Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimized and controlled provisioning of encrypted outsourced data

Recent advances in encrypted outsourced databases support the direct processing of queries on encrypted data. Depend- ing on functionality (i.e. operators) required in the queries the database has to use different encryption schemes with different security properties. Next to these functional re-quirements a security administrator may have to address security policies that may equally determine the used en-cryption schemes. We present an algorithm and tool set that determines an optimal balance between security and functionality as well as helps to identify and resolve possible conflicts. We test our solution on a database benchmark and business-driven security policies.
Predicting the Performance of Virtual Machine Migration

With the ability to move virtual machines between physical hosts, live migration is a core feature of virtualisation. However for migration to be useful, deployable feature on a large (datacentre) scale, we need to predict migration times with accuracy. In this paper, we characterise the parameters affecting live migration with particular emphasis on the Xen virtualisation platform. We discuss the relationships between the important parameters that affect migration and highlight how migration performance can vary considerably depending on the workload. We further provide 2 simulation models that are able to predict migration times to within 90% accuracy for both synthetic and real-world benchmarks.
Grp78 Heterozygosity Promotes Adaptive Unfolded Protein Response and Attenuates Diet-Induced Obesity and Insulin Resistance

OBJECTIVE To investigate the role of the endoplasmic reticulum (ER) chaperone glucose-regulated protein (GRP) 78/BiP in the pathogenesis of obesity, insulin resistance, and type 2 diabetes. RESEARCH DESIGN AND METHODS Male Grp78+/− mice and their wild-type littermates were subjected to a high-fat diet (HFD) regimen. Pathogenesis of obesity and type 2 diabetes was examined by multiple approaches of metabolic phenotyping. Tissue-specific insulin sensitivity was analyzed by hyperinsulinemic-euglycemic clamps. Molecular mechanism was explored via immunoblotting and tissue culture manipulation. RESULTS Grp78 heterozygosity increases energy expenditure and attenuates HFD-induced obesity. Grp78+/− mice are resistant to diet-induced hyperinsulinemia, liver steatosis, white adipose tissue (WAT) inflammation, and hyperglycemia. Hyperinsulinemic-euglycemic clamp studies revealed that Grp78 heterozygosity improves glucose metabolism independent of adiposity and following an HFD increases insulin sensitivity predominantly in WAT. As mechanistic explanations, Grp78 heterozygosity in WAT under HFD stress promotes adaptive unfolded protein response (UPR), attenuates translational block, and upregulates ER degradation-enhancing α-mannosidase–like protein (EDEM) and ER chaperones, thus improving ER quality control and folding capacity. Further, overexpression of the active form of ATF6 induces protective UPR and improves insulin signaling upon ER stress. CONCLUSIONS HFD-induced obesity and type 2 diabetes are improved in Grp78+/− mice. Adaptive UPR in WAT could contribute to this improvement, linking ER homeostasis to energy balance and glucose metabolism.
A simple parallel algorithm for the maximal independent set problem

Simple parallel algorithms for the maximal independent set (MIS) problem are presented. The first algorithm is a Monte Carlo algorithm with a very local property. The local property of this algorithm may make it a useful protocol design tool in distributed computing environments and artificial intelligence. One of the main contributions of this paper is the development of powerful and general techniques for converting Monte Carlo algorithms into deterministic algorithms. These techniques are used to convert the Monte Carlo algorithm for the MIS problem into a simple deterministic algorithm with the same parallel running time.
Interplay of PIWI/Argonaute protein MIWI and kinesin KIF17b in chromatoid bodies of male germ cells

Chromatoid bodies are thought to act as male-germ-cell-specific platforms for the storing and processing of haploid transcripts. The molecular mechanisms governing the formation and function of these germ-cell-specific structures have remained elusive. In this study, we show that the kinesin motor protein KIF17b, which is involved in the nucleocytoplasmic transport of RNA and of a transcriptional coactivator, localizes in chromatoid bodies. The chromatoid body moves actively and non-randomly in the cytoplasm of round spermatids, making frequent contacts with the nuclear envelope. The localization of KIF17b thereby offers a potential mechanism for microtubule-dependent mobility of chromatoid bodies, as well as for the transport of the specific components in and out of the chromatoid body. Interestingly, we demonstrate that KIF17b physically interacts with a testis-specific member of the PIWI/Argonaute family, MIWI, a component of chromatoid bodies implicated in RNA metabolism. A functional interplay between KIF17b and MIWI might be needed for the loading of haploid RNAs in the chromatoid body. Importantly, chromatoid bodies from round spermatids of miwi-null mice are not fully compacted and remain as a diffuse chromatoid material, revealing the essential role played by MIWI in the formation of chromatoid bodies. These results shed new light on the function of chromatoid bodies in the post-transcriptional regulation of gene expression in haploid germ cells.
Ectopic Fat Accumulation and Distant Organ-Specific Insulin Resistance in Japanese People with Nonalcoholic Fatty Liver Disease

Objective The aim of this study was to examine the association between ectopic fat and organ-specific insulin resistance (IR) in insulin-target organs in patients with nonalcoholic fatty liver disease (NAFLD). Methods Organ-specific IR in the liver (hepatic glucose production (HGP)×fasting plasma insulin (FPI) and suppression of HGP by insulin [%HGP]), skeletal muscle (insulin-stimulated glucose disposal [Rd]), and adipose tissue (suppression of FFA by insulin [%FFA]) was measured in 69 patients with NAFLD using a euglycemic hyperinsulinemic clamp with tracer infusion ([6,6-2H2]glucose). Liver fat, intramyocellular lipid (IMCL), and body composition were measured by liver biopsy, proton magnetic resonance spectroscopy, and bioelectrical impedance analysis, respectively. Results HGP×FPI was significantly correlated with Rd (r = −0.57, P<0.001), %HGP with %FFA (r = 0.38, P<0.01), and Rd with %FFA (r = 0.27, P<0.05). Liver steatosis score was negatively associated with Rd (r = −0.47, P<0.001) as well as with HGP×FPI (r = 0.43, P<0.001). Similarly, intrahepatic lipid was negatively associated with Rd (r = −0.32, P<0.05). IMCL was not associated with Rd (r = −0.16, P = 0.26). Fat mass and its percentage were associated with HGP×FPI (r = 0.50, P<0.001; r = 0.48, P<0.001, respectively) and Rd (r = −0.59, P<0.001; r = −0.52, P<0.001, respectively), but not with %FFA (r = −0.21, P = 0.10; r = −0.001, P = 0.99, respectively). Conclusion Unexpectedly, fat accumulation in the skeletal muscle and adipose tissue was not associated with organ-specific IR. Instead, liver fat was associated not only with hepatic IR but also with skeletal muscle IR, suggesting a central role of fatty liver in systemic IR and that a network exists between liver and skeletal muscle.
Topological Considerations for Tuning and Fingering Stringed Instruments

We present a formal language for assigning pitches to strings for fingered multi-string instruments, particularly the six-string guitar. Given the instrument's tuning (the strings' open pitches) and the compass of the fingers of the hand stopping the strings, the formalism yields a framework for simultaneously optimizing three things: the mapping of pitches to strings, the choice of instrument tuning, and the key of the composition. Final optimization relies on heuristics idiomatic to the tuning, the particular musical style, and the performer's proficiency.
Towards Understanding the Impact of Length in Web Search Result Summaries over a Speech-only Communication Channel

Presenting search results over a speech-only communication channel involves a number of challenges for users due to cognitive limitations and the serial nature of speech. We investigated the impact of search result summary length in speech-based web search, and compared our results to a text baseline. Based on crowdsourced workers, we found that users preferred longer, more informative summaries for text presentation. For audio, user preferences depended on the style of query. For single-facet queries, shortened audio summaries were preferred, additionally users were found to judge relevance with a similar accuracy compared to text-based summaries. For multi-facet queries, user preferences were not as clear, suggesting that more sophisticated techniques are required to handle such queries.
Immunoassay based on monoclonal antibodies versus LC-MS: deoxynivalenol in wheat and flour in Southern Brazil

An indirect competitive enzyme-linked immunosorbent assay (ELISA) method using a monoclonal antibody for deoxynivalenol (DON) detection in wheat and flour was standardised and validated (detection limit = 177.1 µg kg−1) and its performance was compared with LC-MS, quantification limit =140 µg kg−1). DON recovery ranged from 88.7% to 122.6% for wheat grain and from 70.6% to 139.3% for flour. Among the 38 wheat samples evaluated, DON was detected in 29 samples (76.3%) by ic-ELISA (281.6–12 291.4 µg kg−1) and in 22 samples (57.9%) by LC-MS (155.3–9906.9 µg kg−1). The 0.93 correlation coefficient between ic-ELISA and LC-MS data in 19 positive DON wheat samples demonstrated the reliability and efficiency of ic-ELISA. Results indicated that standardised ic-ELISA was suitable for DON screening in wheat samples and the need for continuous monitoring of mycotoxin levels in foodstuffs.
An information‐theoretical approach to phylogeography

Data analysis in phylogeographic investigations is typically conducted in either a qualitative manner, or alternatively via the testing of null hypotheses. The former, where inferences about population processes are derived from geographical patterns of genetic variation, may be subject to confirmation bias and prone to overinterpretation. Testing the predictions of null hypotheses is arguably less prone to bias than qualitative approaches, but only if the tested hypotheses are biologically meaningful. As it is difficult to know a priori if this is the case, there is the general need for additional methodological approaches in phylogeographic research. Here, we explore an alternative method for analysing phylogeographic data that utilizes information theory to quantify the probability of multiple hypotheses given the data. We accomplish this by augmenting the model‐selection procedure implemented in ima with calculations of Akaike Information Criterion scores and model probabilities. We generate a ranking of 17 models each representing a set of historical evolutionary processes that may have contributed to the evolution of Plethodon idahoensis, and then quantify the relative strength of support for each hypothesis given the data using metrics borrowed from information theory. Our results suggest that two models have high probability given the data. Each of these models includes population divergence and estimates of ancestral θ that differ from estimates of descendent θ, inferences consistent with prior work in this system. However, the models disagree in that one includes migration as a parameter and one does not, suggesting that there are two regions of parameter space that produce model likelihoods that are similar in magnitude given our data. Results of a simulation study suggest that when data are simulated with migration, most of the optimal models include migration as a parameter, and further that when all of the shared polymorphism results from incomplete lineage sorting, most of the optimal models do not. The results could also indicate a lack of precision, which may be a product of the amount of data that we have collected. In any case, the information‐theoretic metrics that we have applied to the analysis of our data are statistically rigorous, as are hypothesis‐testing approaches, but move beyond the ‘reject/fail to reject’ dichotomy of conventional hypothesis testing in a manner that provides considerably more flexibility to researchers.
Regularized Multidirections and Multiscales Anisotropic Diffusion for Sinogram Restoration of Low-Dosed Computed Tomography

Although most of existing anisotropic diffusion (AD) methods are supported by prefect mathematical theories, they still lead to smoothed edges and anatomy details (EADs). They are caused by not considering the discrete nature of digital signal. In order to improve the performance of AD in sinogram restoration of low-dosed computed tomography (LDCT), we propose a new AD method, named regularized multidirections and multiscales anisotropic diffusion (RMDMS-AD), by extending AD to regularized AD (RAD) in multidirections and multiscales. Since the multidirections can reduce the discrete errors to the maximum extent, meanwhile multiscales and RAD make searching neighborhood of solution be as large as possible which can get more optimal solution to AD, the new proposed method can improve the performance of AD both in denoising and in stability of solution. Moreover, the discrete errors and ill-posed solutions occur mostly near the EADs; the RMDMS-AD will also preserve EADs well. Comparing the proposed new method to existing AD methods using real sinogram, the new method shows good performance in EADs preserving while denoising and suppressing artifacts.
Studies of rare-metal deposits in the Northwest Territories

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Space Localization and Well-Balanced Schemes for Discrete Kinetic Models in Diffusive Regimes

We derive and study well-balanced schemes for quasi-monotone discrete kinetic models. By means of a rigorous localization procedure, we reformulate the collision terms as nonconservative products and solve the resulting Riemann problem, whose solution is self-similar. The construction of an asymptotic preserving (AP) Godunov scheme is straightforward, and various compactness properties are established within different scalings. Finally, some computational results are supplied to show that this approach is realizable and efficient on concrete 2 × 2 models.
Evaluation of MK filters for recovery of enteroviruses from tap water

The MK filter is an electropositively charged filter that can be used to concentrate enteroviruses from large volumes (400 to 1,000 liters) of water. This filter is less expensive than the commonly used 1MDS electropositive filter. In this study, we compared the recovery of poliovirus 1 (PV1) and that of coxsackievirus B3 (CB3) from 378 liters of tap water, using both the MK and the 1MDS filters. Viruses were eluted from the filters with 3% beef extract buffered with 0.05 M glycine (pH 9.5) and reconcentrated via organic flocculation. At high virus inputs (approximately 10(6) PFU), the overall recovery (after elution and reconcentration) of PV1 and CB3 from tap water with the MK filter was less than that achieved with the 1MDS filter (P < 0.05). The recoveries of PV1 from tap water with the MK and 1MDS filters were 73.2% +/- 26% (n = 5 trials) and 90.2% +/- 5.9% (n = 5 trials), respectively. The recoveries of CB3 from tap water with the MK and 1MDS filters were 32.8% +/- 34.5% (n = 4 trials) and 95.8% +/- 12.0% (n = 4 trials), respectively. This study indicated that the MK filter consistently provided lower recovery, with wider variability, of PV1 and CB3 from tap water than the 1MDS filter.
DegenRev: Degeneracy-Based Full Backtranslation Algorithm for Oligopeptide

In order to design microarray oligonucleotides, in the context of new metabolic pathways discovery, it appears that a full backtranslation of oligopeptides is a promising approach. Protein to DNA reverse translation is a time-consuming task that can provide unreasonable quantities of data. This is why most current applications use genetic degenerated code or data mining-based techniques to select the best reverse translation of a short protein sequence called oligopeptide. When the purpose is only to design short oligos it is particularly interesting to have the complete sequences to solve the design problems of enzyme specific oligos for microarrays. In this paper, we revisit existing bioinformatics applications, which bring reverse translation solutions, and we present a new algorithm based on input oligopeptide degeneracy able to efficiently compute a full reverse translation. We propose an implementation with the C programming language and we show its performance statistics on simulated and real biological datasets.
Design and results of the USA-Mexico border human papillomavirus (HPV), cervical dysplasia, and Chlamydia trachomatis study.

OBJECTIVE Mexico has one of the highest mortality rates of invasive cervical cancer in the world. This is particularly true for the states in northern Mexico that border on the United States of America. In addition, Hispanics in the United States have higher rates than do non-Hispanics in the country. Therefore, a binational team was formed to focus on this problem and to determine the risk factors and prevalence of cervical dysplasia and human papillomavirus (HPV) infection, the sexually transmitted disease (STD) known to cause cervical cancer. Chlamydia trachomatis infection, a common STD and potential HPV cofactor, was also assessed. METHODS Research was conducted in 1997 and 1998 in the border region of two states, Arizona in the United States and Sonora in Mexico, applying a cross-sectional study of women attending clinics for routine gynecologic care. Clinical measurements included Pap smears, HPV infection by both polymerase chain reaction (PCR) and Hybrid Capture (HC), and C. trachomatis status by HC and enzyme-linked immunoassay (EIA). A total of 2,436 women were enrolled (mean age 33.3 years +/- 10.3 years). RESULTS The overall prevalence of abnormal cytology was 9.3%, with a significant difference in the prevalence in Mexico (11.4%) vs. the United States (6.6%). Of the participants, 14.5% of them tested positive for HPV by PCR, with no significant difference between the two countries, in spite of a lower behavioral risk profile for the Mexican women. Overall prevalence of C. trachomatis was found to be greater by HC than by EIA (8.2% vs. 3.0%), and in Mexico higher by both methods. CONCLUSIONS An important accomplishment of the project was the implementation of a quality control program for Pap smear collection, which resulted in a significant reduction in inadequate smears in Mexico. Despite numerous potential logistical barriers, the binational team successfully conducted a large-scale study in the border area and developed an infrastructure for future research.
Meta-Features and AdaBoost for Music Classification

One of the biggest challenges facing current methods for classifying music by genre or artist is that features of the sound are computed on very small temporal scales (20 to 50 milliseconds), while the labels need to be assigned at relatively large temporal scales (3 to 5 minutes). We address this challenge by partitioning songs into smaller pieces and classifying each one separately. Our choice of features together with an AdaBoost.MH classifier proved to be the most effective method for genre classification at the recent MIREX 2005 international contests in music information extraction, and the second-best method for recognizing artists. This paper describes our method in detail, from feature extraction to song classification, and presents an evaluation of our method on three genre databases and two artist-recognition databases. Furthermore, we present evidence that the method of partitioning songs is better than classifying either entire songs or individual features, using a variety of popular features and classifiers.
Prospecting Russula senecis: a delicacy among the tribes of West Bengal

Russula senecis, a worldwide distributed mushroom, is exclusively popular among the tribal communities of West Bengal for food purposes. The present study focuses on its reliable taxonomic identification through macro- and micro-morphological features, DNA barcoding, confirmation of its systematic placement by phylogenetic analyses, myco-chemicals and functional activities. For the first time, the complete Internal Transcribed Spacer region of R. senecis has been sequenced and its taxonomic position within subsection Foetentinae under series Ingratae of the subgen. Ingratula is confirmed through phylogenetic analysis. For exploration of its medicinal properties, dried basidiocarps were subjected for preparation of a heat stable phenol rich extract (RusePre) using water and ethanol as solvent system. The antioxidant activity was evaluated through hydroxyl radical scavenging (EC50 5 µg/ml), chelating ability of ferrous ion (EC50 0.158 mg/ml), DPPH radical scavenging (EC50 1.34 mg/ml), reducing power (EC50 2.495 mg/ml) and total antioxidant activity methods (13.44 µg ascorbic acid equivalent/mg of extract). RusePre exhibited antimicrobial potentiality against Listeria monocytogenes, Bacillus subtilis, Pseudomonas aeruginosa and Staphylococcus aureus. Furthermore, different parameters were tested to investigate its chemical composition, which revealed the presence of appreciable quantity of phenolic compounds, along with carotenoids and ascorbic acid. HPLC-UV fingerprint indicated the probable existence of at least 13 phenolics, of which 10 were identified (pyrogallol > kaempferol > quercetin > chlorogenic acid > ferulic acid, cinnamic acid > vanillic acid > salicylic acid > p-coumaric acid > gallic acid). Result from the present work suggests that the fraction, RusePre, may open novel prospect as a functional ingredient in antioxidant supplements and in drugs to treat infectious disease.
A Comprehensive Study of the Past, Present, and Future of Data Deduplication

Data deduplication, an efficient approach to data reduction, has gained increasing attention and popularity in large-scale storage systems due to the explosive growth of digital data. It eliminates redundant data at the file or subfile level and identifies duplicate content by its cryptographically secure hash signature (i.e., collision-resistant fingerprint), which is shown to be much more computationally efficient than the traditional compression approaches in large-scale storage systems. In this paper, we first review the background and key features of data deduplication, then summarize and classify the state-of-the-art research in data deduplication according to the key workflow of the data deduplication process. The summary and taxonomy of the state of the art on deduplication help identify and understand the most important design considerations for data deduplication systems. In addition, we discuss the main applications and industry trend of data deduplication, and provide a list of the publicly available sources for deduplication research and studies. Finally, we outline the open problems and future research directions facing deduplication-based storage systems.