Miracle-dz/UniFAR-FTUs huggingface dataset:
Poly-N-Acetylglucosamine Production by Staphylococcus epidermidis Cells Increases Their In Vivo Proinflammatory Effect

ABSTRACT Poly-N-acetylglucosamine (PNAG) is a major component of the Staphylococcus epidermidis biofilm extracellular matrix. However, it is not yet clear how this polysaccharide impacts the host immune response and infection-associated pathology. Faster neutrophil recruitment and bacterial clearance were observed in mice challenged intraperitoneally with S. epidermidis biofilm cells of the PNAG-producing 9142 strain than in mice similarly challenged with the isogenic PNAG-defective M10 mutant. Moreover, intraperitoneal priming with 9142 cells exacerbated liver inflammatory pathology induced by a subsequent intravenous S. epidermidis challenge, compared to priming with M10 cells. The 9142-primed mice had elevated splenic CD4+ T cells producing gamma interferon and interleukin-17A, indicating that PNAG promoted cell-mediated immunity. Curiously, despite having more marked liver tissue pathology, 9142-primed mice also had splenic T regulatory cells with greater suppressive activity than those of their M10-primed counterparts. By showing that PNAG production by S. epidermidis biofilm cells exacerbates host inflammatory pathology, these results together suggest that this polysaccharide contributes to the clinical features associated with biofilm-derived infections.
Antistaphylococcal Activities of the New Fluoroquinolone JNJ-Q2

ABSTRACT The new broad-spectrum fluoroquinolone JNJ-Q2 displays in vitro activity against Gram-negative and Gram-positive organisms, including methicillin-resistant Staphylococcus aureus (MRSA) and ciprofloxacin-resistant MRSA isolates. Tested with isogenic methicillin-susceptible S. aureus (MSSA) and MRSA strains bearing quinolone-resistant target mutations, JNJ-Q2 displayed MICs ≤ 0.12 μg/ml, values 16- to 32-fold lower than those determined for moxifloxacin. Overexpression of the NorA efflux pump did not impact JNJ-Q2 MICs. Inhibition of S. aureus DNA gyrase and DNA topoisomerase IV enzymes demonstrated that JNJ-Q2 was more potent than comparators against wild-type enzymes and enzymes carrying quinolone-resistant amino acid substitutions, and JNJ-Q2 displayed equipotent activity against both enzymes. In serial-passage studies comparing resistance selection in parallel MRSA cultures by ciprofloxacin and JNJ-Q2, ciprofloxacin readily selected for mutants displaying MIC values of 128 to 512 μg/ml, which were observed within 18 to 24 days of passage. In contrast, cultures passaged in the presence of JNJ-Q2 displayed MICs ≤ 1 μg/ml for a minimum of 27 days of serial passage. A mutant displaying a JNJ-Q2 MIC of 4 μg/ml was not observed until after 33 days of passage. Mutant characterization revealed that ciprofloxacin-passaged cultures with MICs of 256 to 512 μg/ml carried only 2 or 3 quinolone resistance-determining region (QRDR) mutations. Cultures passaged with JNJ-Q2 selection for up to 51 days displayed MICs of 1 to 64 μg/ml and carried between 4 and 9 target mutations. Established in vitro biofilms of wild-type or ciprofloxacin-resistant MRSA exposed to JNJ-Q2 displayed greater decreases in bacterial counts (7 days of exposure produced 4.5 to >7 log10 CFU decreases) than biofilms exposed to ciprofloxacin, moxifloxacin, rifampin, or vancomycin.
Precise score for the prediction of peptides cleaved by the proteasome

MOTIVATION An 8-10mer can become a cytotoxic T lymphocyte epitope only if it is cleaved by the proteasome, transported by TAP and presented by MHC-I molecules. Thus most of the epitopes presented to cytotoxic T cells in the context of MHC-I molecules are products of intracellular proteasomal cleavage. These products are not random, as peptide production is a function of the precise sequence of the proteins processed by the proteasome. RESULTS We have developed a score for the probability that a given peptide results from proteasomal cleavage. High scoring peptides are those that are cleaved in their extremities and not in their center, while low scoring peptides are either cleaved in their centers or not cleaved in their extremities. The current work differs from most previous works, in that it determines the production probability of an entire peptide, rather than trying to predict specific cleavage sites. We further present different score functions for the constitutive and the immunoproteasome. Our results were validated to have low error levels against multiple epitope databases. We provide here a novel computational tool and a website to use it-http://peptibase.cs. biu.ac. il/PepCleave_II/ to assess the probability that a given peptide indeed results from proteasomal cleavage.
A Survey of tooth morphology teaching methods employed in the United Kingdom and Ireland

BACKGROUND Tooth morphology is a central component of the dental curriculum and is applicable to all dental specialities. Traditional teaching methods are being supplemented with innovative strategies to tailor teaching and accommodate the learning styles of the recent generation of students. METHODS An online survey was compiled and distributed to the staff involved in teaching tooth morphology in the United Kingdom and Ireland to assess the importance of tooth morphology in the dentistry curriculum and the methodologies employed in teaching. RESULTS The results of the survey show that tooth morphology constitutes a small module in the dental curriculum. It is taught in the first 2 years of the dental curriculum but is applicable in the clinical years and throughout the dental career. Traditional teaching methods, lecture and practical, are being augmented with innovative teaching including e-learning via virtual learning environment, tooth atlas and e-books leading to blended learning. The majority of the schools teach both normal dental anatomy and morphologic variations of dental anatomy and utilise plastic teeth for practical and examination purposes. Learning the 3D aspects of tooth morphology was deemed important by most of the respondents who also agreed that tooth morphology is a difficult topic for the students. CONCLUSION Despite being core to the dental curriculum, overall minimal time is dedicated to the delivery of tooth morphology, creating a reliance on the student to learn the material. New forms of delivery including computer-assisted learning tools should help sustain learning and previously acquired knowledge.
In vitro rapid organization of endothelial cells into capillary-like networks is promoted by collagen matrices

We have studied the behavior of cloned capillary endothelial cells grown inside a three dimensional collagen matrix. Cell monolayers established on the surface of collagen gels were covered with a second layer of collagen. This induced the monolayers of endothelial cells to reorganize into a network of branching and anastomosing capillary-like tubes. As seen by electron microscopy, the tubes were formed by at least two cells (in transverse sections) delimiting a narrow lumen. In addition, distinct basal lamina material was present between the abluminal face of the endothelial cells and the collagen matrix. These results showed that capillary endothelial cells have the capacity to form vessel-like structures with well-oriented cell polarity in vitro. They also suggest that an appropriate topological relationship of endothelial cells with collagen matrices, similar to that occurring in vivo, has an inducive role on the expression of this potential. This culture system provides a simple in vitro model for studying the factors involved in the formation of new blood vessels (angiogenesis).
Drawing Your Senator from a Jar:Term Length and Legislative Behavior*

This paper studies the effects of term duration on legislative behavior using field experiments that occur in the Arkansas, Illinois, and Texas Senates in the United States. After mandatory changes in senate district boundaries, state senators are randomly assigned to serve either two-year or four-year terms, providing a rare opportunity to study legislative behavior experimentally. Despite important differences across states, when considered together, the results show that senators serving two years abstain more often, introduce fewer bills, and do not seem to be more responsive to their constituents than senators serving four years. In addition, senators serving shorter terms raise and spend significantly more money, although in those states where funds can be raised continuously during the legislative term, the differences arise only when the election is imminent.
Simulating Whole Supercomputer Applications

Detailed simulations of large scale message-passing interface parallel applications are extremely time consuming and resource intensive. A new methodology that combines signal processing and data mining techniques plus a multilevel simulation reduces the simulated data by various orders of magnitude. This reduction makes possible detailed software performance analysis and accurate performance predictions in a reasonable time.
Molecular phylogenetics at the Felsenstein zone: approaching the Strepsiptera problem using 5.8S and 28S rDNA sequences.

Recent efforts to reconstruct the phylogenetic position of the insect order Strepsiptera have elicited a major controversy in molecular phylogenetics. We sequenced the 5.8S rDNA and major parts of the 28S rDNA 5' region of the strepsipteran species Stylops melittae. Their evolutionary dynamics were analyzed together with previously published insect rDNA sequences to identify tree estimation bias risks and to explore additional sources of phylogenetic information. Several major secondary structure changes were found as being autapomorphic for the Diptera, the Strepsiptera, or the Archaeognatha. Besides elevated substitution rates a significant AT bias was present in dipteran and strepsipteran 28S rDNA which, however, was restricted to stem sites in the Diptera while also affecting single-stranded sites in the Strepsiptera. When dipteran taxa were excluded from tree estimation all methods consistently supported the placement of Strepsiptera to within the Holometabola. When dipteran taxa were included maximum likelihood continued to favor a sister-group relationship of Strepsiptera with Mecoptera while remaining methods strongly supported a sister-group relationship with Diptera. Parametric bootstrap analysis revealed maximum likelihood as a consistent estimator if rate heterogeneity across sites was taken into account. Though the position of Strepsiptera within Holometabola remains elusive, we conclude that the evolution of dipteran and strepsipteran rDNA involved similar yet independent changes of substitution parameters.
Concurrency control of nested cooperative transactions in active DBMS

Active database management systems (ADBMSs) use event-condition-action (ECA) rules. Each ECA rule specifies what action is to be taken when an event occurs and the specified condition is satisfied. In this paper, we introduce a concurrency control scheme for handling nested cooperative transactions using detached-mode ECA rules of an ADBMS. A state transition model has been proposed to specify different kinds of nested cooperative transactions using detached-mode ECA rules. The correctness criterion for concurrent execution of such nested cooperative transactions has been stated formally. The problem of verification of the correct schedules and a concurrency control mechanism have also been dealt with.
A Computational Approach to Automatic Prediction of Drunk-Texting

Alcohol abuse may lead to unsociable behavior such as crime, drunk driving, or privacy leaks. We introduce automatic drunk-texting prediction as the task of identifying whether a text was written when under the influence of alcohol. We experiment with tweets labeled using hashtags as distant supervision. Our classifiers use a set of N-gram and stylistic features to detect drunk tweets. Our observations present the first quantitative evidence that text contains signals that can be exploited to detect drunk-texting.
Decision-Theoretic Control of Crowd-Sourced Workflows

Crowd-sourcing is a recent framework in which human intelligence tasks are outsourced to a crowd of unknown people ("workers") as an open call (e.g., on Amazon's Mechanical Turk). Crowd-sourcing has become immensely popular with hoards of employers ("requesters"), who use it to solve a wide variety of jobs, such as dictation transcription, content screening, etc. In order to achieve quality results, requesters often subdivide a large task into a chain of bite-sized subtasks that are combined into a complex, iterative workflow in which workers check and improve each other's results. This paper raises an exciting question for AI — could an autonomous agent control these workflows without human intervention, yielding better results than today's state of the art, a fixed control program? We describe a planner, TurKontrol, that formulates workflow control as a decision-theoretic optimization problem, trading off the implicit quality of a solution artifact against the cost for workers to achieve it. We lay the mathematical framework to govern the various decisions at each point in a popular class of workflows. Based on our analysis we implement the workflow control algorithm and present experiments demonstrating that TurKontrol obtains much higher utilities than popular fixed policies.
Die leichte kognitive Beeinträchtigung

Zusammenfassung Klagen über kognitive Beeinträchtigungen sind ein häufi ges Symptom in der älteren Bevölkerung und werden ent sprechend regelmäßig in der ärztlichen Sprechstunde vor getragen. In diesem Kontext bezeichnet der Begriffjeichte kognitive Beeinträchtigung” ein Syndrom mit diskreten, aber konsistent nachweisbaren kognitiven Defiziten, die je doch noch nicht den Schweregrad einer Demenz erfüllen. Epidemiologischen Studien zufolge ist die leichte kognitive Beeinträchtigung mit einem erhöhten Risiko assoziiert, in den folgenden Jahren eine manifeste Demenz zu ent wickeln. Der vorliegende Beitrag gibt eine Übersicht über aktuelle Konzeptezur Erfassung der leichten kognitiven Be einträchtigung, ihrer Verlaufsdynamik sowie assoziierten neurobiologischen Veränderungen, die auch in der Früh diagnostik einer Demenzerkrankung Relevanz besitzen. Darüber hinaus werden Hinweise für ein strukturiertes Vor gehen in der Diagnostik sowie bezüglich des therapeuti schen Managements dieses für viele Betroffenen mit ho hem Leidensdruck einhergehenden Syndroms gegeben.
The Relation between Fructose-Induced Metabolic Syndrome and Altered Renal Haemodynamic and Excretory Function in the Rat

This paper explores the possible relationships between dietary fructose and altered neurohumoral regulation of renal haemodynamic and excretory function in this model of metabolic syndrome. Fructose consumption induces hyperinsulinemia, hypertriglyceridaemia, insulin resistance, and hypertension. The pathogenesis of fructose-induced hypertension is dubious and involves numerous pathways acting both singly and together. In addition, hyperinsulinemia and hypertension contribute significantly to progressive renal disease in fructose-fed rats. Moreover, increased activity of the renin-angiotensin and sympathetic nervous systems leading to downregulation of receptors may be responsible for the blunted vascular sensitivity to angiotensin II and catecholamines, respectively. Various approaches have been suggested to prevent the development of fructose-induced hypertension and/or metabolic alteration. In this paper, we address the role played by the renin-angiotensin and sympathetic nervous systems in the haemodynamic alterations that occur due to prolonged consumption of fructose.
Bottle Size and Weight Gain in Formula-Fed Infants

BACKGROUND: Formula-fed infants may be at greater risk for overfeeding and rapid weight gain. Different size bottles are used for feeding infants, although little is known about whether bottle size is related to weight gain in bottle-fed infants. METHODS: Data from the Greenlight Intervention Study, a cluster randomized trial to prevent childhood obesity at 4 pediatric resident clinics, were used to analyze the exposure to regular (<6 oz) or large (≥6 oz) bottle size at the 2-month visit on changes in weight, weight-for-age z score (WAZ), and weight-for-length z score (WLZ) at the 6-month visit. Using multivariable regression, we adjusted for potential confounders (birth weight, gender, age, weight measures at 2 months, parent race/ethnicity, education, household income and size, time between 2- and 6-month visits, and first child status). RESULTS: Forty-five percent (n = 386; 41% black, 35% Hispanic, 23% white, 2% other) of infants at the 2-month visit were exclusively formula-fed, and 44% used large (≥6 oz) bottles. Infants whose parents fed with large bottles had 0.21 kg (95% confidence interval [CI]: 0.05 to 0.37) more weight change, 0.24 U (95% CI: 0.07 to 0.41) more change in WAZ, and 0.31 U (95% CI: 0.08 to 0.54) more change in WLZ during this period than infants fed with regular bottles. CONCLUSIONS: Using a large bottle in early infancy independently contributed to greater weight gain and change in WLZ at the 6-month visit. Although growth in infancy is complex, bottle size may be a modifiable risk factor for rapid infant weight gain and later obesity among exclusively formula-fed infants.
A hybrid unsupervised/supervised model for group activity recognition

The new method proposed here recognizes activities performed by a group of users (e.g., attending a meeting, playing sports, and participating in a party) by using sensor data obtained from the users. Note that such group activities (GAs) have characteristics that differ from those of single user activities. For example, the number of users who participate in a GA is different for each activity. The number of meeting participants, for instance, may sometimes be different for each meeting. Also, a user may play different roles (e.g., `moderator' and `presenter' roles) in meetings on different days. We introduce the notion of role into our GA recognition model and try to capture the intrinsic characteristics of GAs with a hybrid unsupervised/supervised approach.
Visualizing programs with Jeliot 3

We present a program visualization tool called Jeliot 3 that is designed to aid novice students to learn procedural and object oriented programming. The key feature of Jeliot is the fully or semi-automatic visualization of the data and control flows. The development process of Jeliot has been research-oriented, meaning that all the different versions have had their own research agenda rising from the design of the previous version and their empirical evaluations. In this process, the user interface and visualization has evolved to better suit the targeted audience, which in the case of Jeliot 3, is novice programmers. In this paper we explain the model for the system and introduce the features of the user interface and visualization engine. Moreover, we have developed an intermediate language that is used to decouple the interpretation of the program from its visualization. This has led to a modular design that permits both internal and external extensibility.
Sensitivity Degree Based Fuzzy SLIQ Decision Tree

The determination of membership function is fairly critical to fuzzy decision tree induction.Unfortunately,generally used heuristics show the pathological behaviour of the attribute tests at split nodes inclining to select a crisp partition.Hence,for generation of binary fuzzy tree,this paper proposes a method depending on the sensitivity degree of attributes to all kinds of classes to determine the transition region of membership function. The method,properly using the pathological characteristic of common heuristics,overcomes drawbacks of G-FDT algorithm proposed by B. Chandra,and it well remedies defects brought on by the pathological behaviour.Moreover,the sensitivity degree based algorithm outperforms G-FDT algorithm in respect to classification accuracy on several datasets from UCI machine learning repository.
Nuclear Actin‐Binding Proteins as Modulators of Gene Transcription

Dynamic transformations in the organization of the cellular microfilament system are the driving force behind fundamental biological processes such as cellular motility, cytokinesis, wound healing and secretion. Eukaryotic cells express a plethora of actin‐binding proteins (ABPs) allowing cells to control the organization of the actin cytoskeleton in a flexible manner. These structural proteins were, not surprisingly, originally described as (major) constituents of the cytoplasm. However, in recent years, there has been a steady flow of reports detailing not only translocation of ABPs into and out of the nucleus but also describing their role in the nuclear compartment. This review focuses on recent developments pertaining to nucleocytoplasmic transport of ABPs, including their mode of translocation and nuclear function. In particular, evidence that structurally and functionally unrelated cytoplasmic ABPs regulate transcription activation by various nuclear (steroid hormone) receptors is steadily accruing. Furthermore, the recent finding that actin is a necessary component of the RNA polymerase II‐containing preinitiation complex opens up new opportunities for nuclear ABPs in gene transcription regulation.
An Authentication Technique Based on Distributed Security Management for the Global Mobility Network

This paper proposes an authentication technique for use in the global mobility network (GLOMONET), which provides a personal communication user with global roaming service. This technique is based on new distributed security management, where authentication management in roaming-service provision is conducted only by the roamed network (the visited network). The original security manager (OSM) administrates the original authentication key (OAK) acquired when a user makes contracts with the home network, while the temporary security manager (TSM) is generated for a roamer in the visited network in order to provide roaming services. The TSM generates and administrates the temporary authentication key (TAK) for a roamer, which key is confidential to the OSM, releases the TAK administration when a roamer moves to other networks, and then disappears. The proposed authentication technique consists of two phases. In the roaming-service-setup phase, triggered by the user's location registration request, authentication control to set up the roaming-service environment is negotiated by the TSM in the visited network, the OSM, and the roamer. In the roaming-service-provision phase, triggered by the user's service request, authentication control to provide the roaming service is negotiated (using the TAK acquired by the roamer in the first phase) only by the visited network and the roamer. This authentication control using the TAK provides a unified authentication procedure with a single logic to both subscribers and roamers. In addition, the security management of the whole GLOMONET is reinforced and the security responsibility is made clear by allocating the subscriber's/roamer's security administration to only the TSM.
A British experience of surgical voice restoration techniques as a secondary procedure following total laryngectomy

Abstract An earlier paper (Cheesman et al., 1985) described assessment procedures for ‘failed’ oesophageal speakers who were referred to Charing Cross Hospital for possible Surgical Voice Restoration in 1983–4. This paper presents the results of surgical voice restoration in the first fifty laryngectomized patients referred and analyses the reasons for failure in those where surgical voice restoration was unsuccessful. 94 per cent of patients who underwent secondary voice restoration were successful at two weeks post-surgery, but this success rate dropped to 73 per cent at three months. Reasons for this are explained and the pre-requisites for a successful surgical voice restoration are indicated.