Impact of alemtuzumab-mediated lymphocyte depletion on SIV reservoir establishment and persistence.

Persistence of the rebound-competent viral reservoir (RCVR) within the CD4+ T cell compartment of people living with HIV remains a major barrier to HIV cure. Here, we determined the effects of the pan-lymphocyte-depleting monoclonal antibody (mAb) alemtuzumab on the RCVR in SIVmac239-infected rhesus macaques (RM) receiving antiretroviral therapy (ART). Alemtuzumab administered during chronic ART or at the time of ART initiation induced >95% depletion of circulating CD4+ T cells in peripheral blood and substantial CD4+ T cell depletion in lymph nodes. However, treatment was followed by proliferation and reconstitution of CD4+ T cells in blood, and despite ongoing ART, levels of cell-associated SIV DNA in blood and lymphoid tissues were not substantially different between alemtuzumab-treated and control RM after immune cell reconstitution, irrespective of the time of alemtuzumab treatment. Upon ART cessation, 19 of 22 alemtuzumab-treated RM and 13 of 13 controls rebounded with no difference in the time to rebound between treatment groups. Time to rebound and reactivation rate was associated with plasma viral loads (pVLs) at time of ART initiation, suggesting lymphocyte depletion had no durable impact on the RCVR. However, 3 alemtuzumab-treated RM that had lowest levels of pre-ART viremia, failed to rebound after ART withdrawal, in contrast to controls with similar levels of SIV replication. These observations suggest that alemtuzumab therapy has little to no ability to reduce well-established RCVRs but may facilitate RCVR destabilization when pre-ART virus levels are particularly low.

Modelling the public health benefits of fibre fortification in the Chinese population through food reformulation.

OBJECTIVES: Various studies have highlighted how consuming adequate dietary fibre (DF) foods could confer multiple potential health benefits to humans, though data suggested that the average intake of the population is below the recommendations. The aim of this study, which involved probabilistic, mathematical and statistical modelling, was to understand, for the first time, how fibre fortification in a broad array of food categories could impact the diet and health status of Chinese consumers. DESIGN: A simulation-based approach was used to examine the potential impact of fibre fortification. The China Health and Nutrition Survey dataset was used to evaluate intakes of DF together with a dietary intake mathematical model. Commercially manufactured foods and beverages eligible for fibre fortification were identified and a total of 296 food and beverages were selected for fibre fortification calculation. Foods and beverages eligible for fibre fortification and the concentration of fibre used at intervention were identified based on Chinese legislations and regulations of nutrition label claims. Populations who meet the dietary reference values of fibre fortification have their health outcomes such as weight, cardiovascular disease (CVD) and type 2 diabetes risk quantified prefibre and postfibre reformulation as per published studies. RESULTS: The simulated fibre fortification intervention model has shown that the mean DF intake increased by 13.28%, from 12.8 g/day of baseline to 14.5 g/day, leading to an increase of 48% (from 6.85% to 10.13%) and 54% (from 14.22% to 21.84%) of the adult and children population, respectively, achieving the recommended fibre guidelines. Additionally, 234 diabetes cases per day (85 340 cases per year) as well as 73 065 deaths secondary to CVD could also potentially be averted or delayed with the increase of DF intake via fibre fortification. CONCLUSIONS: This study provides a practical application implicating the potential public health benefits that could be achieved with food product reformulation.

From worst-case to reality - Case studies illustrating tiered refinement of consumer exposure to cosmetic ingredients.

Consumer exposure to cosmetic ingredients is estimated in a tiered manner. Simple Tier1 deterministic aggregate exposure modelling generates a worst case estimate of exposure. Tier1 assumes that a consumer uses all cosmetic products concomitantly daily, at maximum frequency, and products always contain the ingredient at the maximum allowed % w/w concentration. Refining exposure assessment from worst case to more realistic estimates uses evidence from surveys of actual use levels of ingredients and Tier2 probabilistic models, where distributions of consumer use data can be applied. In Tier2+ modelling, occurrence data provides evidence of products on the market actually containing the ingredient. Three case studies are presented using this tiered approach to illustrate progressive refinement. The scale of refinements from Tier1 to Tier2+ modelling for the ingredients, propyl paraben, benzoic acid and DMDM hydantoin were: 0.492 to 0.026; 1.93 to 0.042 and 1.61 to 0.027 mg/kg/day exposure dose. For propyl paraben, moving from Tier1 to Tier2+ represents a refinement from 49-fold to 3-fold overestimate of exposure when compared to a maximum estimate of 0.01 mg/kg/day exposure seen in human studies. Such refinements from worst case to realistic levels of exposure estimation can be critical in the demonstration of consumer safety.

Estimating the potential public health impact of fibre enrichment: a UK modelling study.

For improving human health, reformulation can be a tool as it allows individuals to consume products of choice while reducing intake of less desirable nutrients, such as sugars and fats, and potentially increasing intake of beneficial nutrients such as fibre. The potential effects of reformulating foods with increased fibre on diet and health need to be better understood. The objective of this statistical modelling study was to understand how fibre enrichment can affect the diet and health of consumers. The UK National Diet and Nutrition Survey datasets from 2014 to 2015 and 2015 to 2016 were utilised to evaluate intakes of fibre and kilocalories with a dietary intake model. Foods and beverages eligible for fibre enrichment were identified (n 915) based on EU legislation for fibre content claims. Those people who meet dietary reference values and fibre enrichment health outcomes such as weight, CVD and type 2 diabetes risk reductions were quantified pre- and post-fibre reformulation via Reynolds et al., D'Agostino et al. and QDiabetes algorithms, respectively. The fibre enrichment intervention showed a mean fibre intake of 19·9 g/d in the UK, signifying a 2·2 g/d increase from baseline. Modelling suggested that 5·9 % of subjects could achieve a weight reduction, 72·2 % a reduction in cardiovascular risk and 71·7 % a reduced risk of type 2 diabetes with fibre fortification (all Ps ≤ 0·05). This study gives a good overview of the potential public health benefits of reformulating food products using a straightforward enrichment scenario.

Gaining traction: Foothold concepts and exemplars in conceptual change.

This paper investigates the emergence of conformational analysis in organic chemistry as a case of conceptual change in science. In this case, the mechanism of conceptual change is identified as the emergence of a new exemplar. This new exemplar was made possible because of the identification of a distinctive chemical structure to which 'foothold' concepts were applicable. These concepts facilitated both clear explanation in the particular case, and the analogical extension of the conceptual innovation throughout the discipline. The case suggests a cognitive explanation for the importance of exemplars to scientific content.

The search process: Integrating the investigation and identification of missing and unidentified persons.

The effective search for the missing and identification of persons, alive or dead, are core components in the prevention and in resolving the issue of Missing Persons. Despite the growing literature on this topic, there is still a lack of publications describing the Search as a process that includes different phases inherently composed of forensic investigative and identification principles for both living and deceased missing persons. This paper is the result of discussions between the Forensic Unit of the International Committee of the Red Cross (ICRC) and members of its external Forensic Advisory Board. It aims to present the Search process as an overarching concept that includes the investigation and identification phases of the missing in any state (dead or alive), in any scenario (with or without bodies), with an integrated, multidisciplinary, and multiagency approach for implementation by all actors involved in the investigation and identification phases of missing persons.

An evaluation of the SureID 23comp Human Identification Kit for kinship testing.

Short tandem repeat (STR) profiling has been routinely used in kinship testing since the introduction of commercial kits in the mid-1990s. While 15 to 23 STR loci normally give definitive results in simple kinship testing, additional loci are sometimes required to resolve complex cases. The SureID 23comp Human Identification Kit, recently released by Health Gene Technologies (China), multiplexes amelogenin and 22 autosomal STRs, 17 of which are non-CODIS STRs. This enables the profiling of 38-40 loci when used in conjunction with widely used commercial kits. In this study, the kit was evaluated for kinship applications as a supplementary STR kit following the minimum criteria for validation recommended by the European Network of Forensic Science Institutes (ENFSI) and the Scientific Working Group on DNA Analysis Methods (SWGDAM) using 500 samples. Performance was comparable with other commercial kits demonstrating: repeatability and reproducibility; precision (maximum s.d. 0.1048 nt); accuracy, all alleles were within ±0.41 nt compared to the actual sizes; heterozygous peak balances at all loci >68%; stutter ratios ranged from 3.8% to 16.15%; full profiles were generated with 125 pg DNA (95.12% of alleles at 62 pg),; and we found 100% concordance over 5 common STRs with the GlobalFiler kit.

Optimization of a reduced volume PCR amplification for PowerPlex® Fusion kit using FTA™ cards and generation of population genetic data for Brunei population.

The commercial PowerPlex® Fusion kit is an autosomal STR multiplex kit that has high discrimination power and is more informative in forensic, paternity, and relationship-testing cases. Key features of this multiplex system are the possibility to direct amplify FTA™ card punches as well as non-FTA cards and commonly used swabs; optimised inhibitor tolerance and high sensitivity generating full profiles from amount as little as 100 pg of human DNA. This study focused on the optimization of performance variables such as FTA™ punch sizes, reduced reaction volumes, and FTA™ purification reagent aiming to increase the analytical sensitivity, decrease the sample consumption, and cost effectiveness. LOD and LOQ values demonstrated high sensitivity of the PowerPlex® Fusion system. In addition, population databases of Brunei Malay and Chinese from the Brunei Darussalam were established, and parameters of forensic importance were calculated. Overall, the forensic parameters indicated an enhanced utility of the PowerPlex® Fusion kit for forensic evidence analysis and paternity testing in Brunei Malay and Chinese populations.

Sequence data of six unusual alleles at SE33 and D1S1656 STR Loci.

When profiling a reference dataset of 500 DNA samples for the population of Saudi Arabia, using the GlobalFiler® PCR amplification kit, six unusual alleles were detected. At the SE33 locus, four novel alleles were found: 2, 14.3, 20.3, and 38; two alleles at the D1S1656 locus: 7 and 8 had been previously reported, but no published sequence data was available. The D1S1656 alleles were sequenced using ForenSeq™ DNA Signature Prep with the MiSeq FGx System (Illumina, USA). As the SE33 is not reported by available Massively Parallel Sequencing (MPS) systems, samples that exhibited the unreported alleles were sequenced using BigDye™ Terminator v3.1 Cycle Sequencing Kit. Here we present the sequence and structure of the previously uncharacterized alleles.

Analysis of the complete mitochondrial genomes of two forensically important blowfly species: Lucilia caesar and Lucilia illustris.

Blowfly species of the family Calliphoridae can be used in forensic investigations to estimate the minimum post-mortem interval (PMImin). Lucilia caesar and Lucilia illustris (Diptera: Calliphoridae) are closely related and phenotypically similar, making reliable identification difficult. To identify potential genetic markers to distinguish these species, five complete mitochondrial genomes were sequenced: three for L. caesar (KM657111-KM657113) and two for L. illustris (KM657109, KM657110). The ND6 gene contained the most species-specific SNPs (1.71%), followed by the ND5 gene (1.68%) and the COI gene (1.56%), identifying ND6 and ND5 as valuable loci for differentiating L. caesar and L. illustris specimens.

The use of forensic DNA analysis in humanitarian forensic action: The development of a set of international standards.

DNA analysis was first applied to the identification of victims of armed conflicts and other situations of violence (ACOSV) in the mid-1990s, starting in South America and the Balkans. Argentina was the first country to establish a genetic database specifically developed to identify disappeared children. Following on from these programs the early 2000s marked major programs, using a largely DNA-led approach, identifying missing persons in the Balkans and following the attack on the World Trade Center in New York. These two identification programs significantly expanded the magnitude of events to which DNA analysis was used to help provide the identity of missing persons. Guidelines developed by Interpol (2014) [1] related to best practice for identification of human remains following DVI type scenarios have been widely disseminated around the forensic community; in numerous cases these guidelines have been adopted or incorporated into national guidelines/standards/practice. However, given the complexity of many humanitarian contexts in which forensic science is employed there is a lack of internationally accepted guidelines, related to these contexts, for authorities to reference. In response the Argentine government's Human Rights Division in the Ministry of Foreign Affairs and Worship (MREC) proposed that the United Nations (UN) should promote best practice in the use of forensic genetics in humanitarian forensic action: this was adopted by the UN in Resolutions A/HRC/RES/10/26 and A/HRC/RES/15/5. Following on from the adoption of the resolutions MREC has coordinated, with the support of the International Committee of the Red Cross (ICRC), the drafting of a set of guidelines (MREC, ICRC, 2014) [2], with input from national and international agencies. To date the guidelines have been presented to South America's MERCOSUR and the UN and have been disseminated to interested parties.

Analysis of four PCR/SNaPshot multiplex assays analyzing 52 SNPforID markers.

The SNPforID consortium identified a panel of 52 SNPs for forensic analysis that has been used by several laboratories worldwide. The original analysis of the 52 SNPs was based on a single multiplex reaction followed by two single-base-extension (SBE) reactions each of which was analyzed using capillary electrophoresis. The SBE assays were designed for high throughput genetic analyzers and were difficult to use on the single capillary ABI PRISM 310 Genetic Analyzer and the latest generation 3500 Genetic Analyzer, as sensitivity on the 310 was low and separation of products on the 3500 with POP-7™ was poor. We have modified the original assay and split it into four multiplex reactions, each followed by an SBE assay. These multiplex assays were analyzed using polymer POP-4™ on ABI 310 PRISM® and polymers POP-4™, POP-6™ and POP-7™ on the 3500 Genetic Analyzer. The assays were sensitive and reproducible with input DNA as low as 60 pg using both the ABI 310 and 3500. In addition, we found that POP-6™ was most effective with the 3500, based on the parameters that we assessed, achieving better separation of the small SBE products; this conflicted with the recommended use of POP-7™ by the instrument manufacturer. To support the use of the SNP panel in casework in Malaysia we have created an allele frequency database from 325 individuals, representing the major population groups within Malaysia. Population and forensic parameters were estimated for all populations and its efficacy evaluated using 51 forensic samples from challenging casework.

The Development and Use of Internal Amplification Controls (IACs) with DNA Profiling Kits for Forensic DNA Analysis.

Biological samples recovered for forensic investigations are often degraded and/or have low amounts of DNA; in addition, in some instances the samples may be contaminated with chemicals that can act as PCR inhibitors. As a consequence this can make interpretation of the results challenging with the possibility of having partial profiles and false negative results. Because of the impact of DNA analysis on forensic investigations, it is important to monitor the process of DNA profiling, in particular the amplification reaction. In this chapter we describe a method for the in-house generation and use of internal amplification controls (IACs) with DNA profiling kits to monitor the success of the PCR proces. In the example we show the use of the SGM Plus® kit. These controls can also be used to aid the interpretation of the DNA profile.

Revolution and progress in medicine.

This paper adapts Kuhn's conceptual framework to developmental episodes in the theory and practice of medicine. Previous attempts to understand the reception of Ignaz Semmelweis's work on puerperal fever in Kuhnian terms are used as a starting point. The author identifies some limitations of these attempts and proposes a new way of understanding the core Kuhnian notions of "paradigm," "progress," and "revolution" in the context of a socially embedded technoscience such as medicine.

Male horse meiosis: metaphase I chromosome configuration and chiasmata distribution.

Chromosome configurations and chiasma frequency during the metaphase I stage of spermatogenesis in the male horse are characterized in this work. The genome-wide frequency and distribution of chiasmata was detected as 49.45 ± 2.07 for 14 fertile stallions. All X and Y chromosomes shared a single chiasma at their pseudoautosomal region, while 1-4 chiasmata were observed in autosomal chromosomes. The chiasma frequency and distribution were further studied for 8 different bivalents identified by FISH in 5 fertile stallions. Genetic length was calculated from chiasmata data for the whole genome as well as for these 8 chromosomes. The findings complement the genetic linkage data and provide insight into the genetic basis of spermatogenesis in normal stallions.

DNA transfer: The role of temperature and drying time.

It has previously been shown, and reconfirmed here, that biological material on a substrate will transfer readily upon contact with another substrate when wet but hardly when dry. There is however a paucity of data regarding the speed at which body fluids dry and how this may affect its transfer upon contact. Here we conduct transfer experiments at 4°C, 22°C and 40°C at multiple time points during the drying process. The speed at which blood dries is dependent on the temperature, with the drying process complete within 15-60min. The percentage of deposited DNA transferred upon contact follows an exponential pattern of decline from soon after deposition, decreasing until the sample is dry. There are no differences in transfer rates upon contact among the different temperature conditions within the first 5min or after 60min since deposit, but significant variation occurs between these time points. When considering the likelihood of a proposed scenario that incorporates one or more contact situations it is important to consider the timing of the potential transfer event(s) relative to when the biological sample in question was initially deposited. The results of this study will assist the interpretation and evaluation of alternative scenarios involving transfer of biological substances.