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

The relationship of dielectric response and water activity in food

This study has deduced a correlation between points of inflection of water activity and loss factor with respect to moisture content. A point of inflection in loss factor with respect to moisture content was found to coincide with the sorption isotherm point of inflection that defines the transition from multilayer to solution in every instance analysed, with an average difference of just 0.01kg.kg-1. Food can support microbial growth and chemical reactions in water activity levels above this critical transition. This correlation was discovered using published dielectric and sorption data for specific foods at similar temperatures. It was found that low sugar foods containing high levels of hydrocolloids generally exhibited different behaviour from fruits. This shows that microwave heating behaviour will be different in fruits compared to low sugar foods with high hydrocolloid content when drying to achieve a certain water activity and therefore shelf life

Economic and Conservation Evaluation of Capital Renovation Projects: Hidalgo County Irrigation District No. 1 (Edinburg) - North Branch / East Main - Final

Initial construction costs and net annual changes in operating and maintenance expenses are identified for a single-component capital renovation project proposed by Hidalgo County Irrigation District No. 1 to the Bureau of Reclamation and North American Development Bank. The proposed project involves installing 4.83 miles of multi-size pipeline to replace a segment of the North Branch / East Main canal. Both nominal and real estimates of water and energy savings and expected economic and financial costs of those savings are identified throughout the anticipated 48-year useful life for the proposed project. Sensitivity results for both the cost of water savings and cost of energy savings are presented for several important parameters. Annual water and energy savings forthcoming from the total project are estimated, using amortization procedures, to be 5,838 ac-ft of water per year and 3,293,049,926 BTUs (965,138 kwh) of energy per year. The calculated economic and financial cost of water savings is estimated to be $15.58 per ac-ft. The calculated economic and financial cost of energy savings is estimated at$0.0000392 per BTU ($0.134 per kwh). In addition, expected real (rather than nominal) values are indicated for the Bureau of Reclamation’s three principal evaluation measures specified in the United States Public Law 106-576 legislation. The initial construction cost per ac-ft of water savings measure is$30.68 per ac-ft of water savings. The initial construction cost per BTU (kwh) of energy savings measure is $0.0000544 per BTU ($0.186 per kwh). The ratio of initial construction costs per dollar of total annual economic savings is estimated to be -1.58

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

Broad anti-hepatitis C virus (HCV) antibody responses are associated with improved clinical disease parameters in chronic HCV infection

During hepatitis C virus (HCV) infection broadly neutralizing antibody (bNAb) responses targeting E1E2 envelope glycoproteins are generated in many individuals. It is unclear if these antibodies play a protective or a pathogenic role during chronic infection. In this study, we investigated whether bNAb responses in individuals with chronic infection were associated with differences in clinical presentation. Patient-derived purified serum IgG was used to assess the breadth of HCV E1E2 binding and neutralization activity of HCV pseudoparticles. Two panels were compared, bearing viral envelope proteins representing either an inter-genotype or an intra-genotype (gt) 1 group. We found that HCV viral load was negatively associated with strong cross-genotypic E1E2 binding (P=0.03). Overall we observed only modest correlation between total E1E2 binding and neutralizing ability. The breadth of inter-genotype neutralization did not correlate with any clinical parameters, however, analysis of individuals with gt 1 HCV infection (n=20), using an intra-genotype pseudoparticle panel, found a strong association between neutralization breadth and reduced liver fibrosis (P=0.006). Broad bNAb response in our chronic cohort was associated with a single nucleotide polymorphism (SNP) in the HLA-DQB1 gene (P=0.038) as previously reported in an acute cohort. Furthermore bNAbs in these individuals targeted more than one region of E2 neutralizing epitopes as assessed through cross-competition of patient bNAbs with well-characterized E2 antibodies. We conclude that bNAb responses in chronic gt1 infection are associated with lower rates of fibrosis and host genetics may play a role in the ability to raise such responses. IMPORTANCE: Globally there are 130-150 million people with chronic HCV infection. Typically the disease is progressive and is a major cause of severe liver cirrhosis and hepatocellular carcinoma. While it is known that neutralizing antibodies have a role in spontaneous clearance during acute infection, little is known about their role in chronic infection. In the present work we investigate the antibody response in a cohort of chronically infected individuals and find that a broad neutralizing antibody response is protective, with reduced levels of liver fibrosis and cirrhosis. We also find an association with SNPs in class II HLA genes and the presence of a broad neutralizing response indicating that antigen presentation may be important for production of HCV neutralizing antibodies

Economic and Conservation Evaluation of Capital Renovation Projects: Harlingen Irrigation District Cameron County No. 1 Canal Meters and Telemetry Equipment, Impervious-Lining of Delivery Canals, Pipelines Replacing Delivery Canals, and On-Farm Delivery-Site Meters

Initial construction costs and net annual changes in operating and maintenance expenses are identified for the capital renovation project proposed by Harlingen Irrigation District Cameron County No. 1 to the North American Development Bank (NADBank). Both nominal and real, expected economic and financial costs of water and energy savings are identified throughout the anticipated useful lives for each of the four components of the proposed project (i.e., canal meters and telemetry equipment, impervious-lining of delivery canals, 24" pipelines replacing delivery canals, and on-farm delivery-site meters). Sensitivity results for both the cost of water savings and cost of energy savings are presented for several important parameters. Expected cost of water savings and cost of energy savings for each of the four components are aggregated into a composite set of cost measures for the total proposed project. Aggregate cost of water savings is estimated to be $31.37 per ac-ft and energy savings are measured at an aggregate value of$0.0002253 per BTU (i.e., $0.769 per kwh). In addition, expected values are indicated for the Bureau of Reclamation’s three principal evaluation measures specified in the Public Law 106-576 legislation. The aggregate initial construction cost per ac-ft of water savings measure is$26.87 per ac-ft of water savings. The aggregate initial construction cost per BTU (kwh) of energy savings measure is $0.0001603 per BTU ($0.547 per kwh). The amount of initial construction costs per dollar of total annual economic savings is estimated to be -1.30

Economic and Conservation Evaluation of Capital Renovation Projects: Cameron County Irrigation District No. 2 (San Benito) – Interconnect Between Canals 39 and 13-A1 and Replacement of Rio Grande Diversion Pumping Plant

Initial construction costs and net annual changes in operating and maintenance expenses are identified for the capital renovation project proposed by the Cameron County Irrigation District No. 2 (a.k.a. San Benito) to the North American Development Bank (NADBank) and Bureau of Reclamation. Both nominal and real, expected economic and financial costs of water and energy savings are identified throughout the anticipated useful lives for both components of the proposed project (i.e., a lined interconnect between Canals 39 and 13-A1 and replacement of the Rio Grande diversion pumping plant). Sensitivity results for both the cost of water savings and cost of energy savings are presented for several important parameters. Expected cost of water savings and cost of energy savings for both components are aggregated into a composite set of cost measures for the total proposed project. Aggregate cost of water savings is estimated to be $41.26 per ac-ft and energy savings are measured at an aggregate value of$0.0001586 per BTU (i.e., $0.541 per kwh). In addition, expected values are indicated for the Bureau of Reclamation’s three principal evaluation measures specified in the United States Public Law 106-576 legislation. The aggregate initial construction cost per ac-ft of water savings measure is$157.07 per ac-ft of water savings. The aggregate initial construction cost per BTU (kwh) of energy savings measure is $0.0001777 per BTU ($0.606 per kwh). The ratio of initial construction costs per dollar of total annual economic savings is estimated to be -3.80

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

Economic and Conservation Evaluation of Capital Renovation Projects: Edinburg Irrigation District Hidalgo County No. 1 - 72" Pipeline Replacing Delivery Canal and Multi-Size Pipeline Replacing Delivery Canal

Initial construction costs and net annual changes in operating and maintenance expenses are identified for the capital renovation project proposed by Edinburg Irrigation District Hidalgo County No. 1 to the North American Development Bank (NADBank). Both nominal and real, expected economic and financial costs of water and energy savings are identified throughout the anticipated useful lives for both components of the proposed project (i.e., 72" pipeline replacing a segment of delivery canal along the "Curry Main" and multi-size pipeline replacing a segment of delivery canal along the "North Branch / East Main"). Sensitivity results for both the cost of water savings and cost of energy savings are presented for several important parameters. Expected cost of water savings and cost of energy savings for both components are aggregated into a composite set of cost measures for the total proposed project. Aggregate cost of water savings is estimated to be $29.87 per ac-ft and energy savings are measured at an aggregate value of$0.0000595 per BTU (i.e., $0.203 per kwh). In addition, expected values are indicated for the Bureau of Reclamation's three principal evaluation measures specified in the United States Public Law 106-576 legislation. The aggregate initial construction cost per ac-ft of water savings measure is$50.90 per ac-ft of water savings. The aggregate initial construction cost per BTU (kwh) of energy savings measure is $0.0000777 per BTU ($0.265 per kwh). The ratio of initial construction costs per dollar of total annual economic savings is estimated to be -2.01