Miracle-dz/UniFAR-FTUs huggingface dataset:
A discrete time queueing analysis of ATM systems with heterogeneous traffic sources

A discrete time queueing model for the performance of an ATM system is analyzed using matrix analytic methods. Time is segmented into slots with each slot equal to the transmission time of one ATM cell. The ATM system is modeled as a single server queue with Markovian arrivals and service time equal to one slot. The arrival process includes as a special case the superposition of on-off sources, possibly heterogeneous. The queueing model is of the "M/G/1 type". By exploring the structure of the "M/G/1 type" Markov chain, the complexity of the solution to the problem is reduced to only the inversion of a 2/spl times/2 matrix irrespective of the size of the Markov chain. This simplification allows us to solve problems of large sizes. In this paper, we extend the model to the heterogeneous case with L types of traffic sources and demonstrate that the solution to the model now involves the inversion of an L+1 by L+1 matrix. Derivations of the steady-state solutions and numerical analysis are given for the case of L=2.
Activation of dopamine receptor 2 (DRD2) prompts transcriptomic and metabolic plasticity in glioblastoma

Glioblastoma (GBM) is one of the most aggressive and lethal tumor types. Evidence continues to accrue indicating that the complex relationship between GBM and the brain microenvironment contributes to this malignant phenotype. However, the interaction between GBM and neurotransmitters, signaling molecules involved in neuronal communication, remains incompletely understood. Here we examined, in both sexes of humans and mice, how the monoamine dopamine influences GBM cells. We demonstrate that GBM cells express DRD2, with elevated expression in the glioma-initiating cell (GIC) population. Stimulation of DRD2 caused neuron-like depolarization exclusively in GICs. In addition, long-term activation of DRD2 heightened the sphere-forming capacity of GBM cells as well as tumor engraftment efficiency. Mechanistic investigation revealed that DRD2 signaling activates the hypoxia response and functionally alters metabolism. Finally, we found that GBM cells synthesize and secrete dopamine themselves, suggesting a potential autocrine mechanism. These results identify dopamine signaling as a potential therapeutic target in GBM and further highlight neurotransmitters as a key feature of the pro-tumor microenvironment. Significance Statement This work offers critical insight into the role of the neurotransmitter dopamine in the progression of GBM. We show that dopamine induces specific changes in the state of tumor cells, augmenting their growth and shifting them to a more stem-cell like state. Further, we show that dopamine can alter the metabolic behavior of GBM cells, increasing glycolysis. Finally, we show that GBM cells, including tumor samples from patients, can synthesize and secrete dopamine, suggesting an autocrine signaling process underlying these results. These results describe a novel connection between neurotransmitters and brain cancer, further highlighting the critical influence of the brain milieu on GBM.
Novel cholera toxin variant and ToxT regulon in environmental Vibrio mimicus strains: potential resources for the evolution of Vibrio cholerae hybrid strains

Atypical El Tor strains of Vibrio cholerae O1 harboring variant ctxB genes of cholera toxin (CT) are gradually becoming a major cause of recent cholera epidemics. Vibrio mimicus occasionally contains virulence factors associated with cholera, e.g., CT, encoded by ctxAB on CTXФ genome; and TCP, the CTXФ-specific receptor. This study carried out extensive molecular characterization of CTXФ and ToxT regulon in ctx+ve strains of V. mimicus isolated from the Bengal coast. Southern hybridization, PCR, and DNA sequencing of virulence related-genes revealed the presence of an El Tor type CTX prophage (CTXET) carrying a novel ctxAB, tandem copies of environmental type pre-CTX prophage (pre-CTXEnv), and RS1 elements, which were organized in an array of RS1-CTXET-RS1-pre-CTXEnv-pre-CTXEnv. Additionally, a novel variant of tcpA and toxT respectively, showing clonal lineage to a phylogenetic clade of V. cholerae non-O1/O139, was identified. The V. mimicus strains lacked the RTX and TLC elements, and Vibrio seventh pandemic islands of the El Tor strains, but contained five heptamer (TTTTGAT) repeats in ctxAB promoter region like some classical strains of V. cholerae O1. PFGE analysis showed all the ctx+ve V. mimicus strains were clonally related. However, their in vitro CT production and in vivo toxigenecity were variable, which could be explained by differential transcription of virulence genes along with ToxR regulon. Taken together, our findings strongly suggest that environmental V. mimicus strains act as potential reservoir of atypical virulence factors, including variant CT and ToxT regulon, and may contribute to the evolution of V. cholerae hybrid strains. IMPORTANCE Natural diversification of CTXФ and ctxAB genes certainly influences disease severity and shifting patterns in major etiological agents of cholera, e.g., the overwhelming emergence of hybrid El Tor variants, replacing the prototype El Tor strains of V. cholerae. This study showing the occurrence of CTXET comprising a novel variant of ctxAB in V. mimicus points out a previously unnoticed evolutionary event, independent to that of the El Tor strains of V. cholerae. Identification and cluster analysis of the newly-discovered alleles of tcpA and toxT indicates their horizontal transfer from an uncommon clone of V. cholerae. The genomic content of ToxT regulon, and tandemly arranged multiple pre-CTXФEnv and a CTXФET in V. mimicus probably act as salient raw materials inducing natural recombination among the hallmark virulence genes of hybrid V. cholerae strains. This study will facilitate deeper understanding of the evolution of new variant CT and ToxT regulon, influencing cholera epidemiology.
bin3C : Exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes (MAGs)

Most microbes inhabiting the planet cannot be easily grown in the lab. Metagenomic techniques provide a means to study these organisms, and recent advances in the field have enabled the resolution of individual genomes from metagenomes, so-called Metagenome Assembled Genomes (MAGs). In addition to expanding the catalog of known microbial diversity, the systematic retrieval of MAGs stands as a tenable divide and conquer reduction of metagenome analysis to the simpler problem of single genome analysis. Many leading approaches to MAG retrieval depend upon time-series or transect data, whose effectiveness is a function of community complexity, target abundance and depth of sequencing. Without the need for time-series data, promising alternative methods are based upon the high-throughput sequencing technique called Hi-C. The Hi-C technique produces read-pairs which capture in-vivo DNA-DNA proximity interactions (contacts). The physical structure of the community modulates the signal derived from these interactions and a hierarchy of interaction rates exists (īntra-chromosomal > Inter-chromosomal > Inter-cellular). We describe an unsupervised method that exploits the hierarchical nature of Hi-C interaction rates to resolve MAGs from a single time-point. As a quantitative demonstration, next, we validate the method against the ground truth of a simulated human faecal microbiome. Lastly, we directly compare our method against a recently announced proprietary service ProxiMeta, which also performs MAG retrieval using Hi-C data. bin3C has been implemented as a simple open-source pipeline and makes use of the unsupervised community detection algorithm Infomap (https://github.com/cerebis/bin3C).
Characterization of the Spectrum of Solar Irradiance under Different Crop Protection Coverings in Mediterranean Conditions and Effect on the Interception of Photosynthetically Active Radiation

Plants use visible light and part of adjacent ultraviolet and near infrared regions for photosynthesis. Crop protection coverings enable plant cultivation in areas or seasons not suitable open field. However, the use of covering materials is a detriment to solar irradiance, which may decrease the photosynthetic rate. Here, the effect of two different covering materials, tempered glass and white polyethylene mesh, on solar irradiance was compared to open field (control) under real farming conditions. Relative irradiance (RI) and photosynthetic photon flux density (PPFD) were recorded along 380-780 nm wavelength spectrums in the two conditions at 10:00 h and 13:00 h. Also the efficiency of Capsicum peppers in capturing solar irradiance was evaluated in leaves as the reflectance of both RI and PPFD under the mentioned growing conditions. Low differences in RI among the three conditions were found, and the lowest values corresponded to glasshouse conditions. Differences were more obvious in PPFD and, compared to open field, both mesh greenhouse and glasshouse conditions provoked remarkable decreases in all the spectral bands, 50-55% and 75-80% respectively. Covering materials also differed on the ratio of reflected PPFD and incident PPFD. Glasshouse plants displayed the highest reflectance at both 10:00 h and 13:00 h (0.05-0.20), followed by mesh greenhouse (0.05-0.10), suggesting that glasshouse conditions might decrease the photosynthesis rate due to both PPFD decrease and reflectance, although the effect of polyethylene mesh should not be disregarded as it also decreases considerably PPFD. Our results have important implications for the physiology and the productivity of crops under different covering materials.
GRID: A Geographic Routing with Identified Void in Ad Hoc and Sensor Networks

The geographic routing in ad hoc and sensor networks takes advantage of stateless nature to achieve outstanding scalability. However, it is also the statelessness constrain current geographic routing algorithms at best delivery guaranteed solutions, while the path optimality is of little concerned. In this paper, we present a novel geographic routing algorithm, called GRID, as attempt to find optimal path from source to destination even if some parts of the network are unavailable for forwarding due to low density or obstacles. To break the limitation of statelessness, GRID identifies the boundary of communication void and spread information about it in vicinity. With the knowledge of void, intermediate node divert the path in advance to achieve less hop count and shorter travel distance. By means of simulations under various scenarios, we compare its performance with existing state of the art protocols, showing that it performs better in terms of delivery delay and delivery ratio.
A Survey on Data Integrity of Cloud Storage in Cloud Computing

A B S T R A C T Cloud computing is an emerging technology aimed at providing various computing and storage services over the Internet. In cloud computing, the computing resources are Memory, storage and processor are not physically present at the user’s location. Instead, they are located outside the premises and managed by a service provider . The user can access the resources via the Internet. The main focus is data security and Integrity of cloud computing. This survey paper aims to analyses various security issue in cloud computing and data integrity proof. This paper describes the various security issue related to cloud computing. To check integrity of data, the user must be able to use the assist of a TPA. The TPA has experience in checking integrity of the data . It also help low computational devices like PDA check the data integrity of large data file. The data in the cloud should be correct, consistent, accessible and high quality. The aim of this survey paper is to analyses ensuring the integrity of the data and provides the proof that data is in secured manner.
Ultra-high throughput multiplexing and sequencing of >500 bp amplicon regions on the Illumina HiSeq 2500 platform

Amplification, sequencing and analysis of the 16S rRNA gene affords characterization of microbial community composition. As this tool has become more popular and projects have grown in size and scope, greater sample multiplexing is becoming necessary while maintaining high quality sequencing. Here, modifications to the Illumina HiSeq 2500 platform are described that afford greater multiplexing and 300 bp paired-end reads of higher quality than produced by the current Illumina MiSeq platform. To improve the feasibility and flexibility of this method, a 2-Step PCR amplification protocol is also described that allows for targeting of different amplicon regions, thus improving amplification success from low bacterial bioburden samples.
Comparative length weight relationship and condition factor in Alepes kleinii (Bloch 1793) along Mumbai and Goa coast of India

The length weight relationships and condition factors of the two populations of Alepes kleinii (Bloch 1793) along Mumbai and Goa Coasts were calculated out for males and females, separately. The length weight relationship (LWR) was established as Log W= -2.799 + 2.037 Log L for females, Log W= 1.245+1.313 Log L for males, and Log W= -2.103+ 1.721 Log L for pooled data for population of Mumbai Coast. Similarly, Log W= -2.712 + 2.001 Log L for females, Log W= -1.100 + 1.264 Log L for males and Log W= 1.922 + 1.643 Log L for pooled data for population of Goa Coast. The coefficient of correlation “r” between length and weight was found to be higher in females at Mumbai (0.909) and Goa (0.921) Coast than in males. The values of condition factor “K” was found to be higher in males (2.0609Mumbai Coast and 2.0962 Goa Coast) than in females (1.5329 Mumbai and 1.4879 Goa Coast). from both the Coast.
Open prediction of polysaccharide utilisation loci (PUL) in 5414 public Bacteroidetes genomes using PULpy

Polysaccharide utilisation loci (PUL) are regions within bacterial genomes that encode all the necessary machinery for the cleavage of particular carbohydrates. For the Bacteroidetes phylum, prediction of PUL from genomic data alone involves the identification of carbohydrate-active enzymes (CAZymes) co-localised with susCD gene pairs. Here we present the open prediction of PUL in 5414 public Bacteroidetes genomes, and an open-source pipeline to reproduce or extend the results.
Towards the Development of Integrated Reuse Environments for UML Artifacts

Systematic software reuse is recognized to achieve better software, faster and at a lower cost. The benefits of reuse can be maximized if types of early stage software artifacts can be easily reused. In early-stage reuse, once a match is found, all related later stages artifacts for the match can also be reused. However, the development of integrated reuse environments to allow managing and reusing repositories of early stage artifacts has not caught adequate attention of researchers yet. In response to this problem, we propose an approach to the development of environments integrated with CASE tools and capable facilitating early-stage artifacts reuse. Successful implementation of such environments is expected to improve the software quality and developers productivity. Keywords-early-stage artifacts; design reuse; integrated reuse environment; similarity metrics; multi-view similarity.
COMPARATIVE ANALYSIS OF THE EFICENCY OF POWERPLEX 16 AND POWERPLEX FUSION MULTIPLEX STR KITS IN THE ANALYSIS OF THE CHALLENGING FORENSIC SAMPLES

Since the introduction of the term low copy number DNA, also referred as low template DNA, touch DNA or trace DNA analysis, it has quickly become focal point of forensic DNA testing as well as other DNA based studies. Low template DNA (ltDNA) samples can be described as the samples which involve single source samples with template DNA in concentrations below 100 picograms (pg). Due to sensitivity of ltDNA samples to contamination, it is of great importance to optimize performance of the multiplex STR systems and existing protocols to increase chance of successful analysis. The main objective of this study was analysis of 20 challenging samples (skeletal remains, cigarette buts, chewing gum, poorly collected buccal swabs etc.) mostly low template DNA samples, preliminarily profiled by PowerPlex® 16 multiplex STR systems and additionally processed with new generation multiplex STR kit PowerPlex® Fusion. Sample isolation was done using a standard phenol-chloroform method for bone samples and DNeasy® Blood and Tissue Kit for other forensic samples. PowerPlex® 16 (PP16), multiplex STR system and PowerPlex® Fusion (PP Fusion) were used for co-amplification of 15 and 24 autosomal STR loci respectively. Results of this preliminary study suggest that PP Fusion primer set is better optimized for the analysis of ltDNA samples, and it is more robust regarding presence of the potential PCR inhibitors.
Apprentissage de dictionnaire pour les représentations parcimonieuses

A popular approach within the signal processing and machine learning communities consists in modelling high-dimensional data as sparse linear combinations of atoms selected from a dictionary. Given the importance of the choice of the dictionary for the operational deployment of these tools, a growing interest for \emph{learned} dictionaries has emerged. The most popular dictionary learning techniques, which are expressed as large-scale matrix factorization through the optimization of a non convex cost function, have been widely disseminated thanks to extensive empirical evidence of their success and steady algorithmic progress. Yet, until recently they remained essentially heuristic. We will present recent work on statistical aspects of sparse dictionary learning, contributing to the characterization of the excess risk as a function of the number of training samples. The results cover non only sparse dictionary learning but also a much larger class of constrained matrix factorization problems.
A FRAMEWORK FOR FAST CLASSIFICATION ALGORITHMS

Today, due to globalization of the world the size of data set is increasing, it is necessary to discover the knowledge. The discovery of knowledge can be typically in the form of association rules, classification rules, clustering, discovery of frequent episodes and deviation detection. Fast and accurate classifiers for large databases are an important task in data mining. There is growing evidence that integrating classification and association rules mining, classification approaches based on heuristic, greedy search like decision tree induction. Emerging associative classification algorithms have shown good promises on producing accurate classifiers. In this paper we focus on performance of associative classification and present a parallel model for classifier building. For classifier building some parallel-distributed algorithms have been proposed for decision tree induction but so far no such work has been reported for associative classification.
DNA copy number imbalances in primary cutaneous lymphomas (PCL)

Cutaneous lymphomas (CL) represent a clinically defined group of extranodal non-Hodgkin lymphomas harboring heterogeneous and incompletely delineated molecular aberrations. Over the past decades, molecular studies have identified several chromosomal aberrations, but the interpretation of individual genomic studies can be challenging. We conducted a meta-analysis to delineate genomic alterations for different types of PCL. Searches of PubMed and ISI Web of Knowledge for the years 1996 to 2016 identified 32 publications reporting the investigation of PCL for genome-wide copy number alterations, by means of comparative genomic hybridization techniques and whole genome and exome sequencing. For 449 samples from 22 publications, copy number variation data was accessible for sample based meta-analysis. Summary profiles for genomic imbalances, generated from case-specific data, identified complex genomic imbalances, which could discriminate between different subtypes of CL and promise a more accurate classification. The collected data presented in this study are publicly available through the “Progenetix” online repository.
Critical Reflection in Health and Social Care and Practising Critical Reflection: A Resource Handbook

synthesising the results from studies across different countries, the wide variability commonly found in data quality among studies can lead to considerable difficulties in producing valid results (Altman, 2001). Despite these issues, the book makes a dynamic and useful contribution to outlining ways in which social workers can move beyond thinking globally but acting locally, to thinking globally and acting globally.
Mass mortality of Eunicella singularis (Anthozoa: Octocorallia) in the Chafarinas Islands (North Africa, Western Mediterranean Sea)

Records of mortality after a high temperature event in 2014 in the white gorgonian Eunicella singularis were compiled in six different locations around the Chafarinas Islands. Quadrats were used to quantify dead colonies, colonies affected by epibionts and healthy colonies at different depths. No relationship was found between depth and percentage of affected colonies; however, differences in the mortality among sites were detected. On average, 43% of the colonies of E. singularis were found dead, 1% damaged and 36% healthy. These results highlight the need of further researches for monitoring the colonies of this species considering future scenarios of rising temperature.
Bats adjust temporal features of echolocation calls but not those of communication calls in response to traffic noise

Summary statement This study reveals the impact of anthropogenic noise on spectrally distinct vocalizations and the limitations of the acoustic masking hypothesis to explain the vocal response of bats to chronic noise. Abstract The acoustic masking hypothesis states that auditory masking may occur if the target sound and interfering sounds overlap spectrally, and it suggests that animals exposed to noise will modify their acoustic signals to increase signal detectability. However, it is unclear if animals will put more effort into changing their signals that spectrally overlap more with the interfering sounds than when the signals overlap less. We examined the dynamic changes in the temporal features of echolocation and communication vocalizations of the Asian particolored bat (Vespertilio sinensis) when exposed to traffic noise. We hypothesized that traffic noise has a greater impact on communication vocalizations than on echolocation vocalizations and predicted that communication vocalization change would be greater than echolocation. The bats started to adjust echolocation vocalizations on the fourth day of noise exposure, including an increased number of call sequences, decreased number of calls, and vocal rate within a call sequence. However, there was little change in the duration of the call sequence. In contrast, these communication vocalization features were not significantly adjusted under noise conditions. These findings suggest that the degree of spectral overlap between noise and animal acoustic signals does not predict the level of temporal vocal response to the noise.