionais são estabelecidas e a sua percepção sobre o emprego. Em um processo natural de evolução, o comportamento das pessoas se modifica e, consequentemente, as empresas precisam atender tanto as demandas de mercado como as de seus profissionais, com visões e valores diferenciados entre as gerações. Considerando este cenário, a pesquisa teve por objetivo identificar a percepção dos estudantes de um centro universitário pertencentes à Geração Y sobre o emprego ideal. A metodologia utilizada foi um survey aplicado aos estudantes universitários de um Centro Universitário do município de Guarulhos. O instrumento teve origem em Berthon et al. (2005), com 25 itens classificados em cinco dimensões: rotina de trabalho, interação pessoal, benefícios econômicos, desenvolvimento profissional e responsabilidade social. A escala apresentou-se em formato tipo Likert de sete pontos, variando de 1: discordo totalmente a 7: concordo totalmente. Os resultados apontam que os profissionais da Geração Y gostam de trabalhar em empresas que aplicam novas práticas de trabalho e consideram importante o bom relacionamento com a chefia e colegas.