Tracking TCRß sequence clonotype expansions during antiviral therapy using high-throughput sequencing of the hypervariable region

To maintain a persistent infection viruses such as hepatitis C virus (HCV) employ a range of mechanisms that subvert protective T cell responses. The suppression of antigen-specific T cell responses by HCV hinders efforts to profile T cell responses during chronic infection and antiviral therapy. Conventional methods of detecting antigen-specific T cells utilize either antigen stimulation (e.g., ELISpot, proliferation assays, cytokine production) or antigen-loaded tetramer staining. This limits the ability to profile T cell responses during chronic infection due to suppressed effector function and the requirement for prior knowledge of antigenic viral peptide sequences. Recently, high-throughput sequencing (HTS) technologies have been developed for the analysis of T cell repertoires. In the present study, we have assessed the feasibility of HTS of the TCRβ complementarity determining region (CDR)3 to track T cell expansions in an antigen-independent manner. Using sequential blood samples from HCV-infected individuals undergoing antiviral therapy, we were able to measure the population frequencies of >35,000 TCRβ sequence clonotypes in each individual over the course of 12 weeks. TRBV/TRBJ gene segment usage varied markedly between individuals but remained relatively constant within individuals across the course of therapy. Despite this stable TRBV/TRBJ gene segment usage, a number of TCRβ sequence clonotypes showed dramatic changes in read frequency. These changes could not be linked to therapy outcomes in the present study; however, the TCRβ CDR3 sequences with the largest fold changes did include sequences with identical TRBV/TRBJ gene segment usage and high junction region homology to previously published CDR3 sequences from HCV-specific T cells targeting the HLA-B*0801-restricted 1395HSKKKCDEL1403 and HLA-A*0101-restricted 1435ATDALMTGY1443 epitopes. The pipeline developed in this proof of concept study provides a platform for the design of future experiments to accurately address the question of whether T cell responses contribute to SVR upon antiviral therapy. This pipeline represents a novel technique to analyze T cell dynamics in situations where conventional antigen-dependent methods are limited due to suppression of T cell functions and highly diverse antigenic sequences

Characterisation of potato crisp effective porosity using micro-CT

Background The effective porosity is an important quantitative parameter for food products that has a significant effect on taste and quality. It is challenging to quantify the apparent porosity of fried potato crisps as they have a thin irregularly shaped cross section containing oil and water. This study uses a novel micro-CT technique to determine the solid volume fraction and hence the effective porosity of three types of potato crisps: standard continuously fried crisps, microwaved crisps, and continuously fried ‘kettle’ crisps. Results It was found that continuously fried kettle crisps had the lowest effective porosity at 0.54, providing the desired crunchy taste and lower oil contents. Crisps produced using a microwave process designed to mimic the dehydration process of standard continuous fried crisps had an effective porosity of 0.65, which was very similar to the effective porosity of 0.63 for standard continuously fried crisps. The results were supported by the findings of a forced preference consumer test. Conclusion The effective porosity affects the product taste and is therefore a critical parameter. This study shows that micro-CT analysis can be used to characterise the change in effective porosity of a thin irregularly shaped food product, caused by a change of cooking procedure

Rapid and accurate broadband absorption cross-section measurement of human bodies in a reverberation chamber

A measurement methodology for polarization and angle of incidence averaged electromagnetic absorption cross-section using a reverberation chamber is presented. The method is optimized for simultaneous rapid and accurate determination of average absorption cross-section over the frequency range 1–15 GHz, making it suitable for use in human absorption and exposure studies. The typical measurement time of the subject is about 8 min with a corresponding statistical uncertainty of about 3% in the measured absorption cross-section. The method is validated by comparing measurements on a spherical phantom with Mie series calculations. The efficacy of the method is demonstrated with measurements of the posture dependence of the absorption cross-section of a human subject and an investigation of the effects of clothing on the measured absorption which are important considerations for the practical design of experiments for studies on human subjects

The characteristics of cognitive neuroscience tests in a schizophrenia cognition clinical trial: Psychometric properties and correlations with standard measures.

In comparison to batteries of standard neuropsychological tests, cognitive neuroscience tests may offer a more specific assessment of discrete neurobiological processes that may be aberrant in schizophrenia. However, more information regarding psychometric properties and correlations with standard neuropsychological tests and functional measures is warranted to establish their validity as treatment outcome measures. The N-back and AX-Continuous Performance Task (AX-CPT) are two promising cognitive neuroscience tests designed to measure specific components of working memory and contextual processing respectively. In the current study, we report the psychometric properties of multiple outcome measures from these two tests as well as their correlations with standard neuropsychological measures and functional capacity measures. The results suggest that while the AX-CPT and N-back display favorable psychometric properties, they do not exhibit greater sensitivity or specificity with functional measures than standard neurocognitive tests

Engaging with community researchers for exposure science: lessons learned from a pesticide biomonitoring study

A major challenge in biomonitoring studies with members of the general public is ensuring their continued involvement throughout the necessary length of the research. The paper presents evidence on the use of community researchers, recruited from local study areas, as a mechanism for ensuring effective recruitment and retention of farmer and resident participants for a pesticides biomonitoring study. The evidence presented suggests that community researchers' abilities to build and sustain trusting relationships with participants enhanced the rigour of the study as a result of their on-the-ground responsiveness and flexibility resulting in data collection beyond targets expected

Proof of Bose-Einstein Condensation for Interacting Gases with a One-Particle Spectral Gap

Using a specially tuned mean-field Bose gas as a reference system, we establish a positive lower bound on the condensate density for continuous Bose systems with superstable two-body interactions and a finite gap in the one-particle excitations spectrum, i.e. we prove for the first time standard homogeneous Bose-Einstein condensation for such interacting systems

Odours of Plasmodium falciparum-infected participants influence mosquito-host interactions.

Malaria parasites are thought to influence mosquito attraction to human hosts, a phenomenon that may enhance parasite transmission. This is likely mediated by alterations in host odour because of its importance in mosquito host-searching behaviour. Here, we report that the human skin odour profile is affected by malaria infection. We compared the chemical composition and attractiveness to Anopheles coluzzii mosquitoes of skin odours from participants that were infected by Controlled Human Malaria Infection with Plasmodium falciparum. Skin odour composition differed between parasitologically negative and positive samples, with positive samples collected on average two days after parasites emerged from the liver into the blood, being associated with low densities of asexual parasites and the absence of gametocytes. We found a significant reduction in mosquito attraction to skin odour during infection for one experiment, but not in a second experiment, possibly due to differences in parasite strain. However, it does raise the possibility that infection can affect mosquito behaviour. Indeed, several volatile compounds were identified that can influence mosquito behaviour, including 2- and 3-methylbutanal, 3-hydroxy-2-butanone, and 6-methyl-5-hepten-2-one. To better understand the impact of our findings on Plasmodium transmission, controlled studies are needed in participants with gametocytes and higher parasite densities

Record Maximum Oscillation Frequency in C-face Epitaxial Graphene Transistors

The maximum oscillation frequency (fmax) quantifies the practical upper bound for useful circuit operation. We report here an fmax of 70 GHz in transistors using epitaxial graphene grown on the C-face of SiC. This is a significant improvement over Si-face epitaxial graphene used in the prior high frequency transistor studies, exemplifying the superior electronics potential of C-face epitaxial graphene. Careful transistor design using a high {\kappa} dielectric T-gate and self-aligned contacts, further contributed to the record-breaking fmax

Planetary Nebulae as standard candles XI. Application to Spiral Galaxies

We report the results of an [O III] lambda 5007 survey for planetary nebulae (PN) in three spiral galaxies: M101 (NGC 5457), M51 (NGC 5194/5195) and M96 (NGC 3368). By comparing on-band/off-band [O III] lambda 5007 images with images taken in H-alpha and broadband R, we identify 65, 64 and 74 PN candidates in each galaxy, respectively. From these data, an adopted M31 distance of 770 kpc, and the empirical planetary nebula luminosity function (PNLF), we derive distances to M101, M51, and M96 of 7.7 +/- 0.5, 8.4 +/- 0.6, and 9.6 +/- 0.6 Mpc. These observations demonstrate that the PNLF technique can be successfully applied to late-type galaxies, and provide an important overlap between the Population I and Population II distance scales. We also discuss some special problems associated with using the PNLF in spiral galaxies, including the effects of dust and the possible presence of [O III] bright supernova remnants.Comment: 38 pages, TeX, with tables included but not figures. Uses epsf.tex and kpnobasic.tex. To be published in the Astophysical Journal. Full paper is available at http://www.astro.psu.edu/users/johnf/Text/research.htm