Miracle-dz/UniFAR-FTUs huggingface dataset:
Human Immunodeficiency Virus Type 1 Vpr Impairs Dendritic Cell Maturation and T-Cell Activation: Implications for Viral Immune Escape

ABSTRACT Antigen presentation and T-cell activation are dynamic processes involving signaling molecules present in both APCs and T cells. Effective APC function and T-cell activation can be compromised by viral immune evasion strategies, including those of human immunodeficiency virus type 1 (HIV-1). In this study, we determined the effects of HIV-1 Vpr on one of the initial target of the virus, dendritic cells (DC), by investigating DC maturation, cytokine profiling, and CD8-specific T-cell stimulation function followed by a second signal. Vpr impaired the expression of CD80, CD83, and CD86 at the transcriptional level without altering normal cellular transcription. Cytokine profiling indicated that the presence of Vpr inhibited production of interleukin 12 (IL-12) and upregulated IL-10, whereas IL-6 and IL-1β were unaltered. Furthermore, DC infected with HIV-1 vpr+ significantly reduced the activation of antigen-specific memory and recall cytotoxic-T-lymphocyte responses. Taken together, these results indicate that HIV-1 Vpr may in part be responsible for HIV-1 immune evasion by inhibiting the maturation of costimulatory molecules and cytokines essential for immune activation.
MST construction in O(log log n) communication rounds

We consider a simple model for overlay networks, where all n processes are connected to all other processes, and each message contains at most O(log n) bits. For this model, we present a distributed algorithm that constructs a minimum-weight spanning tree in O(log log n) communication rounds, where in each round any process can send a message to each other process. This result is the first to break the ω(log n) parallel time complexity barrier with small message sizes.
Good, Giving, and Game

In two dyadic studies (a short-term longitudinal study and a daily experience study), we demonstrate that people high in sexual communal strength (i.e., those motivated to meet a romantic partner’s sexual needs) have partners who are more satisfied with and committed to their relationships. In Study 1, people higher in sexual communal strength had partners who felt more satisfied and committed to the relationship both at that time and 3 weeks later. In Study 2, the partners of people high in sexual communal strength perceived their partners as more responsive to their needs during sex, and this was one reason why they reported feeling more satisfied and committed in the relationship. Implications for theories of communal motivation and approaches to sexuality in romantic relationships are discussed.
Detection of T and B cells specific complement-fixing alloantibodies using flow cytometry: A diagnostic approach for a resource limited laboratory

Background and Objectives: Various methods have been reported for the detection of antibodies in recipient sera, which can be human leukocyte antigens (HLAs) or non-HLA specific, complement- or noncomplement fixing, as well as donor T (HLA-Class-I) and/or B cell (HLA-Class-I and II) specific. These alloantibodies play a pivotal role in antibody-mediated renal transplantation rejection. Deposition of C4d in peritubular capillaries of a kidney biopsy is a marker of antibody-mediated rejection. The C4d flow-panel reactive antibodies (PRAs) are a screening method for HLA-specific and complement fixing antibodies. However, the method is limited by the lack of donor specificity. Design and Settings: Here, we present a new and simple flow cytometric method referred to as C4d-flow cytometry crossmatch (C4d-FCXM) for the detection of donor-specific (T and/or B cell) and C4d-fixing alloantibodies. Results: The method was applied in a series of clinical cases and judged to be useful. The method may limit unwanted deferral of the donor due to positivity in C4d Flow-PRA and/or FCXM and may be helpful in prediction of antibody mediated rejections. Furthermore, this method can provide information pretransplant in contrast to kidney biopsy and C4d evaluation done posttransplant. Conclusions: We postulate that this method incorporates most of the features of all the available modalities (i.e., National Institute of Health-complement dependent lymphocytotoxicity, FCXM, cytotoxic FCXM and C4d-flowPRA) yet cost-effective and best suited for resource-limited laboratory/ies which is a common scenario in developing countries.
The Genetic Basis of Baculum Size and Shape Variation in Mice

The rapid divergence of male genitalia is a preeminent evolutionary pattern. This rapid divergence is especially striking in the baculum, a bone that occurs in the penis of many mammalian species. Closely related species often display diverse baculum morphology where no other morphological differences can be discerned. While this fundamental pattern of evolution has been appreciated at the level of gross morphology, nearly nothing is known about the genetic basis of size and shape divergence. Quantifying the genetic basis of baculum size and shape variation has been difficult because these structures generally lack obvious landmarks, so comparing them in three dimensions is not straightforward. Here, we develop a novel morphometric approach to quantify size and shape variation from three-dimensional micro-CT scans taken from 369 bacula, representing 75 distinct strains of the BXD family of mice. We identify two quantitative trait loci (QTL) that explain ∼50% of the variance in baculum size, and a third QTL that explains more than 20% of the variance in shape. Together, our study demonstrates that baculum morphology may diverge relatively easily, with mutations at a few loci of large effect that independently modulate size and shape. Based on a combination of bioinformatic investigations and new data on RNA expression, we prioritized these QTL to 16 candidate genes, which have hypothesized roles in bone morphogenesis and may enable future genetic manipulation of baculum morphology.
‘Neutrality Comes From Inside Us’: British-Asian and Indian Perspectives on Television News after 11 September

This paper focuses on responses to the viewing of television news channels during and after 11 September 2001 by a sample of Indian viewers in Bombay and British-Asian viewers in South-East England. Viewers’ perceptions of neutrality, bias, reliability and vested interests within news channels and organisations are discussed, alongside the manner in which issues of gender, age and religion impact on the meanings made from and imputed to the news coverage of the attacks on America and Afghanistan. As well as considering the ways in which multilingual and sometimes transnational families experience television news in the contemporary arena, the paper addresses questions about the political significance and social impact of news broadcasts within communities with pre-existing beliefs and world views. We argue that the ways in which many so-called ‘international’ news channels covered issues of blame, evidence and retribution with regard to the Twin Tower and Pentagon attacks raised levels of tension, increased communal dislikes and reinforced pre-existing animosities against Muslim communities across the world.
CD4+ T cell activation and tolerance induction in B cell knockout mice

B cell knockout mice microMT/microMT were used to examine the requirement for B cell antigen (Ag) presentation in the establishment of CD4+ T cell tolerance. CD4+T cells from microMT mice injected with exogenous protein Ag in adjuvant responded to in vitro challenge by transcription of cytokine mRNA, cytokine secretion, and proliferation. Peripheral tolerance could be established in microMT mice with a single dose of deaggragated protein. This tolerance was manifested by a loss of T cell proliferation and cytokine production (including both T helper cell type 1 [Th1]- and Th2-related cytokines), indicating that B cells are not required for the induction of peripheral T cell tolerance and suggesting that the dual zone tolerance theory is not applicable to all protein Ags and is not mediated through Ag presentation by B cells.
Isolation and identification of bacterial endophytes from pharmaceutical agarwood-producing Aquilaria species

Background: Resins and gums are used in traditional medicine and do have potential applications in pharmacy and medicine. Agarwood is the fragrant resinous wood, which is an important commodity from Aquilaria species and has been used as a sedative, analgesic, and digestive in traditional medicine. Endophytic bacteria are potentially important in producing pharmaceutical compounds found in the plants. Hence, it was important to understand which types of endophytic bacteria are associated with pharmaceutical agarwood-producing Aquilaria species. Objective: This study was undertaken to isolate and identify endophytic bacteria associated with agarwood-producing seven (7) Aquilaria species from Malaysia. Materials and Methods: Botanical samples of seven Aquilaria species were collected, and endophytic bacteria were isolated from surface-sterilized-tissue samples. The 16S rRNA gene fragments were amplified using PCR method, and endophytic bacterial isolates (EBIs) were identified based on 16S rRNA gene sequence similarity based method. Results: Culturable, 77 EBIs were analyzed, and results of 16S rRNA gene sequences analysis suggest that 18 different types of endophytic bacteria are associated with (seven) Aquilaria species. From 77 EBIs, majority (36.4%) of the isolates were of Bacillus pumilus. Conclusion: These findings indicate that agarwood-producing Aquilaria species are harboring 18 different types of culturable endophytic bacteria.
Communicating Student Evaluation of Teaching Results: Rating Interpretation Guides (RIGs)

In the past decade student evaluation of teaching has expanded within Australian universities, with the results of evaluations increasingly being used to make judgements about teaching quality, career advancement and the funding of teaching. An important component of any student evaluation of teaching system is, therefore, the communication of rating results in a manner that enables fair and meaningful interpretations and comparisons of results by the wide range of evaluation users. This paper describes the development in one Australian university of Rating Interpretation Guides (RIGs) which take into account the influence of different teaching contexts on ratings and encourage evaluation users to explore ratings in terms of a range of scores rather than focusing on a single mean score. RIGs represent an important innovation in the communication of evaluation results for both formative and summative evaluation purposes. They are designed to enable meaningful interpretations of ratings which in turn will encourage appropriate use of results.
Healthy Eating in Schools, Overweight and ‘Eating Disorders’: are they connected?

Abstract This paper raises questions about the increase in ‘eating disorders’ and the widespread preoccupation with diet and weight among girls in both primary and secondary schools. Obesity and overweight are also on the increase (in adults and children) and are seen as priorities to be tackled by health promotion. Empirical research is required to investigate the effects of educational messages aimed at children about fat in the diet and healthy eating, and their possible implication in the increase in both overweight and in pre‐occupation with body size. Is health education actually part of the problem, making girls more conscious of their weight? The paper reviews some of the relevant literature and also suggests practices in schools which may help or hinder true ‘healthy eating’ and healthy perceptions of self. Whilst teachers should not be expected to tackle clinical cases of ‘eating disorders’, there is much that can be achieved in schools to promote children's self‐esteem and positive body image, .
Socio-economic differences in fruit and vegetable consumption among Australian adolescents and adults

Abstract Objectives: To determine whether socio-economic groups differ in their fruit and vegetable consumption, and the variety eaten, and whether socio-economic differences are similar for adolescents and adults. The study also examined whether socio-economic groups vary in their reported desire to increase the amount of fruit and vegetables consumed, and the perceived barriers to achieving this. Design, setting and subjects: The 1995 Australian National Nutrition Survey collected fruit and vegetable intake data from adolescents aged 13–17 years (n = 654) and adults 18–64 years (n = 7695) using a 24-hour dietary recall. Gross annual household income was used to measure socio-economic position. Results: Approximately 44% of males and 34% of females did not consume fruit in the 24 hours preceding the survey, and 20% of males and 17% of females did not consume vegetables. Among adolescents and adults, fruit and vegetable consumption was positively related to income. The only exception was vegetable consumption among adolescent males, which did not vary by income Lower-income adults consumed a smaller variety of fruits and vegetables than their higher-income counterparts. Fruit and vegetable variety did not vary by income among adolescents. Lower-income adults expressed less desire to increase their fruit and vegetable consumption, and were more likely to report that price and storage were barriers to doing so. Socio-economic differences in consumption and variety were more apparent for adults than for adolescents. Conclusions: In addition to increasing the consumption of fruits and vegetables among the general population, nutrition interventions, programmes and policy aiming to improve diet should target adolescents and adults from low socio-economic groups. Strategies should address price and storage barriers.
Bilingual Generation Effect: Variations in Participant Bilingual Type and List Type

Abstract Slamecka and Katsaiti (1987, Experiment 1) reported that there is no generation effect with bilingual materials under intentional learning instructions. In contrast, O'Neill, Roy, and Tremblay (1993, Experiment 1) demonstrated a bilingual generation effect when an incidental learning set was induced. In the present experiment, the possibility that another procedural variation between the two studies accounts for the disparate findings was examined. A 2-stimuli (read bilingual translations, generate bilingual translations) list was compared with a 3-stimuli (read bilingual translations, generate bilingual translations, read unilingual repetitions) list, in accordance with the procedures used in the earlier experiments. Under incidental learning conditions, for both list types, a strong generation effect was found. Participant type—coordinate or compound bilingualism—was also varied. The generation effect was much larger for compound bilinguals than for coordinate bilinguals, presumably because of .
Barriers to women’s progression into nurse management in the National Health Service

Women are failing to enter senior management levels across all occupational groupings. Barriers to the progression of women into nurse management (NHS) are examined. Substantial evidence of gender‐based disadvantage is found. Women with dependent children, especially those working part‐time, are located in the lower nurse grades irrespective of their qualifications and experience. The resultant outcome is one where otherwise comparable groups of female nurses experience unequal access to the nurse management grades. Three problems are identified: the low status of part‐time work; inflexible working practices and management inertia. Therefore, despite rhetorical support for the introduction of initiatives which would overcome some of these barriers, little has materialised by way of introducing such initiatives.
Phorbol Esters and SDF-1 Induce Rapid Endocytosis and Down Modulation of the Chemokine Receptor CXCR4

The chemokine receptor CXCR4 is required, together with CD4, for entry by some isolates of HIV-1, particularly those that emerge late in infection. The use of CXCR4 by these viruses likely has profound effects on viral host range and correlates with the evolution of immunodeficiency. Stromal cell-derived factor-1 (SDF-1), the ligand for CXCR4, can inhibit infection by CXCR4-dependent viruses. To understand the mechanism of this inhibition, we used a monoclonal antibody that is specific for CXCR4 to analyze the effects of phorbol esters and SDF-1 on surface expression of CXCR4. On human T cell lines SupT1 and BC7, CXCR4 undergoes slow constitutive internalization (1.0% of the cell surface pool/min). Addition of phorbol esters increased this endocytosis rate >6-fold and reduced cell surface CXCR4 expression by 60 to 90% over 120 min. CXCR4 was internalized through coated pits and coated vesicles and subsequently localized in endosomal compartments from where it could recycle to the cell surface after removal of the phorbol ester. SDF-1 also induced the rapid down modulation (half time ∼5 min) of CXCR4. Using mink lung epithelial cells expressing CXCR4 and a COOH-terminal deletion mutant of CXCR4, we found that an intact cytoplasmic COOH-terminal domain was required for both PMA and ligand-induced CXCR4 endocytosis. However, experiments using inhibitors of protein kinase C indicated that SDF-1 and phorbol esters trigger down modulation through different cellular mechanisms. SDF-1 inhibited HIV-1 infection of mink cells expressing CD4 and CXCR4. The inhibition of infection was less efficient for CXCR4 lacking the COOH-terminal domain, suggesting at least in part that SDF-1 inhibition of virus infection was mediated through ligand-induced internalization of CXCR4. Significantly, ligand induced internalization of CXCR4 but not CD4, suggesting that CXCR4 and CD4 do not normally physically interact on the cell surface. Together these studies indicate that endocytosis can regulate the cell-surface expression of CXCR4 and that SDF-1–mediated down regulation of cell-surface coreceptor expression contributes to chemokine-mediated inhibition of HIV infection.
Scalable approaches for analysis of human genome-wide expression and genetic variation data

One of the major tasks in bioinformatics and computational biology is prediction of phenotype from molecular data. Predicting phenotypes such as disease opens the way to better diagnostic tools, potentially identifying disease earlier than would be detectable using other methods. Examining molecular signatures rather than clinical phenotypes may help refine disease classification and prediction procedures, since many diseases are known to have multiple molecular subtypes with differing etiology, prognosis, and treatment options. Beyond prediction itself, identifying predictive markers aids our understanding of the biological mechanisms underlying phenotypes such as disease, generating hypotheses that can be tested in the lab. The aims of this thesis are to develop effective and efficient computational and statistical tools for analysing large scale gene expression and genetic datasets, with an emphasis on predictive models. Several key challenges include high dimensionality of the data, which has important statistical and computational implications, noisy data due to measurement error and stochasticity of the underlying biology, and maintaining biological interpretability without sacrificing predictive performance. We begin by examining the problem of predicting breast cancer metastasis and relapse from gene expression data. We present an alternative approach based on gene set statistics. Second, we address the problem of analysing large human case/control genetic (single nucleotide polymorphism) data, and present an efficient and scalable algorithm for fitting sparse models to large datasets. Third, we apply sparse models to genetic case/control datasets from eight complex human diseases, evaluating how each one can be predicted from genotype. Fourth, we apply sparse models lasso methods to a multi-omic dataset consisting of genetic variation, gene expression, and serum metabolites, for reconstruction of genetic regulatory networks. Finally, we propose a novel multi-task statistical approach, intended for modelling multiple correlated phenotypes. In summary, this thesis discusses a range of predictive models and applies them to a wide range of problems, including gene expression, genetic, and multi-omic datasets. We demonstrate that such models, and particularly sparse models, are computationally feasible and can scale to large datasets, provide increased insight into the biological causes of disease, and for some diseases have high predictive performance, allowing high-confidence disease diagnosis to be made based on genetic data.
Antigenic specificity of immunoprotective therapeutic vaccination for glaucoma.

PURPOSE To investigate the antigenic specificity of the immune neuroprotective mechanism that can protect retinal ganglion cells (RGCs) against death caused by high intraocular pressure (IOP). METHODS A unilateral increase in IOP was induced in rats by argon laser photocoagulation of the episcleral veins and limbal plexus. Rats with high IOP were immunized with glatiramer acetate (Cop-1, a synthetic copolymer) or with myelin-derived or uveitogenic peptides. When the steroid drug methylprednisolone was used, it was administered intraperitoneally every other day for 12 days. RESULTS Vaccination with myelin-derived peptides that reside in the axons failed to protect RGCs from death caused by high IOP. In contrast, IOP-induced RGC loss was reduced by vaccination with R16, a peptide derived from interphotoreceptor retinoid-binding protein, an immunodominant antigen residing in the eye. The benefit of protection against IOP-induced RGC loss outweighed the cost of the monophasic experimental autoimmune uveitis (EAU) that transiently developed in a susceptible rat strain. Treatment with methylprednisolone alleviated the disease symptoms, but caused further loss of RGCs. Cop-1 vaccination was effective in both EAU-resistant and EAU-susceptible strains. CONCLUSIONS To benefit damaged neurons, immune neuroprotection should be directed against immunodominant antigens that reside in the site of damage. In a rat model of high IOP, RGCs can benefit from vaccination with peptides derived from proteins that are immunodominant in the eye but not from myelin-associated proteins. This suggests that the site of primary degeneration in IOP-induced RGC loss is in the eye. Cop-1 vaccination apparently circumvents the site-specificity barrier and provides protection without risk of inducing autoimmune disease.
Cognitive processes in children's multimedia text learning

The cognitive processes underlying children's multimedia text learning were studied using a self-paced task and authentic school texts with mostly representational pictures in an elementary school setting. Both the quantity and quality of learning were assessed immediately following intervention and 1 week later. In a within-subjects design, all of the children were taught four lessons of a different format: (1) written presentation only; (2) written presentation accompanied by pictures; (3) oral presentation only and (4) oral presentation accompanied by pictures. With respect to the quantity of learning, a short-term modality effect was found with oral presentation producing better results than written presentation when accompanied by pictures. A multimedia effect was found for only the oral conditions. With respect to the quality of the children's learning, an initial short-term modality effect was found but reversed 1 week following intervention with no evidence of a multimedia effect. Copyright © 2008 John Wiley & Sons, Ltd.