Miracle-dz/UniFAR-FTUs huggingface dataset:
Rabbit Order: Just-in-Time Parallel Reordering for Fast Graph Analysis

Ahead-of-time data layout optimization by vertex reordering is a widely used technique to improve memory access locality in graph analysis. While reordered graphs yield better analysis performance, the existing reordering algorithms use significant amounts of computation time to provide efficient vertex ordering, hence, they fail to reduce end-to-end processing time. This paper presents a first algorithm for just-in-time parallel reordering, named Rabbit Order. It reduces end-to-end runtime by achieving high locality and fast reordering at the same time through two approaches. The first approach is hierarchical community-based ordering, which exploits the locality derived from hierarchical community structures in real-world graphs. Our ordering fully leverages low-latency cache levels by mapping hierarchical communities into hierarchical caches. The second approach is parallel incremental aggregation, which improves the runtime efficiency of reordering by decreasing the number of vertices to be processed. In addition, this approach utilizes lightweight atomic operations for concurrency control to avoid locking overheads and achieve high scalability. Our experiments show that Rabbit Order significantly outperforms state-of-the-art reordering algorithms.
Privacy-safe network trace sharing via secure queries

Privacy concerns relating to sharing network traces have traditionally been handled via sanitization, which includes removal of sensitive data and IP address anonymization. We argue that sanitization is a poor solution for data sharing that offers insufficient research utility to users and poor privacy guarantees to data providers. We claim that a better balance in the utility/privacy trade-off, inherent to network data sharing, can be achieved via a new paradigm we propose: secure queries. In this paradigm, a data owner publishes a query language and an online portal, allowing researchers to submit sets of queries to be run on data. Only certain operations are allowed on certain data fields, and in specific contexts. Query restriction is achieved via the provider's privacy policy, and enforced by the language's interpreter. Query results, returned to researchers, consist of aggregate information such as counts, histograms, distributions, etc. and not of individual packets. We discuss why secure queries provide higher privacy guarantees and higher research utility than sanitization, and present a design of the secure query language and a privacy policy.
Impact of a Single Nucleotide Polymorphism in the MDM2 Gene on Neuroblastoma Development and Aggressiveness: Results of a Pilot Study on 239 Patients

Purpose: MDM2 is a key negative regulator of p53 activity, and a single nucleotide polymorphism (SNP309, T>G change; rs 2279744) in its promoter increases the affinity for the transcription factor SP1, enhancing MDM2 expression. We carried out a pilot study to investigate the effect of this polymorphism on development and behavior of neuroblastoma, an extracranial pediatric tumor with unfrequent genetic inactivation of p53. Experimental Design: We genotyped the MDM2-SNP309 alleles of tumor DNA from 239 neuroblastoma patients and peripheral blood DNA from 237 controls. In 40 of 239 neuroblastomas, the MDM2-SNP309 alleles were also genotyped in peripheral blood DNA. Data were analyzed by two-sided Fisher's exact test, log-rank test, and Kaplan-Meier statistics. Where appropriate, data are reported with 95% confidence intervals (CI). Results: The frequency of both the T/G and G/G genotypes or the G/G or T/G genotype only was higher in neuroblastoma DNA samples than in controls: 60.3% (95% CI, 54.1-66.5) versus 47.3% (95% CI, 40.9-53.6), 30.4% (95% CI, 22.4-37.8) versus 15.0% (95% CI, 9.2-20.7), and 52.0% (95% CI, 45.0-59.9) versus 41.9% (95% CI, 35.3-48.5), respectively; Two-Sided Fisher's Exact Test P values were 0.006, 0.003, and 0.048, respectively; Odds ratios were 1.69 (95% CI, 1.18-2.43), 2.45 (95% CI, 1.37-4.39) and 1.51 (95% CI, 1.02-2.22), respectively. A significant association (P = 0.016) between heterozygous (T/G)/homozygous (G/G) genotypes at SNP309 and advanced clinical stages was also shown. Homozygous/heterozygous SNP309 variant carriers had a shorter 5-year overall survival than patients with the wild-type allele (P = 0.046; log-rank test). A shorter overall survival in patients with heterozygous/homozygous SNP309 was also observed in the subgroups with age at diagnosis >1 year and adrenal primary tumor (P = 0.024 and P = 0.014, respectively). Conclusions: Data from this pilot study suggest that the MDM2 G/G and T/G-SNP309 alleles are markers of increased predisposition to tumor development and disease aggressiveness in neuroblastoma. However, additional studies with larger patient cohorts are required for a definitive assessment of the clinical relevance of these data.
Implementation of an Energy Management Control Strategy for WSNs using the LINC Middleware

Energy optimisation in Wireless Sensor Networks (WSNs) is traditionally done either at the sensor node level or at the network level. To obtain even more energy savings, the final application must be considered. Control theory offers promising solutions to tackle this challenge. This paper details an implementation of a control strategy to minimise energy consumption of a WSN, while ensuring the application Quality of Service (QoS). The application QoS is expressed with the sampling period for sensor nodes and a minimum number of samples that must be available at the application level at each sampling time. With a Model Predictive Control strategy, the lifetime of the WSN is doubled compared to the basic case. The control strategy has been implemented and evaluated on a real test-bed, formed of heterogeneous sensor nodes, thanks to the LINC coordination middleware.
Early hyaluronate injection improves quality of life but not neural recovery in unilateral vocal fold paralysis: an open-label randomized controlled study.

PURPOSE To investigate the neurologic and functional effect of intracordal hyaluronate injections in acute unilateral vocal fold paralysis (UVFP) in a randomized controlled trial. METHODS In this open-label, randomized controlled study, 29 patients with UVFP were recruited within 6 months of their first outpatient visit and were randomized to receive either single hyaluronate injection (HI group) or conservative management (CM group). Quantitative laryngeal electromyography, videolaryngostroboscopy, UVFP-related quality of life (Voice Outcomes Survey, VOS), laboratory voice analysis, and health-related quality of life (SF-36) were evaluated at baseline, and at 1, 3 and 6 months post-injection in the HI group, and at baseline and 6 months in the CM group. RESULTS Improvements in most quality of life domains and other assessments were comparable between the HI and CM groups; however, the HI group had a greater improvement in the mental health domain of quality of life at the end of follow-up. CONCLUSIONS Early hyaluronate injection cannot improve nerve regeneration but can result in long-lasting improvements in patients' psychosocial well-being, thus highlighting the importance of early intervention for patients with UVFP.
Defining Groups: Identifying Characteristics of the Mars Scientific Community

Scientific communities are composed of interconnected and disparate groupings of individuals. The connections between those communities and the backgrounds of individuals can influence how those groups approach and solve problems. A question then becomes, what aspects of their connections and backgrounds are important to characterize that community? How do you characterize a community that spans multiple disciples, locations, and research interests? The current research sought to identify defining aspects of the Mars scientific community by looking at connections represented by co-authorship on papers. A subset of the Mars community was studied, specifically, those taking part in two separate panels. These panels consisted of the recent (2009) and previous (2003) Planetary Science Decadal Survey for Mars. The data suggests the community holds a diverse background with a fair amount of crossover in their academic achievements. Results also point to the influence of universities in the composition of these two panels.
The RNA Virus Database

The RNA Virus Database is a database and web application describing the genome organization and providing analytical tools for the 938 known species of RNA virus. It can identify submitted nucleotide sequences, can place them into multiple whole-genome alignments (in species where more than one isolate has been fully sequenced) and contains translated genome sequences for all species. It has been created for two main purposes: to facilitate the comparative analysis of RNA viruses and to become a hub for other, more specialised virus Web sites. It is available at the following four mirrored sites. http://virus.zoo. ox.ac. uk/rnavirusdb http://hivweb.sanbi. ac.za/rnavirusdb http://bioinf.cs. auckland.ac. nz/rnavirusdb http://tree.bio. ed.ac. uk/rnavirusdb
Ambient Air Quality Assessment in the Grand Casablanca Area (Morocco): Impact of Road Traffic Emissions for the 2013-2016 Period

<p><em>Air Pollution is a serious hazard worldwide especially in urban areas. Road traffic is the main cause of pollution in agglomerations that are confronted to an excess of pollutants due to traffic intensity and the dominance of diesel cars. This paper presents the assessment of road traffic pollution in the Grand Casablanca</em><em> </em><em>area. Data used are the result of simultaneous measurements at thirteen sites located in the Grand Casablanca. Available data cover 4 years period (2013</em><em>-</em><em>2016). Traffic-related air pollutants are reviewed in order to assess their impact on the local air quality. It include nitrogen dioxide (NO<sub>2</sub>), particulate matter (PM<sub>10</sub>), carbon monoxide (CO) and Benzene (C<sub>6</sub>H<sub>6</sub>). Annual evolutions are presented and compared to national air quality standards;</em><em> </em><em>NO<sub>2</sub> annual trends are also evaluated. The [NO]/[NO<sub>2</sub>] emissions ratio calculation allows then to characterize the measurement sites against road traffic. The paper focuses on determining the contribution of road traffic emissions on air quality modifying; we found spatial variability in traffic</em><em> </em><em>pollutants. The results pointed out that road traffic and conditions are the main causes of air pollution in the area and the analysis provide a quick view of the relatively critical areas that need more action to reduce this pollution. </em></p>
Grouping Android Tag Synonyms on Stack Overflow

On Stack Overflow, more than 38,000 diverse tags are used to classify posts. The Stack Overflow community provides tag synonyms to reduce the number of tags that have the same or similar meaning. In our previous research, we used those synonym pairs to derive a number of strategies to create tag synonyms automatically.In this work, we continue this line of research and present an approach to group tag synonyms to meaningful topics. We represent our synonyms as directed, weighted graphs, and investigate several graph community detection algorithms to build meaningful groups of tags, also called tag communities.We apply our approach to the tags obtained from Android-related Stack Overflow posts and evaluate the resulting tag communities quantitatively with various community metrics. In addition, we evaluate our approach qualitatively through a manual inspection and comparison of a random sample of tag communities. Our results show that we can cluster the Android tags to 2,481 meaningful tag communities. We also show how these tag communities can be used to derive trends of topics of Android-related questions on Stack Overflow.
The Effects of Reading Racetracks on the Sight Word Fluency and Acquisitionfor Two Elementary Students with Disabilities: A Further Replicationand Analysis

The purpose of this research was to determine the effectiveness of reading racetracks on the sight word acquisi- tion and fluency of two elementary students who qualified for special education services. An ABABA' reversal, single subject design provided data on the number of words the participants read correctly during a 1-minute timing as well as his or her error rate during that same 1-minute timing. The overall outcomes indicated an increase in the acquisition and fluency of sight words and a decrease in errors. Maintenance of treatment gains were noted for both corrects and errors during the post-testing of each participant. Very small declines in corrects were noted as were small increases in errors.
TreeSha: 3D Shape Retrieval with a Tree Graph Representation based on the Autodiffusion Function Topology

In this paper we present a new method for shape description and matching based on a tree representation built upon the scale space analysis of maxima of the Autodiffusion function (ADF). The use of the Heat Kernel based approach makes the method invariant to articulated deformations. By coupling maxima of the Autodiffusion function with the related basins of attraction, it is possible to link the information at different scales encoding spatial relationships in a tree structure. Furthermore, texture information can be easily included in the descriptor by adding regional color histograms to the node attributes of the tree. Dedicated graph kernels have been designed to evaluate shape dissimilarity from the obtained representations using both structural, geometric and color information. Preliminary experiments performed on the SHREC 2013 non-rigid textured dataset showed very good retrieval performances.
Multi-objective scheduling of micro-services for optimal service function chains

Lately application service providers (ASPs) and Internet service providers (ISPs) are being confronted with the unprecedented challenge of accommodating increasing service and traffic demands from their geographically distributed users. Many ASPs and ISPs, such as Facebook, Netflix, AT&T and others have adopted micro-service architecture to tackle this problem. Instead of building a single, monolithic application, the idea is to split the application into a set of smaller, interconnected services, called micro-services (or simply services). Such services are lightweight and perform distinct tasks independent of each other. Hence, they can be deployed quickly and independently as user demands vary. Nevertheless, scheduling of micro-services is a complex task and is currently under-researched. In this work, we address the problem of scheduling micro-services across multiple clouds, including micro-clouds. We consider different user-level SLAs, such as latency and cost, while scheduling such services. Our aim is to reduce overall turnaround time for the complete end-to-end service in service function chains and reduce the total traffic generated. In this work we present a novel fair weighted affinity-based scheduling heuristic to solve this problem. We also compare the results of proposed solution with standard biased greedy scheduling algorithms presented in the literature and observe significant improvements.
ICFHR2016 Competition on the Analysis of Handwritten Text in Images of Balinese Palm Leaf Manuscripts

This paper presents the results of the Competition on the Analysis of Handwritten Text in Images of Balinese Palm Leaf Manuscripts that was organized in the context of the 15th International Conference on Frontiers in Handwriting Recognition (ICFHR-2016). This competition provides a suitable challenge for testing and evaluation of robustness for some methods, image features and descriptors which were already proposed for handwritten text analysis of document image. In this competition, three different challenges in document analysis of palm leaf manuscript images are proposed: Challenge 1: Binarization of Palm Leaf Manuscript Images, Challenge 2: Query-by-Example Word Spotting on Palm Leaf Manuscript Images, and Challenge 3: Isolated Character Recognition of Balinese Script in Palm Leaf Manuscript Images. The first handwritten Balinese palm leaf manuscript dataset, the AMADI_LontarSet, is used for performance evaluation. This paper describes the competition details including the dataset creation and the ground truth construction, the evaluation measures used, a short description of each participant as well as the performance of the all submitted methods.
Evaluating a Process-Based Mitigation Wetland Water Budget Model

Correctly predicting water levels is key to the success of created wetlands. The Pierce method is a commonly used technique for modeling and designing mitigation wetlands that assumes minimal groundwater interaction with the wetland. This technique for mitigation wetland design relies primarily on surface water inputs, assuming a relatively impermeable substrate (perched system), and level pool routing. The Pierce method was applied utilizing two different evapotranspiration estimation methods: Thornthwaite (IPM) and FAO-56 PenmanMonteith (IPM-FAO). A second process-based model, utilizing MODFLOW-2005, was constructed to better predict water levels in mitigation wetlands. Modeled processes included groundwater movement and vegetative resistance to flow, which can be a significant factor in wetland water levels. The two versions of the Pierce method were compared to the process-based wetland representation developed in MODFLOW-2005 using data from an existing mitigation
Confinement, Desolvation, And Electrosorption Effects on the Diffusion of Ions in Nanoporous Carbon Electrodes

Supercapacitors are electrochemical devices which store energy by ion adsorption on the surface of a porous carbon. They are characterized by high power delivery. The use of nanoporous carbon to increase their energy density should not hinder their fast charging. However, the mechanisms for ion transport inside electrified nanopores remain largely unknown. Here we show that the diffusion is characterized by a hierarchy of time scales arising from ion confinement, solvation, and electrosorption effects. By combining electrochemistry experiments with molecular dynamics simulations, we determine the in-pore conductivities and diffusion coefficients and their variations with the applied potential. We show that the diffusion of the ions is slower by 1 order of magnitude compared to the bulk electrolyte. The desolvation of the ions occurs on much faster time scales than electrosorption.
Modeling OOV Words With Letter N-Grams in Statistical Taggers: Preliminary Work in Biomedical Entity Recognition

,We discuss sequential tagging problems in natural language processing using statistical methodology. We propose an automatic and domain-independent approach to modeling out-ofvocabulary (OOV) words, that is words that do not occur in training data. Our method is based on using probabilistic letter n-gram models to model orthography of different tags. We show how to combine the approach with two widely used statistical models Hidden Markov Models and Conditional Random Fields. Instead of taking the common approach of directly using sub-strings as features resulting in an explosion in the number of model parameters, we compress orthographic information into a small number of parameters. Experiments in biomedical entity recognition on the Genia corpus show that the approach can alleviate the OOV problem resulting in improvement in overall model performance.
Utilization of DNA as a Sole Source of Phosphorus, Carbon, and Energy by Shewanella spp.: Ecological and Physiological Implications for Dissimilatory Metal Reduction

ABSTRACT The solubility of orthophosphate (PO43−) in iron-rich sediments can be exceedingly low, limiting the bioavailability of this essential nutrient to microbial populations that catalyze critical biogeochemical reactions. Here we demonstrate that dissolved extracellular DNA can serve as a sole source of phosphorus, as well as carbon and energy, for metal-reducing bacteria of the genus Shewanella. Shewanella oneidensis MR-1, Shewanella putrefaciens CN32, and Shewanella sp. strain W3-18-1 all grew with DNA but displayed different growth rates. W3-18-1 exhibited the highest growth rate with DNA. While strain W3-18-1 displayed Ca2+-independent DNA utilization, both CN32 and MR-1 required millimolar concentrations of Ca2+ for growth with DNA. For S. oneidensis MR-1, the utilization of DNA as a sole source of phosphorus is linked to the activities of extracellular phosphatase(s) and a Ca2+-dependent nuclease(s), which are regulated by phosphorus availability. Mass spectrometry analysis of the extracellular proteome of MR-1 identified one putative endonuclease (SO1844), a predicted UshA (bifunctional UDP-sugar hydrolase/5′ nucleotidase), a predicted PhoX (calcium-activated alkaline phosphatase), and a predicted CpdB (bifunctional 2′,3′ cyclic nucleotide 2′ phosphodiesterase/3′ nucleotidase), all of which could play important roles in the extracellular degradation of DNA under phosphorus-limiting conditions. Overall, the results of this study suggest that the ability to use exogenous DNA as the sole source of phosphorus is widespread among the shewanellae, and perhaps among all prokaryotes, and may be especially important for nutrient cycling in metal-reducing environments.
Investigation of the Phenylalkylamine Binding Site in hKv1.3 (H399T), a Mutant with a Reduced C-Type Inactivated State

To screen for residues of hKv1.3 important for current block by the phenylalkylamine verapamil, the inactivated-state-reduced H399T mutant was used as a background for mutagenesis studies. This approach was applied mainly to abolish the accumulation in the inactivated blocked state, recovery from which in the wild type is normally slow. Substitution of amino acids in the S6 transmembrane helix indicated a heavy disruption of verapamil block by the A413C mutation, reducing the IC50 from 2.4 to 267 μM. Subsequent scanning for verapamil moieties essential for current block was performed by application of derivatives with altered side groups. Neither the removal of the nitrile or the methyl group nor the addition of a methoxy group resulted in major variations of IC50 values for hKv1.3 (H399T) current block. However, disruption of current block by A413C was 4- to 10-fold less pronounced for derivatives lacking the 4-methoxy group of the (3,4-dimethoxyphenyl)ethylmethyl-amino part (devapamil) or all four methoxy groups (emopamil), respectively. Emopamil displayed a Hill coefficient of 2 for hKv1.3 (H399T/A413C) instead of 1 for hKv1.3 (H399T) current block. These results might indicate that the alteration of Ala413 modulates the access of phenylalkylamines to their binding site depending on the occupancy of the phenyl rings with methoxy groups. A computer-based docking model shows a subset of docked PAA conformations, with a spatial proximity between the (4-methoxyphenyl)ethyl-methyl-amino group and Ala413. The PAA binding site might therefore include a binding pocket for the aromatic ring of the ethyl-methyl-amino part in an S6–S6 interface gap.