Miracle-dz/UniFAR-FTUs huggingface dataset:
Plasmids from Shiga Toxin-Producing Escherichia coli Strains with Rare Enterohemolysin Gene (ehxA) Subtypes Reveal Pathogenicity Potential and Display a Novel Evolutionary Path

ABSTRACT Most Shiga toxin-producing Escherichia coli (STEC) strains associated with severe disease, such as hemolytic-uremic syndrome (HUS), carry large enterohemolysin-encoding (ehxA) plasmids, e.g., pO157 and pO103, that contribute to STEC clinical manifestations. Six ehxA subtypes (A through F) exist that phylogenetically cluster into eae-positive (B, C, F), a mix of eae-positive (E) and eae-negative (A), and a third, more distantly related, cluster of eae-negative (D) STEC strains. While subtype B, C, and F plasmids share a number of virulence traits that are distinct from those of subtype A, sequence data have not been available for subtype D and E plasmids. Here, we determined and compared the genetic composition of four subtype D and two subtype E plasmids to establish their evolutionary relatedness among ehxA subtypes and define their potential role in pathogenicity. We found that subtype D strains carry one exceptionally large plasmid (>200 kbp) that carries a variety of virulence genes that are associated with enterotoxigenic and enterohemorrhagic E. coli, which, quite possibly, enables these strains to cause disease despite being food isolates. Our data offer further support for the hypothesis that this subtype D plasmid represents a novel virulence plasmid, sharing very few genetic features with other plasmids; we conclude that these plasmids have evolved from a different evolutionary lineage than the plasmids carrying the other ehxA subtypes. In contrast, the 50-kbp plasmids of subtype E (pO145), although isolated from HUS outbreak strains, carried only few virulence-associated determinants, suggesting that the clinical presentation of subtype E strains is largely a result of chromosomally encoded virulence factors. IMPORTANCE Bacterial plasmids are known to be key agents of change in microbial populations, promoting the dissemination of various traits, such as drug resistance and virulence. This study determined the genetic makeup of virulence plasmids from rare enterohemolysin subtype D and E Shiga toxin-producing E. coli strains. We demonstrated that ehxA subtype D plasmids represent a novel E. coli virulence plasmid, and although subtype D plasmids were derived from nonclinical isolates, they encoded a variety of virulence determinants that are associated with pathogenic E. coli. In contrast, subtype E plasmids, isolated from strains recovered from severely ill patients, carry only a few virulence determinants. The results of this study reemphasize the plasticity and vast diversity among E. coli plasmids. This work demonstrates that, although E. coli strains of certain serogroups may not be frequently associated with disease, they should not be underestimated in protecting human health and food safety.
Characterizing Developer Behavior in Cloud Based IDEs

Background: Cloud based integrated development environments (IDEs) are rapidly gaining popularity for its native support and potential to accelerate DevOps. However, there is little research of how developers behave when interacting with these environments. Aims: To develop empirical knowledge about how developers behave when interacting with cloud based IDEs to deal with programming tasks at various difficulty levels. Method: We conducted a user study using a cloud based IDE, JazzHub. We collected and coded session trace data, self-reported effort and frustration levels, and screen recordings. Results: We built a Markov activity transition model that describes the transitions among common development activities such as coding, debugging, and searching for information. It also captures extended interactions with remote resources. We correlated activity transition with different code growth trajectories. Conclusion: The findings are an early step toward realizing the potential for enhanced interactions in cloud based IDEs. Our study provides empirical evidence that may inspire the future evolution of cloud based IDE designs and features.
Sleep‐disordered breathing and cognitive functioning in preschool children with and without Down syndrome

BACKGROUND Sleep affects children's cognitive development, preparedness for school and future academic outcomes. People with Down syndrome (DS) are particularly at risk for sleep-disordered breathing (SDB). To our knowledge, the association between SDB and cognition in preschoolers with DS is unknown. METHODS We assessed sleep by using cardiorespiratory polygraphy in 22 typically developing (TD) preschoolers and 22 with DS. Cognition was assessed by using the Mullen Scales of Early Learning and behaviour by using the Strengths and Difficulties Questionnaire (SDQ). The MacArthur Communicative Development Inventory (MCDI) measured language level. We predicted that sleep problems would be associated with lower cognitive and behavioural functioning. RESULTS In TD children, longer sleep duration was associated with higher scores on MCDI expressive language and fewer emotional symptoms such as fear and unhappiness on the SDQ, whilst SDB was associated with increased conduct problems and less prosocial behaviour on the SDQ. Conversely, for children with DS, SDB was associated with increased language understanding and use of actions and gestures on the MCDI. CONCLUSIONS The findings in the TD group support our hypotheses. We recommend that sleep problems are screened for and treated as even mild SDB may prompt poorer cognition and behaviour. For children with DS, we expect that multiple factors in this complex syndrome mask or mediate the association between sleep and cognitive development and tighter controls are necessary to uncover effects of sleep. We propose longitudinal studies as a necessary tool to assess the precise impact of sleep on cognitive development in accounting for individual differences in DS.
A Broad-Host-Range Tailocin from Burkholderia cenocepacia

ABSTRACT The Burkholderia cepacia complex (Bcc) consists of 20 closely related Gram-negative bacterial species that are significant pathogens for persons with cystic fibrosis (CF). Some Bcc strains are highly transmissible and resistant to multiple antibiotics, making infection difficult to treat. A tailocin (phage tail-like bacteriocin), designated BceTMilo, with a broad host range against members of the Bcc, was identified in B. cenocepacia strain BC0425. Sixty-eight percent of Bcc representing 10 species and 90% of non-Bcc Burkholderia strains tested were sensitive to BceTMilo. BceTMilo also showed killing activity against Pseudomonas aeruginosa PAO1 and derivatives. Liquid chromatography-mass spectrometry analysis of the major BceTMilo proteins was used to identify a 23-kb tailocin locus in a draft BC0425 genome. The BceTMilo locus was syntenic and highly similar to a 24.6-kb region on chromosome 1 of B. cenocepacia J2315 (BCAL0081 to BCAL0107). A close relationship and synteny were observed between BceTMilo and Burkholderia phage KL3 and, by extension, with paradigm temperate myophage P2. Deletion mutants in the gene cluster encoding enzymes for biosynthesis of lipopolysaccharide (LPS) in the indicator strain B. cenocepacia K56-2 conferred resistance to BceTMilo. Analysis of the defined mutants in LPS biosynthetic genes indicated that an α-d-glucose residue in the core oligosaccharide is the receptor for BceTMilo. IMPORTANCE BceTMilo, presented in this study, is a broad-host-range tailocin active against Burkholderia spp. As such, BceTMilo and related or modified tailocins have potential as bactericidal therapeutic agents against plant- and human-pathogenic Burkholderia.
Handwritten Chinese Text Recognition Using Separable Multi-Dimensional Recurrent Neural Network

The Long Short-Term Memory Recurrent Neural Network (LSTM-RNN) has been demonstrated successful in handwritten text recognition of Western and Arabic scripts. It is totally segmentation free and can be trained directly from text line images. However, the application of LSTM-RNNs (including Multi-Dimensional LSTM-RNN (MDLSTM-RNN)) to Chinese text recognition has shown limited success, even when training them with large datasets and using pre-training on datasets of other languages. In this paper, we propose a handwritten Chinese text recognition method by using Separable MDLSTMRNN (SMDLSTM-RNN) modules, which extract contextual information in various directions, and consume much less computation efforts and resources compared with the traditional MDLSTMRNN. Experimental results on the ICDAR-2013 competition dataset show that the proposed method performs significantly better than the previous LSTM-based methods, and can compete with the state-of-the-art systems.
Learning Structural Loss Parameters on Graph Embedding Applied on Symbolic Graphs

We propose an amelioration of proposed Graph Embedding (GEM) method in previous work that takes advantages of structural pattern representation and the structured distortion. it models an Attributed Graph (AG) as a Probabilistic Graphical Model (PGM). Then, it learns the parameters of this PGM presented by a vector, as new signature of AG in a lower dimensional vectorial space. We focus to adapt the structured learning algorithm via 1_slack formulation with a suitable risk function, called Graph Edit Distance (GED). It defines the dissimilarity of the ground truth and predicted graph labels. It determines by the error tolerant graph matching using bipartite graph matching algorithm. We apply Structured Support Vector Machines (SSVM) to process classification task. During our experiments, we got our results on the GREC dataset.
AMPA glutamate receptors are required for sensory-organ formation and morphogenesis in the basal chordate

Significance In mammals, AMPA-type glutamate receptors (GluAs) are expressed ubiquitously in the central nervous system and play critical roles in synaptic plasticity, learning, and memory. Here we examined GluAs in the ascidian, Ciona intestinalis, and determined that they are expressed in a limited subset of cells during early development. We further find that GluAs are required for development of the ocellus, a photoreceptive organ used during the swimming stage, and for tail resorption and body axis rotation during metamorphosis. These functions require ion influx through GluAs. This is a demonstration of an in vivo requirement for GluAs in organ formation and morphogenesis. GluAs are also expressed during mammalian development, suggesting that developmental roles of GluAs may be functionally conserved. AMPA-type glutamate receptors (GluAs) mediate fast excitatory transmission in the vertebrate central nervous system (CNS), and their function has been extensively studied in the mature mammalian brain. However, GluA expression begins very early in developing embryos, suggesting that they may also have unidentified developmental roles. Here, we identify developmental roles for GluAs in the ascidian Ciona intestinalis. Mammals express Ca2+-permeable GluAs (Ca-P GluAs) and Ca2+-impermeable GluAs (Ca-I GluAs) by combining subunits derived from four genes. In contrast, ascidians have a single gluA gene. Taking advantage of the simple genomic GluA organization in ascidians, we knocked down (KD) GluAs in Ciona and observed severe impairments in formation of the ocellus, a photoreceptive organ used during the swimming stage, and in resorption of the tail and body axis rotation during metamorphosis to the adult stage. These defects could be rescued by injection of KD-resistant GluAs. GluA KD phenotypes could also be reproduced by expressing a GluA mutant that dominantly inhibits glutamate-evoked currents. These results suggest that, in addition to their role in synaptic communication in mature animals, GluAs also have critical developmental functions.
Sex Differences in the Psychometric Properties of the Pittsburgh Sleep Quality Index.

BACKGROUND The Pittsburgh Sleep Quality Index (PSQI) is a well-known, validated, and reliable instrument used to measure the clinical construct of sleep quality. Little research has been done to measure its psychometric properties by sex. Previous researchers have established the validity of a three-factor structure, but it is unknown whether it applies to both men and women equally. MATERIALS AND METHODS This study examined 198 participants; women (n = 104), men (n = 94) who were participants in the Diabetes Sleep Treatment Trial, an ongoing study examining the effect of continuous positive airway pressure on glycemic control in people with type 2 diabetes. A principal components analysis with varimax rotation, scree plots, parallel analysis, and Eigenvalues confidence intervals were all computed to determine factor structure using the seven components measured in the PSQI. RESULTS Component one, a question about perceived sleep quality, loaded with "sleep efficiency" and "sleep duration" in men and with "daytime dysfunction" and "sleep disturbances" in women. CONCLUSION This study confirms a three-factor structure as previously suggested; however, "perceived sleep quality" may load differently depending on the sex being examined. This result suggests that men and women may interpret what is meant by "overall sleep quality" differently.
SAFE: A Simple Approach for Feature Extraction from App Descriptions and App Reviews

A main advantage of app stores is that they aggregate important information created by both developers and users. In the app store product pages, developers usually describe and maintain the features of their apps. In the app reviews, users comment these features. Recent studies focused on mining app features either as described by developers or as reviewed by users. However, extracting and matching the features from the app descriptions and the reviews is essential to bear the app store advantages, e.g. allowing analysts to identify which app features are actually being reviewed and which are not. In this paper, we propose SAFE, a novel uniform approach to extract app features from the single app pages, the single reviews and to match them. We manually build 18 part-of-speech patterns and 5 sentence patterns that are frequently used in text referring to app features. We then apply these patterns with several text pre-and post-processing steps. A major advantage of our approach is that it does not require large training and configuration data. To evaluate its accuracy, we manually extracted the features mentioned in the pages and reviews of 10 apps. The extraction precision and recall outperformed two state-of-the-art approaches. For well-maintained app pages such as for Google Drive our approach has a precision of 87% and on average 56% for 10 evaluated apps. SAFE also matches 87% of the features extracted from user reviews to those extracted from the app descriptions.
Agile Quality Requirements Engineering Challenges: First Results from a Case Study

Agile software development methods have become increasingly popular in the last years. Despite their popularity, they have been criticized for focusing on delivering functional requirements and neglecting the quality requirements. Several studies have reported this shortcoming. However, there is little known about the challenges organizations currently face when dealing with quality requirements. Based on a qualitative exploratory case study, this research investigated real life large-scale distributed Agile projects to understand the challenges Agile teams face regarding quality requirements. Eighteen semi-structured open-ended in-depth interviews were conducted with Agile practitioners representing six different organizations in the Netherlands. Based on the analysis of the collected data, we have identified nine challenges Agile practitioners face when engineering quality requirements in large-scale distributed Agile projects that could harm the implementation of the quality requirements and result in neglecting them.
Modelling the Evolution of Enterprise Architectures Using Ontologies

Enterprise architecture supports enterprise transformation through model-based holistic descriptions that capture and share the knowledge, concepts, and relationships representing the enterprise. Although enterprise architecture models portray the gap between the as-is and to-be enterprise, they disregard the underlying aspects that together enact enterprise transformation. This paper proposes an ontology-based approach for the specification of the concepts and relationships used to express and analyze the evolution of enterprise architecture models.
Virological and immunological determinants of intrahepatic virus‐specific CD8+ T‐cell failure in chronic hepatitis C virus infection

Virus‐specific CD8+ T‐cells play an important role in the outcome of acute hepatitis C virus (HCV) infection. In the chronic phase, however, HCV can persist despite the presence of virus‐specific T‐cell responses. Therefore, we set out to perform a full‐breadth analysis of the intrahepatic virus‐specific CD8+ T‐cell response, its relation to the peripheral T‐cell response, and the overall influence of viral escape and the genetic restriction on intrahepatic CD8+ T‐cell failure. Intrahepatic and peripheral CD8+ T‐cells from 20 chronically HCV infected patients (genotype 1) were comprehensively analyzed using overlapping peptides spanning the entire HCV polyprotein in concert with autologous viral sequences that were obtained for all targeted regions. HCV‐specific CD8+ T‐cell responses were detectable in most (90%) chronically HCV‐infected patients, and two thirds of these responses targeted novel previously undescribed epitopes. Most of the responses were detectable only in the liver but not in the peripheral blood, indicating accumulation and enrichment at the site of disease. Of note, only approximately half of the responses were associated with viral sequence variations supported by functional analysis as viral escape mutations. Escape mutations were more often associated with HLA‐B alleles. Conclusion: Our results show an unexpected high frequency of intrahepatic virus‐specific CD8+ T‐cells, a large part of which continue to target the present viral antigens. Thus, our results suggest that factors other than mutational escape contribute to the failure of intrahepatic virus‐specific CD8+ T‐cells. (HEPATOLOGY 2008.)
Interleukin 37 reverses the metabolic cost of inflammation, increases oxidative respiration, and improves exercise tolerance

Significance Interleukin 1 family member IL-37 is a naturally occurring inhibitor of inflammation. In this study, exogenous administration of recombinant human IL-37 reversed the decrease in exercise performance observed during systemic inflammation. IL-37 also increased exercise performance in healthy mice. IL-37 treatment acted through a dual mechanism of suppression of inflammation and modulation of metabolic pathways. The implications of the present findings impact on patients with chronic inflammatory diseases spanning from rheumatoid arthritis to cancer, in which fatigue is often incapacitating, and provide rationale for exploring recombinant IL-37 in the treatment of inflammation-mediated fatigue. IL-1 family member interleukin 37 (IL-37) has broad antiinflammatory properties and functions as a natural suppressor of innate inflammation. In this study, we demonstrate that treatment with recombinant human IL-37 reverses the decrease in exercise performance observed during systemic inflammation. This effect was associated with a decrease in the levels of plasma and muscle cytokines, comparable in extent to that obtained upon IL-1 receptor blockade. Exogenous administration of IL-37 to healthy mice, not subjected to an inflammatory challenge, also improved exercise performance by 82% compared with vehicle-treated mice (P = 0.01). Treatment with eight daily doses of IL-37 resulted in a further 326% increase in endurance running time compared with the performance level of mice receiving vehicle (P = 0.001). These properties required the engagement of the IL-1 decoy receptor 8 (IL-1R8) and the activation of AMP-activated protein kinase (AMPK), because both inhibition of AMPK and IL-1R8 deficiency abrogated the positive effects of IL-37 on exercise performance. Mechanistically, treatment with IL-37 induced marked metabolic changes with higher levels of muscle AMPK, greater rates of oxygen consumption, and increased oxidative phosphorylation. Metabolomic analyses of plasma and muscles of mice treated with IL-37 revealed an increase in AMP/ATP ratio, reduced levels of proinflammatory mediator succinate and oxidative stress-related metabolites, as well as changes in amino acid and purine metabolism. These effects of IL-37 to limit the metabolic costs of chronic inflammation and to foster exercise tolerance provide a rationale for therapeutic use of IL-37 in the treatment of inflammation-mediated fatigue.
Risk-Based Packet Routing for Privacy and Compliance-Preserving SDN

Software Defined Networking (SDN) is increasingly being used in data centers as well as enterprise networks. In an environment that has strict compliance requirements, such as HIPAA compliance, a critical role for an SDN controller is to route all data packets while considering data privacy preservation and compliance-preservation. In this paper, we address this problem by proposing a routing protocol for SDN which is an efficient risk-based swarm routing protocol. The programmable capability of controllers is exploited in order to minimize privacy and compliance risks in data transmission. The proposed routing protocol is based on the Ant Colony Optimization technique and machine learning, while the data for learning is obtained from OVSDB and the OpenvSwitch Database management protocol. We collect a history of packet transfers for training purposes and learn from the training data to efficiently and intelligently route sensitive data packets while it preserves the target compliance. This routing is obtained by intelligent eviction of rules that are downloaded to the switches. We have implemented the proposed schemes based on an RYU controller.