Fitness Ranking of Individual Mutants Drives Patterns of Epistatic Interactions in HIV-1

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Performance of the CMS Cathode Strip Chambers with Cosmic Rays

The Cathode Strip Chambers (CSCs) constitute the primary muon tracking device in the CMS endcaps. Their performance has been evaluated using data taken during a cosmic ray run in fall 2008. Measured noise levels are low, with the number of noisy channels well below 1%. Coordinate resolution was measured for all types of chambers, and fall in the range 47 microns to 243 microns. The efficiencies for local charged track triggers, for hit and for segments reconstruction were measured, and are above 99%. The timing resolution per layer is approximately 5 ns

Population mechanics: A mathematical framework to study T cell homeostasis

Unlike other cell types, T cells do not form spatially arranged tissues, but move independently throughout the body. Accordingly, the number of T cells in the organism does not depend on physical constraints imposed by the shape or size of specific organs. Instead, it is determined by competition for interleukins. From the perspective of classical population dynamics, competition for resources seems to be at odds with the observed high clone diversity, leading to the so-called diversity paradox. In this work we make use of population mechanics, a non-standard theoretical approach to T cell homeostasis that accounts for clone diversity as arising from competition for interleukins. The proposed models show that carrying capacities of T cell populations naturally emerge from the balance between interleukins production and consumption. These models also suggest remarkable functional differences in the maintenance of diversity in naïve and memory pools. In particular, the distribution of memory clones would be biased towards clones activated more recently, or responding to more aggressive pathogenic threats. In contrast, permanence of naïve T cell clones would be determined by their affinity for cognate antigens. From this viewpoint, positive and negative selection can be understood as mechanisms to maximize naïve T cell diversity

Identification and Filtering of Uncharacteristic Noise in the CMS Hadron Calorimeter

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Routine use of ancillary investigations in staging diffuse large B-cell lymphoma improves the International Prognostic Index (IPI)

<p>Abstract</p> <p>Background</p> <p>The International Prognostic Index (IPI) is used to determine prognosis in diffuse large B-cell lymphoma (DLBCL). One of the determinants of IPI is the stage of disease with bone marrow involvement being classified as stage IV. For the IPI, involvement on bone marrow is traditionally defined on the basis of histology with ancillary investigations used only in difficult cases to aid histological diagnosis. This study aimed to determine the effect of the routine use of flow cytometry, immunohistochemistry and molecular studies in bone marrow staging upon the IPI.</p> <p>Results</p> <p>Bone marrow trephines of 156 histologically proven DLBCL cases at initial diagnosis were assessed on routine histology, and immunohistochemistry using two T-cell markers (CD45RO and CD3), two B-cell markers (CD20 and CD79a) and kappa and lambda light chains. Raw flow cytometry data on all samples were reanalysed and reinterpreted blindly. DNA extracted from archived paraffin-embedded trephine biopsy samples was used for immunoglobulin heavy chain and light chain gene rearrangement analysis. Using immunophenotyping (flow cytometry and immunohistochemistry), 30 (19.2%) cases were upstaged to stage IV. A further 8 (5.1%) cases were upstaged using molecular studies. A change in IPI was noted in 18 cases (11.5%) on immunophenotyping alone, and 22 (14.1%) cases on immunophenotyping and molecular testing. Comparison of two revised IPI models, 1) using immunophenotyping alone, and 2) using immunophenotyping with molecular studies, was performed with baseline IPI using a Cox regression model. It showed that the revised IPI model using immunophenotyping provides the best differentiation between the IPI categories.</p> <p>Conclusion</p> <p>Improved bone marrow staging using flow cytometry and immunohistochemistry improves the predictive value of the IPI in patients with DLBCL and should be performed routinely in all cases.</p

Analysis of the IDS Gene in 38 Patients with Hunter Syndrome: The c.879G>A (p.Gln293Gln) Synonymous Variation in a Female Create Exonic Splicing

BACKGROUND: Hunter syndrome (mucopolysaccharidosis type II, MPS II) is a rare disease inherited in an X-linked autosomal recessive pattern. It is the prevailing form of the mucopolysaccharidoses in China. Here we investigated mutations of IDS (iduronate 2-sulfatase) gene in 38 unrelated Chinese patients, one of which is a female. METHODS: Peripheral leucocytes were collected from the patients and the IDS gene was amplified to looking for the variations. For a female patient, the X chromosome status was analyzed by androgen receptor X-inactivation assay and the mutation impact on RNA level was further performed by reverse transcription polymerase chain reaction. RESULTS: We discovered that point mutations constituted the major form while mutations in codon p.R468 defined the largest number of patients in our cohort. Consistent with data from other ethnic groups, exons 9 and 3 had comparatively more mutations, while exon 2 had quite a few mutations unique to Chinese patients. Of the 30 different mutations identified, only 9 were novel: one was a premature termination mutation, i.e., c.196C>T (p.Gln66X); three were missense mutations, i.e., c.200T>C (p.Leu67Pro), c.215T>C (p.Leu72Pro), c.389C>T (p.Thr130Ile); one was a small deletion, i.e., c.1104_1122del19 (p.Ser369ArgfsX16); and one was a deletion that spanned both exons 8 and 9 deletion leading to gross structural changes in the IDS gene. In addition, a synonymous mutation c.879G>A (p.Gln293Gln) was identified in a female Hunter disease patient, which resulted in loss of the original splicing site, activated a cryptic splicing site upstream, leading to a 28 bp deletion and a premature termination at p. Tyr285GlufsX47. Together with concurrent skewed X-inactivation this was believed to facilitate the development of Hunter disease in this girl. CONCLUSIONS: In conclusion, the molecular analysis of IDS gene in Chinese patients confirmed the Hunter disease diagnosis and expanded the mutation and clinical spectrum of this devastating disorder

Evaluation of the Sublingual Route for Administration of Influenza H5N1 Virosomes in Combination with the Bacterial Second Messenger c-di-GMP

Avian influenza A H5N1 is a virus with pandemic potential. Mucosal vaccines are attractive as they have the potential to block viruses at the site of entry, thereby preventing both disease and further transmission. The intranasal route is safe for the administration of seasonal live-attenuated influenza vaccines, but may be less suitable for administration of pandemic vaccines. Research into novel mucosal routes is therefore needed. In this study, a murine model was used to compare sublingual administration with intranasal and intramuscular administration of influenza H5N1 virosomes (2 µg haemagglutinin; HA) in combination with the mucosal adjuvant (3′,5′)-cyclic dimeric guanylic acid (c-di-GMP). We found that sublingual immunisation effectively induced local and systemic H5N1-specific humoral and cellular immune responses but that the magnitude of response was lower than after intranasal administration. However, both the mucosal routes were superior to intramuscular immunisation for induction of local humoral and systemic cellular immune responses including high frequencies of splenic H5N1-specific multifunctional (IL-2+TNF-α+) CD4+ T cells. The c-di-GMP adjuvanted vaccine elicited systemic haemagglutination inhibition (HI) antibody responses (geometric mean titres ≥40) both when administered sublingually, intranasally and inramuscularly. In addition, salivary HI antibodies were elicited by mucosal, but not intramuscular vaccination. We conclude that the sublingual route is an attractive alternative for administration of pandemic influenza vaccines

The effect of the COACH program (Continuity Of Appropriate pharmacotherapy, patient Counselling and information transfer in Healthcare) on readmission rates in a multicultural population of internal medicine patients

BACKGROUND: Medication errors occur frequently at points of transition in care. The key problems causing these medication errors are: incomplete and inappropriate medication reconciliation at hospital discharge (partly arising from inadequate medication reconciliation at admission), insufficient patient information (especially within a multicultural patient population) and insufficient communication to the next health care provider. Whether interventions aimed at the combination of these aspects indeed result in less discontinuity and associated harm is uncertain. Therefore the main objective of this study is to determine the effect of the COACH program (Continuity Of Appropriate pharmacotherapy, patient Counselling and information transfer in Healthcare) on readmission rates in patients discharged from the internal medicine department. METHODS/DESIGN: An experimental study is performed at the internal medicine ward of a general teaching hospital in Amsterdam, which serves a multicultural population. In this study the effects of the COACH program is compared with usual care using a pre-post study design. All patients being admitted with at least one prescribed drug intended for chronic use are included in the study unless they meet one of the following exclusion criteria: no informed consent, no medication intended for chronic use prescribed at discharge, death, transfer to another ward or hospital, discharge within 24 hours or out of office hours, discharge to a nursing home and no possibility to counsel the patient.The intervention consists of medication reconciliation, patient counselling and communication between the hospital and primary care healthcare providers.The following outcomes are measured: the primary outcome readmissions within six months after discharge and the secondary outcomes number of interventions, adherence, patient's attitude towards medicines, patient's satisfaction with medication information, costs, quality of life and finally satisfaction of general practitioners and community pharmacists.Interrupted time series analysis is used for data-analysis of the primary outcome. Descriptive statistics is performed for the secondary outcomes. An economic evaluation is performed according to the intention-to-treat principle. DISCUSSION: This study will be able to evaluate the clinical and cost impact of a comprehensive program on continuity of care and associated patient safety. TRIAL REGISTRATION: Dutch trial register: NTR151

Healthcare providers' knowledge, experience and challenges of reporting adverse events following immunisation: a qualitative study

Background: Healthcare provider spontaneous reporting of suspected adverse events following immunisation (AEFI) is central to monitoring post-licensure vaccine safety, but little is known about how healthcare professionals recognise and report to surveillance systems. The aim of this study was explore the knowledge, experience and attitudes of medical and nursing professionals towards detecting and reporting AEFI. Methods: We conducted a qualitative study, using semi-structured, face to face interviews with 13 Paediatric Emergency Department consultants from a tertiary paediatric hospital, 10 General Practitioners, 2 local council immunisation and 4 General Practice nurses, recruited using purposive sampling in Adelaide, South Australia, between December 2010 and September 2011. We identified emergent themes related to previous experience of an AEFI in practice, awareness and experience of AEFI reporting, factors that would facilitate or impede reporting and previous training in vaccine safety. Thematic analysis was used to analyse the data. Results: AEFI reporting was infrequent across all groups, despite most participants having reviewed an AEFI. We found confusion about how to report an AEFI and variability, according to the provider group, as to the type of events that would constitute a reportable AEFI. Participants’ interpretation of a “serious” or “unexpected” AEFI varied across the three groups. Common barriers to reporting included time constraints and unsatisfactory reporting processes. Nurses were more likely to have received formal training in vaccine safety and reporting than medical practitioners. Conclusions: This study provides an overview of experience and beliefs of three healthcare professional groups in relation to identifying and reporting AEFI. The qualitative assessment reveals differences in experience and awareness of AEFI reporting across the three professional groups. Most participants appreciated the importance of their role in AEFI surveillance and monitoring the ongoing safety of vaccines. Future initiatives to improve education, such as increased training to health care providers, particularly, medical professionals, are required and should be included in both undergraduate curricula and ongoing, professional development.Adriana Parrella, Annette Braunack-Mayer, Michael Gold, Helen Marshall and Peter Baghurs