Miracle-dz/UniFAR-FTUs huggingface dataset:
Melanotic Pathology and Vertical Transmission of the Gut Commensal Elizabethkingia meningoseptica in the Major Malaria Vector Anopheles gambiae

Background The resident gut flora is known to have significant impacts on the life history of the host organism. Endosymbiotic bacterial species in the Anopheles mosquito gut are potent modulators of sexual development of the malaria parasite, Plasmodium, and thus proposed as potential control agents of malaria transmission. Results Here we report a melanotic pathology in the major African malaria vector Anopheles gambiae, caused by the dominant mosquito endosymbiont Elizabethkingia meningoseptica . Transfer of melanised tissues into the haemolymph of healthy adult mosquitoes or direct haemolymph inoculation with isolated E . meningoseptica bacteria were the only means for transmission and de novo formation of melanotic lesions, specifically in the fat body tissues of recipient individuals. We show that E . meningoseptica can be vertically transmitted from eggs to larvae and that E . meningoseptica -mono-associated mosquitoes display significant mortality, which is further enhanced upon Plasmodium infection, suggesting a synergistic impact of E . meningoseptica and Plasmodium on mosquito survival. Conclusion The high pathogenicity and permanent association of E . meningoseptica with An. Gambiae through vertical transmission constitute attractive characteristics towards the potential design of novel mosquito/malaria biocontrol strategies.
Semantic Support for Visualisation in Collaborative AI Planning

In the last decades, many advances have been made in intelligent planning systems. Significant improvements related to core problems, providing faster search algorithms and shortest plans have been proposed. However, there is a lack in researches allowing a better support for a proper use and interaction with planners, where, for instance, visualization can play an important role. This work proposes a general framework for visu-alisation of planning information using an approach based on semantic modelling. It intends to enhance the notion of knowledge-based planning applying it to other aspects of planning, such as visualisation. The approach consists in an integrated ontology set and reasoning mechanism for multi-modality visualisation destined to collabora-tive planning environments. This framework will permit organizing and modelling the domain from the visualisation perspective, and give a tailored support for presentation of information.
Incomplete response of inflammatory arthritis to TNFα blockade is associated with the Th17 pathway

Objectives To establish if changes in Th1/Th17 cell populations previously reported in experimental arthritis occur in patients with rheumatoid arthritis (RA) treated with anti-tumour necrosis factor α (TNFα) agents, and whether the therapeutic response to anti-TNFα is compromised in patients and mice because of elevated Th17/IL-17 levels. Finally, to assess the efficacy of combined blockade of anti-TNFα and anti-IL-17 in experimental arthritis. Methods A longitudinal study of two independent cohorts (cohort 1, n=24; cohort 2, n=19) of patients with RA treated with anti-TNFα biological agents was carried out to assess their Th17/IL-17 levels before and after the start of anti-TNFα therapy. IL-12/23p40 production was assessed in plasma Peripheral blood lymphocytes (PBLs) and monocytes. Mice with collagen-induced arthritis (CIA) were treated with anti-TNFα alone, anti-IL17 alone or a combination of the two. Efficacy of treatment and response was assessed from changes in Disease Activity Score 28–erythrocyte sedimentation rate scores in patients, and in clinical scores and histological analysis in CIA. Results Significant increases in circulating Th17 cells were observed in patients after anti-TNFα therapy and this was accompanied by increased production of IL-12/23p40. There was an inverse relationship between baseline Th17 levels and the subsequent response of patients with RA to anti-TNFα therapy. In addition, PBLs from non-responder patients showed evidence of increased IL-17 production. Similarly, in anti-TNFα-treated mice, there was a strong correlation between IL-17 production and clinical score. Finally combined blockade of TNFα and IL-17 in CIA was more effective than monotherapy, particularly with respect to the duration of the therapeutic effect. Conclusions These findings, which need to be confirmed in a larger cohort, suggest that a Th17-targeted therapeutic approach may be useful for anti-TNFα non-responder patients or as an adjunct to anti-TNFα therapy, provided that safety concerns can be addressed.
A reconfigurable supercomputing library for accelerated parallel lagged-Fibonacci pseudorandom number generation

To help promote more widespread adoption of hardware acceleration in parallel scientific computing we present portable, flexible design components for pseudorandom number generation. Due to the success of the Scalable Parallel Random Number Generators (SPRNG) software library in stochastic computations (e.g., Monte Carlo simulations), we developed an efficient and portable hardware architecture fully compatible with SPRNG's Parallel Additive Lagged Fibonacci Generator (PALFG). Our general design produces identical results for all the parameter sets that SPRNG supports and yields high performance parallel random number generators, which can each generate 162 million 31 bit uniform random integers per second on Xilinx Virtex II Pro FPGAs. The friendly design interface makes it easy for users to integrate into their applications, particularly computational scientists unfamiliar with reconfigurable hardware. Due to its fast generation speed and friendly interface, this uniform random number generator is being targeted as an open core for parallel scientific computing.
The Efficacy of Pramipexole, a Dopamine Receptor Agonist, as an Adjunctive Treatment in Treatment-Resistant Depression: An Open-Label Trial

Dopaminergic dysfunction is implicated in the pathophysiology of treatment-resistant depression. Although the efficacy of adjunctive pramipexole treatment has been demonstrated in treatment-resistant bipolar depression, such data are scarce for major depressive disorder (MDD). We recruited 17 patients with DSM-IV major depressive episode who have failed to respond to previous treatment with a selective serotonin reuptake inhibitor. Five patients were diagnosed as having bipolar II disorder and 12 as having unipolar MDD. Patients were monitored at an ambulatory care facility every two weeks until 12 weeks. Pramipexole was added to existing medication. Depression severity was assessed with the Hamilton Depression Rating Scale 21-item version (HDRS-21). The mean maximum dosage of pramipexole was 1.6 mg (SD 0.9). The HDRS-21 total score decreased from 19.4 (SD 3.8) at baseline to 7.2 (SD 5.4) at endpoint (P < 0.000001). Twelve patients (71%) were responders based on the definition of 50% or more reduction in the HDRS-21 score. Ten patients (59%) remitted (HDRS-21 total score at endpoint <8). These results were almost unchanged when the sample was confined to patients with MDD. No serious adverse events were observed. Our findings indicate that pramipexole augmentation therapy may be effective and well tolerated in refractory depressed patients.
EduSpeak®: A speech recognition and pronunciation scoring toolkit for computer-aided language learning applications

SRI International’s EduSpeak® system is a software development toolkit that enables developers of interactive language education software to use state-of-the-art speech recognition and pronunciation scoring technology. Automatic pronunciation scoring allows the computer to provide feedback on the overall quality of pronunciation and to point to specific production problems. We review our approach to pronunciation scoring, where our aim is to estimate the grade that a human expert would assign to the pronunciation quality of a paragraph or a phrase. Using databases of nonnative speech and corresponding human ratings at the sentence level, we evaluate different machine scores that can be used as predictor variables to estimate pronunciation quality. For more specific feedback on pronunciation, the EduSpeak toolkit supports a phone-level mispronunciation detection functionality that automatically flags specific phone segments that have been mispronounced. Phone-level information makes it possible to provide the student with feedback about specific pronunciation mistakes.Two approaches to mispronunciation detection were evaluated in a phonetically transcribed database of 130,000 phones uttered in continuous speech sentences by 206 nonnative speakers. Results show that classification error of the best system, for the phones that can be reliably transcribed, is only slightly higher than the average pairwise disagreement between the human transcribers.
Associations of autophagy with lung diffusion capacity and oxygen saturation in severe COPD: effects of particulate air pollution

Although traffic exposure has been associated with the development of COPD, the role of particulate matter <10 μm in aerodynamic diameter (PM10) in the pathogenesis of COPD is not yet fully understood. We assessed the 1-year effect of exposure to PM10 on the pathogenesis of COPD in a retrospective cohort study. We recruited 53 subjects with COPD stages III and IV and 15 healthy controls in a hospital in Taiwan. We estimated the 1-year annual mean levels of PM10 at all residential addresses of the cohort participants. Changes in PM10 for the 1-year averages in quintiles were related to diffusion capacity of the lung for carbon monoxide levels (r=−0.914, P=0.029), changes in the pulse oxygen saturation (ΔSaO2; r=−0.973, P=0.005), receptor for advanced glycation end-products (r=−0.881, P=0.048), interleukin-6 (r=0.986, P=0.002), ubiquitin (r=0.940, P=0.017), and beclin 1 (r=0.923, P=0.025) in COPD. Next, we observed that ubiquitin was correlated with ΔSaO2 (r=−0.374, P=0.019). Beclin 1 was associated with diffusion capacity of the lung for carbon monoxide (r=−0.362, P=0.028), ΔSaO2 (r=−0.354, P=0.032), and receptor for advanced glycation end-products (r=−0.471, P=0.004). Autophagy may be an important regulator of the PM10-related pathogenesis of COPD, which could cause deterioration in the lung diffusion capacity and oxygen saturation.
Informal specification-based performance evaluation of security protocols

We propose a performance evaluation method for security protocols. Based on the informal specification, we construct a canonical model which includes, alongside protocol messages, cryptographic operations performed by participants in the process of message construction. Each cryptographic operation is assigned a cost modeled as a function of the size of processed message components. We model not only the size of regular message components but also the size of ciphertext produced by various cryptographic operations. We illustrate the applicability of our method by comparatively analyzing the performance of the original CCITT X.509 protocol and a slightly modified version of the same protocol.
Materials and Methods Briefdefinitive Report Disseminated Tuberculosis in Interferon 7 Gene-disrupted Mice

The expression of protective immunity to Mycobacterium tuberculosis in mice is mediated by T lymphocytes that secrete cytokines. These molecules then mediate a variety of roles, including the activation ofparasitized host macrophages, and the recruitment of other mononuclear phagocytes to the site of the infection in order to initiate granuloma formation. Among these cytokines, interferon y (IFN-y) is believed to play a key role is these events. In confirmation ofthis hypothesis, we show in this study that mice in which the IFN-y gene has been disrupted were unable to contain or control a normally sublethal dose of M. tuberculosis, delivered either intravenously or aerogenically. In such mice, a progressive and widespread tissue destruction and necrosis, associated with very high numbers ofacid-fast bacilli, was observed. In contrast, despite the lack of protective immunity, some DTH-like reactivity could still be elicited. These data, therefore, indicate that although IFN-y may not be needed for DTH expression, it plays a pivotal and essential role in protective cellular immunity to tuberculosis infection. C urrent murine models of experimental Mycobacterium tuberculosis infection indicate that the emergence of acquired immunity to this organism is mediated by populations of both class I and II MHC-restricted T lymphocytes, which secrete cytokines that result in the activation of para-sitized macrophages and promotion of the granulomatous response (1-4). The cytokine IFN-y, which is an effective inducer of antimicrobial mechanisms in several systems (5, 6) has been shown to inhibit the growth of mycobacteria in vitro (7-9), but its role in vivo has yet to be precisely defined. In this regard, we report here that mice in which the IFN-y gene has been disrupted (IFN-y gene knockout mice [GKO mice]), develop a fatal, disseminated form of disease when inoculated with a normally sublethal inoculum of M. tuberculosis . These results indicate, therefore, that IFN-'Y plays a pivotal role in the expression ofprotective immunity to this infection in the mouse. Moreover, this new immunodeficient mouse model may prove highly useful in the evaluation of therapeutic intervention strategies in the severely immunocom-promised host. Mice. GKO mice were generated as described previously (10). Briefly, a normal IFN-y allele in mouse embryonic stem cells was replaced with a defective gene using a targeted vector which introduced a termination codon after the first 30 amino acids of the mature IFN-y protein. The altered stem cells were injected into C57BL/6J blastocysts and transmitted via the germline. Heterozy-gous offspring …
Preoperative diagnosis of infection in patients with nonunions.

BACKGROUND The surgical treatment of a fracture nonunion is complicated in the presence of infection. The purpose of the present study is to report on the utility of a standardized protocol to rule out infection in high-risk patients and to evaluate the efficacy of each component of the protocol. METHODS A single protocol of preoperative laboratory tests (white blood-cell count, C-reactive protein level, and erythrocyte sedimentation rate) and a combined white blood cell/sulfur colloid scan were performed for patients with a high risk of fracture nonunion. Infection was diagnosed on the basis of positive intraoperative cultures, evidence of gross infection at the time of the procedure, or evidence of gross infection during the immediate postoperative period. With use of infection as the end point, univariate analysis and multiple logistic regression analysis were used to compare tests. A risk stratification method was used to combine tests. RESULTS Ninety-three patients with ninety-five nonunions were evaluated. Thirty of the ninety-five nonunions were ultimately diagnosed as being infected. With use of a combination of elevated white blood-cell count, erythrocyte sedimentation rate, and C-reactive protein level and a positive scan, the predicted probabilities of infection associated with zero, one, two, and three positive tests were 18%, 24%, 50%, and 86%, respectively. With the elimination of the nuclear scan, the predicted probabilities for zero, one, two, and three risk factors were 20%, 19%, 56%, and 100%. CONCLUSIONS The erythrocyte sedimentation rate and the C-reactive protein level were both independently accurate predictors of infection. Use of a risk stratification method showed that the likelihood of infection increased with each additional positive test. A combined white blood cell/sulfur colloid scan was the least predictive method of revealing infection and is not cost effective, even as part of a stratification scheme. LEVEL OF EVIDENCE Diagnostic level III. See instructions for authors for a complete description of levels of evidence.
Prognostic and Therapeutic Implications of Aromatase Expression in Lung Adenocarcinomas with EGFR Mutations

Purpose: Lung adenocarcinomas among never-smokers are more common in females than in males. This implies that gender-dependent hormones promote smoking unrelated lung adenocarcinoma. We therefore investigated mRNA expression of aromatase, an intrinsic estrogen synthetase, in lung adenocarcinoma and assessed its correlation to clinicopathologic factors, including EGFR mutations and postsurgical prognosis. Experimental Design: Aromatase mRNA expression in primary tumor samples from 110 patients with lung adenocarcinoma was evaluated with qRT-PCR. Inhibitory effects of the aromatase inhibitor exemestane were assessed in lung adenocarcinoma cell lines (11-18 and HCC4006), which have EGFR mutations, separately and combined with EGFR tyrosine kinase inhibitor erlotinib. Results: Aromatase gene expression was not correlated with patients' clinicopathologic factors, including EGFR mutation status. High aromatase expression was associated with poor prognosis for both recurrence-free survival (P = 0.004) and overall survival (P = 0.003). In addition, the prognostic significance of aromatase expression was limited to females, never-smokers, and patients with EGFR mutations, but not in their counterparts. HCC4006, which has a low aromatase mRNA expression level, was not sensitive to exemestane, either alone or combined with erlotinib. In contrast, growth of 11-18 cells, which have high aromatase expression, was significantly inhibited by exemestane, both alone and combined with erlotinib. Conclusions: Aromatase is a candidate prognostic factor in patients with lung adenocarcinoma, especially in those with EGFR mutations, and may also be a beneficial therapeutic target in those patients. Clin Cancer Res; 20(13); 3613–22. ©2014 AACR.
Extended algorithm for spatial characterization and discrimination rules

Spatial data mining, i.e., mining knowledge from large amounts of spatial data, is a demanding field since huge amounts of spatial data have been collected in various applications, ranging from remote sensing to geographical information systems (GIS), computer cartography, environmental assessment and planning. The collected data far exceed people's ability to analyze it. The number and the size of spatial databases are rapidly growing which results in an increasing need for spatial data mining. In this paper, we have presented a new spatial data mining algorithm for spatial characterization and discrimination rules. For spatial data mining algorithm, it is important that class membership of a database object is not only determined by its non-spatial attributes but also by the attributes of objects in its neighborhood. We have implemented the algorithm within a general framework for spatial data mining providing a small set of database primitives on top of a commercial spatial database management system. At the end, performance analysis using a real geographic database demonstrates the effectiveness of the proposed algorithms.
Evolving the input space for a decision system

This paper addresses the problem of classifying data sets. The aim of this research is to extend the discrimination of a decision system by adding polynomials of the base inputs to the available inputs. The polynomials used to extend the inputs are evolved using the quality of the decision trees resulting from the extended inputs as a fitness function. The system has been integrated into the WEKA framework and so allows other components to be used in the decision system. So far our approach has focused on decision trees using the base inputs and compares it with a decision tree built using the extended input space. NSGA-II, a multi-objective optimisation algorithm, has also been integrated into the system to investigate the effects of added selection pressure on the generated polynomials. Because we have a library of procedures which we can apply we have also used Reduct systems in concert with the extension system and experiments show that although these reduce the input space the overall decision system is no better and can take longer to develop.
The Movement Tracker: A Flexible System for Automated Movement Analysis in Invertebrate Model Organisms

Phenotyping strategies in simple model organisms such as D. melanogaster and C. elegans are often broadly limited to growth, aging, and fitness. Recently, a number of physical setups and video tracking software suites have been developed to allow for accurate, quantitative, and high‐throughput analysis of movement in flies and worms. However, many of these systems require precise experimental setups and/or fixed recording formats. We report here an update to the Parallel Worm Tracker software, which we termed the Movement Tracker. The Movement Tracker allows variable experimental setups to provide cross‐platform automated processing of a variety of movement characteristics in both worms and flies and permits the use of simple physical setups that can be readily implemented in any laboratory. This software allows high‐throughput processing capabilities and high levels of flexibility in video analysis, providing quantitative movement data on C. elegans and D. melanogaster in a variety of different conditions. © 2016 by John Wiley & Sons, Inc.
Creativity: Can It Be Taught? The Case of Engineering Education.

Summary Creativity in higher education is analyzed as an intentional act and related to a number of ideas from cognitive psychology. It is claimed that the culture of engineering education entails a too narrow view on creativity and is based on outdated learning theories. The deeper philosophical implications of creativity, i.e. the quest for meaning, will have to be readdressed if engineering education is to prepare its graduates for future tasks.
Malware behavior image for malware variant identification

Several methods have been devised by researchers to facilitate malware analysis and one of them is through malware visualization. Malware visualization is a field that focuses on representing malware features in a form of visual cues that could be used to convey more information about a particular malware. There has been works in malware visualization but unfortunately, there seems to be a lack of focus in visualizing malware behavior. In this paper, we highlight our findings in visualizing malware behavior and its potential benefit for malware classification. Our research shows that malware behavior visualization can be used as a way to identify malware variants with high accuracy.
Using population data for assessing next-generation sequencing performance

Motivation: During the past 4 years, whole-exome sequencing has become a standard tool for finding rare variants causing Mendelian disorders. In that time, there has also been a proliferation of both sequencing platforms and approaches to analyse their output. This requires approaches to assess the performance of different methods. Traditionally, criteria such as comparison with microarray data or a number of known polymorphic sites have been used. Here we expand such approaches, developing a maximum likelihood framework and using it to estimate the sensitivity and specificity of whole-exome sequencing data. Results: Using whole-exome sequencing data for a panel of 19 individuals, we show that estimated sensitivity and specificity are similar to those calculated using microarray data as a reference. We explore the effect of frequency misspecification arising from using an inappropriately selected population and find that, although the estimates are affected, the rankings across procedures remain the same. Availability and implementation: An implementation using Perl and R can be found at busso.ncl. ac.uk (Username: igm101; Password: Z1z1nts). Contact: Darren.Houniet@ogt.com; mauro.santibanez-koref@newcastle.ac.uk