Genome-wide association study identifies new HLA class II haplotypes strongly protective against narcolepsy

Narcolepsy is a rare sleep disorder with the strongest human leukocyte antigen (HLA) association ever reported. Since the associated HLA-DRB1*1501-DQB1*0602 haplotype is common in the general population (15-25%), it has been suggested that it is almost necessary but not sufficient for developing narcolepsy. To further define the genetic basis of narcolepsy risk, we performed a genome-wide association study (GWAS) in 562 European individuals with narcolepsy (cases) and 702 ethnically matched controls, with independent replication in 370 cases and 495 controls, all heterozygous for DRB1*1501-DQB1*0602. We found association with a protective variant near HLA-DQA2 (rs2858884; P < 3 x 10(-8)). Further analysis revealed that rs2858884 is strongly linked to DRB1*03-DQB1*02 (P < 4 x 10(-43)) and DRB1*1301-DQB1*0603 (P < 3 x 10(-7)). Cases almost never carried a trans DRB1*1301-DQB1*0603 haplotype (odds ratio = 0.02; P < 6 x 10(-14)). This unexpected protective HLA haplotype suggests a virtually causal involvement of the HLA region in narcolepsy susceptibility.

Pinocchio: Bringing Reflection to Life with First-Class Interpreters

To support development tools like debuggers, runtime systems need to provide a meta-programming interface to alter their semantics and access internal data. Reflective capabilities are typically fixed by the Virtual Machine (VM). Unanticipated reflective features must either be simulated by complex program transformations, or they require the development of a specially tailored VM. We propose a novel approach to behavioral reflection that eliminates the barrier between applications and the VM by manipulating an explicit tower of first-class interpreters. Pinocchio is a proof-of-concept implementation of our approach which enables radical changes to the interpretation of programs by explicitly instantiating subclasses of the base interpreter. We illustrate the design of Pinocchio through non-trivial examples that extend runtime semantics to support debugging, parallel debugging, and back-in-time object-flow debugging. Although performance is not yet addressed, we also discuss numerous opportunities for optimization, which we believe will lead to a practical approach to behavioral reflection.

The catalytic class I(A) PI3K isoforms play divergent roles in breast cancer cell migration

Transforming growth factor-β (TGFβ) plays an important role in breast cancer metastasis. Here phosphoinositide 3-kinase (PI3K) signalling was found to play an essential role in the enhanced migration capability of fibroblastoid cells (FibRas) derived from normal mammary epithelial cells (EpH4) by transduction of oncogenic Ras (EpRas) and TGFβ1. While expression of the PI3K isoform p110δ was down-regulated in FibRas cells, there was an increase in the expression of p110α and p110β in the fibroblastoid cells. The PI3K isoform p110β was found to specifically contribute to cell migration in FibRas cells, while p110α contributed to the response in EpH4, EpRas and FibRas cells. Akt, a downstream targets of PI3K signalling, had an inhibitory role in the migration of transformed breast cancer cells, while Rac, Cdc42 and the ribosomal protein S6 kinase (S6K) were necessary for the response. Together our data reveal a novel specific function of the PI3K isoform p110β in the migration of cells transformed by oncogenic H-Ras and TGF-β1.

Structural basis for the regulation of cysteine-protease activity by a new class of protease inhibitors in Plasmodium

Plasmodium cysteine proteases are essential for host-cell invasion and egress, hemoglobin degradation, and intracellular development of the parasite. The temporal, site-specific regulation of cysteine-protease activity is a prerequisite for survival and propagation of Plasmodium. Recently, a new family of inhibitors of cysteine proteases (ICPs) with homologs in at least eight Plasmodium species has been identified. Here, we report the 2.6 A X-ray crystal structure of the C-terminal, inhibitory domain of ICP from P. berghei (PbICP-C) in a 1:1 complex with falcipain-2, an important hemoglobinase of Plasmodium. The structure establishes Plasmodium ICP as a member of the I42 class of chagasin-like protease inhibitors but with large insertions and differences in the binding mode relative to other family members. Furthermore, the PbICP-C structure explains why host-cell cathepsin B-like proteases and, most likely, also the protease-like domain of Plasmodium SERA5 (serine-repeat antigen 5) are no targets for ICP.

Pancreatic carcinoma, pancreatitis, and healthy controls: metabolite models in a three-class diagnostic dilemma

Metabolomics as one of the most rapidly growing technologies in the "-omics" field denotes the comprehensive analysis of low molecular-weight compounds and their pathways. Cancer-specific alterations of the metabolome can be detected by high-throughput mass-spectrometric metabolite profiling and serve as a considerable source of new markers for the early differentiation of malignant diseases as well as their distinction from benign states. However, a comprehensive framework for the statistical evaluation of marker panels in a multi-class setting has not yet been established. We collected serum samples of 40 pancreatic carcinoma patients, 40 controls, and 23 pancreatitis patients according to standard protocols and generated amino acid profiles by routine mass-spectrometry. In an intrinsic three-class bioinformatic approach we compared these profiles, evaluated their selectivity and computed multi-marker panels combined with the conventional tumor marker CA 19-9. Additionally, we tested for non-inferiority and superiority to determine the diagnostic surplus value of our multi-metabolite marker panels. Compared to CA 19-9 alone, the combined amino acid-based metabolite panel had a superior selectivity for the discrimination of healthy controls, pancreatitis, and pancreatic carcinoma patients [Formula: see text] We combined highly standardized samples, a three-class study design, a high-throughput mass-spectrometric technique, and a comprehensive bioinformatic framework to identify metabolite panels selective for all three groups in a single approach. Our results suggest that metabolomic profiling necessitates appropriate evaluation strategies and-despite all its current limitations-can deliver marker panels with high selectivity even in multi-class settings.

Selection and recombination drive the evolution of MHC class II DRB diversity in ungulates

Major histocompatibility complex (MHC) antigen-presenting genes are the most variable loci in vertebrate genomes. Host-parasite co-evolution is assumed to maintain the excessive polymorphism in the MHC loci. However, the molecular mechanisms underlying the striking diversity in the MHC remain contentious. The extent to which recombination contributes to the diversity at MHC loci in natural populations is still controversial, and there have been only few comparative studies that make quantitative estimates of recombination rates. In this study, we performed a comparative analysis for 15 different ungulates species to estimate the population recombination rate, and to quantify levels of selection. As expected for all species, we observed signatures of strong positive selection, and identified individual residues experiencing selection that were congruent with those constituting the peptide-binding region of the human DRB gene. However, in addition for each species, we also observed recombination rates that were significantly different from zero on the basis of likelihood-permutation tests, and in other non-quantitative analyses. Patterns of synonymous and non-synonymous sequence diversity were consistent with differing demographic histories between species, but recent simulation studies by other authors suggest inference of selection and recombination is likely to be robust to such deviations from standard models. If high rates of recombination are common in MHC genes of other taxa, re-evaluation of many inference-based phylogenetic analyses of MHC loci, such as estimates of the divergence time of alleles and trans-specific polymorphism, may be required.

Evidence of viral adaptation to HLA class I-restricted immune pressure in chronic hepatitis C virus infection

Cellular immune responses are an important correlate of hepatitis C virus (HCV) infection outcome. These responses are governed by the host's human leukocyte antigen (HLA) type, and HLA-restricted viral escape mutants are a critical aspect of this host-virus interaction. We examined the driving forces of HCV evolution by characterizing the in vivo selective pressure(s) exerted on single amino acid residues within nonstructural protein 3 (NS3) by the HLA types present in two host populations. Associations between polymorphisms within NS3 and HLA class I alleles were assessed in 118 individuals from Western Australia and Switzerland with chronic hepatitis C infection, of whom 82 (69%) were coinfected with human immunodeficiency virus. The levels and locations of amino acid polymorphisms exhibited within NS3 were remarkably similar between the two cohorts and revealed regions under functional constraint and selective pressures. We identified specific HCV mutations within and flanking published epitopes with the correct HLA restriction and predicted escaped amino acid. Additional HLA-restricted mutations were identified that mark putative epitopes targeted by cell-mediated immune responses. This analysis of host-virus interaction reveals evidence of HCV adaptation to HLA class I-restricted immune pressure and identifies in vivo targets of cellular immune responses at the population level.

Avoiding misclassification bias with the traditional Charnley classification: rationale for a fourth Charnley class BB

Long-term follow up of patients with total hip arthroplasty (THA) revealed a marked deterioration of walking capacities in Charnley class B after postoperative year 4. We hypothesized that a specific group of patients, namely those with unilateral hip arthroplasty and an untreated but affected contralateral hip was responsible for this observation. Therefore, we conducted a study taking into consideration the two subclasses that make up Charnley class B: patients with unilateral THA and contralateral hip disease and patients with bilateral THA. A sample of 15,160 patients with 35,773 follow ups that were prospectively collected over 10 years was evaluated. The sample was categorized into four classes according to a new modified Charnley classification. Annual analyses of the proportion of patients with ambulation longer than 60 min were conducted. The traditionally labeled Charnley class B consists of two very different patient groups with respect to their walking capacities. Those with unilateral THA and contralateral hip disease have underaverage walking capacities and a deterioration of ambulation beginning 3 to 4 years after surgery. Those with bilateral THA have stable overaverage walking capacities similar to Charnley class A. An extension of the traditional Charnley classification is proposed, taking into account the two different patient groups in Charnley class B. The new fourth Charnley class consists of patients with bilateral THA and was labeled BB in order to express the presence of two artificial hip joints and to preserve the traditional classification A through C.

Curing capability of halogen and LED light curing units in deep class II cavities in extracted human molars

Class II cavities were prepared in extracted lower molars filled and cured in three 2-mm increments using a metal matrix. Three composites (Spectrum TPH A4, Ceram X mono M7 and Tetric Ceram A4) were cured with both the SmartLite PS LED LCU and the Spectrum 800 continuous cure halogen LCU using curing cycles of 10, 20 and 40 seconds. Each increment was cured before adding the next. After a seven-day incubation period, the composite specimens were removed from the teeth, embedded in self-curing resin and ground to half the orofacial width. Knoop microhardness was determined 100, 200, 500, 1000, 1500, 2500, 3500, 4500 and 5500 microm from the occlusal surface at a distance of 150 microm and 1000 microm from the metal matrix. The total degree of polymerization of a composite specimen for any given curing time and curing light was determined by calculating the area under the hardness curve. Hardness values 150 microm from the metal matrix never reached maximum values and were generally lower than those 1000 microm from the matrix. The hardest composite was usually encountered between 200 microm and 1000 microm from the occlusal surface. For every composite-curing time combination, there was an increase in microhardness at the top of each increment (measurements at 500, 2500 and 4500 microm) and a decrease towards the bottom of each increment (measurements at 1500, 3500 and 5500 microm). Longer curing times were usually combined with harder composite samples. Spectrum TPH composite was the only composite showing a satisfactory degree of polymerization for all three curing times and both LCUs. Multiple linear regression showed that only the curing time (p < 0.001) and composite material (p < 0.001) had a significant association with the degree of polymerization. The degree of polymerization achieved by the LED LCU was not significantly different from that achieved by the halogen LCU (p = 0.54).

Cost effectiveness of home based population screening for Chlamydia trachomatis in the UK: economic evaluation of chlamydia screening studies (ClaSS) project

OBJECTIVE: To investigate the cost effectiveness of screening for Chlamydia trachomatis compared with a policy of no organised screening in the United Kingdom. DESIGN: Economic evaluation using a transmission dynamic mathematical model. SETTING: Central and southwest England. PARTICIPANTS: Hypothetical population of 50,000 men and women, in which all those aged 16-24 years were invited to be screened each year. MAIN OUTCOME MEASURES: Cost effectiveness based on major outcomes averted, defined as pelvic inflammatory disease, ectopic pregnancy, infertility, or neonatal complications. RESULTS: The incremental cost per major outcome averted for a programme of screening women only (assuming eight years of screening) was 22,300 pounds (33,000 euros; $45,000) compared with no organised screening. For a programme screening both men and women, the incremental cost effectiveness ratio was approximately 28,900 pounds. Pelvic inflammatory disease leading to hospital admission was the most frequently averted major outcome. The model was highly sensitive to the incidence of major outcomes and to uptake of screening. When both were increased the cost effectiveness ratio fell to 6200 pound per major outcome averted for screening women only. CONCLUSIONS: Proactive register based screening for chlamydia is not cost effective if the uptake of screening and incidence of complications are based on contemporary empirical studies, which show lower rates than commonly assumed. These data are relevant to discussions about the cost effectiveness of the opportunistic model of chlamydia screening being introduced in England.

Influence of beveling and ultrasound application on marginal adaptation of box-only Class II (slot) resin composite restorations

A laboratory study was performed to assess the influence of beveling the margins of cavities and the effects on marginal adaptation of the application of ultrasound during setting and initial light curing. After minimal access cavities had been prepared with an 80 microm diamond bur, 80 box-only Class II cavities were prepared mesially and distally in 40 extracted human molars using four different oscillating diamond coated instruments: (A) a U-shaped PCS insert as the non-beveled control (EMS), (B) Bevelshape (Intensiv), (C) SonicSys (KaVo) and (D) SuperPrep (KaVo). In groups B-D, the time taken for additional bevel finishing was measured. The cavities were filled with a hybrid composite material in three increments. Ultrasound was also applied to one cavity per tooth before and during initial light curing (10 seconds). The specimens were subjected to thermomechanical stress in a computer-controlled masticator device. Marginal quality was assessed by scanning electron microscopy and the results were compared statistically. The additional time required for finishing was B > D > C (p < or = 0.05). In all groups, thermomechanical loading resulted in a decrease in marginal quality. Beveling resulted in higher values for "continuous" margins compared with that of the unbeveled controls. The latter showed better marginal quality at the axial walls when ultrasound was used. Beveling seems essential for good marginal adaptation but requires more preparation time. The use of ultrasonic vibrations may improve the marginal quality of unbeveled fillings and warrants further investigation.

Interrelation of peri-operative morbidity and ASA class assignment in patients undergoing gynaecological surgery

OBJECTIVE: The aim of this study was to estimate intra- and post-operative risk using the American Society of Anaesthesiologists (ASA) classification which is an important predictor of an intervention and of the entire operating programme. STUDY DESIGN: In this retrospective study, 4435 consecutive patients undergoing elective and emergency surgery at the Gynaecological Clinic of the University Hospital of Zurich were included. The ASA classification for pre-operative risk assessment was determined by an anaesthesiologist after a thorough physical examination. We observed several pre-, intra- and post-operative parameters, such as age, body-mass-index, duration of anaesthesia, duration of surgery, blood loss, duration of post-operative stay, complicated post-operative course, morbidity and mortality. The investigation of different risk factors was achieved by a multiple linear regression model for log-transformed duration of hospitalisation. RESULTS: Age and obesity were responsible for a higher ASA classification. ASA grade correlates with the duration of anaesthesia and the duration of the surgery itself. There was a significant difference in blood loss between ASA grades I (113+/-195 ml) and III (222+/-470 ml) and between classes II (176+/-432 ml) and III. The duration of post-operative hospitalisation could also be correlated with ASA class. ASA class I=1.7+/-3.0 days, ASA class II=3.6+/-4.3 days, ASA class III=6.8+/-8.2 days, and ASA class IV=6.2+/-3.9 days. The mean post-operative in-hospital stay was 2.5+/-4.0 days without complications, and 8.7+/-6.7 days with post-operative complications. Multiple linear regression model showed that not only the ASA classification contained an important information for the duration of hospitalisation. Parameters such as age, class of diagnosis, post-operative complications, etc. also have an influence on the duration of hospitalisation. CONCLUSION: This study shows that the ASA classification can be used as a good and early available predictor for the planning of an intervention in gynaecological surgery. The ASA classification helps the surgeon to assess the peri-operative risk profile of which important information can be derived for the planning of the operation programme.