Miracle-dz/UniFAR-FTUs huggingface dataset:
Who is Who in the Mailing List? Comparing Six Disambiguation Heuristics to Identify Multiple Addresses of a Participant

Many software projects adopt mailing lists for the communication of developers and users. Researchers have been mining the history of such lists to study communities' behavior, organization, and evolution. A potential threat of this kind of study is that users often use multiple email addresses to interact in a single mailing list. This can affect the results and tools, when, for example, extracting social networks. This issue is particularly relevant for popular and long-term Open Source Software (OSS) projects, which attract participation of thousands of people. Researchers have proposed heuristics to identify multiple email addresses from the same participant, however there are few studies analyzing the effectiveness of these heuristics. In addition, many studies still do not use any heuristics for authors' disambiguation, which can compromise the results. In this paper, we compare six heuristics from the literature using data from 150 mailing lists from Apache Software Foundation projects. We found that the heuristics proposed by Oliva et al. and a Naïve heuristic outperformed the others in most cases, when considering the F-measure metric. We also found that the time window and the size of the dataset influence the effectiveness of each heuristic. These results may help researchers and tool developers to choose the most appropriate heuristic to use, besides highlighting the necessity of dealing with identity disambiguation, mainly in open source software communities with a large number of participants.
Frequency and Fidelity of Translesion Synthesis of Site-specific N-2-Acetylaminofluorene Adducts during DNA Replication in a Human Cell Extract (*)

We have previously analyzed the effects of site-specific N-2-acetylaminofluorene (AAF) adducts on the efficiency and frameshift fidelity of SV40-based DNA replication in a human cell extract (Thomas, D. C., Veaute, X., Kunkel, T. A., and Fuchs, R. P. P.(1994) Proc. Natl. Acad. Sci. U.S.A. 91, 7752-7756). Here we use two sets of substrates to examine the probability of replication termination and error-free and error-prone bypass of AAF adducts. The substrates contained site-specific adducts at one of three guanines in a NarI sequence (5′-GGCGCC-3′) placed within the lacZα reporter gene and located on the template for either leading or lagging strand replication. The presence of the adduct at any position strongly reduces the efficiency of a single round of replication in a HeLa cell extract. Product analysis reveals preferential replication of the undamaged strand and termination of replication of the damaged strand occurring one nucleotide before incorporation opposite either a leading or lagging strand adduct. Products resistant to restriction endonuclease cleavage at the adducted site were generated in amounts consistent with 16-48% lesion bypass during replication. Most of this bypass was error-free. However, two-nucleotide deletion errors were detected in the replication products of DNA containing an AAF adduct in either the leading or lagging strand, but only when present at the third guanine position. Collectively, the data suggest that the replication apparatus in a HeLa cell extract generates a template-primer slippage error at an AAF adduct once for every 30-100 bypass events.
Non-Lytic, Actin-Based Exit of Intracellular Parasites from C. elegans Intestinal Cells

The intestine is a common site for invasion by intracellular pathogens, but little is known about how pathogens restructure and exit intestinal cells in vivo. The natural microsporidian parasite N. parisii invades intestinal cells of the nematode C. elegans, progresses through its life cycle, and then exits cells in a transmissible spore form. Here we show that N. parisii causes rearrangements of host actin inside intestinal cells as part of a novel parasite exit strategy. First, we show that N. parisii infection causes ectopic localization of the normally apical-restricted actin to the basolateral side of intestinal cells, where it often forms network-like structures. Soon after this actin relocalization, we find that gaps appear in the terminal web, a conserved cytoskeletal structure that could present a barrier to exit. Reducing actin expression creates terminal web gaps in the absence of infection, suggesting that infection-induced actin relocalization triggers gap formation. We show that terminal web gaps form at a distinct stage of infection, precisely timed to precede spore exit, and that all contagious animals exhibit gaps. Interestingly, we find that while perturbations in actin can create these gaps, actin is not required for infection progression or spore formation, but actin is required for spore exit. Finally, we show that despite large numbers of spores exiting intestinal cells, this exit does not cause cell lysis. These results provide insight into parasite manipulation of the host cytoskeleton and non-lytic escape from intestinal cells in vivo.
Near-optimal Supervised Feature Selection among Frequent Subgraphs

Graph classification is an increasingly important step in numerous application domains, such as function prediction of molecules and proteins, computerised scene analysis, and anomaly detection in program flows. Among the various approaches proposed in the literature, graph classification based on frequent subgraphs is a popular branch: Graphs are represented as (usually binary) vectors, with components indicating whether a graph contains a particular subgraph that is frequent across the dataset. On large graphs, however, one faces the enormous problem that the number of these frequent subgraphs may grow exponentially with the size of the graphs, but only few of them possess enough discriminative power to make them useful for graph classification. Efficient and discriminative feature selection among frequent subgraphs is hence a key challenge for graph mining. In this article, we propose an approach to feature selection on frequent subgraphs, called CORK, that combines two central advantages. First, it optimizes a submodular quality criterion, which means that we can yield a near-optimal solution using greedy feature selection. Second, our submodular quality function criterion can be integrated into gSpan, the state-of-the-art tool for frequent subgraph mining, and help to prune the search space for discriminative frequent subgraphs even during frequent subgraph mining.
Supplementary File of “ Formal Specification and Runtime Detection of Dynamic Properties in Asynchronous Pervasive Computing Environments ”

In our paper “Formal Specification and Runtime Detection of Dynamic Properties in Asynchronous Pervasive Computing Environments”, we propose the Property Detection for Asynchronous Context (PDAC) framework to support formal specification and runtime detection of dynamic properties in asynchronous pervasive computing environments. Three essential parts of the framework are discussed: modeling of the temporal evolution of environment state, specification of dynamic properties, and detection of the specified dynamic property by the proposed SurfMaint algorithm.
The enzyme activities of Caf1 and Ccr4 are both required for deadenylation by the human Ccr4–Not nuclease module

Enzymatic shortening of mRNA poly(A) tails is important for translation and mRNA degradation. Ccr4–Not, a major eukaryotic deadenylase, contains two catalytic subunits. Using a nuclease module reconstituted with human subunits, we demonstrate that both nuclease subunits are required for deadenylation.
Nystrom Method for Approximating the GMM Kernel

The GMM (generalized min-max) kernel was recently proposed (Li, 2016) as a measure of data similarity and was demonstrated effective in machine learning tasks. In order to use the GMM kernel for large-scale datasets, the prior work resorted to the (generalized) consistent weighted sampling (GCWS) to convert the GMM kernel to linear kernel. We call this approach as ``GMM-GCWS''. In the machine learning literature, there is a popular algorithm which we call ``RBF-RFF''. That is, one can use the ``random Fourier features'' (RFF) to convert the ``radial basis function'' (RBF) kernel to linear kernel. It was empirically shown in (Li, 2016) that RBF-RFF typically requires substantially more samples than GMM-GCWS in order to achieve comparable accuracies. The Nystrom method is a general tool for computing nonlinear kernels, which again converts nonlinear kernels into linear kernels. We apply the Nystrom method for approximating the GMM kernel, a strategy which we name as ``GMM-NYS''. In this study, our extensive experiments on a set of fairly large datasets confirm that GMM-NYS is also a strong competitor of RBF-RFF.
A Potential Benefit of Albinism in Astyanax Cavefish: Downregulation of the oca2 Gene Increases Tyrosine and Catecholamine Levels as an Alternative to Melanin Synthesis

Albinism, the loss of melanin pigmentation, has evolved in a diverse variety of cave animals but the responsible evolutionary mechanisms are unknown. In Astyanax mexicanus, which has a pigmented surface dwelling form (surface fish) and several albino cave-dwelling forms (cavefish), albinism is caused by loss of function mutations in the oca2 gene, which operates during the first step of the melanin synthesis pathway. In addition to albinism, cavefish have evolved differences in behavior, including feeding and sleep, which are under the control of the catecholamine system. The catecholamine and melanin synthesis pathways diverge after beginning with the same substrate, L-tyrosine. Here we describe a novel relationship between the catecholamine and melanin synthesis pathways in Astyanax. Our results show significant increases in L-tyrosine, dopamine, and norepinephrine in pre-feeding larvae and adult brains of Pachón cavefish relative to surface fish. In addition, norepinephrine is elevated in cavefish adult kidneys, which contain the teleost homologs of catecholamine synthesizing adrenal cells. We further show that the oca2 gene is expressed during surface fish development but is downregulated in cavefish embryos. A key finding is that knockdown of oca2 expression in surface fish embryos delays the development of pigmented melanophores and simultaneously increases L-tyrosine and dopamine. We conclude that a potential evolutionary benefit of albinism in Astyanax cavefish may be to provide surplus L-tyrosine as a precursor for the elevated catecholamine synthesis pathway, which could be important for adaptation to the challenging cave environment.
Muscle Recruitment and Coordination following Constraint-Induced Movement Therapy with Electrical Stimulation on Children with Hemiplegic Cerebral Palsy: A Randomized Controlled Trial

Objective To investigate changes of muscle recruitment and coordination following constraint-induced movement therapy, constraint-induced movement therapy plus electrical stimulation, and traditional occupational therapy in treating hand dysfunction. Methods In a randomized, single-blind, controlled trial, children with hemiplegic cerebral palsy were randomly assigned to receive constraint-induced movement therapy (n = 22), constraint-induced movement therapy plus electrical stimulation (n = 23), or traditional occupational therapy (n = 23). Three groups received a 2-week hospital-based intervention and a 6-month home-based exercise program following hospital-based intervention. Constraint-induced movement therapy involved intensive functional training of the involved hand during which the uninvolved hand was constrained. Electrical stimulation was applied on wrist extensors of the involved hand. Traditional occupational therapy involved functional unimanual and bimanual training. All children underwent clinical assessments and surface electromyography (EMG) at baseline, 2 weeks, 3 and 6 months after treatment. Surface myoelectric signals were integrated EMG, root mean square and cocontraction ratio. Clinical measures were grip strength and upper extremity functional test. Results Constraint-induced movement therapy plus electrical stimulation group showed both a greater rate of improvement in integrated EMG of the involved wrist extensors and cocontraction ratio compared to the other two groups at 3 and 6 months, as well as improving in root mean square of the involved wrist extensors than traditional occupational therapy group (p<0.05). Positive correlations were found between both upper extremity functional test scores and integrated EMG of the involved wrist as well as grip strength and integrated EMG of the involved wrist extensors (p<0.05). Conclusions Constraint-induced movement therapy plus electrical stimulation is likely to produce the best outcome in improving muscle recruitment and coordination in children with hemiplegic cerebral palsy compared to constraint-induced movement therapy alone or traditional occupational therapy. Trial registration chictr.org ChiCTR-TRC-13004041
Unsupervised Context-Driven Recommendations Based On User Reviews

In this work we present Rich-Context, a context-driven recommender system that extracts contextual information using topic modeling without the need to define keywords. Our system uses the mined context to produce recommendations. We propose a methodology to measure the quality of context topic models along with a novel way to represent context that allows it to be used as side-information in a recommendation engine. Results show that Rich-Context makes more accurate predictions than five well-established recommendation algorithms.
Bargaining, Mergers and Technology Choice in Bilaterally Oligopolistic Industries

This Paper provides a conceptual framework of multilateral bargaining in a bilaterally oligopolistic industry to analyse the motivations for horizontal mergers, technology choice, and their welfare implications. We first analyse the implication of market structure for the distribution of industry profits. We find that retailer mergers are more likely (less likely) if suppliers have increasing (decreasing) unit costs, while supplier mergers are more likely (less likely) if goods are substitutes (complements). In a second step we explore how market structure affects suppliers' technology choice, which reflects a trade-off between infra-marginal and marginal production costs. We find that suppliers focus more on marginal cost reduction if (i) retailers are integrated and (ii) suppliers are non-integrated. In a final step we consider the whole picture where both market structure and (subsequent) technology choice are endogenous. Analysing the equilibrium market structure, we find cases where retailers become integrated to induce suppliers to choose a more efficient technology, even though integration weakens their bargaining position. In this case the merger benefits all parties, i.e., suppliers, retailers, and even consumers. We also show that the equilibrium market structure does often not maximize welfare.
On a CCA2-secure variant of McEliece in the standard model

We consider public-key encryption schemes based on error-correcting codes that are IND-CCA2 secure in the standard model. We analyze a system due to Dowsley, Muller-Quade and Nascimento. We then show how to instantiate the Rosen-Segev framework with the McEliece scheme.
Workshop on Configuration a Graphical Framework for Supporting Mass Customization……………………………………………..1 Incremental Prediction of Configurator Input Values Based on Association Rules – a Case Study……………………………………………………………………………………….….32 Iulia Nica and Franz Wotawa Simol – a Modeling Language for Simula

Many companies deploying mass customization strategies adopt product configuration systems to support their activities. While such systems focus mainly on configuration process support, mass customization needs to cover the management of the whole customizable product cycle. In this paper, we describe a graphical modeling framework that allows one to model both a product and its production process. We first introduce our framework. Then, we outline a possible implementation based on Constraint Logic Programming of such product/process configuration system. A comparison with some existing product configuration systems and process modeling tools concludes the paper.
Expanded decorrelating detector with reduced noise enhancement for multipath frequency-selective fading channels

A novel hybrid multiuser detection scheme that jointly uses linear and nonlinear interference suppression techniques is developed for high-speed direct-sequence code-division multiple-access communications in multipath frequency-selective fading channels. The detector detects signals in a symbol-by-symbol style. Conventional decorrelating detectors suffer from the noise enhancement problem, which becomes more serious for dispersive multipath channels. The proposed detector uses interference cancellation technology to reduce the rank of the expanded signal subspace and hence it preserves the advantages of the expanded decorrelating detector in terms of complete multiple access interference and intersymbol interference suppression and meanwhile avoids its disadvantage in terms of noise enhancement. Computer simulation shows clear superiority of the new detector to other existing methods.
Quality Assurance Strategies in Microtask Crowdsourcing

Crowdsourcing is the outsourcing of a unit of work to a crowd of people via an open call for contributions. While there are various forms of crowdsourcing, such as open innovation, civic engagement and crowdfunding in this work we specifically focus on microtasking. Microtasking is a branch of crowdsourcing, where a work is presented as a set of identical microtasks, each requiring contributors only several minutes to complete usually in exchange for a reward of less than 1 USD. Labeling images, transcribing documents, analyzing sentiments of short sentences and cleaning datasets are popular examples of work which could be solved as microtasks. Available up to date microtask crowdsourcing platforms, such as CrowdFlower and Amazon Mechanical Turk, allow thousands of microtasks to be solved in parallel by hundreds of contributors available online. To tackle the problem of quality in microtask crowdsourcing, it is necessary to study different quality attributes, to investigate what causes low quality of results and slow task execution in microtask crowdsourcing, to identify effective methods to both assess and assure that these quality attributes are of high level. We conducted the most extensive literature review analysis of quality attributes, assessment and assurance techniques ever done in the area of microtasking and crowdsourcing in general. We further advanced the state of the art in three research tracks: i) Improving accuracy and execution speed (the major track), where we monitor in-page user activity of each individual worker, automatically predict abandoned assignments causing delays and assignments with low quality of results, and relaunch them to other workers using our tool ReLauncher; ii) Crowdsourcing complex processes, where we introduce BPMN-extensions to design business processes of both crowd and machine tasks, and the crowdsourcing platform Crowd Computer to deploy these tasks; and iii) Improving workers user experience, where we identify problems workers face searching for tasks to work on, address these problems in our prototype of the task listing interface and introduce a new mobile crowdsourcing platform, CrowdCafe, designed in a way to optimize task searching time and to motivate workers with tangible rewards, such as a coffee.
The Bragg peak of a proton beam in intracranial therapy of tumors.

Results are reported on four patients with tumors treated by intracranial irradiation with the Bragg peak of a proton beam from the 160-Mev Harvard cyclotron, as well as radiobiological investigations in 100 monkeys demonstrating experimentally the feasibility of the method. Protons, emerging from the portal of the cyclotron at great speeds, can be directed in nearly straight lines so that at the end of their range (the Bragg peak) they stop at the brain target and liberate greater amounts of ionizing radiation than elsewhere along their path. Combining the Bragg peak with multiple portals of entry permits large doses of radiation, up to 20,000 rad, to be delivered to an intracranial target while surrounding zones receive a significantly lower dose. Use of the Bragg peak has advantages over the full penetration techniques. The fact that the beam penetrates only to target, combined with the greater ionizing energy yield of the Bragg peak, reduces by approximates 1/3--1/6 the dose to nontarget portions of the brain produced by a full-penetration method. Furthermore, a variety of portals can be selected because no emerging beam threatens radiosensitive structures such as the eyes, gonads, or blood-forming tissues. Cebus monkeys were used to assess such factorsmore » as the total dose and dose rate. The technique permits focal cerebral destructtons through skin, bone, and brain without making any opening along the path of the beam. To ensure that the brain target is superimposed on the Bragg peak, a precise stereotactic system is required. An instrument was designed that provides bony fixation to the small by tiny drill rods that enter the outer table of the skall to maintain the head position most firmly. The brain target is identified by bone landmarks or encephalography. The instrument is adjusted to bring the centers of rotation of the instrument precisely on the brain target, and the Bragg peak is precisely superimposed on the center of instrument rotation. Thus, the patient's head is rotated around Lhe two axes, permitting a large number of beam path portals while the brain target remains on the Bragg peak. A telescoping water absorber permits the proper penetration into the brain after a small correction is made to compensate for the difference in absorption of brain and bone from water. The technique makes it possible to irradiate malignant brain tumors (gliomas), tumors of the pituitary region, and vascular malformations. Hypophysectomy can be done with reduced risk to surrounding structures in an awake, comfortable patient. Successful results are reported in three patients with intracranial malignancies and one who underwent palliative hypophysectomy for breast cancer. Its use in alleviation of Parkinson's disease is planned. (BBB)« less
Statistical analysis of molecule colocalization in bioimaging

The quantitative analysis of molecule interactions in bioimaging is key for understanding the molecular orchestration of cellular processes and is generally achieved through the study of the spatial colocalization between the different populations of molecules. Colocalization methods are traditionally divided into pixel‐based methods that measure global correlation coefficients from the overlap between pixel intensities in different color channels, and object‐based methods that first segment molecule spots and then analyze their spatial distributions with second‐order statistics. Here, we present a review of such colocalization methods and give a quantitative comparison of their relative merits in different types of biological applications and contexts. We show on synthetic and biological images that object‐based methods are more robust statistically than pixel‐based methods, and allow moreover to quantify accurately the number of colocalized molecules. © 2015 International Society for Advancement of Cytometry