Miracle-dz/UniFAR-FTUs huggingface dataset:
A study of a KVM-based cluster for grid computing

We present a performance study of a virtualized cluster based on the virtualization system KVM. We show benchmark results from the High Performance Computing Challenge (HPCC) application suite including the High Performance Linpack (HPL) benchmark. We also present the mechanism by which this cluster is connected to the Open Science Grid (OSG). Our results show that jobs with low amounts of network communication will only suffer moderate overhead (≈10%) due to virtualization, while MPI applications will suffer from a considerable overhead in the 60% range. The KVM cluster under investigation does prove to be suitable for current High Throughput Computing (HTC) grid usage on OSG where the Condor middleware is used.
Prevalence of Listeria monocytogenes in Raw Meats Marketed in Bangkok and Characterization of the Isolates by Phenotypic and Molecular Methods

Listeria monocytogenes causes listeriosis characterized by septicaemia, encephalitis, and abortion or stillbirth. Regular monitoring of its prevalence in food and characterization of its phenotypes and genotypes are necessary for disease surveillance and tracing the epidemic outbreaks. In this study, the prevalence of L. monocytogenes in raw meats marketed in Bangkok was 15.4%. The bacteria isolated from meat were serotyped and genotyped using enterobacterial repetitive intergenic consensus–polymerase chain reaction (ERIC-PCR). Their virulence-associated genes, antimicrobial susceptibility, and ability to invade intestinal epithelial cells were studied. All 22 L. monocytogenes strains isolated from 104 raw meat samples carried virulence-associated genes, such as actA, flaA, hlyA, iap, inlA, inlB, and prfA. These were serotype 4b, suggesting their pathogenic and epidemic potential. These isolates could be classified into six ERIC-PCR groups: A-F. The majority (59.1%) of the isolates belonged to Group A, and three isolates were Group D which was closely related to the Group A. Two isolates each were Group C and E, and one isolate each was group B and F. Although the isolates belonged to the same serotype and genotype and were all equipped with the virulence-associated genes, they showed a different cell invasion capability and antibiotic susceptibility. All the isolates were susceptible to ampicillin, amikacin, chloramphenicol, gentamicin, imipenem, penicillin G, sulphamethoxazole-trimethoprim, and tetracycline. However, one isolate showed only intermediate susceptibility to tetracycline. The data provide the first molecular insight into the L. monocytogenes isolates in Thailand and elucidate a potential risk of people contracting listeriosis.
DNA hypermethylation as a predictor of PSA recurrence in patients with low- and intermediate-grade prostate cancer.

BACKGROUND DNA CpG island hypermethylation causes gene silencing and is a common event in prostate carcinogenesis and progression. We investigated its role as a possible prognostic marker in patients with PCA Gleason score ≤7. PATIENTS AND METHODS We used a quantitative, methylation-specific PCR to analyze methylation patterns at five gene loci (APC, GSTP1, PTGS2, RARbeta and TIG1) in 84 prostate cancer (PCA) tissues (Gleason Score ≤7). Methylation was correlated with established clinico-pathological parameters (preoperative PSA, pathological Gleason score, extraprostatic extension, seminal vesicle penetration, lymph node involvement, surgical margins and age) and PSA recurrence. RESULTS DNA hypermethylation was frequently detected at APC (95.2%), GSTP1 (84.5%), PTGS2 (100%), RAR-beta (81.0%) and TIG1 (95.2%). DNA hypermethylation was correlated with Gleason Score (p=0.027; PTGS2) and lymph node involvement (p=0.024; RARbeta). High methylation levels at RARbeta (p=0.023) was a significant predictor of PSA recurrence following radical prostatectomy. CONCLUSION The analysis of DNA hypermethylation provides prognostic information in prognosis of low- and intermediate-grade PCA.
Combination of kernels applied to face verification

In this paper a novel method of information fusion at classifier level is applied to face verification. Three complementary kinds of facial data have been considered: texture, range data and curvature images. Three different kernels have been defined from each representation and finally a combined kernel has been developed. The resulting kernel has been used to train a classifier based on Support Vector Machines and it has been applied to face verification. The method has been deeply tested using the Face Recognition Grand Challenge database. The experiments show that in all cases the combined proposed classifier improves individual classifiers.
SOLO Taxonomy for Assessing Novices' Algorithmic Design

We present the utilization of the educational SOLO taxonomy for assessing algorithmic features of introductory programming. The SOLO taxonomy was recently studied by CS research educators, with respect to code reading and code writing. Most of the studies focused on code reading. In this paper we offer a framework of SOLO utilization for assessing basic algorithmic design features of code writing. Our novelty stems from focusing on: selection, flexible manipulation, and composition of basic design patterns, as well as on capitalization on unfolded task characteristics. We specify SOLO levels with respect to algorithmic design, and relate to common errors. We display our findings of applying the suggested framework in an ordered study with CS1 students.
Investigations into cochannel interference in microcellular mobile radio systems

A microcell interference model termed the Nakagami m/sub x//m/sub y/ model is introduced. The desired signal and the cochannel interferers are assumed to have Nakagami statistics but with different amounts of fading. A special case of this model is obtained when the desired signal has Nakagami statistics while the cochannel interferers are subject to Rayleigh fading. The probability density function of the signal-to-interference ratio in the Nakagami model is derived. This model is also compared with a Rician/Rayleigh microcellular model. Expressions for the outage probabilities in microcell systems are derived. Numerical results show that, compared to medium/large cell systems, the microcellular systems have a lower outage probability. The impact of diversity on the microcellular system is also studied. An improvement of the outage probability due to diversity is observed. >
MicroRNA Expression Variability in Human Cervical Tissues

MicroRNAs (miRNAs) are short (∼22 nt) non-coding regulatory RNAs that control gene expression at the post-transcriptional level. Deregulation of miRNA expression has been discovered in a wide variety of tumours and it is now clear that they contribute to cancer development and progression. Cervical cancer is one of the most common cancers in women worldwide and there is a strong need for a non-invasive, fast and efficient method to diagnose the disease. We investigated miRNA expression profiles in cervical cancer using a microarray platform containing probes for mature miRNAs. We have evaluated miRNA expression profiles of a heterogeneous set of cervical tissues from 25 different patients. This set included 19 normal cervical tissues, 4 squamous cell carcinoma, 5 high-grade squamous intraepithelial lesion (HSIL) and 9 low-grade squamous intraepithelial lesion (LSIL) samples. We observed high variability in miRNA expression especially among normal cervical samples, which prevented us from obtaining a unique miRNA expression signature for this tumour type. However, deregulated miRNAs were identified in malignant and pre-malignant cervical tissues after tackling the high expression variability observed. We were also able to identify putative target genes of relevant candidate miRNAs. Our results show that miRNA expression shows natural variability among human samples, which complicates miRNA data profiling analysis. However, such expression noise can be filtered and does not prevent the identification of deregulated miRNAs that play a role in the malignant transformation of cervical squamous cells. Deregulated miRNAs highlight new candidate gene targets allowing for a better understanding of the molecular mechanism underlying the development of this tumour type.
Design of an active one-degree-of-freedom lower-limb exoskeleton with inertia compensation

Limited research has been done on exoskeletons to enable faster movements of the lower extremities. An exoskeleton’s mechanism can actually hinder agility by adding weight, inertia and friction to the legs; compensating inertia through control is particularly difficult due to instability issues. The added inertia will reduce the natural frequency of the legs, probably leading to lower step frequency during walking. We present a control method that produces an approximate compensation of an exoskeleton’s inertia. The aim is making the natural frequency of the exoskeleton-assisted leg larger than that of the unaided leg. The method uses admittance control to compensate for the weight and friction of the exoskeleton. Inertia compensation is emulated by adding a feedback loop consisting of low-pass filtered acceleration multiplied by a negative gain. This gain simulates negative inertia in the low-frequency range. We tested the controller on a statically supported, single-degree-of-freedom exoskeleton that assists swing movements of the leg. Subjects performed movement sequences, first unassisted and then using the exoskeleton, in the context of a computer-based task resembling a race. With zero inertia compensation, the steady-state frequency of the leg swing was consistently reduced. Adding inertia compensation enabled subjects to recover their normal frequency of swing.
Bidding Against Competitors

Consideration is given to a system of n competitors, where if a competitor selects its bids equally likely from a given set of bid values, its probability of winning is guaranteed to be 1/n, regardless of the bid values selected by other competitors in the system. A discussion is presented of several variations of this basic scheme, namely, bidding with unequal weights, bidding with more than one winner, and bidding with an unknown number of competitors. Two economical, but approximate, bidding schemes are discussed. In the first scheme, the competitors select their bids from a set with a constant size, and in the second, each competitor selects only one bid even though the total number of competitors is not known a priori. It is shown how to use these bidding schemes to construct solutions to several problems in distributed systems, including the mutual exclusion problem and the dining philosophers problem. >
Mitochondrial DNA Evidence for a Diversified Origin of Workers Building Mausoleum for First Emperor of China

Variant studies on ancient DNA have attempted to reveal individual origin. Here, based on cloning sequencing and polymerase chain reaction-restriction fragment length polymorphisms, we analyzed polymorphisms in the first hypervariable region and coding regions of mitochondrial DNA of 19 human bone remains which were excavated from a tomb near the Terra Cotta Warriors and dated some 2,200 years before present. With the aim of shedding light on origins of these samples who were supposed to be workers building the mausoleum for the First Emperor of China, we compared them with 2,164 mtDNA profiles from 32 contemporary Chinese populations at both population and individual levels. Our results showed that mausoleum-building workers may be derived from very diverse sources of origin.
Control of hyperactivation in sperm.

BACKGROUND Sperm hyperactivation is critical to fertilization, because it is required for penetration of the zona pellucida. Hyperactivation may also facilitate release of sperm from the oviductal storage reservoir and may propel sperm through mucus in the oviductal lumen and the matrix of the cumulus oophorus. Hyperactivation is characterized by high amplitude, asymmetrical flagellar bending. METHODS This is a review of the original literature on the mechanisms that regulate hyperactivation, including physiological factors and signaling pathways. RESULTS Computer-assisted semen analysis systems can be used to identify hyperactivated sperm by setting minimum thresholds for curvilinear velocity (VSL) and lateral head movement and a maximum threshold for path linearity. Hyperactivation is triggered by a rise in flagellar Ca(2+) resulting from influx primarily through plasma membrane CatSper channels and possibly also by release of Ca(2+) from a store in the redundant nuclear envelope. It requires increased pH and ATP production. The physiological signals that trigger the rise in Ca(2+) remain elusive, but there is evidence that the increased Ca(2+) acts through a calmodulin/calmodulin kinase pathway. Hyperactivation is considered part of the capacitation process; however, the regulatory pathway that triggers hyperactivation can operate independently from that which prepares sperm to undergo the acrosome reaction. Hyperactivation may be modulated by chemotactic signals to turn sperm toward the oocyte. CONCLUSIONS Little is known about exactly what triggers hyperactivation in human sperm. This information could enable clinicians to develop reliable fertility assays to assess normal hyperactivation in human sperm samples.
Simple rational guidance for chopping up transactions

Chopping transactions into pieces is good for performance but may lead to non-serializable executions. Many researchers have reacted to this fact by either inventing new concurrency control mechanisms, weakening serializability, or both. We adopt a different approach. We assume a user who • has only the degree 2 and degree 3 consistency options offered by the vast majority of conventional database systems; and •knows the set of transactions that may run during a certain interval (users are likely to have such knowledge for online or real-time transactional applications). Given this information, our algorithm finds the finest partitioning of a set of transactions TranSet with the following property; if the partitioned transactions execute serializably, then TranSet executes serializably. This permits users to obtain more concurrency while preserving correctness. Besides obtaining more inter-transaction concurrency, chopping transactions in this way can enhance intra-transaction parallelism. The algorithm is inexpensive, running in O(n x (e + m)) time using a naive implementation where n is the number of edges in the conflict graph among the transactions, and m is the maximum number of accesses of any transaction. This makes it feasible to add as a tuning knob to practical systems.
Author Profiling: Predicting Age and Gender from Blogs Notebook for PAN at CLEF 2013

Author profiling is the task of determining age, gender, native language or personality type of author by studying their sociolect aspect, that is, how lan- guage is shared by people. In this paper, we propose a Machine Learning ap- proach to determine unknown author's age and gender. The approach uses three types of features: content based, style based and topic based. We were able to achieve an accuracy of 64.08%, 64.30% for age and 56.53%, 64.73% for gender in English and Spanish respectively.
Efficacy and tissue distribution of DHP107, an oral paclitaxel formulation

Paclitaxel is indispensable in treating human cancers. Due to poor drug solubility and efflux systems in the gastrointestinal tract, peroral delivery of paclitaxel has been a significant challenge. We developed a mucoadhesive oral formulation (DHP107) that can directly and effectively deliver paclitaxel to intestinal endothelial cells without concomitant use of P-glycoprotein inhibitors. Here, we evaluated the tissue distribution of paclitaxel, the antitumor efficacy and the absorption mechanism of DHP107. DHP107, which contains 10 mg/mL of paclitaxel in a mixture of monoolein, tricarprylin, and Tween 80 was administered p.o. to female BALB/c mice at a 50 mg/kg dose. Diluted Taxol was administered via bolus tail-vein injection at 10 mg/kg as a control. Blood and tissue samples were harvested at various time points and analyzed by high-performance liquid chromatography. Tissue sections were observed using light microscopy after immunohistochemical and Oil Red O staining. By day 27, tumor volume after DHP107 and Taxol treatments was one-third of that in the untreated group. After p.o. administration, paclitaxel was widely distributed in various organs (Tmax = 2 h), especially liver, spleen, and lung. DHP107 was effectively absorbed through the intestinal lipid transport system. DHP107 changed spontaneously into <100-μm droplets and micelles in the intestine, which in turn adhered to mucoepithelial cells, were absorbed via lipid uptake mechanism, and formed lipid bodies in the epithelium. Paclitaxel in DHP107 was effectively absorbed through the gastrointestinal tract via lipid uptake mechanism and was distributed in various tissues. The detailed uptake mechanism is currently under investigation. [Mol Cancer Ther 2007;6(12):3239–47]
Camouflage images

Camouflage images contain one or more hidden figures that remain imperceptible or unnoticed for a while. In one possible explanation, the ability to delay the perception of the hidden figures is attributed to the theory that human perception works in two main phases: feature search and conjunction search. Effective camouflage images make feature based recognition difficult, and thus force the recognition process to employ conjunction search, which takes considerable effort and time. In this paper, we present a technique for creating camouflage images. To foil the feature search, we remove the original subtle texture details of the hidden figures and replace them by that of the surrounding apparent image. To leave an appropriate degree of clues for the conjunction search, we compute and assign new tones to regions in the embedded figures by performing an optimization between two conflicting terms, which we call immersion and standout, corresponding to hiding and leaving clues, respectively. We show a large number of camouflage images generated by our technique, with or without user guidance. We have tested the quality of the images in an extensive user study, showing a good control of the difficulty levels.
Tolerance of didanosine as enteric-coated capsules versus buffered tablets.

329 E Didanosine (ddI) is a nucleoside analogue that competitively inhibits the HIV reverse transcriptase enzyme. The lability of the molecule in acid milieu reduces its bioavailability to 10% when administered orally.1 A first approach to overcome this limitation was the formulation of ddI as buffered tablets, so that the absorption of the drug was improved by gastric-acid neutralization.2 Gastrointestinal symptoms such as dyspepsia, nausea/vomiting, flatulence or diarrhea, are among the most frequent complaints in subjects receiving ddI. In addition to the inner toxicity of ddI, the citrate/phosphate/sucrose vehicle in buffered tables seems to play a significant part in these gastrointestinal toxicities.3 Since the year 2001, ddI has been available in the form of capsules containing gastro-resistant pellets that liberate the drug’s active ingredient within the intestinal lumen. The main pharmacokinetic parameters are approximately equivalent for enteric-coated and buffered preparations, but the former was expected to be more well tolerated.4 Herein, we present the results of a small retrospective study, in which we assessed the incidence of side effects in HIV-positive subjects who initiated a triple regimen containing buffered versus enteric-coated ddI. All HIV-positive patients who initiated a ddI-containing triple regimen, either with buffered tablets or enteric capsules (400 mg once daily in both instances), at one HIV/AIDS reference center in 2001 and 2002 were retrospectively analyzed. All recruited patients had not had prior ddI experience and a minimum follow-up of 12 months. Subjects with prior history of chronic gastrointestinal disease, pancreatitis, neuropathy, or alcohol abuse were not considered eligible. The main laboratory parameters were recorded through chart review. Adverse reactions were identified from clinical records. Treatment adherence was ascertained examining the pharmacy records, because all subjects had to obtain the medication monthly from the pharmacy. A total of 133 HIV-positive patients starting a ddI-containing triple regimen were retrospectively analyzed. Overall, 83 received buffered tablets (b-ddI) and 50 received entericcoated capsules (e-ddI). Overall, baseline demographics were comparable between both groups. Mean age was 38 8 years old, 80% were male, 55% had acquired HIV through sexual contacts, and 45% were former intravenous drug users. The virologic and immunologic status when ddI was started were comparable between both treatment groups: patients on b-ddI had an average CD4 count of 429 272 cells per microliter and a median viral load of 2249 HIV-RNA copies per milliliter, while these parameters
Estimation of percentage body fat by dual-energy x-ray absorptiometry: evaluation by in vivo human elemental composition

Dual-energy x-ray absorptiometry (DXA) is widely applied for estimating body fat. The percentage of body mass as fat (%fat) is predicted from a DXA-estimated RST value defined as the ratio of soft tissue attenuation at two photon energies (e.g., 40 keV and 70 keV). Theoretically, the RST concept depends on the mass of each major element in the human body. The DXA RST values, however, have never been fully evaluated by measured human elemental composition. The present investigation evaluated the DXA RST value by the total body mass of 11 major elements and the DXA %fat by the five-component (5C) model, respectively. Six elements (i.e. C, N, Na, P, Cl and Ca) were measured by in vivo neutron activation analysis, and potassium (i.e. K) by whole-body 40K counting in 27 healthy adults. Models were developed for predicting the total body mass of four additional elements (i.e. H, O, Mg and S). The elemental content of soft tissue, after correction for bone mineral elements, was used to predict the RST values. The DXA RST values were strongly associated with the RST values predicted from elemental content (r = 0.976, P < 0.001), although there was a tendency for the elemental-predicted RST to systematically exceed the DXA-measured RST (mean ± SD, 1.389 ± 0.024 versus 1.341 ± 0.024). DXA-estimated %fat was strongly associated with 5C %fat (24.4 ± 12.0% versus 24.9 ± 11.1%, r = 0.983, P < 0.001). DXA RST is evaluated by in vivo elemental composition, and the present study supports the underlying physical concept and accuracy of the DXA method for estimating %fat.