Miracle-dz/UniFAR-FTUs huggingface dataset:
SH3-Domain binding function of HIV-1 Nef is required for association with a PAK-related kinase.

HIV-1 Nef has previously been shown to bind to Src homology-3 (SH3) domains of a subset of Src family tyrosine kinases. In addition, Nef has been reported to coprecipitate with a serine/threonine kinase activity termed NAK (for Nef-associated kinase). The identity of NAK remains uncertain, but it has been suggested to represent a novel member of the p21-activated kinase (PAK) family. We report here that NAK autophosphorylation is increased not only by an activated form of the p21-family GTPase cdc42 but also by a plasma membrane-targeted fragment of the adapter protein Nck, thus providing further evidence that NAK is related to PAKs. A detailed structure-based mutational analysis of Nef revealed that all amino acid changes that inhibited the Nef/Hck-SH3 interaction, as measured by surface-plasmon resonance, also abolished coprecipitation of NAK. As PAK family proteins do not contain SH3 domains, these observations are best explained by a protein complex in which Nef, NAK, and an SH3-protein all contact each other. In addition, a number of conserved amino acids in Nef that are not involved in SH3 binding were also found to be crucial for association with NAK. Molecular modeling suggests that these residues are involved in formation of an adjacent binding surface for NAK or another critical component of the NAK/Nef complex.
CT of prominent pericolic or perienteric vasculature in patients with Crohn's disease: correlation with clinical disease activity and findings on barium studies.

UNLABELLED OBJECTIVE. The purpose of this study was to correlate CT findings of prominent pericolic or perienteric vasculature with clinical disease activity, treatment methods, and barium enema study findings in patients with Crohn's disease. MATERIALS AND METHODS We retrospectively analyzed 33 patients with Crohn's disease who had undergone both barium enema study and abdominal CT. CT scans were evaluated for the presence and location of prominent vasculature. On the basis of the Crohn's disease activity index, the patients were assigned to one of three categories--active, intermediate, or quiescent disease groups--and the frequency of prominent vasculature was compared among them. Thereafter, erythrocyte sedimentation rates, C-reactive protein levels, treatment methods, and radiographic findings were compared in groups with and without prominent vasculature. RESULTS Prominent vasculature was more frequently found in patients with active disease (81%) than in those with intermediate (33%) and quiescent disease (0%) (p < 0.001). The erythrocyte sedimentation rates and C-reactive protein levels were higher in patients with prominent vasculature (but not at a statistically significant rate). Patients with prominent vasculature were more frequently admitted to the hospital (p = 0.024) and received more aggressive treatment (p = 0.049) than patients without prominent vasculature. The main differences of radiographic findings between the group with prominent vasculature and the group without prominent vasculature included the common occurrence of longitudinal and perpendicular ulceration (p = 0.017 for small bowel; p = 0.041 for colon) and the extensive length of organ involvement (p = 0.004 for small bowel; p = 0.036 for colon). CONCLUSION Prominent pericolic or perienteric vasculature seen on CT in patients with Crohn's disease suggests that the disease is clinically active, advanced, and extensive and that these patients require more aggressive treatment than patients without this CT finding.
Using Deep and Convolutional Neural Networks for Accurate Emotion Classification on DEAP Dataset

Emotion recognition is an important field of research in Brain Computer Interactions. As technology and the understanding of emotions are advancing, there are growing opportunities for automatic emotion recognition systems. Neural networks are a family of statistical learning models inspired by biological neural networks and are used to estimate functions that can depend on a large number of inputs that are generally unknown. In this paper we seek to use this effectiveness of Neural Networks to classify user emotions using EEG signals from the DEAP (Koelstra et al (2012)) dataset which represents the benchmark for Emotion classification research. We explore 2 different Neural Models, a simple Deep Neural Network and a Convolutional Neural Network for classification. Our model provides the state-of-the-art classification accuracy, obtaining 4.51 and 4.96 percentage point improvements over (Rozgic et al (2013)) classification of Valence and Arousal into 2 classes (High and Low) and 13.39 and 6.58 percentage point improvements over (Chung and Yoon(2012)) classification of Valence and Arousal into 3 classes (High, Normal and Low). Moreover our research is a testament that Neural Networks could be robust classifiers for brain signals, even outperforming traditional learning techniques.
Using speech recognition for real-time captioning and lecture transcription in the classroom

Speech recognition (SR) technologies were evaluated in different classroom environments to assist students to automatically convert oral lectures into text. Two distinct methods of SR-mediated lecture acquisition (SR-mLA), real-time captioning (RTC) and postlecture transcription (PLT), were evaluated in situ life and social sciences lecture courses employing typical classroom equipment. Both methods were compared according to technical feasibility and reliability of classroom implementation, instructors' experiences, word recognition accuracy, and student class performance. RTC provided near-instantaneous display of the instructor's speech for students during class. PLT employed a user-independent SR algorithm to optimally generate multimedia class notes with synchronized lecture transcripts, instructor audio, and class PowerPoint slides for students to access online after class. PLT resulted in greater word recognition accuracy than RTC. During a science course, students were more likely to take optional online quizzes and received higher quiz scores with PLT than when multimedia class notes were unavailable. Overall class grades were also higher when multimedia class notes were available. The potential benefits of SR-mLA for students who have difficulty taking notes accurately and independently were discussed, particularly for nonnative English speakers and students with disabilities. Field-tested best practices for optimizing SR accuracy for both SR-mLA methods were outlined.
Antigen mediated and polyclonal stimulation of human cytokine production elicit qualitatively different patterns of cytokine gene expression.

Polyclonal activators are widely used as surrogate antigens in analysis of human cytokine gene expression. An implicit assumption is that the T cell activation and cytokine production observed in response to polyclonal activation provides a more intense, but qualitatively identical, reflection of results that would be obtained with antigen. Here we demonstrate that stimulation using accessory cell independent (immobilized anti-CD3 mAb) or dependent [phytohemagglutinin (PHA) or soluble anti-CD3 mAb] polyclonal activators yields different conclusions from those that are obtained in response to antigen-specific T cell activation. Cytokine synthesis in 1-5 day bulk cultures of fresh peripheral blood mononuclear cells (PBMC) from 52 subjects evenly divided between grass pollen sensitive allergic rhinitis subjects and normal, non-atopic controls were examined. Antigen-specific re-stimulation elicited elevated IL-4 and IL-10 production and lower IFN-gamma synthesis among allergic subjects than normal non-atopic control subjects. This commitment of fresh PBMC towards a Th2-like response in atopics and the dominance of the IFN-gamma response seen in non-allergic subjects was reinforced when the ratio of IFN-gamma:IL-4 production in bulk culture was examined. Atopic individuals exhibited median IFN-gamma:IL-4 values of 0.07, whereas grass pollen stimulated cytokine production by normal subjects yielded a ratio of 4.8. In marked contrast, IL-2, IL-4, IL-10 and IFN-gamma production elicited using polyclonal activators, though much more intense, did not differ between allergic and non-allergic subjects (Wilcoxon rank sum test P > > 0.05). (ABSTRACT TRUNCATED AT 250 WORDS)
Mechanism of Control of Arabidopsis thaliana Aspartate Kinase-Homoserine Dehydrogenase by Threonine*

The regulatory domain of the bifunctional threonine-sensitive aspartate kinase homoserine dehydrogenase contains two homologous subdomains defined by a common loop-αhelix-loop-β strand-loop-β strand motif. This motif is homologous with that found in the two subdomains of the biosynthetic threonine-deaminase regulatory domain. Comparisons of the primary and secondary structures of the two enzymes allowed us to predict the location and identity of the amino acid residues potentially involved in two threonine-binding sites ofArabidopsis thaliana aspartate kinase-homoserine dehydrogenase. These amino acids were then mutated and activity measurements were carried out to test this hypothesis. Steady-state kinetic experiments on the wild-type and mutant enzymes demonstrated that each regulatory domain of the monomers of aspartate kinase-homoserine dehydrogenase possesses two nonequivalent threonine-binding sites constituted in part by Gln443 and Gln524. Our results also demonstrated that threonine interaction with Gln443 leads to inhibition of aspartate kinase activity and facilitates the binding of a second threonine on Gln524. Interaction of this second threonine with Gln524 leads to inhibition of homoserine dehydrogenase activity.
On the use of two QMR algorithms for solving singular systems and applications in Markov chain modeling

Recently, Freund and Nachtigal proposed the quasi-minimal residual algorithm (QMR) for solving general nonsingular non-Hermitian linear systems. The method is based on the Lanczos process, and thus it involves matrix—vector products with both the coefficient matrix of the linear system and its transpose. Freund developed a variant of QMR, the transpose-free QMR algorithm (TFQMR), that only requires products with the coefficient matrix. In this paper, the use of QMR and TFQMR for solving singular systems is explored. First, a convergence result for the general class of Krylov-subspace methods applied to singular systems is presented. Then, it is shown that QMR and TFQMR both converge for consistent singular linear systems with coefficient matrices of index 1. Singular systems of this type arise in Markov chain modeling. For this particular application, numerical experiments are reported.
The phylogeny of plant and animal pathogens in the Ascomycota

Abstract What makes a fungus pathogenic? In this review, phylogenetic inference is used to speculate on the evolution of plant and animal pathogens in the fungal Phylum Ascomycota. A phylogeny is presented using 297 18S ribosomal DNA sequences from GenBank and it is shown that most known plant pathogens are concentrated in four classes in the Ascomycota. Animal pathogens are also concentrated, but in two ascomycete classes that contain few, if any, plant pathogens. Rather than appearing as a constant character of a class, the ability to cause disease in plants and animals was gained and lost repeatedly. The genes that code for some traits involved in pathogenicity or virulence have been cloned and characterized, and so the evolutionary relationships of a few of the genes for enzymes and toxins known to play roles in diseases were explored. In general, these genes are too narrowly distributed and too recent in origin to explain the broad patterns of origin of pathogens. Co-evolution could potentially be part of an explanation for phylogenetic patterns of pathogenesis. Robust phylogenies not only of the fungi, but also of host plants and animals are becoming available, allowing for critical analysis of the nature of co-evolutionary warfare. Host animals, particularly human hosts have had little obvious effect on fungal evolution and most cases of fungal disease in humans appear to represent an evolutionary dead end for the fungus. Plants have been important in the evolution of fungi, and the rapid nature of co-evolutionary change might partially explain the lack of obvious, global characters uniting all plant pathogens.
Recurrent outbreaks of measles, chickenpox and mumps. II. Systematic differences in contact rates and stochastic effects.

Yorke, J. A. and W. P. London (Mathematical Research Branch, National Institute of Arthritis, Metabolism, and Digestive Diseases, Bethesda, Maryland 20014). Recurrent outbreaks of measles, chickenpox and mumps. I I . Systematic differences in contact rates and stochastic effects. Am J Epidemiol 98:469-482, 1973. —The mean monthly contact rates for measles, chickenpox and mumps estimated from the monthly reported cases show systematic differences between the years with many cases and the years with few cases. In New York City, the mean contact rates for chickenpox were different during the years 1931-1945 than during 1946-1960. The clustering of cases within social groups is proposed to account for these differences in the contact rates and for other empirical observations. The irregularity of outbreaks of measles in cities of fewer than two million people can be explained by stochastic effects. Outbreaks of measles in distant large metropolitan areas are highly correlated in time, but the reasons for the correlation are not clear.
Lipidomic analysis of patients with microbial invasion of the amniotic cavity reveals up‐regulation of leukotriene B4

Bioactive lipids derived from the metabolism of polyunsaturated fatty acids are important mediators of the inflammatory response. Labor per se is considered a sterile inflammatory process. Intra‐amniotic inflammation (IAI) due to microorganisms (i.e., intra‐amniotic infection) or danger signals (i.e., sterile IAI) has been implicated in the pathogenesis of preterm labor and clinical chorioamnionitis at term. Early and accurate diagnosis of microbial invasion of the amniotic cavity (MIAC) requires analysis of amniotic fluid (AF). It is possible that IAI caused by microorganisms is associated with a stereotypic lipidomic profile, and that analysis of AF may help in the identification of patients with this condition. To test this hypothesis, we analyzed the fatty acyl lipidome of AF by liquid chromatography—mass spectrometry from patients in spontaneous labor at term and preterm gestations. We report that the AF concentrations of proinflammatory lipid mediators of the 5‐lipoxygenase pathway are significantly higher in MIAC than in cases of sterile IAI. These results suggest that the concentrations of 5‐lipoxygenase metabolites of arachidonic acid, 5‐hydroxyeicosatetraenoic acid, and leukotriene B4 in particular could serve as potential biomarkers of MIAC. This finding could have important implications for the rapid identification of patients who may benefit from antimicrobial treatment. —Maddipati, K. R. , Romero, R. , Chaiworapongsa, T. , Chaemsaithong, P., Zhou, S. ‐L. , Xu, Z. , Tarca, A. L. , Kusanovic, J. P., Gomez, R. , Chaiyasit, N. , Honn, K. V. Lipidomic analysis of patients with microbial invasion of the amniotic cavity reveals up‐regulation of leukotriene B4. FASEBJ. 30, 3296–3307 (2016). www.fasebj. org
A Pilot Study Evaluating Liquid-Based Fine Needle Aspiration Cytology of Breast Lesions: A Cytomorphological Comparison of SurePath® Liquid-Based Preparations and Conventional Smears

Objective: Fine needle aspiration cytology (FNAC) is recommended by the World Health Organization as a diagnostic method for breast lesions. The morphological interpretation of liquid-based preparations (LBPs) remains a diagnostic challenge due to considerably altered cytomorphology. The aim of the current study was to compare cytomorphological characteristics of SurePath® (SP)-based LBP and conventional smear (CS) in breast FNACs. Study Design: The study included 77 benign and 60 malignant breast FNACs obtained by both SP and CS, all with tissue confirmation. Cases analyzed with both preparations were reviewed and compared, focusing on 10 cytomorphological features. Results: SP aspirates demonstrated notable cytomorphological alterations. Among them, a prominent three-dimensional configuration of cell clusters and frequent and conspicuous nucleoli were the most prominent characteristics of SP compared with CS. Overall diagnostic performances were comparable but were slightly lower for SP than CS (diagnostic accuracy of two reviewers; 87.6 and 90.5% for SP vs. 91.2 and 92.7% for CS, respectively). Conclusion: Although the reviewer should be aware of distinctive cytomorphological alterations, the SP technique is reliable for the evaluation of breast lesions with the advantage of easy interpretation and a diagnostic accuracy equivalent to CS.
Study of nanopattern forming with chemical coatings for silicon-based stamp in nanoimprint process

The aim of this study is to present a silane molecule self-assembled monolayer (octadecyltrimethoxysilane (CH3(CH2)17Si(OCH3)3): OTS-SAM) as anti-adhesive coatings to improve of silicon-based stamps for the developed nanoimprint lithography (NIL). In this work, the nanostructures of stamps are fabricated by electron-beam lithography (EBL). The diameters of period pillar nanopatterns on the silicon-based stamps are 150 nm and 200 nm, receptively. The influence of silicon-based stamp substrate can be investigated by contact angle measurement after modifying the chemical coating treatment for imprinted thin polymethyl methacrylate (PMMA) films. To control the forming of fabricated nanopatterns, the simulation can be done to obtain the effects of patterning distortion during this NIL process. In addition, the study employs atomic force microscopy (AFM) to obtain a simultaneous observation for the morphologies of silicon-based and imprinted PMMA polymer nanostructures interface. The results indicate an over 95% improvement for silicon-based nanopatterns with the anti-adhesive properties in NIL process.
Direct Vocabulary Instruction in Kindergarten: Teaching for Breadth versus Depth

The purpose of this study was to compare 2 methods for directly teaching word meanings to kindergarten students within storybook read‐alouds that varied in instructional time and depth of instruction along with a control condition that provided students with incidental exposure to target words. Embedded instruction introduces target word meanings during storybook readings in a time‐efficient manner. Extended instruction is more time intensive but provides multiple opportunities to interact with target words outside the context of the story. Participants included 42 kindergarten students who were taught 9 target words, 3 with each method. Target words were counterbalanced in a within‐subjects design. Findings indicated that extended instruction resulted in more full and refined word knowledge, while embedded instruction resulted in partial knowledge of target vocabulary. Implications are discussed in relation to the strengths and limitations of different approaches to direct vocabulary instruction in kindergarten and the trade‐offs between instruction that focuses on teaching for breadth versus depth.
Aromatase inhibitors and breast cancer prevention

Introduction: Endocrine therapy with selective estrogen receptor modulators (SERMs) has been the mainstay of breast cancer prevention trials to date. The aromatase inhibitors, which inhibit the final chemical conversion of androgens to estrogens, have shown increased disease-free survival benefit over tamoxifen in patients with primary hormone receptor-positive breast cancer, as well as reducing the risk of developing contralateral breast cancers. The aromatase inhibitors are being actively evaluated as prevention agents for women with a history of ductal carcinoma in situ as well as for women who are considered to be at high risk for developing primary invasive breast cancer. Areas covered: This review evaluates the available prevention data, as evidenced by the decrease in contralateral breast cancers, when aromatase inhibitors are used in the adjuvant setting, as well as the emerging data of the aromatase inhibitors specifically tested in the prevention setting for women at high risk. Expert opinion: Exemestane is a viable option for breast cancer prevention. We continue to await further follow-up on exemestane as well as other aromatase inhibitors in the prevention setting for women at high risk of developing breast cancer or with a history of ductal carcinoma in situ.
Evaluation of Scenarios for Reducing Human Salmonellosis Through Household Consumption of Fresh Minced Pork Meat

Nontyphoidal salmonellosis is the second most frequently reported zoonotic disease in the European Union (EU) and is considered to be a major threat to human health worldwide. The most reported Salmonella serovar in the EU is S. Enteritidis, mainly associated with egg contamination, followed by S. Typhimurium, with the latter being the most predominant serovar isolated from pork. These findings suggest that reducing the Salmonella contamination in the pork production might be a good strategy to prevent and control human salmonellosis in the EU. Recently, a quantitative microbial risk assessment (QMRA) has been developed to assess the risks for human salmonellosis due to home consumption of fresh minced pork meat in Belgium. ( 1) The newly developed risk model is called the METZOON model. In the current study, the METZOON model was used to evaluate the effectiveness of different hypothetical Salmonella mitigation strategies implemented at different stages of the minced pork production and consumption chain by means of a scenario analysis. To efficiently evaluate the mitigation strategies, model results were obtained by running simulations using the randomized complete block design. The effectiveness of a mitigation strategy is expressed using point and interval estimates of the effect size for dependent observations, expressed as the standardized difference in population means. The results indicate that the most effective strategies are taken during the slaughter processes of polishing, evisceration, and chilling, and during postprocessing, whereas interventions in the primary production and at the beginning of the slaughter process seem to have only a limited effect. Improving consumer awareness is found to be effective as well.
A Miniature Electrical Impedance Tomography Sensor and 3-D Image Reconstruction for Cell Imaging

Real-time quantitative imaging is becoming highly desirable to study nondestructively the biological behavior of 3-D cell culture systems. In this paper, we investigate the feasibility of quantitative imaging/monitoring of 3-D cell culture processes via electrical impedance tomography (EIT), which is capable of generating conductivity images in a non-destructive manner with high temporal resolution. To this end, a planar miniature EIT sensor amenable to standard cell culture format is designed, and a 3-D forward model for the sensor is developed for 3-D imaging. Furthermore, a novel 3-D-Laplacian and sparsity joint regularization algorithm is proposed for enhanced 3-D image reconstruction. Simulation phantoms with spheres at various vertical and horizontal positions were imaged for 3-D performance evaluation. In addition, experiments on human breast cancer cell spheroid and a triangular breast cancer cell pellet were carried out for experimental verification. The results have shown that the stable measurement on high conductive cell culture medium and the significant improvement of image quality based on the proposed regularization method are achieved. It demonstrates the feasibility of using the miniature EIT sensor and 3-D image reconstruction algorithm to visualize 3-D cell cultures, such as spheroids or artificial tissues and organs. The established work would expedite real-time quantitative imaging of 3-D cell culture for assessment of cellular dynamics.