Miracle-dz/UniFAR-FTUs huggingface dataset:
The impact of human leukocyte antigen (HLA) micropolymorphism on ligand specificity within the HLA-B*41 allotypic family

Background Polymorphic differences between human leukocyte antigen (HLA) molecules affect the specificity and conformation of their bound peptides and lead to differential selection of the T-cell repertoire. Mismatching during allogeneic transplantation can, therefore, lead to immunological reactions. Design and Methods We investigated the structure-function relationships of six members of the HLA-B*41 allelic group that differ by six polymorphic amino acids, including positions 80, 95, 97 and 114 within the antigen-binding cleft. Peptide-binding motifs for B*41:01, *41:02, *41:03, *41:04, *41:05 and *41:06 were determined by sequencing self-peptides from recombinant B*41 molecules by electrospray ionization tandem mass spectrometry. The crystal structures of HLA-B*41:03 bound to a natural 16-mer self-ligand (AEMYGSVTEHPSPSPL) and HLA-B*41:04 bound to a natural 11-mer self-ligand (HEEAVSVDRVL) were solved. Results Peptide analysis revealed that all B*41 alleles have an identical anchor motif at peptide position 2 (glutamic acid), but differ in their choice of C-terminal pΩ anchor (proline, valine, leucine). Additionally, B*41:04 displayed a greater preference for long peptides (>10 residues) when compared to the other B*41 allomorphs, while the longest peptide to be eluted from the allelic group (a 16mer) was obtained from B*41:03. The crystal structures of HLA-B*41:03 and HLA-B*41:04 revealed that both alleles interact in a highly conserved manner with the terminal regions of their respective ligands, while micropolymorphism-induced changes in the steric and electrostatic properties of the antigen-binding cleft account for differences in peptide repertoire and auxiliary anchoring. Conclusions Differences in peptide repertoire, and peptide length specificity reflect the significant functional evolution of these closely related allotypes and signal their importance in allogeneic transplantation, especially B*41:03 and B*41:04, which accommodate longer peptides, creating structurally distinct peptide-HLA complexes.
Morpholino-based gene knockdown screen of novel genes with developmental function in Ciona intestinalis

In the present study, we conducted an extensive analysis to identify novel genes with developmental function among Ciona intestinalis genes discovered by cDNA projects. Translation of a total of 200 genes expressed during embryogenesis was suppressed by using specific morpholino antisense oligonucleotides. Suppression of the translation of any of 40 genes (one-fifth of the genes tested) was thereby shown to cause specific embryonic defects. Most of these genes have counterpart(s) in mouse and human, suggesting that the present approach will be useful for identifying candidate genes essential for the development of vertebrates. Suppression of translation of 14 of these 40 genes resulted in the `disorganized body plan' phenotype characterized by gross morphological abnormalities caused by early defects in embryogenesis. These genes encode zinc-finger, transmembrane or Pbx homeodomain proteins. The morphological features of larvae of this phenotypic class varied according to the gene suppressed, suggesting that a distinct developmental event such as tissue specification or cell cycle progression was affected in each type of larva. Suppression of the remaining 26 genes resulted in the `abnormal tail' phenotype. Some of these genes encode proteins with known functional structures such as Zn-finger and HLH motifs. Twelve genes among them are especially interesting, because their suppression produced defects in the nervous system, as demonstrated by the loss of the sensory pigment cells or palps of the adhesive organ in the knockdown larvae. These results suggest that screening for developmental genes by the reverse genetic approach in Ciona intestinalis embryos is effective for identifying novel genes with developmental functions required for the development of chordates.
Fel d 4, a cat lipocalin allergen

Background Cat allergy is unique among allergy to mammals in that the major allergen Fel d 1 is a uteroglobin‐like protein and not a lipocalin. The biochemical spectrum of the cat allergens is thus uncertain, particularly with regard to the role that a cat lipocalin protein may play in sensitization to cats in allergic individuals.
Exploring the determinants of uncertainty in contingent valuation surveys

This paper uses the interval data model to explore the determinants of uncertainty in two-way payment ladder and in multiple-bounded uncertainty choice surveys. It estimates the uncertainty function that relates the size of the willingness-to-pay range to explanatory variables, where one of them is a proxy of the actual willingness-to-pay. The combination of the interval data model and the inclusion of the proxy variable present some advantages over the ordinary least square estimations currently used in the literature. In particular, it reduces the risk of the omitted variable bias and it takes into account that the dependent variable is not fully observed.
The Demise of the Golden Toad and the Creation of a Climate Change Icon Species

There is an unavoidable degree of uncertainty associated with future climate projections, and even more unpredictability about the potential impact of different climate scenarios on the ecology and distribution of organisms. Conservationists face a major public communications challenge to both raise awareness and mobilise support for conservation and climate change mitigation/adaptation policies while realistically representing complex and uncertain scientific information. Here, we illustrate the interplay of these competing communication goals through a review of the representations of the golden toad in the print media and peer-reviewed literature (in English and Spanish). Since its disappearance in 1989 the toad has become an important conservation flagship species that has been frequently portrayed as the first verified extinction attributable to global warming. Moreover, there was an increase in the certainty of published news items regarding the toad and its demise, especially in the late 1990s. The uncertainty surrounding the toad's disappearance (apparent in the primary research literature) was poorly represented in the popular press. The transformation of the toad into an iconic species for climate change advocacy may reflect a perceived need to supply tangible evidence of biodiversity consequences arising from climate change and highlights the challenges facing conservation scientists in communicating scientific concerns and uncertainty via the media.
Elder abuse as a risk factor for hospitalization in older persons.

IMPORTANCE Elder abuse is associated with increased mortality risk. However, the relationship between elder abuse and health care services utilization remains unclear. OBJECTIVE To examine the relationship between overall elder abuse and specific subtypes of elder abuse and rate of hospitalization in a community-dwelling population of older adults. DESIGN Prospective population-based study. SETTING Chicago Health and Aging Project. PARTICIPANTS Of the 6674 community-dwelling older adults who participated in the Chicago Health and Aging Project, 106 were identified by social services agencies for elder abuse. MAIN OUTCOMES AND MEASURES The primary predictor was elder abuse (reported and confirmed) reported to social services agency. The outcome of interest was the annual rate of hospitalization obtained from the Centers for Medicare and Medicaid Services. Poisson regression models were used to assess these longitudinal relationships. RESULTS The unadjusted mean annual rate of hospitalization was 0.62 (95% CI, 0.59-0.66) for those without elder abuse and 1.97 (95% CI, 1.33-2.61) for those with reported elder abuse. After adjusting for sociodemographic and socioeconomic variables, medical comorbidities, cognitive and physical function, and psychosocial well-being, reported elder abuse had higher rates of hospitalization (rate ratio [RR], 2.00 [95% CI, 1.45-2.75]). Psychological abuse (RR, 2.22 [95% CI, 1.44-3.43]), financial exploitation (RR, 1.75 [95% CI, 1.06-2.90]), caregiver neglect (RR, 2.43 [95% CI, 1.60-3.69]), and 2 or more types of elder abuse (RR, 2.59 [95% CI, 1.82-3.66]) were associated with increased rates of hospitalization, after considering the same potential confounders. Results from interaction term analyses suggested that the association between elder abuse and hospitalization did not differ across the levels of medical comorbidities, cognitive and functional impairment, or psychosocial distress. CONCLUSIONS AND RELEVANCE Elder abuse was associated with increased rates of hospitalization in this community population. Future research is needed to explore the causal mechanisms between elder abuse and hospitalization. As we enter the era of health care reform, an improved understanding of factors that increase rates of hospitalization could also have significant implications for social and health policy as well as clinical care of the vulnerable patients.
Analysis of Spamming Threats and Some Possible Solutions for Online Social Networking Sites (OSNS)

 Abstract — In this paper we are presenting some spamming techniques their behaviour and possible solutions. We have analyzed how Spammers enters into online social networking sites (OSNSs) to target them and diverse techniques used by them for this purpose. Spamming is very common issue in present era of Internet especially through Online Social Networking Sites (like Facebook, Twitter, and Google+ etc.). Spam messages keep wasting Internet bandwidth and the storage space of servers. On social networking sites; spammers often disguise themselves by creating fake accounts and hijacking user’s accounts for personal gains. They behave like normal user and they continue to change their spamming strategy. Following spamming techniques are discussed in this paper like clickjacking, social engineered attacks, cross site scripting, URL shortening, and drive by download. We have used elgg framework for demonstration of some of spamming threats and respective implementation of solutions.
Gustatory Receptors Required for Avoiding the Insecticide l-Canavanine

Insect survival depends on contact chemosensation to sense and avoid consuming plant-derived insecticides, such as l-canavanine. Members of a family of ∼60 gustatory receptors (GRs) comprise the main peripheral receptors responsible for taste sensation in Drosophila. However, the roles of most Drosophila GRs are unknown. In addition to GRs, a G protein-coupled receptor, DmXR, has been reported to be required for detecting l-canavanine. Here, we showed that GRs are essential for responding to l-canavanine and that flies missing DmXR displayed normal l-canavanine avoidance and l-canavanine-evoked action potentials. Mutations disrupting either Gr8a or Gr66a resulted in an inability to detect l-canavanine. We found that l-canavanine stimulated action potentials in S-type sensilla, which were where Gr8a and Gr66a were both expressed, but not in Gr66a-expressing sensilla that did not express Gr8a. l-canavanine-induced action potentials were also abolished in the Gr8a and Gr66a mutant animals. Gr8a was narrowly required for responding to l-canavanine, in contrast to Gr66a, which was broadly required for responding to other noxious tastants. Our data suggest that GR8a and GR66a are subunits of an l-canavanine receptor and that GR8a contributes to the specificity for l-canavanine.
Role of Homologous Recombination in Adaptive Diversification of Extraintestinal Escherichia coli

ABSTRACT The contribution of homologous exchange (recombination) of core genes in the adaptive evolution of bacterial pathogens is not well understood. To investigate this, we analyzed fully assembled genomes of two Escherichia coli strains from sequence type 131 (ST131), a clonal group that is both the leading cause of extraintestinal E. coli infections and the main source of fluoroquinolone-resistant E. coli. Although the sequences of each of the seven multilocus sequence typing genes were identical in the two ST131 isolates, the strains diverged from one another by homologous recombination that affected at least 9% of core genes. This was on a par with the contribution to genomic diversity of horizontal gene transfer and point gene mutation. The genomic positions of recombinant and mobile genetic regions were partially linked, suggesting their concurrent occurrence. One of the genes affected by homologous recombination was fimH, which encodes mannose-specific type 1 fimbrial adhesin, resulting in functionally distinct copies of the gene in ST131 strains. One strain, a uropathogenic isolate, had a pathoadaptive variant of fimH that was acquired by homologous replacement into the commensal strain background. Close examination of FimH structure and function in additional ST131 isolates revealed that recombination led to acquisition of several functionally distinct variants that, upon homologous exchange, were targeted by a variety of pathoadaptive mutations under strong positive selection. Different recombinant fimH strains also showed a strong clonal association with ST131 isolates that had distinct fluoroquinolone resistance profiles. Thus, homologous recombination of core genes plays a significant role in adaptive diversification of bacterial pathogens, especially at the level of clonally related groups of isolates.
More Than Morningness: The Effect of Circadian Rhythm Amplitude and Stability on Resilience, Coping, and Sleep Duration

Self-report tools that measure circadian rhythms have focused primarily on phase. We add to the sparse literature on assessing amplitude and stability. We randomly recruited 1,163 participants who completed several measures. The correlation between the LV scale (amplitude) and FR scale (stability) was −0.12 (p < 0.01). As expected, amplitude was negatively associated with phase (r = −0.64, p < 0.01) while stability showed a weak link with phase (r = 0.07, p < 0.05). Structural equation modeling suggested a close model-fit of the factor structure in the sample (RMSEA = 0.033). The LV scale explained 22% of the variance, while the FR scale explained 23%. Scale reliability was satisfactory for the LV scale (0.68) and good for the FR scale (0.73). Participants with low amplitude or flexible rhythms reported significantly better resilience, coping, and required less daily sleep. We constructed a composite circadian categorical variable to combine the best attributes from the LV and FR scales; participants with both low amplitude and flexible rhythms, reported significantly better resilience, coping, and less sleep need. We found rhythm amplitude decreased with age, while stability remained constant.
Discovering Community Assets: Master of Public Health Culminating Experience

The Sonoma County Department of Health Services, through Cradle to Career, promotes collective impact around educational attainment and workforce development, and has become a leader in developing a framework for community schools. The first step in developing a community schools model is to understand and inventory what is already going on in the community. This process, known more formally as asset mapping, is a participatory process focused on documenting the strengths and resources of a community. The collaborative nature of the process helps to promote community involvement and build community cohesion. In order to assist schools wanting to begin an asset mapping process, the Department of Health Services sought to develop a toolkit for community asset mapping. The following paper is a summary on a 300-hour fieldwork experience at the Department of Health Services specific to understanding asset mapping and developing a guide for communities and schools wanting to discover their assets. DISCOVERING COMMUNITY ASSETS 3 Discovering Community Assets: Master of Public Health Culminating Experience There are two paths typically used to explore solutions and make decisions in a community. The first path, which is used more often, highlights the needs, deficits and problems within a community to drive solutions. The high use of needs assessments and tertiary care reflects a journey down this path. In contrast, the second path focuses on assets, emphasizing the existing strengths of individuals, organizations, and communities as a way to mobilize and build community capacity for action. Taking an asset approach allows communities to redefine their truth, and serves as a way to help community members take an active role in developing solutions. When community members become involved in and lead the process from beginning to end, they are able to take ownership of the process and build community cohesion. This paper will provide an introduction to asset mapping as a method for discovering community assets, and a summary of 300 hours of fieldwork experience completed at the Sonoma County Department of Health Services as a culminating experience for the University of San Francisco’s Master of Public Health program.
Assessment of three methods to reduce the influence of mathematical coupling on oxygen consumption and delivery relationships.

STUDY OBJECTIVES To determine if oxygen consumption/oxygen delivery (VO2/DO2) relationships derived using calorimetry (which are not influenced by shared measurement error) agreed with those obtained using the pulmonary artery (PA) catheter alone. To evaluate three strategies to reduce the influence of shared measurement error to determine if agreement between the two methods could be improved. METHODS Twenty-seven patients were studied following coronary artery bypass surgery. Calorimetric VO2, six thermodilution cardiac outputs (COs), and arterial and mixed venous oxygen content measurements were made at baseline and were repeated 30 min following dobutamine administrations of 3 microg/kg/min and 5 microg/kg/min. RESULTS Dobutamine produced a dose-dependent increase in DO2, from 378+/-65 mL/min/m2 to 446+/-78 mL/min/m2 (p<0.01) and in both PA catheter and calorimetric-derived VO2, from 104+/-18 mL/min/Mi2 to 114+/-22 mL/min/m2 (p<0.05) and from 117+/-15 mL/min/m2 to 126+/-19 mL/min/m2 (p<0.01), respectively. Agreement was poor (bias=12%, SD=21%) between the calorimetric and PA catheter methods of determining VO2/DO2 slope. When three CO measurements were used to calculate VO2, and three separate CO measurements were used to calculate DO2, the level of agreement between the two methods improved (bias=2%, SD=15%). Increasing the number of COs resulted in a similar improvement in the level of agreement between the two methods. Weighting the slope to the observed change in DO2 was the best method to improve the level of agreement (bias=2%, SD=6% for three COs). CONCLUSIONS To reduce the influence of shared measurement error, the best strategy to improve the measurement of VO2/DO2 slope is to maximize the change in DO2 (optimally over 100 mL/min/m2).
Sustainability: Reviewing Australia's progress, 1992-2002

In late 2002, nations will meet for the World Summit on Sustainable Development, and review a decade of progress since the UN Conference on Environment and Development held in Rio in 1992. This anniversary also presents an opportunity to review domestic policy progress, such as that of Australia in the ten years since its 1992 National Strategy for Ecologically Sustainable Development (ESD). This paper reviews the past decade of environmental policy and progress to ESD in Australia, noting some globally significant advances as well as under-achievement. The paper identifies two reasons for under-achievement: the unprecedented nature and difficulty of sustainability problems, and the lack of suitable policy processes and institutional arrangements to address these, and suggests policy and institutional reforms.
Knowledge visualisation techniques for revealing advanced research and trends

Revealing themes and trends in scientific work are important research tasks. However, the challenging effort is to make knowledge visualization distinct and straightforward to interpret. In this paper, different perspectives and methods were introduced to analyze leading projects and research theme. Factor analysis and pathfinder network were carried out to picture research directions by clustering scientific papers taken from the Web (CiteSeer papers). Ontology technology was applied to discover foremost research topics based on Taiwan NSC project proposals. The results obtained show that recent popular research towards to pursue Web related work. Of particular interest is that the proposed techniques could be re-used in a number of ways and could possibly be shared across different domains.
Design of control-group conditions in clinical trials of behavioral interventions.

PURPOSE To review considerations in the design of placebo (attention) control conditions for community-based clinical trials of health behavior change interventions and to provide practical strategies for the design of control conditions. ORGANIZING CONSTRUCTS A well-designed control condition is an essential component of a clinical trial to foster the unambiguous interpretation of study findings. METHODS Pitfalls in the design of control conditions in clinical trials of behavioral interventions are identified and strategies to address them are offered. Types of control conditions that have been used in fall prevention trials are described, along with their strengths and weaknesses. The control condition used in the recent fall evaluation and prevention program (FEPP) was designed to overcome limitations of previous trial designs; it is provided to illustrate how to apply specific design principles. CONCLUSIONS Pitfalls in the design of behavioral intervention studies may be avoided with the application of sound design principles. The FEPP active control condition can be used as a model in the design of future studies.
The effects of news on exchange rates when the risk premium is considered

Poor performance of forward exchange rates to predict future spot rates has caused researchers to analyse other approaches to exchange rate determination. One such approach is to treat exchange rates as prices of foreign currency assets. Thus, these prices should be highly sensitive to new information. This paper analyses, as news variables, unanticipated changes in the USA and home country money supplies, incomes, and interest rates. Two different methods are used to account for the unobservable risk premium. Results suggest that news does not significantly influence exchange rates for the four countries involved-Germany, Italy, Canada and Japan. Possible reasons are discussed.
Comparison of standing balance between female collegiate dancers and soccer players.

STUDY DESIGN This study was designed as a comparison study of two cohorts. OBJECTIVES The hypothesis of this study was that soccer players and dancers have different balance abilities and that these differences could be objectively measured using center of pressure measurements. BACKGROUND Center of pressure (COP) measurements are reproducible and have been validated in the literature for assessing standing balance. The literature does not provide sensitive enough techniques for discriminating between two groups of athletes with excellent standing balance. METHODS AND MEASURES A Matscan pressure mat (Tekscan, Boston, MA) was used to compare COP change variability between 32 female collegiate soccer players and 32 dancers. COP was used to calculate sway index, center acquisition time, sway path length and sway velocity as measures of standing balance. RESULTS The dancers had significantly better balance scores (p<0.05) in 5 of 20 balance tests. Results for the remaining 15 balance tests were not significantly different. CONCLUSION These data show that standing balance characteristics of dancers and soccer players can be objectively measured using COP data. Dancers have certain standing balance abilities that are better than those of soccer players. The COP measurements in this study can be used as a tool in future studies investigating standing balance in different groups of athletes.