Miracle-dz/UniFAR-FTUs huggingface dataset:
A Matrix-based Method for Analysing Stochastic Process Algebras

This paper demonstrates how three stochastic process algebras can be mapped on to a generally-distributed stochastic transition system. We demonstrate an aggregation technique on these stochastic transition systems and show how this can be implemented as a matrix-analysis method for finding steady-state distributions. We verify that the time complexity of the algorithm is a considerable improvement upon a previous method and discuss how the technique can be used to generate partial steady-state distributions for SPA systems.
Dicer-2-Dependent Activation of Culex Vago Occurs via the TRAF-Rel2 Signaling Pathway

Despite their importance as vectors of human and livestock diseases, relatively little is known about innate antiviral immune pathways in mosquitoes and other insects. Previous work has shown that Culex Vago (CxVago), which is induced and secreted from West Nile virus (WNV)-infected mosquito cells, acts as a functional homolog of interferon, by activating Jak-STAT pathway and limiting virus replication in neighbouring cells. Here we describe the Dicer-2-dependent pathway leading to WNV-induced CxVago activation. Using a luciferase reporter assay, we show that a NF-κB-like binding site in CxVago promoter region is conserved in mosquito species and is responsible for induction of CxVago expression following WNV infection. Using dsRNA-based gene knockdown, we show that the NF-κB ortholog, Rel2, plays significant role in the signaling pathway that activates CxVago in mosquito cells in vitro and in vivo. Using similar approaches, we also show that TRAF, but not TRAF-3, is involved in activation of Rel2 after viral infection. Overall the study shows that a conserved signaling pathway, which is similar to mammalian interferon activation pathway, is responsible for the induction and antiviral activity of CxVago.
An Optimization-Based Heuristic for the Split Delivery Vehicle Routing Problem

The split delivery vehicle routing problem is concerned with serving the demand of a set of customers with a fleet of capacitated vehicles at minimum cost. Contrary to what is assumed in the classical vehicle routing problem, a customer can be served by more than one vehicle, if convenient. We present a solution approach that integrates heuristic search with optimization by using an integer program to explore promising parts of the search space identified by a tabu search heuristic. Computational results show that the method improves the solution of the tabu search in all but one instance of a large test set.
Storage of human milk and the influence of procedures on immunological components of human milk

The storage of human milk for use later by the mother's own infant or an unrelated recipient has an impact on its constituents. These effects involve the storage container, heating, cooling and freezing the milk. Overall, glass is the least destructive container. Milk can be safely refrigerated for 72 h with little change. Freezing destroys cellular activity and reduces vitamins B6 and C. Boiling, in addition, destroys lipase and reduces the effect of immunoglobulin A and secretory immunoglobulin A. The nutrient value of human milk is essentially unchanged, but the immunological properties are reduced by various storage techniques.
[Construction of the XZ113 delta eaeA, XZ113 delta stx2 and XZ113 delta ehxA mutants of STEC O18 XZ113 and their pathogenicity in mice].

OBJECTIVE To study the contribution of virulence genes of STEC O18 XZ113 isolate to the pathogenicity in mice. METHODS The eaeA, stx2 and ehxA knock-out mutants of STEC strain XZ113 were generated using lambda-Red recombination system. RESULTS Bacterial adherence test showed that the eaeA mutant adhered to HEp-2 cells in a diffuse manner with no microcolony formation. Vero cells assay showed that the stx mutant had no cytotoxicity to Vero cells. Enterohemolytic activity test showed that the ehxA mutant lost the ability to express the enterohemolytic activity. Competition assay between the wild-type strain XZ113 and its mutants in vivo and in vitro showed that all mutants were mildly attenuated in vitro, but in vivo, XZ113 delta eaeA was moderate attenuated, XZ113 delta stx2 and XZ113 delta ehxA were all highly attenuated. CONCLUSIONS These results indicate that the virulence factors encoded by the stx2 and ehxA genes were important for the pathogenesis of STEC O18 in mice.
Differences in Crenate Broomrape Parasitism Dynamics on Three Legume Crops Using a Thermal Time Model

Root parasitic weeds are a major limiting production factor in a number of crops, and control is difficult. Genetic resistance and chemical control lead the fight, but without unequivocal success. Models that help to describe and even predict the evolution of parasitism underground are a valuable tool for herbicide applications, and even could help in breeding programs. Legumes are heavily affected by Orobanche crenata (crenate broomrape) in the Mediterranean basin. This work presents a descriptive model based on thermal time and correlating growing degree days (GDD) with the different developmental stages of the parasite. The model was developed in three different legume crops (faba bean, grass pea and lentil) attacked by crenate broomrape. The developmental stages of the parasite strongly correlated with the GDD and differences were found depending on the host crop.
Not Your Typical Strongyloides Infection: A Literature Review and Case Study

Strongyloides hyperinfection syndrome is one of several clinical manifestations of strongyloidiasis and has a mortality rate exceeding 85%. The syndrome is characterized by a high organism burden owing to autoinfection and is most common in immunocompromised hosts. The recovery of multiple pathogens is likely due to a piggyback phenomenon that occurs when enteric pathogens are transferred to the bloodstream attached to Strongyloides larvae. Herein, we describe a case of Strongyloides hyperinfection syndrome with a novel feature in a 69-year-old Venezuelan man. To our knowledge, this is the first case of Strongyloides hyperinfection syndrome and Pneumocystis jiroveci pneumonia occurring simultaneously. Owing to its extremely high mortality rate, Strongyloides hyperinfection syndrome must be considered early in the differential diagnosis for respiratory failure when multiple pathogens are recovered in patients from endemic areas.
Test Collection for Legal IR from Online Discussion Forums

With proliferation of online discussion forums, legal data on the Web is increasing. A number of online sites provide platforms for discussion, counselling and assistance pertaining to legal problems where a lay person can ask questions and/or seek assistance and volunteers share their views, expert opinions. Although these forums can provide legal help at rudimentary level, increasing number of users consult and often their legal information need gets complemented by the forums. Lack of easy natural language search facility in these forums, however, deprives a novice user from quickly retrieving answers to similar questions asked in the past. Like all other empirical discipline, measurable technological progress in legal IR requires a quantitative evaluation framework that provides standard, well-defined experimental setup, benchmark datasets and evaluation metrics. The aim of building this test collection is to provide a credible testbed for legal IR from online discussion forums. The data has been collected by crawling a number of free online legal discussion forums such as lawguru.com, legalservice.co.in covering different type of legal cases like criminal law, consumer law, constitutional law etc.
Mood induction and instructions to sustain moods: A test of the subject compliance hypothesis of mood congruent memory

Abstract Laboratory mood induction procedures that enlist subjects' co-operation in creating and sustaining moods tend to bias memory toward mood congruence, but this phenomenon may be explained in ways that are not directly related to mood. One such account is the “subject compliance hypothesis” (proposed by Blaney, 1986). which argues that mood congruent recall is the result of subjects' attempts to maintain or boost their moods, not the result of the moods per se. To test this hypothesis, happy and sad moods were induced using the musical mood induction procedure, which enlists subjects' co-operation in altering their moods. After subjects had performed several tasks, however, they were told that they could stop maintaining their mood. When asked to recall autobiographical memories a minute later, subjects nevertheless exhibited mood congruent bias. This finding argues against the subject compliance hypothesis, and suggests that subjects' moods persisted without active maintenance. Implications concern.
SPDW: A Software Development Process Performance Data Warehousing Environment

Metrics are essential in the assessment of the quality of software development processes (SDP). However, the adoption of a metrics program requires an information system for collecting, analyzing, and disseminating measures of software processes, products and services. This paper describes SPDW, an SPD data warehousing environment developed in the context of the metrics program of a leading software operation in Latin America, currently assessed as CMM Level 3. SDPW architecture encompasses: 1) automatic project data capturing, considering different types of heterogeneity present in the software development environment; 2) the representation of project metrics according to a standard organizational view; and 3) analytical functionality that supports process analysis. The paper also describes current implementations, and reports experiences on the use of SPDW by the organization
A Review of Data Mining Techniques and Applications

Data mining is the analytics and knowledge discovery process of analyzing large volumes of data from various sources and transforming the data into useful information. Various disciplines have contributed to its development and is becoming increasingly important in the scientific and industrial world. This article presents a review of data mining techniques and applications from 1996 to 2016. Techniques are divided into two main categories: predictive methods and descriptive methods. Due to the huge number of publications available on this topic, only a selected number are used in this review to highlight the developments of the past 20 years. Applications are included to provide some insights into how each data mining technique has evolved over the last two decades. Recent research trends focus more on large data sets and big data. Recently there have also been more applications in area of health informatics with the advent of newer algorithms.
Treadmill Gait Analysis Characterizes Gait Alterations in Parkinson's Disease and Amyotrophic Lateral Sclerosis Mouse Models

ABSTRACT Guillot, Asress, Richardson, Glass, and Miller (2008) recently reported that treadmill gait analysis does not detect motor deficits in animal models of Parkinson's disease (PD) or amyotrophic lateral sclerosis (ALS). The authors studied aged C57BL/6J mice administered the neurotoxin 1-methyl 4-phenyl 1-, 2-, 3-, 6-tetrahydropyridine to model PD, and a small number of presymptomatic superoxide dismutase 1 G93A mice to study ALS. Several key issues merit discussion to put their observations in perspective. An increasing number of research groups are applying treadmill gait analysis to their rodent models of numerous movement disorders. The conclusions Guillot et al. drew undermine the potential importance of the paradigm of treadmill gait analysis for understanding and treating PD and ALS.
Excap: Maximization of Haplotypic Diversity of Linked Markers

Genetic markers, defined as variable regions of DNA, can be utilized for distinguishing individuals or populations. As long as markers are independent, it is easy to combine the information they provide. For nonrecombinant sequences like mtDNA, choosing the right set of markers for forensic applications can be difficult and requires careful consideration. In particular, one wants to maximize the utility of the markers. Until now, this has mainly been done by hand. We propose an algorithm that finds the most informative subset of a set of markers. The algorithm uses a depth first search combined with a branch-and-bound approach. Since the worst case complexity is exponential, we also propose some data-reduction techniques and a heuristic. We implemented the algorithm and applied it to two forensic caseworks using mitochondrial DNA, which resulted in marker sets with significantly improved haplotypic diversity compared to previous suggestions. Additionally, we evaluated the quality of the estimation with an artificial dataset of mtDNA. The heuristic is shown to provide extensive speedup at little cost in accuracy.
De novo Transcriptome Assembly of Phomopsis liquidambari Provides Insights into Genes Associated with Different Lifestyles in Rice (Oryza sativa L.)

The mechanisms that trigger the switch from endophytic fungi to saprophytic fungi are largely unexplored. Broad host range Phomopsis liquidambari is established in endophytic and saprophytic systems with rice (Oryza sativa L.). Endophytic P. liquidambari promotes rice growth, increasing rice yield and improving the efficiency of nitrogen fertilizer. This species's saprophytic counterpart can decompose rice litterfall, promoting litter organic matter cycling and the release of nutrients and improving the soil microbial environment. Fluorescence microscopy, confocal laser scanning microscopy and quantitative PCR investigated the colonization dynamics and biomass of P. liquidambari in rice in vivo. P. liquidambari formed infection structures similar to phytopathogens with infected vascular tissues that systematically spread to acrial parts. However, different from pathogenic infection, P. liquidambari colonization exhibits space restriction and quantity restriction. Direct comparison of a fungal transcriptome under three different habitats provided a better understanding of lifestyle conversion during plant-fungi interactions. The isolated total RNA of Ck (pure culture), EP (endophytic culture) and FP (saprophytic culture) was subjected to Illumina transcriptome sequencing. To the best of our knowledge, this study is the first to investigate Phomopsis sp. using RNA-seq technology to obtain whole transcriptome information. A total of 27,401,258 raw reads were generated and 22,700 unigenes were annotated. Functional annotation indicated that carbohydrate metabolism and biosynthesis of secondary metabolites played important roles. There were 2522 differentially expressed genes (DEGs) between the saprophytic and endophytic lifestyles. Quantitative PCR analysis validated the DEGs of RNA-seq. Analysis of DEGs between saprophytic and endophytic lifestyles revealed that most genes from amino acids metabolism, carbohydrate metabolism, fatty acid biosynthesis, secondary metabolism and terpenoid and steroid biosynthesis were up-regulated in EP. Secondary metabolites of these pathways may affect fungal growth and development and contribute to signaling communication with the host. Most pathways of xenobiotic biodegradation and metabolism were upregulated in FP. Cytochrome P450s play diverse vital roles in endophytism and saprophytism, as their highly specialized functions are evolutionarily adapted to various ecological niches. These results help to characterize the relationship between fungi and plants, the diversity of fungi for ecological adaptations and the application prospects for fungi in sustainable agriculture.
Productivity Effects of Information Diffusion in Networks

We examine what drives the diffusion of different types of information through email networks and the effects of these diffusion patterns on the productivity and performance of information workers. In particular, we ask: What predicts the likelihood of an individual becoming aware of a strategic piece of information, or becoming aware of it sooner? Do different types of information exhibit different diffusion patterns, and do different characteristics of social structure, relationships and individuals in turn affect access to different kinds of information? Does better access to information predict an individual's ability to complete projects or generate revenue? We characterize the social network of a medium sized executive recruiting firm using accounting data on project co-work relationships and ten months of email traffic. We identify two distinct types of information diffusing over this network - 'event news' and 'discussion topics' - by their usage characteristics, and observe several thousand diffusion processes of each type of information. We find the diffusion of news, characterized by a spike in communication and rapid, pervasive diffusion through the organization, is influenced by demographic and network factors but not by functional relationships (e.g. prior co-work, authority) or the strength of ties. In contrast, diffusion of discussion topics, which exhibit shallow diffusion characterized by 'back-and-forth' conversation, is heavily influenced by functional relationships and the strength of ties, as well as demographic and network factors. Discussion topics are more likely to diffuse vertically up and down the organizational hierarchy, across relationships with a prior working history, and across stronger ties, while news is more likely to diffuse laterally as well as vertically, and without regard to the strength or function of relationships. We also find access to information strongly predicts project completion and revenue generation. The effects are economically significant, with each additional 'word seen' correlated with about $70 of additional revenue generated. Our findings provide some of the first evidence of the economic significance of information diffusion in email networks.
On the privacy provisions of Bloom filters in lightweight bitcoin clients

Lightweight Bitcoin clients are gaining increasing adoption among Bitcoin users, owing to their reduced resource and bandwidth consumption. These clients support a simplified payment verification (SPV) mode as they are only required to download and verify a part of the block chain---thus supporting the usage of Bitcoin on constrained devices, such as smartphones. SPV clients rely on Bloom filters to receive transactions that are relevant to their local wallet. These filters embed all the Bitcoin addresses used by the SPV clients, and are outsourced to more powerful Bitcoin nodes which then only forward to those clients transactions relevant to their outsourced Bloom filters. In this paper, we explore the privacy of existing SPV clients. We show analytically and empirically that the reliance on Bloom filters within existing SPV clients leaks considerable information about the addresses of Bitcoin users. Our results show that an SPV client who uses a modest number of Bitcoin addresses (e.g., < 20) risks revealing almost all of his addresses. We also show that this information leakage is further exacerbated when users restart their SPV clients and/or when the adversary has access to more than one Bloom filter pertaining to the same SPV client. Motivated by these findings, we propose an efficient countermeasure to enhance the privacy of users which rely on SPV clients; our proposal can be directly integrated within existing SPV client implementations.
Pattern-Based Compaction for ProbLog Inference

The probabilistic inference of current Probabilistic Logic Programming systems uses weighted model counting (WMC). To compute the success probability of a query, first the set of proofs of the query is computed. Next, the set of proofs is converted into a corresponding Boolean formula which is compiled into a suitable representation that allows WMC in polynomial time. The computational cost of each step depends on the size and the complexity of the output of the previous step. The set of proofs, computed in the first step, can become large. In this paper we propose a way to reduce the size of the collected proofs in order to improve the next steps. We use an AND-OR graph to represent the collected proofs. Our method compacts the AND-OR graph by detecting several patterns and applying transformations on them. Experiments confirm that by decreasing the size of the AND-OR graph, we reduce the time and memory consumption of the next steps. Our algorithm enables probabilistic inference on problems previously unsolvable.
Prediction of promiscuous peptides that bind HLA class I molecules

Promiscuous T‐cell epitopes make ideal targets for vaccine development. We report here a computational system, multipred, for the prediction of peptide binding to the HLA‐A2 supertype. It combines a novel representation of peptide/MHC interactions with a hidden Markov model as the prediction algorithm. multipred is both sensitive and specific, and demonstrates high accuracy of peptide‐binding predictions for HLA‐A∗0201, ∗0204, and ∗0205 alleles, good accuracy for ∗0206 allele, and marginal accuracy for ∗0203 allele. multipred replaces earlier requirements for individual prediction models for each HLA allelic variant and simplifies computational aspects of peptide‐binding prediction. Preliminary testing indicates that multipred can predict peptide binding to HLA‐A2 supertype molecules with high accuracy, including those allelic variants for which no experimental binding data are currently available.
In Vivo Persistence of Codominant Human CD8+ T Cell Clonotypes Is Not Limited by Replicative Senescence or Functional Alteration1

T cell responses to viral epitopes are often composed of a small number of codominant clonotypes. In this study, we show that tumor Ag-specific T cells can behave similarly. In a melanoma patient with a long lasting HLA-A2/NY-ESO-1-specific T cell response, reaching 10% of circulating CD8 T cells, we identified nine codominant clonotypes characterized by individual TCRs. These clonotypes made up almost the entire pool of highly differentiated effector cells, but only a fraction of the small pool of less differentiated “memory” cells, suggesting that the latter serve to maintain effector cells. The different clonotypes displayed full effector function and expressed TCRs with similar functional avidity. Nevertheless, some clonotypes increased, whereas others declined in numbers over the observation period of 6 years. One clonotype disappeared from circulating blood, but without preceding critical telomere shortening. In turn, clonotypes with increasing frequency had accelerated telomere shortening, correlating with strong in vivo proliferation. Interestingly, the final prevalence of the different T cell clonotypes in circulation was anticipated in a metastatic lymph node withdrawn 2 years earlier, suggesting in vivo clonotype selection driven by metastases. Together, these data provide novel insight in long term in vivo persistence of T cell clonotypes associated with continued cell turnover but not replicative senescence or functional alteration.