Miracle-dz/UniFAR-FTUs huggingface dataset:
Chronic pulmonary cavitary tuberculosis in rabbits: a failed host immune response

The molecular determinants of the immune response to Mycobacterium tuberculosis HN878 infection in a rabbit model of pulmonary cavitary tuberculosis were studied. Aerosol infection of rabbits resulted in a highly differentially expressed global transcriptome in the lungs at 2 weeks, which dropped at 4 weeks and then gradually increased. While IFNγ was progressively upregulated throughout the infection, several other genes in the IFNγ network were not. T-cell activation network genes were gradually upregulated and maximally induced at 12 weeks. Similarly, the IL4 and B-cell activation networks were progressively upregulated, many reaching high levels between 12 and 16 weeks. Delayed peak expression of genes associated with macrophage activation and Th1 type immunity was noted. Although spleen CD4+ and CD8+ T cells showed maximal tuberculosis antigen-specific activation by 8 weeks, macrophage activation in lungs, lymph nodes and spleen did not peak until 12 weeks. In the lungs, infecting bacilli grew exponentially up to 4 weeks, followed by a steady-state high bacillary load to 12 weeks that moderately increased during cavitation at 16 weeks. Thus, the outcome of HN878 infection of rabbits was determined early during infection by a suboptimal activation of innate immunity and delayed T-cell activation.
Predictors of Coping for Mothers of Separated/Divorced Offspring

RÉSUMÉ Cette étude examine la relation entre, d'une part, la cohésion familiale, le contrôle subjectif, et trois formes de soutien social (soutien émotionnel, apport d'information, aide concrète), et, d'autre part, les stratégies d'adaptation utilisées par les mères de personnes séparées ou divorcées. Les données ont été obtenues auprès de 84 mères âgées de 45 à 78 ans (moyenne: 61). Deux analyses de régression multiple ont été conduites en utilisant l'adaptation de type évitement (accent mis sur la ventilation des émotions, sur le désengagement mental et comportemental) et l'adaptation de type implication active (adaptation active, planification, réinterprétation positive et croissance) à titre de variables critères. Un recours plus fréquent à l'adaptation de type évitement s'est avéré être associé à une faible cohésion familiale, un bas niveau de contrôle subjectif, et à un haut niveau de soutien émotionnel. De plus, une utilisation plus importante de l'adaptation active était associé à un haut niveau de soutien émotionnel. ABSTRACT The relationship between family cohesion, perceived control, received social support types (emotional, informational, and tangible), and the coping strategies used by mothers of separated or divorced offspring was examined. Data were obtained from 84 mothers aged 45 to 78 (M age 61). Two multiple regression analyses were conducted with avoidant coping (focus on and venting emotion, behavioural disengagement, mental disengagement) and active coping (active coping, planning, positive reinterpretation and growth) serving as criterion variables. Greater use of avoidant coping was associated with low family cohesion, low perceived control, and high received emotional support. In addition, greater use of active coping was associated with high received emotional support.
UvA-DARE (Digital Detecting and disrupting criminal networks

Background: criminal networks are essentially defined as sets of actors that are connected by one or more ties. While many empirical studies of criminal networks have focused on the properties of actors (i.e. key-players), less attention is paid to the importance of ties in terms of tie-strength and its influence on emerging criminal networks. Aim: The aim of this study is to empirically study the associations between the structural, temporal and demographical dimensions of the strength of ties within organized criminal networks Method: We use a combination of social network-, statistical- and qualitative analysis to study the associations between three dimensions of tie-strength: the structural-, temporal-and demographical- dimension. Network-data: A criminal meso-network consisting of N= 5178 actors Results and conclusions: Our findings suggest that weak ties are important for the exchange of information particularly at a meso-level, but not exclusively due to a small-world effect. The majority of these ties are fluid, instrumental in nature, and often based on trust in a third party instead of between actors at both ends. ‘Freelance’ co-operation emerges out of the fluid pools of potential co-offenders. The strong ties in the network rely heavily on kinship and attachment to local neighborhoods. Different clusters of strong ties are associated with an overarching ‘old-boys’ network’ that remains more durable over time and forms a sustainable pool of criminal cooperation within the overall fluid criminal network.
A bayesian network based approach for software defects prediction

Since the inception of software project management, the quality of a software project is always a priority. Defects in a software development project lead to degradation of the quality which might be the cause of its failure. In order to predict the defects in a software development project we propose a Bayesian Network based approach. It is developed by using project repositories which store software metrics and defect information. In this approach we combine subjective judgements from experienced project managers and available defect rate data to produce a network and use this to forecast and hence control defect rates.
Lexical Tightness and Text Complexity

We present a computational notion of Lexical Tightness that measures global cohesion of content words in a text. Lexical tightness represents the degree to which a text tends to use words that are highly inter-associated in the language. We demonstrate the utility of this measure for estimating text complexity as measured by US school grade level designations of texts. Lexical tightness strongly correlates with grade level in a collection of expertly rated reading materials. Lexical tightness captures aspects of prose complexity that are not covered by classic readability indexes, especially for literary texts. We also present initial findings on the utility of this measure for automated estimation of complexity for poetry.
Rothamsted Repository Download

, Host plant shifts of herbivorous insects may be a ﬁ rst step toward sympatric speciation and can create new pests of agriculturally important crops; however, the molecular mechanisms that mediate this process are poorly understood. Certain races of the polyphagous aphid Myzus persicae have recently adapted to feed on tobacco ( Myzus persicae nicotianae ) and show a reduced sensitivity to the plant alkaloid nicotine and cross-resistance to neon- icotinoids a class of synthetic insecticides widely used for control. Here we show constitutive overexpression of a cytochrome P450 (CYP6CY3) allows tobacco-adapted races of M. persicae to ef ﬁ ciently detoxify nicotine and has preadapted them to resist neonicotinoid insecticides. CYP6CY3, is highly overexpressed in M. persicae nicotianae clones from three continents compared with M. persicae s.s. and expression level is signi ﬁ cantly correlated with tolerance to nicotine. CYP6CY3 is highly ef ﬁ cient (com-pared with the primary human nicotine-metabolizing P450) at me- tabolizing nicotine and neonicotinoids to less toxic metabolites in vitro and generation of transgenic Drosophila expressing CYP6CY3 demonstrate that it confers resistance to both compounds in vivo. Overexpression of CYP6CY3 results from the expansion of a dinucleotide microsatellite in the promoter region and a recent gene ampli ﬁ cation, with some aphid clones carrying up to 100 copies. We conclude that the mutations leading to overexpression of CYP6CY3 were a prerequisite for the host shift of M. persicae to tobacco and that gene ampli ﬁ cation and microsatellite polymorphism are evolutionary drivers in insect host adaptation.
Factors Predicting Volunteer Engagement Among Urban-Residing African American Women

Research has shown that urban-residing African American women engage in volunteer work at impressive rates. However, few studies have empirically assessed the factors that account for volunteerism within this population. This study explores the relationship between demographic variables, early religious involvement, current religious involvement, empathy, perspective taking, and volunteer engagement among African American women residing in a large urban center (N = 211). Findings from multivariate analyses revealed that current religious involvement positively predicted women’s volunteer engagement. Age was found to negatively predict volunteer engagement but positively predict the number of hours women spend volunteering per year. The implications of these findings are discussed and future lines of research considered.
“Where Are the Field Investigations?” An Investigation of the (Implied) Paradox of Learning About Environmental Education in a Virtual Classroom

There is an inherent paradox in the tenets of environmental education and the constructs of virtual classrooms. Is there a role for distance education in environmental education? Does learning about environmental education in an online course context contradict the basic principles of environmental education? This article discusses a collaborative inquiry research study that investigated student learning in an online environmental education course. RésuméIl y a un paradoxe intrinsèque dans les principes qui sous-tendent la formation environnementale et les construits des classes virtuelles. La formation à distance a-t-elle une place dans la formation sur l’environnement? L’apprentissage sur la formation environnementale dans le contexte d’un cours en ligne contredit-il les principes de base de la formation environnementale? Cet article se penche sur une étude collaborative visant à analyser l’apprentissage des étudiants dans un cours à distance portant sur la formation environnementale.
Scary warnings and rational precautions: A review of the psychology of fear appeals

Abstract Research into the effects of fear-arousal on precautionary motivation and action is reviewed. Current models do not adequately distinguish between emotional (i.e., fear arousal) and cognitive (i.e., threat perception) responses to fear appeals and, in general, are not well supported. Evidence suggesting that (i) coping appraisals are more powerful predictors of precautionary action than threat perception and that (ii) fear control processes may interfere with precautionary motivation, recommends cautious and limited use of fear appeals in health promotion. It seems likely that fear arousal is less important in motivating precautionary action than perceptions of action effectiveness and self-efficacy. Moreover, perceived personal relevance may be critical to the emotional and cognitive impact of threat information. Available findings are summarised in the form of a process model that highlights the potential complexity of fear arousal effects. Sequential measurement of fear arousal, other than by self-report, is recommended in studies seeking to clarify these effects.
Control of Spontaneous Firing Patterns by the Selective Coupling of Calcium Currents to Calcium-Activated Potassium Currents in Striatal Cholinergic Interneurons

The spontaneous firing patterns of striatal cholinergic interneurons are sculpted by potassium currents that give rise to prominent afterhyperpolarizations (AHPs). Large-conductance calcium-activated potassium (BK) channel currents contribute to action potential (AP) repolarization; small-conductance calcium-activated potassium channel currents generate an apamin-sensitive medium AHP (mAHP) after each AP; and bursts of APs generate long-lasting slow AHPs (sAHPs) attributable to apamin-insensitive currents. Because all these currents are calcium dependent, we conducted voltage- and current-clamp whole-cell recordings while pharmacologically manipulating calcium channels of the plasma membrane and intracellular stores to determine what sources of calcium activate the currents underlying AP repolarization and the AHPs. The Cav2.2 (N-type) blocker ω-conotoxin GVIA (1 μm) was the only blocker that significantly reduced the mAHP, and it induced a transition to rhythmic bursting in one-third of the cells tested. Cav1 (L-type) blockers (10 μm dihydropyridines) were the only ones that significantly reduced the sAHP. When applied to cells induced to burst with apamin, dihydropyridines reduced the sAHPs and abolished bursting. Depletion of intracellular stores with 10 mm caffeine also significantly reduced the sAHP current and reversibly regularized firing. Application of 1 μm ω-conotoxin MVIIC (a Cav2.1/2.2 blocker) broadened APs but had a negligible effect on APs in cells in which BK channels were already blocked by submillimolar tetraethylammonium chloride, indicating that Cav2.1 (Q-type) channels provide the calcium to activate BK channels that repolarize the AP. Thus, calcium currents are selectively coupled to the calcium-dependent potassium currents underlying the AHPs, thereby creating mechanisms for control of the spontaneous firing patterns of these neurons.
Identification of MiRNAs as specific biomarkers in prostate cancer diagnostics : A combined in silico and molecular approach

Cancer is a class of diseases, classified by the organ of origin and characterized by uncontrollable cell growth. Our focus is on prostate cancer (PC) which starts in the prostate and is generally a walnut-sized gland located below the bladder. Approximately 4500 males in South Africa are diadnosed annually, thus making it the second most common cause of cancer death in men. Current diagnostic methods include digital rectal examinations (DRE), prostate specific antigen test (PSA), biopsy and ultrasound however, they are invasive and lack specificity and sensitivity. Therefore, the development of a noninvasive, specific and sensitive early detection method is required. Biomarkers are biological indicators i.e. DNA, proteins and miRNA, which have recently been identified as targets for the early detection of disease. MiRNAs are small, naturally occurring, non-coding RNA molecules directly involved in regulating gene expression at the post-transcriptional level. They offer great potential as biomarkers for cancer detection due to their remarkable stability in blood and characteristic expression in different diseases. The aim of this study is therefore to identify miRNAs as specific biomarkers for the early detection of PC. The identification of specific miRNAs and their targets will be done using various bioinformatics techniques including programming and statistical analyses. Once identified, these miRNAs will be experimentally validated to generate expression profiles using molecular techniques. Furthermore, newly identified, experimentally validated miRNAs will be used in combination with nanotechnology to develop a diagnostic kit for the early detection of PC. IWBBIO 2013. Proceedings Granada, 18-20 March, 2013 161
Cytoplasmic ATP Hydrolysis Powers Transport of Lipopolysaccharide Across the Periplasm in E. coli

Powering LPS Export The surface of Gram-negative bacteria such as Escherichia coli is covered in lipopolysaccharide (LPS), which must be synthesized within the cytoplasm and then exported across the periplasm to the outer leaflet of the outer membrane. Okuda et al. (p. 1214, published online 8 November) describe the detection of LPS molecules bound to specific components of the E. coli lipopolysaccharide exporter during transport in vivo. In vitro reconstitution of LPS transport revealed the energetic requirements for the first two steps of transport, release from the membrane and transit along the periplasmic bridge of the exporter that connects the inner and outer membrane components. The findings suggest that adenosine triphosphate hydrolysis by a cytoplasmic component of the machine provides energy to push a continuous stream of LPS against its concentration gradient to the cell surface. Transporting lipopolysaccharide from inside the bacterial cell to the surface requires multiple molecules of adenosine triphosphate. Millions of molecules of lipopolysaccharide (LPS) must be assembled on the Escherichia coli cell surface each time the cell divides. The biogenesis of LPS requires seven essential lipopolysaccharide transport (Lpt) proteins to move LPS from the inner membrane through the periplasm to the cell surface. However, no intermediate transport states have been observed. We developed methods to observe intermediate LPS molecules bound to Lpt proteins in the process of being transported in vivo. Movement of individual LPS molecules along these binding sites required multiple rounds of adenosine triphosphate (ATP) hydrolysis in vitro, which suggests that ATP is used to push a continuous stream of LPS through a transenvelope bridge in discrete steps against a concentration gradient.
SPARQL Update for Materialized Triple Stores under DL-Lite_RDFS Entailment

Updates in RDF stores have recently been standardised in the SPARQL 1.1 Update specification. However, computing answers entailed by ontologies in triple stores is usually treated orthogonally to updates. Even W3C’s SPARQL 1.1 Update language and SPARQL 1.1 Entailment Regimes specifications explicitly exclude a standard behaviour for entailment regimes other than simple entailment in the context of updates. In this paper, we take a first step to close this gap. We define a fragment of SPARQL basic graph patterns corresponding to (the RDFS fragment of) DL-Lite and the corresponding SPARQL update language, dealing with updates both of ABox and of TBox statements. We discuss possible semantics along with potential strategies for implementing them. Particularly, we treat materialised RDF stores, which store all entailed triples explicitly, and preservation of materialisation upon ABox and TBox updates.
Variations in Alveolar Partial Pressure for Carbon Dioxide and Oxygen Have Additive Not Synergistic Acute Effects on Human Pulmonary Vasoconstriction

The human pulmonary vasculature constricts in response to hypercapnia and hypoxia, with important consequences for homeostasis and adaptation. One function of these responses is to direct blood flow away from poorly-ventilated regions of the lung. In humans it is not known whether the stimuli of hypercapnia and hypoxia constrict the pulmonary blood vessels independently of each other or whether they act synergistically, such that the combination of hypercapnia and hypoxia is more effective than the sum of the responses to each stimulus on its own. We independently controlled the alveolar partial pressures of carbon dioxide (Paco 2) and oxygen (Pao 2) to examine their possible interaction on human pulmonary vasoconstriction. Nine volunteers each experienced sixteen possible combinations of four levels of Paco 2 (+6, +1, −4 and −9 mmHg, relative to baseline) with four levels of Pao 2 (175, 100, 75 and 50 mmHg). During each of these sixteen protocols Doppler echocardiography was used to evaluate cardiac output and systolic tricuspid pressure gradient, an index of pulmonary vasoconstriction. The degree of constriction varied linearly with both Paco 2 and the calculated haemoglobin oxygen desaturation (1-So 2). Mixed effects modelling delivered coefficients defining the interdependence of cardiac output, systolic tricuspid pressure gradient, ventilation, Paco 2 and So 2. No interaction was observed in the effects on pulmonary vasoconstriction of carbon dioxide and oxygen (p>0.64). Direct effects of the alveolar gases on systolic tricuspid pressure gradient greatly exceeded indirect effects arising from concurrent changes in cardiac output.
CPHmodels-3.0—remote homology modeling using structure-guided sequence profiles

CPHmodels-3.0 is a web server predicting protein 3D structure by use of single template homology modeling. The server employs a hybrid of the scoring functions of CPHmodels-2.0 and a novel remote homology-modeling algorithm. A query sequence is first attempted modeled using the fast CPHmodels-2.0 profile–profile scoring function suitable for close homology modeling. The new computational costly remote homology-modeling algorithm is only engaged provided that no suitable PDB template is identified in the initial search. CPHmodels-3.0 was benchmarked in the CASP8 competition and produced models for 94% of the targets (117 out of 128), 74% were predicted as high reliability models (87 out of 117). These achieved an average RMSD of 4.6 Å when superimposed to the 3D structure. The remaining 26% low reliably models (30 out of 117) could superimpose to the true 3D structure with an average RMSD of 9.3 Å. These performance values place the CPHmodels-3.0 method in the group of high performing 3D prediction tools. Beside its accuracy, one of the important features of the method is its speed. For most queries, the response time of the server is <20 min. The web server is available at http://www.cbs. dtu.dk/services/CPHmodels/.
Newspaper Treatment of a Candidate's News Releases

for women is 58% of that of men. (See Table I.) Why such discrepancies in salaries? The key element in determining salaries is usually journalism experience. And this is where women fall behind. Women and men congressionally accredited correspondents do not have equal professional experience. Median amount of journalism experience for women was nine years compared to the man's 15 years. This is not surprising, given the eight-year age difference. (See Table 2). This difference in journalistic experience partially explains the great differential in salaries, but not entirely. Years of experience is not the only element in setting pay scales for men and women journalists. Women, often times, are brought on the j o b at lower wages than men. For example, the majority of men with five years journalism expenence or less made $20,000 per year or more, Most women with less than five years experience earned between $ 10,000 and 520,OOO per year and 17% of the women with less than five years experience earned less than $1O,OOO per year. Despite the discrepancies in income and experience, there is a bright spot in this analysis. Women correspondents are making headway in the type of work being done. Once, almost exclusively, women reporters covered such "lady like" beats as religion and society.6 Now women are holding higher positions in the news business. Nearly 28% of the women journalists interviewed in this study were editors, compared to 19% of the men. These percentages should not be interpreted as a massive takeover of the editors' chairs by women. This merely indicates that women interviewed were given some responsible positions in journalism. The majority of the editors in Washington and in the country are men. The women correspondents also worked for a diversity of news organizations, including the growing trade, o r specialized press. Women d o not appear to be excluded from any particular type of news organization.
Patterns of Daily Time Use of Young Adults With or Without First-Episode Psychosis

This study compared patterns of daily activities and satisfaction with time use of young adults with first-episode psychosis and healthy volunteers. Fifty young adults participated in retrospective structured interviews on time use. Young adults with first-episode psychosis spend more time in sleep, passive leisure, and personal care activities, and less in total productive activities and education. No difference appeared for leisure, paid work, and household work, or satisfaction with daily time use. Reasons underlying dissatisfaction with daily time use differed between the groups. Clinical and research implications are discussed.