Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural basis for recognition and remodeling of the TBP:DNA:NC2 complex by Mot1

Swi2/Snf2 ATPases remodel substrates such as nucleosomes and transcription complexes to control a wide range of DNA-associated processes, but detailed structural information on the ATP-dependent remodeling reactions is largely absent. The single subunit remodeler Mot1 (modifier of transcription 1) dissociates TATA box-binding protein (TBP):DNA complexes, offering a useful system to address the structural mechanisms of Swi2/Snf2 ATPases. Here, we report the crystal structure of the N-terminal domain of Mot1 in complex with TBP, DNA, and the transcription regulator negative cofactor 2 (NC2). Our data show that Mot1 reduces DNA:NC2 interactions and unbends DNA as compared to the TBP:DNA:NC2 state, suggesting that Mot1 primes TBP:NC2 displacement in an ATP-independent manner. Electron microscopy and cross-linking data suggest that the Swi2/Snf2 domain of Mot1 associates with the upstream DNA and the histone fold of NC2, thereby revealing parallels to some nucleosome remodelers. This study provides a structural framework for how a Swi2/Snf2 ATPase interacts with its substrate DNA:protein complex. DOI: http://dx.doi. org/10.7554/eLife.07432. 001
Formation of 7-dehydrocholesterol-containing membrane rafts in vitro and in vivo, with relevance to the Smith-Lemli-Opitz syndrome Published, JLR Papers in Press, November 1, 2003. DOI 10.1194/jlr.M300232-JLR200

Smith-Lemli-Opitz syndrome (SLOS) is a recessive disease typified by 7-dehydrocholesterol (7DHC) accumulation and depletion of cholesterol. Because cholesterol is a primary component of detergent-resistant membrane domains (“rafts”), we examined the compatibility of 7DHC with raft formation. Liposomes containing bovine brain phosphatidylcholine, sphingomyelin, cerebrosides, and either cholesterol, 7DHC, or coprostanol (the latter being incompatible with raft formation) were prepared. 7DHC was indistinguishable from cholesterol in its ability to become incorporated into membrane rafts, as judged by physical and chemical criteria, whereas coprostanol did not form rafts. The in vivo compatibility of 7DHC with raft formation was evaluated in brains of rats treated with trans-1,4-bis(2-dichlorobenzylamino-ethyl)cyclohexane dihydrochloride (AY9944), which mimics the SLOS biochemical defect. 7DHC/cholesterol ratios in rafts and whole brains from AY9944-treated rats were similar, indicating comparable efficiency of 7DHC and cholesterol incorporation into brain rafts. In contrast, dolichol (a nonsterol isoprenoid incompatible with raft formation) was greatly depleted in brain rafts relative to whole brain. Although brain raft fractions prepared from AY9944-treated and control rats yielded similar sterol-protein ratios, their gel electrophoresis profiles exhibited multiple differences, suggesting that altered raft sterol composition perturbs raft protein content. These results are discussed in the context of the SLOS phenotype, particularly with regard to the associated central nervous system defects.
Multiple-locus VNTR Analyses of Methicillin-resistant Staphylococcus aureus from Jamaica

Background This study assessed the antimicrobial susceptibilities and the presence of inducible macrolide–lincosamide–streptogramin B (iMLSB) resistance in methicillin-resistant Staphylococcus aureus (MRSA) of Jamaica as well as the relatedness using polymerase chain reaction-based staphylococcal cassette chromosome mec (SCCmec) and multiple-locus variable numbers of tandem repeat analyses (MLVAs). Materials and Methods Antimicrobial susceptibility, the presence of MLSB resistance, and SCCmec and MLVA patterns were assessed for 61 nonduplicate isolates of MRSA from hospitalized patients. Results While no isolate was resistant to vancomycin, 53 (86.9%) isolates were resistant to ciprofloxacin, 52 (85.3%) to erythromycin, 49 (80%) to lincomycin, and 45 (74%) to clindamycin. Of the 52 erythromycin-resistant isolates, 48% exhibited constitutive resistance and 8% showed inducible MLSB (iMLSB) resistance. Most (85%) of typable isolates were SCCmec type IV, and among these, 16 MLVA patterns were identified. Conclusion Multidrug resistance continues to characterize MRSA. Among the erythromycin-resistant isolates, constitutive resistance and iMLSB resistance are common. These facts will complicate the treatment of MRSA infections and warrant continued surveillance and judicial use of antimicrobial agents.
Sub-Telomere Directed Gene Expression during Initiation of Invasive Aspergillosis

Aspergillus fumigatus is a common mould whose spores are a component of the normal airborne flora. Immune dysfunction permits developmental growth of inhaled spores in the human lung causing aspergillosis, a significant threat to human health in the form of allergic, and life-threatening invasive infections. The success of A. fumigatus as a pathogen is unique among close phylogenetic relatives and is poorly characterised at the molecular level. Recent genome sequencing of several Aspergillus species provides an exceptional opportunity to analyse fungal virulence attributes within a genomic and evolutionary context. To identify genes preferentially expressed during adaptation to the mammalian host niche, we generated multiple gene expression profiles from minute samplings of A. fumigatus germlings during initiation of murine infection. They reveal a highly co-ordinated A. fumigatus gene expression programme, governing metabolic and physiological adaptation, which allows the organism to prosper within the mammalian niche. As functions of phylogenetic conservation and genetic locus, 28% and 30%, respectively, of the A. fumigatus subtelomeric and lineage-specific gene repertoires are induced relative to laboratory culture, and physically clustered genes including loci directing pseurotin, gliotoxin and siderophore biosyntheses are a prominent feature. Locationally biased A. fumigatus gene expression is not prompted by in vitro iron limitation, acid, alkaline, anaerobic or oxidative stress. However, subtelomeric gene expression is favoured following ex vivo neutrophil exposure and in comparative analyses of richly and poorly nourished laboratory cultured germlings. We found remarkable concordance between the A. fumigatus host-adaptation transcriptome and those resulting from in vitro iron depletion, alkaline shift, nitrogen starvation and loss of the methyltransferase LaeA. This first transcriptional snapshot of a fungal genome during initiation of mammalian infection provides the global perspective required to direct much-needed diagnostic and therapeutic strategies and reveals genome organisation and subtelomeric diversity as potential driving forces in the evolution of pathogenicity in the genus Aspergillus.
Using Portfolios in Program Evaluation: An Investigation of Interrater Reliability

Portfolios and other open-ended assessments are increasingly incorporated into evaluations and testing programs. However, questions about the reliability of such assessments continue to be raised. After reviewing forces that may be leading to increased interest in and use of portfolio assessment, we investigate the interrater reliability of a portfolio assessment used in a small-scale program evaluation. Three types of portfolio scores were investigated—analytic, combined analytic (formed by summing across analytic scores), and holistic. The interrater reliability coefficient was highest for summed analytic scores (r 5 .86). Results indicate that at least three raters are required to obtain acceptable levels of reliability for holistic and individual analytic scores.
Remember and transfer what you have learned - recognizing composite activities based on activity spotting

Activity recognition approaches have shown to enable good performance for a wide variety of applications. Most approaches rely on machine learning techniques requiring significant amounts of training data for each application. Consequently they have to be retrained for each new application limiting the real-world applicability of today's activity recognition methods. This paper explores the possibility to transfer learned knowledge from one application to others thereby significantly reducing the required training data for new applications. To achieve this transferability the paper proposes a new layered activity recognition approach that lends itself to transfer knowledge across applications. Besides allowing to transfer knowledge across applications this layered approach also shows improved recognition performance both of composite activities as well as of activity events.
Language identification : how to distinguish similar languages ?

The goal of this paper is to discuss the language identification problem of Croatian, language that even state-of-the-art language identification tools find hard to distinguish from similar languages, such as Serbian, Slovenian or Slovak language. We developed the tool that implements the list of Croatian most frequent words with the threshold that each document needs to satisfy, we added the specific characters elimination rule, applied second-order Markov model classification and a rule of forbidden words. Finally, we built up the tool that overperforms current tools in discriminating between these similar languages.
Antiepidermal Growth Factor Receptor Monoclonal Antibodies: Applications in Colorectal Cancer

Patients with metastatic colorectal cancer have a poor prognosis and present a challenge to clinicians. The role of the antiepidermal growth factor receptor (EGFR) pathway in tumorogenesis and tumor progression has been well defined. This paper will review the use of anti-EGFR monoclonal antibodies in the treatment of operable, as well as metastatic colorectal cancer both in the setting of KRAS mutation unselected patients and later in KRAS wild-type patients. Active investigations designed to further identify predictive biomarkers that may be potentially druggable are reviewed as well.
Cocaine-induced Modification of Synaptic Plasticity in Rat Medial Prefrontal Cortex

Copyright Information: All rights reserved unless otherwise indicated. Contact the author or original publisher for any necessary permissions. eScholarship is not the copyright owner for deposited works. Learn more at http://www.escholarship. org/help_copyright. html#reuse Cocaine-induced Modification of Synaptic Plasticity in Rat Medial Prefrontal Cortex
Learning Global Term Weights for Content-based Recommender Systems

Recommender systems typically leverage two types of signals to effectively recommend items to users: user activities and content matching between user and item profiles, and recommendation models in literature are usually categorized into collaborative filtering models, content-based models and hybrid models. In practice, when rich profiles about users and items are available, and user activities are sparse (cold-start), effective content matching signals become much more important in the relevance of the recommendation. The de-facto method to measure similarity between two pieces of text is computing the cosine similarity of the two bags of words, and each word is weighted by TF (term frequency within the document) x IDF (inverted document frequency of the word within the corpus). In general sense, TF can represent any local weighting scheme of the word within each document, and IDF can represent any global weighting scheme of the word across the corpus. In this paper, we focus on the latter, i.e., optimizing the global term weights, for a particular recommendation domain by leveraging supervised approaches. The intuition is that some frequent words (lower IDF, e.g. ``database'') can be essential and predictive for relevant recommendation, while some rare words (higher IDF, e.g. the name of a small company) could have less predictive power. Given plenty of observed activities between users and items as training data, we should be able to learn better domain-specific global term weights, which can further improve the relevance of recommendation. We propose a unified method that can simultaneously learn the weights of multiple content matching signals, as well as global term weights for specific recommendation tasks. Our method is efficient to handle large-scale training data generated by production recommender systems. And experiments on LinkedIn job recommendation data justify the effectiveness of our approach.
Teaching Software Engineering Using Lightweight Analysis

In teaching software engineering, it is a major challenge to integrate methodology and theory into the practice of software development. The goal of this pro ject is to explore a new pedagogical approach to teaching software engineering centered on the c lose integration of analysis tools with instruction in programming methodologies. Instead of learning m ethodologies as abstract ideas, students will directly benefit from applying analysis tools t hat embody methodologies to large, realistic programs.
Thiazolidinedione-8 Alters Symbiotic Relationship in C. albicans-S. mutans Dual Species Biofilm

The small molecule, thiazolidinedione-8 (S-8) was shown to impair biofilm formation of various microbial pathogens, including the fungus Candida albicans and Streptococcus mutans. Previously, we have evaluated the specific molecular mode of S-8 action against C. albicans biofilm-associated pathogenicity. In this study we investigated the influence of S-8 on dual species, C. albicans-S. mutans biofilm. We show that in the presence of S-8 a reduction of the co-species biofilm formation occurred with a major effect on C. albicans. Biofilm biomass and exopolysaccharide (EPS) production were significantly reduced by S-8. Moreover, the agent caused oxidative stress associated with a strong induction of reactive oxygen species and hydrogen peroxide uptake inhibition by a mixed biofilm. In addition, S-8 altered symbiotic relationship between these species by a complex mechanism. Streptococcal genes associated with quorum sensing (QS) (comDE and luxS), EPS production (gtfBCD and gbpB), as well as genes related to protection against oxidative stress (nox and sodA) were markedly upregulated by S-8. In contrast, fungal genes related to hyphae formation (hwp1), adhesion (als3), hydrophobicity (csh1), and oxidative stress response (sod1, sod2, and cat1) were downregulated in the presence of S-8. In addition, ywp1 gene associated with yeast form of C. albicans was induced by S-8, which is correlated with appearance of mostly yeast cells in S-8 treated dual species biofilms. We concluded that S-8 disturbs symbiotic balance between C. albicans and S. mutans in dual species biofilm.
High voltage passive harmonic filter design

This paper presents a developed graphic user interface (GUI)-based program for high-voltage passive harmonic filter design. The developed program composes of four modules: load flow analysis, harmonic analysis, passive harmonic filter design, and capacitor bank design. Simulation results of a case study on 13-bus balanced transmission systems are summarized. Three types of externally fused capacitor bank design are described.
E-Collaboration Within the Dispersed Sales Force Training Process of Multinational Pharmaceutical Companies

In this paper the authors propose an ICT architecture for the support of collaborative tasks within a dispersed sales force training process in multinational pharmaceutical companies. Four areas of collaboration are identified through case studies. Each of these areas comprises a certain number of collaborative tasks. The equivocality and complexity of these tasks have to be taken into account when considering ICT support. The authors used a task-media-fit-matrix to decide on and justify usage of certain information and communication technologies for the support of collaborative tasks. The task-media-fitmatrix, in our opinion, can help both practitioners and researchers in either justifying investments in e-collaboration tools or evaluating ICT architectures in the field of ecollaboration.
Assessment the relationship between reflux and body mass index with comparing different regression models

Aim The aim of this study was to determine whether there is relation between body mass index and symptoms of gastro-esophageal reflux disease in our community using Logit, Probit and Complementary log-log models. Background The most frequent statistical tool to address the relationship among a dichotomous response and other covariates is logistic regression. However logistic regression is familiar for researchers, some other models with similar results are favorable to assess such relationship like as Probit and Complementary log-log. Patients and methods We carried out a population-based study to estimate the strength of the association between body mass and reflux symptoms. During interview, participants completed a valid Gastro-esophageal Reflux Questionnaire. The coefficients calculated by logistic, Probit and Complementary log-log regression with multivariate adjustments for covariates. Results Reflux symptoms at least once a week over the last three months were reported by 522 (9.1%) of the 5733 interviewees. There were no evidence in all models to address the significant relation between Reflux and BMI and all models derived in same efficacy. Conclusion Our results showed that the choice of the link function in this analysis is not the most important issue but still a user could also look forward to some other link functions like Probit and Complementary log-log.
3D reconstruction of an outdoor archaeological site through a multi-view stereo technique

This paper describes the experimentation of a common multi-view stereo technique on a particularly complex test case: the “Via Colonnata" in the archaeological site of Kyme Eolica in Turkey. The study demonstrates that it is possible to create a detailed 3D model of an area sized tens of square meters without the need to use any dedicated device like laser scanners, drones or helium balloons, but just employing a digital camera and open source software. The reconstruction process implemented in this study addresses and solves some of the most relevant problems related to the reconstruction of large areas and the subsequent mapping of a texture on the geometrical model. In particular, we suggest some guidelines for the acquisition phase that help to reduce the subsequent problems related both to 3D geometry creation and texture mapping. In the pre-processing phase, we propose an automated technique for filtering of unimportant areas, based on the analysis of the disparity maps related to each image pair (the farther areas from the current point of view are masked out, in order to obtain a 3D model free of artifacts/defects). For the texture mapping process, in order to reduce the blur resulting from averaging and blending operations in overlapping areas, we propose a method that automatically identifies the most appropriate subset of images to be projected on the 3D model.
Computational Models of Moral Perception , Conflict and Elevation

Computational models of moral cognition will be critical to the creation of agents and robots that operate autonomously in morally sensitive and complex domains. We propose a framework for developing computational models of moral cognition based on behavioral and neurobiological experimental results and field observations. Specifically, we discuss the following critical issues in building such models: 1. Managing conflicts between different moral concerns; 2. The role of moral perceptions in moral judgments; 3. Mechanisms and consequences of moral emotions; 4. Learning and adjusting moral behavior. Moreover, we discuss computational architectures for building and exploring models of moral cognition at different levels of analysis: individual, small groups and large groups.
Going for the Online Customer - An Interpretive Case Study of Internetworked Customer Reach in Online Entertainment

This paper explores efforts to reach the online customer in online entertainment. It does so on the basis of an interpretive case study conducted at the Swedish computer game developer Daydream Software, where the the specific objects of study were the customer reach efforts involved in the release of the game developer s new on-line game Clusterball. The Clusterball case illustrates a radical change effort in that it represents a break with the common method to distribute a computer game. Basically, it also represents a break with the conventional wisdom of competitive strategy in that it combines a mass-market strategy with a differentiation one. We explore how the unfolding process of customer reach was deeply influenced by the intertwined nature of information technology and business processes. In addition, we suggest how understanding these intertwinings would add to both the practice of online entertainement business and the body of competitive strategy knowledge.
One-Shot Rates for Entanglement Manipulation Under Non-entangling Maps

We obtain expressions for the optimal rates of one-shot entanglement manipulation under operations which generate a negligible amount of entanglement. As the optimal rates for entanglement distillation and dilution in this paradigm, we obtain the max- and min-relative entropies of entanglement, the two logarithmic robustnesses of entanglement, and smoothed versions thereof. This gives a new operational meaning to these entanglement measures. Moreover, by considering the limit of many identical copies of the shared entangled state, we partially recover the recently found reversibility of entanglement manipulation under the class of operations which asymptotically do not generate entanglement.
HIV-1 gp120 envelope glycoprotein determinants for cytokine burst in human monocytes

The first step of HIV infection involves the interaction of the gp120 envelope glycoprotein to its receptor CD4, mainly expressed on CD4+ T cells. Besides its role on HIV-1 entry, the gp120 has been shown to be involved in the production of IL-1, IL-6, CCL20 and other innate response cytokines by bystander, uninfected CD4+ T cells and monocytes. However, the gp120 determinants involved in these functions are not completely understood. Whether signalling leading to cytokine production is due to CD4 or other receptors is still unclear. Enhanced chemokine receptor binding and subsequent clustering receptors may lead to cytokine production. By using a comprehensive panel of gp120 mutants, here we show that CD4 binding is mandatory for cytokine outburst in monocytes. Our data suggest that targeting monocytes in HIV-infected patients might decrease systemic inflammation and the potential tissue injury associated with the production of inflammatory cytokines. Understanding how gp120 mediates a cytokine burst in monocytes might help develop new approaches to improve the chronic inflammation that persists in these patients despite effective suppression of viremia by antiretroviral therapy.
The monetary transmission mechanism in Italy: the credit channel and a missing ring

Research on how money affects economic activity has revived interest in the socalled "credit view". In this paper we focus on current developments in the credit view in order to assess the results of the past decade's research and its legacy for macroeconomics and monetary policy. We expound the main models of the "credit channels" of monetary transmission, drawing a distinction between models of aggregate demand, which are predominant, and models of aggregate supply, which are less developed despite theory suggests a potential connection between credit conditions and firms' production activity. Each approach is accompanied by a survey of the main empirical results with particular reference to Italy, where bankfirm relations are traditionally regarded as particularly important.