Statistical Resolution of Ambiguous HLA Typing Data

High-resolution HLA typing plays a central role in many areas of immunology, such as in identifying immunogenetic risk factors for disease, in studying how the genomes of pathogens evolve in response to immune selection pressures, and also in vaccine design, where identification of HLA-restricted epitopes may be used to guide the selection of vaccine immunogens. Perhaps one of the most immediate applications is in direct medical decisions concerning the matching of stem cell transplant donors to unrelated recipients. However, high-resolution HLA typing is frequently unavailable due to its high cost or the inability to re-type historical data. In this paper, we introduce and evaluate a method for statistical, in silico refinement of ambiguous and/or low-resolution HLA data. Our method, which requires an independent, high-resolution training data set drawn from the same population as the data to be refined, uses linkage disequilibrium in HLA haplotypes as well as four-digit allele frequency data to probabilistically refine HLA typings. Central to our approach is the use of haplotype inference. We introduce new methodology to this area, improving upon the Expectation-Maximization (EM)-based approaches currently used within the HLA community. Our improvements are achieved by using a parsimonious parameterization for haplotype distributions and by smoothing the maximum likelihood (ML) solution. These improvements make it possible to scale the refinement to a larger number of alleles and loci in a more computationally efficient and stable manner. We also show how to augment our method in order to incorporate ethnicity information (as HLA allele distributions vary widely according to race/ethnicity as well as geographic area), and demonstrate the potential utility of this experimentally. A tool based on our approach is freely available for research purposes at http://microsoft.com/science

Inverse correlation between quasiparticle mass and Tc in a cuprate high-Tc superconductor

Close to a zero-temperature transition between ordered and disordered electronic phases, quantum fluctuations can lead to a strong enhancement of electron mass and to the emergence of competing phases such as superconductivity. A correlation between the existence of such a quantum phase transition and superconductivity is quite well established in some heavy fermion and iron-based superconductors, and there have been suggestions that high-temperature superconductivity in copper-oxide materials (cuprates) may also be driven by the same mechanism. Close to optimal doping, where the superconducting transition temperature Tc is maximal in cuprates, two different phases are known to compete with superconductivity: a poorly understood pseudogap phase and a charge-ordered phase. Recent experiments have shown a strong increase in quasiparticle mass m* in the cuprate YBa2Cu3O7-δ as optimal doping is approached, suggesting that quantum fluctuations of the charge-ordered phase may be responsible for the high-Tc superconductivity. We have tested the robustness of this correlation between m* and Tc by performing quantum oscillation studies on the stoichiometric compound YBa2Cu4O8 under hydrostatic pressure. In contrast to the results for YBa2Cu3O7-δ, we find that in YBa2Cu4O8, the mass decreases as Tc increases under pressure. This inverse correlation between m* and Tc suggests that quantum fluctuations of the charge order enhance m* but do not enhance Tc

Microstructural characterisation of subsurface deformation and the degradation of Stellite 6 induced by self-mated sliding contact in a simulated PWR environment

© 2021 Elsevier Ltd Stellite 6 (Co-29.5%Cr-5%W-1.2%C in wt%) is traditionally used as a hardfacing material in the primary circuit of pressurised water reactors (PWRs) due to its good corrosion and wear resistance in water at up to 300 °C. In this study, pin-on-disc type sliding contact tribocorrosion testing was conducted on HIPed Stellite 6 at 20 °C and 250 °C using a bespoke tribometer to simulate a primary circuit environment. Transmission electron microscopy (TEM), scanning electron microscopy (SEM), and X-ray diffraction (XRD) were used to characterize, for the first time, the material affected by tribocorrosion. Whilst the material loss increases by 16–39 times when the test temperature is increased from 20 °C to 250 °C, the mechanisms of degradation and deformation remain largely unchanged. Furthest from the sliding contact, strain is principally accommodated by the deformation-induced transformation of the γ Co-based matrix to ε-martensite. Closer to the sliding contact, the ε-martensite phase accommodates further strain via twinning and dislocation slip. At the sliding contact the intense deformation generates a nanocrystalline structure. The tribologically affected material is resistant to plastic strain localisation; this confines wear to the nanoscale where the synergistic effects of chemical degradation and mechanical deformation permit the removal of nanoscale particulates (corrosion enhanced nanowear (tribocorrosion)). The increased wear rate at 250 °C is attributed to a temperature dependent increase in corrosion enhanced nanowear. The degradation mechanisms revealed are important for the design of future hardfacings

A single dose of antibody-drug conjugate cures a stage 1 model of African trypanosomiasis.

Infections of humans and livestock with African trypanosomes are treated with drugs introduced decades ago that are not always fully effective and often have severe side effects. Here, the trypanosome haptoglobin-haemoglobin receptor (HpHbR) has been exploited as a route of uptake for an antibody-drug conjugate (ADC) that is completely effective against Trypanosoma brucei in the standard mouse model of infection. Recombinant human anti-HpHbR monoclonal antibodies were isolated and shown to be internalised in a receptor-dependent manner. Antibodies were conjugated to a pyrrolobenzodiazepine (PBD) toxin and killed T. brucei in vitro at picomolar concentrations. A single therapeutic dose (0.25 mg/kg) of a HpHbR antibody-PBD conjugate completely cured a T. brucei mouse infection within 2 days with no re-emergence of infection over a subsequent time course of 77 days. These experiments provide a demonstration of how ADCs can be exploited to treat protozoal diseases that desperately require new therapeutics

Phenotypic Expressions of CCR5-Δ32/Δ32 Homozygosity

Objective: As blockade of CC-chemokine receptor 5 (CCR5) has been proposed as therapy for HIV-1, we examined whether the CCR5-Δ32/Δ32 homozygous genotype has phenotypic expressions other than those related to HIV-1. Design: Study subjects were white homosexual men or men with hemophilia who were not infected with HIV-1. In this study, 15 CCR5-Δ32/Δ32 homozygotes were compared with 201 CCR5 wild-type (+/+) subjects for a wide range of clinical conditions and laboratory assay results ascertained during prospective cohort studies and routine clinical care. CCR5-Δ32 genotype was determined by polymerase chain reaction, followed by single-stranded conformational polymorphism analysis. Results: Hypertension and conditions attributable to hemophilia were the only diagnoses frequently found in clinical records of CCR5-Δ32/Δ32 study subjects. Based on blood pressure measurement and treatment history, CCR5-Δ32/Δ32 homozygotes had a 2.8-fold higher prevalence of hypertension than age-matched CCR5-+/+ study subjects (95% confidence interval [CI], 1.2-6.4; p = .01); none of the homozygotes had severe hypertension. Hematologic measures were generally similar across the genotypes, but total lymphocyte counts were ~20% higher in CCR5-Δ32/Δ32 study subjects than in CCR5-+/+ study subjects (p \u3c .05). Among patients with hemophilia who were infected with hepatitis C virus (HCV), mean alanine aminotransferase levels were 117% higher among CCR5-Δ32/Δ32 homozygotes (p \u3c .05), but serum HCV levels did not differ by CCR5-Δ32 genotype. CCR5-Δ32/Δ32 homozygous study subjects had a lower prevalence of antibodies to measles virus than those with other genotypes, but this association was not confirmed in a group of blood donors. The prevalence of antibodies to nine other common viruses, HBV, and HCV was not related to CCR5 genotype. Conclusions: CCR5-Δ32/Δ32 homozygotes are generally similar to wild-type persons. Confirmatory investigations are required to determine whether hypertension, increased lymphocyte counts, and higher hepatic enzyme levels in the presence of HCV infection represent true phenotypic expressions of this genotype. CCR5-Δ32/Δ32 homozygosity does not provide broad protection against viral infections

Bridging Alone: Religious Conservatism, Marital Homogamy, and Voluntary Association Membership

This study characterizes social insularity of religiously conservative American married couples by examining patterns of voluntary associationmembership. Constructing a dataset of 3938 marital dyads from the second wave of the National Survey of Families and Households, the author investigates whether conservative religious homogamy encourages membership in religious voluntary groups and discourages membership in secular voluntary groups. Results indicate that couples’ shared affiliation with conservative denominations, paired with beliefs in biblical authority and inerrancy, increases the likelihood of religious group membership for husbands and wives and reduces the likelihood of secular group membership for wives, but not for husbands. The social insularity of conservative religious groups appears to be reinforced by homogamy—particularly by wives who share faith with husbands

Tricks and treats: designing technology to support mobility assistance dogs

Assistance dogs are a key intervention to support the autonomy of people with tetraplegia. Previous research on assistive technologies have investigated ways to, ultimately, replace their labour using technology, for instance through the design of smart home environments. However, both the disability studies literature and our interviews suggest there is an immediate need to support these relationships, both in terms of training and bonding. Through a case study of an accessible dog treats dispenser, we investigate a technological intervention responding to these needs, detailing an appropriate design methodology and contributing insights into user requirements and preferences

Broad and Gag-Biased HIV-1 Epitope Repertoires Are Associated with Lower Viral Loads

Background: HLA class-I alleles differ in their ability to control HIV replication through cell-mediated immune responses. No consistent associations have been found between the breadth of Cytotoxic T Lymphocytes (CTL) responses and the control of HIV-1, and it is unknown whether the size or distribution of the viral proteome-wide epitope repertoire, i.e., the intrinsic ability to present fewer, more or specific viral epitopes, could affect clinical markers of disease progression. Methodology/Principal Findings: We used an epitope prediction model to identify all epitope motifs in a set of 302 HIV-1 full-length proteomes according to each individual's HLA (Human Leukocyte Antigen) genotype. The epitope repertoire, i.e., the number of predicted epitopes per HIV-1 proteome, varied considerably between HLA alleles and thus among individual proteomes. In a subgroup of 270 chronically infected individuals, we found that lower viral loads and higher CD4 counts were associated with a larger predicted epitope repertoire. Additionally, in Gag and Rev only, more epitopes were restricted by alleles associated with low viral loads than by alleles associated with higher viral loads. Conclusions/Significance: This comprehensive analysis puts forth the epitope repertoire as a mechanistic component of the multi-faceted HIV-specific CTL response. The favorable impact on markers of disease status of the propensity to present more HLA binding peptides and specific proteins gives impetus to vaccine design strategies that seek to elicit responses to a broad array of HIV-1 epitopes, and suggest a particular focus on Gag