Two polymorphisms facilitate differences in plasticity between two chicken major histocompatibility complex class I proteins

Major histocompatibility complex class I molecules (MHC I) present peptides to cytotoxic T-cells at the surface of almost all nucleated cells. The function of MHC I molecules is to select high affinity peptides from a large intracellular pool and they are assisted in this process by co-factor molecules, notably tapasin. In contrast to mammals, MHC homozygous chickens express a single MHC I gene locus, termed BF2, which is hypothesised to have co-evolved with the highly polymorphic tapasin within stable haplotypes. The BF2 molecules of the B15 and B19 haplotypes have recently been shown to differ in their interactions with tapasin and in their peptide selection properties. This study investigated whether these observations might be explained by differences in the protein plasticity that is encoded into the MHC I structure by primary sequence polymorphisms. Furthermore, we aimed to demonstrate the utility of a complimentary modelling approach to the understanding of complex experimental data. Combining mechanistic molecular dynamics simulations and the primary sequence based technique of statistical coupling analysis, we show how two of the eight polymorphisms between BF2*15:01 and BF2*19:01 facilitate differences in plasticity. We show that BF2*15:01 is intrinsically more plastic than BF2*19:01, exploring more conformations in the absence of peptide. We identify a protein sector of contiguous residues connecting the membrane bound ?3 domain and the heavy chain peptide binding site. This sector contains two of the eight polymorphic residues. One is residue 22 in the peptide binding domain and the other 220 is in the ?3 domain, a putative tapasin binding site. These observations are in correspondence with the experimentally observed functional differences of these molecules and suggest a mechanism for how modulation of MHC I plasticity by tapasin catalyses peptide selection allosterically

Prevalence of sulfonamide resistance genes in bacterial isolates from manured agricultural soils and pig slurry in the United Kingdom

Prevalence of three sulfonamide resistance genes, sul1, sul2 and sul3 and sulfachloropyridazine (SCP) resistance was determined in bacteria isolated from UK manured agricultural clay soils and slurry samples, over a two year period. Slurry from tylosin-fed pigs amended with SCP and oxytetracycline (OTC) was used for manuring. Sul gene positive isolates were further screened for the presence of class 1 and 2 integrons. Phenotypic resistance to SCP was significantly higher in pig slurry and post application soil than in pre-application soil. Of 5isolates, 23 % carried sul1, 18 % sul2 and 9 % sul3 only. Two percent of isolates contained all three sul genes. Class 1 and class 2 integrons were identified in 5 % and 11.7 % of sul positive isolates. In previous reports, sul1 was linked to class 1 integrons, but in this study only 8 % of sul1 positive isolates carried the intI1 gene. Sulfonamide resistant pathogens were identified in slurry amended soil and soil leachate, including Shigella flexneri, Aerococcus spp. and Acinetobacter baumanni, suggesting a potential environmental reservoir. Sulfonamide resistance in Psychrobacter, Enterococcus and Bacillus spp. is reported for the first time, and this study also provides the first description of the genotype sul1, sul2 and sul3 outside the Enterobacteriacae, and in the soil environment

Integron prevalence and diversity in manured soil

Integron abundance and diversity were studied in soil amended with pig slurry. Real-time PCR illustrated a significant increase in class 1 integron prevalence post slurry-application with increased prevalence still evident at 10 months post-application. Culture dependent data revealed 10 genera, including putative human pathogens, carrying class 1 and 2 integrons

Qualitative critical incident study of patients’ experiences leading to emergency hospital admission with advanced respiratory illness

Objectives: The high volume of emergency admissions to hospital is a challenge for health systems internationally. Patients with lung cancer and chronic obstructive pulmonary disease (COPD) are frequently admitted to hospital as emergency cases. While the frequency of emergency admission has been investigated, few studies report patient experiences, particularly in relation to the decision-making process prior to emergency admission. We sought to explore patient and carer experiences and those of their healthcare professionals in the period leading up to emergency admission to hospital. Setting: 3 UK hospitals located in different urban and rural settings. Design: Qualitative critical incident study. Participants: 24 patients with advanced lung cancer and 15 with advanced COPD admitted to hospital as emergencies, 20 of their carers and 50 of the health professionals involved in the patients' care. Results: The analysis of patient, carer and professionals' interviews revealed a detailed picture of the complex processes involved leading to emergency admission to hospital. 3 phases were apparent in this period: self-management of deteriorating symptoms, negotiated decision-making and letting go. These were dynamic processes, characterised by an often rapidly changing clinical condition, uncertainty and anxiety. Patients considered their options drawing on experience, current and earlier advice. Patients tried to avoid admission, reluctantly accepting it, albeit often with a sense of relief, as anxiety increased with worsening symptoms. Conclusions: Patients with advanced respiratory illness, and their carers, try to avoid emergency admission, and use logical and complex decision-making before reluctantly accepting it. Clinicians and policy-makers need to understand this complex process when considering how to reduce emergency hospital admissions rather than focusing on identifying and labelling admissions as 'inappropriate'

“It's been quite a challenge”: Redesigning end-of-life care in acute hospitals

AbstractObjective:This paper reports the findings of an interview-based study undertaken to investigate the introduction of end-of-life (EoL) care pathways in three acute trusts, as part of a larger project examining service redesign. The aim was to examine the barriers to and facilitators of change.Method:Twenty-one in-depth qualitative interviews were conducted with staff working in three National Health Service (NHS) acute hospital trusts. These staff members were involved in end-of-life care, and their accounts were analyzed to identify the key issues when introducing service changes in these settings.Results:Thematic analysis revealed five major themes—two of which, leadership and facilitation, and education and training, indicate what needs to be in place if end-of-life care pathways are to be adopted by staff. However, the remaining three themes of difficult conversations, diagnosing dying, and communication across boundaries highlight particular areas of practice and organization that need to be addressed before end-of-life care in hospitals can be improved.Significance of results:Organization of end-of-life care in acute hospitals is challenging, and care pathways provide a degree of guidance as to how services can be delivered. However, even when there is effective leadership at all levels of an organization and an extensive program of education for all staff support the use of care pathways, significant barriers to their introduction remain. These include staff anxieties concerning diagnosing dying and discussing dying and end-of-life care planning with patients and their families. It is hoped these findings can inform the development of the proposed new care plans which are set to replace end of life care pathways in England.</jats:sec

Selector function of MHC I molecules is determined by protein plasticity

The selection of peptides for presentation at the surface of most nucleated cells by major histocompatibility complex class I molecules (MHC I) is crucial to the immune response in vertebrates. However, the mechanisms of the rapid selection of high affinity peptides by MHC I from amongst thousands of mostly low affinity peptides are not well understood. We developed computational systems models encoding distinct mechanistic hypotheses for two molecules, HLA-B*44:02 (B*4402) and HLA-B*44:05 (B*4405), which differ by a single residue yet lie at opposite ends of the spectrum in their intrinsic ability to select high affinity peptides. We used &lt;em&gt;in vivo&lt;/em&gt; biochemical data to infer that a conformational intermediate of MHC I is significant for peptide selection. We used molecular dynamics simulations to show that peptide selector function correlates with protein plasticity, and confirmed this experimentally by altering the plasticity of MHC I with a single point mutation, which altered &lt;em&gt;in vivo&lt;/em&gt; selector function in a predictable way. Finally, we investigated the mechanisms by which the co-factor tapasin influences MHC I plasticity. We propose that tapasin modulates MHC I plasticity by dynamically coupling the peptide binding region and {\alpha}&lt;sub&gt;3&lt;/sub&gt; domain of MHC I allosterically, resulting in enhanced peptide selector function

User Variability and IR System Evaluation

ABSTRACT Test collection design eliminates sources of user variability to make statistical comparisons among information retrieval (IR) systems more affordable. Does this choice unnecessarily limit generalizability of the outcomes to real usage scenarios? We explore two aspects of user variability with regard to evaluating the relative performance of IR systems, assessing effectiveness in the context of a subset of topics from three TREC collections, with the embodied information needs categorized against three levels of increasing task complexity. First, we explore the impact of widely differing queries that searchers construct for the same information need description. By executing those queries, we demonstrate that query formulation is critical to query effectiveness. The results also show that the range of scores characterizing effectiveness for a single system arising from these queries is comparable or greater than the range of scores arising from variation among systems using only a single query per topic. Second, our experiments reveal that searchers display substantial individual variation in the numbers of documents and queries they anticipate needing to issue, and there are underlying significant differences in these numbers in line with increasing task complexity levels. Our conclusion is that test collection design would be improved by the use of multiple query variations per topic, and could be further improved by the use of metrics which are sensitive to the expected numbers of useful documents

Dynamic lactate indices as predictors of outcome in critically ill patients

INTRODUCTION: Dynamic changes in lactate concentrations in the critically ill may predict patient outcome more accurately than static indices. We aimed to compare the predictive value of dynamic indices of lactatemia in the first 24 hours of intensive care unit (ICU) admission with the value of more commonly used static indices. METHODS: This was a retrospective observational study of a prospectively obtained intensive care database of 5,041 consecutive critically ill patients from four Australian university hospitals. We assessed the relationship between dynamic lactate values collected in the first 24 hours of ICU admission and both ICU and hospital mortality. RESULTS: We obtained 36,673 lactate measurements in 5,041 patients in the first 24 hours of ICU admission. Both the time weighted average lactate (LACTW₂₄) and the change in lactate (LACΔ₂₄) over the first 24 hours were independently predictive of hospital mortality with both relationships appearing to be linear in nature. For every one unit increase in LACTW₂₄ and LACΔ₂₄ the risk of hospital death increased by 37% (OR 1.37, 1.29 to 1.45; P < 0.0001) and by 15% (OR 1.15, 1.10 to 1.20; P < 0.0001) respectively. Such dynamic indices, when combined with Acute Physiology and Chronic Health Evaluation II (APACHE II) scores, improved overall outcome prediction (P < 0.0001) achieving almost 90% accuracy. When all lactate measures in the first 24 hours were considered, the combination of LACTW₂₄ and LACΔ₂₄ significantly outperformed (P < 0.0001) static indices of lactate concentration, such as admission lactate, maximum lactate and minimum lactate. CONCLUSIONS: In the first 24 hours following ICU admission, dynamic indices of hyperlactatemia have significant independent predictive value, improve the performance of illness severity score-based outcome predictions and are superior to simple static indices of lactate concentration