Codon-precise, synthetic, antibody fragment libraries built using automated hexamer codon additions and validated through next generation sequencing

We have previously described ProxiMAX, a technology that enables the fabrication of precise, combinatorial gene libraries via codon-by-codon saturation mutagenesis. ProxiMAX was originally performed using manual, enzymatic transfer of codons via blunt-end ligation. Here we present Colibra™: an automated, proprietary version of ProxiMAX used specifically for antibody library generation, in which double-codon hexamers are transferred during the saturation cycling process. The reduction in process complexity, resulting library quality and an unprecedented saturation of up to 24 contiguous codons are described. Utility of the method is demonstrated via fabrication of complementarity determining regions (CDR) in antibody fragment libraries and next generation sequencing (NGS) analysis of their quality and diversity

Systematic reviews of complementary therapies - an annotated bibliography. Part 1: Acupuncture

Background Complementary therapies are widespread but controversial. We aim to provide a comprehensive collection and a summary of systematic reviews of clinical trials in three major complementary therapies (acupuncture, herbal medicine, homeopathy). This article is dealing with acupuncture. Potentially relevant reviews were searched through the register of the Cochrane Complementary Medicine Field, the Cochrane Library, Medline, and bibliographies of articles and books. To be included articles had to review prospective clinical trials of acupuncture; had to describe review methods explicitly; had to be published; and had to focus on treatment effects. Information on conditions, interventions, methods, results and conclusions was extracted using a pretested form and summarized descriptively. Results From a total of 48 potentially relevant reviews preselected in a screeening process 39 met the inclusion criteria. 22 were on various pain syndromes or rheumatic diseases. Other topics addressed by more than one review were addiction, nausea, asthma and tinnitus. Almost unanimously the reviews state that acupuncture trials include too few patients. Often included trials are heterogeneous regarding patients, interventions and outcome measures, are considered to have insufficient quality and contradictory results. Convincing evidence is available only for postoperative nausea, for which acupuncture appears to be of benefit, and smoking cessation, where acupuncture is no more effective than sham acupuncture. Conclusions A large number of systematic reviews on acupuncture exists. What is most obvious from these reviews is the need for (the funding of) well-designed, larger clinical trials

Cost-effectiveness of HBV and HCV screening strategies:a systematic review of existing modelling techniques

Introduction: Studies evaluating the cost-effectiveness of screening for Hepatitis B Virus (HBV) and Hepatitis C Virus (HCV) are generally heterogeneous in terms of risk groups, settings, screening intervention, outcomes and the economic modelling framework. It is therefore difficult to compare cost-effectiveness results between studies. This systematic review aims to summarise and critically assess existing economic models for HBV and HCV in order to identify the main methodological differences in modelling approaches. Methods: A structured search strategy was developed and a systematic review carried out. A critical assessment of the decision-analytic models was carried out according to the guidelines and framework developed for assessment of decision-analytic models in Health Technology Assessment of health care interventions. Results: The overall approach to analysing the cost-effectiveness of screening strategies was found to be broadly consistent for HBV and HCV. However, modelling parameters and related structure differed between models, producing different results. More recent publications performed better against a performance matrix, evaluating model components and methodology. Conclusion: When assessing screening strategies for HBV and HCV infection, the focus should be on more recent studies, which applied the latest treatment regimes, test methods and had better and more complete data on which to base their models. In addition to parameter selection and associated assumptions, careful consideration of dynamic versus static modelling is recommended. Future research may want to focus on these methodological issues. In addition, the ability to evaluate screening strategies for multiple infectious diseases, (HCV and HIV at the same time) might prove important for decision makers

Modelling the risk of Taenia solium exposure from pork produced in western Kenya

The tapeworm Taenia solium is the parasite responsible for neurocysticercosis, a neglected tropical disease of public health importance, thought to cause approximately 1/3 of epilepsy cases across endemic regions. The consumption of undercooked infected pork perpetuates the parasite’s life-cycle through the establishment of adult tapeworm infections in the community. Reducing the risk associated with pork consumption in the developing world is therefore a public health priority. The aim of this study was to estimate the risk of any one pork meal in western Kenya containing a potentially infective T. solium cysticercus at the point of consumption, an aspect of the parasite transmission that has not been estimated before. To estimate this, we used a quantitative food chain risk assessment model built in the @RISK add-on to Microsoft Excel. This model indicates that any one pork meal consumed in western Kenya has a 0.006 (99% Uncertainty Interval (U.I). 0.0002–0.0164) probability of containing at least one viable T. solium cysticercus at the point of consumption and therefore being potentially infectious to humans. This equates to 22,282 (99% U.I. 622–64,134) potentially infective pork meals consumed in the course of one year within Busia District alone. This model indicates a high risk of T. solium infection associated with pork consumption in western Kenya and the work presented here can be built upon to investigate the efficacy of various mitigation strategies for this locality

Antibody Repertoires in Humanized NOD-scid-IL2Rγnull Mice and Human B Cells Reveals Human-Like Diversification and Tolerance Checkpoints in the Mouse

Immunodeficient mice reconstituted with human hematopoietic stem cells enable the in vivo study of human hematopoiesis. In particular, NOD-scid-IL2Rγnull engrafted mice have been shown to have reasonable levels of T and B cell repopulation and can mount T-cell dependent responses; however, antigen-specific B-cell responses in this model are generally poor. We explored whether developmental defects in the immunoglobulin gene repertoire might be partly responsible for the low level of antibody responses in this model. Roche 454 sequencing was used to obtain over 685,000 reads from cDNA encoding immunoglobulin heavy (IGH) and light (IGK and IGL) genes isolated from immature, naïve, or total splenic B cells in engrafted NOD-scid-IL2Rγnull mice, and compared with over 940,000 reads from peripheral B cells of two healthy volunteers. We find that while naïve B-cell repertoires in humanized mice are chiefly indistinguishable from those in human blood B cells, and display highly correlated patterns of immunoglobulin gene segment use, the complementarity-determining region H3 (CDR-H3) repertoires are nevertheless extremely diverse and are specific for each individual. Despite this diversity, preferential DH-JH pairings repeatedly occur within the CDR-H3 interval that are strikingly similar across all repertoires examined, implying a genetic constraint imposed on repertoire generation. Moreover, CDR-H3 length, charged amino-acid content, and hydropathy are indistinguishable between humans and humanized mice, with no evidence of global autoimmune signatures. Importantly, however, a statistically greater usage of the inherently autoreactive IGHV4-34 and IGKV4-1 genes was observed in the newly formed immature B cells relative to naïve B or total splenic B cells in the humanized mice, a finding consistent with the deletion of autoreactive B cells in humans. Overall, our results provide evidence that key features of the primary repertoire are shaped by genetic factors intrinsic to human B cells and are principally unaltered by differences between mouse and human stromal microenvironments

Children, civilianhood, and humanitarian securitization

In this paper, the influence of the construction of children as civilians over the processes of securitization in the US intervention in Somalia is examined. This is done through an analysis of the US print news media coverage of that event. The study employs two key theoretical frameworks: the first is the social understanding of civilianhood; and the second is the Copenhagen School’s theory of securitization. The work concludes that a failure to unpack the value of referent objects of security diminishes the insights that securitization theory can offer. The grammar of securitizing moves cannot be fully comprehended in instances of militarized humanitarian interventions, in particular, without this kind of analysis. Children as suffering civilians draw considerable attention from the world’s media and thus an investigation of their role in securitization can be highly informative

Randomized Controlled Trials of HIV/AIDS Prevention and Treatment in Africa: Results from the Cochrane HIV/AIDS Specialized Register

INTRODUCTION: To effectively address HIV/AIDS in Africa, evidence on preventing new infections and providing effective treatment is needed. Ideally, decisions on which interventions are effective should be based on evidence from randomized controlled trials (RCTs). Our previous research described African RCTs of HIV/AIDS reported between 1987 and 2003. This study updates that analysis with RCTs published between 2004 and 2008. OBJECTIVES: To describe RCTs of HIV/AIDS conducted in Africa and reported between 2004 and 2008. METHODS: We searched the Cochrane HIV/AIDS Specialized Register in September 2009. Two researchers independently evaluated studies for inclusion and extracted data using standardized forms. Details included location of trials, interventions, methodological quality, location of principal investigators and funders. RESULTS: Our search identified 834 RCTs, with 68 conducted in Africa. Forty-three assessed prevention-interventions and 25 treatment-interventions. Fifteen of the 43 prevention RCTs focused on preventing mother-to-child HIV transmission. Thirteen of the 25 treatment trials focused on opportunistic infections. Trials were conducted in 16 countries with most in South Africa (20), Zambia (12) and Zimbabwe (9). The median sample size was 628 (range 33-9645). Methods used for the generation of the allocation sequence and allocation concealment were adequate in 38 and 32 trials, respectively, and 58 reports included a CONSORT recommended flow diagram. Twenty-nine principal investigators resided in the United States of America (USA) and 18 were from African countries. Trials were co-funded by different agencies with most of the funding obtained from USA governmental and non-governmental agencies. Nineteen pharmaceutical companies provided partial funding to 15 RCTs and African agencies co-funded 17 RCTs. Ethical approval was reported in 65 trials and informed consent in 61 trials. CONCLUSION: Prevention trials dominate the trial landscape in Africa. Of note, few principal investigators and funders are from Africa. These findings mirror our previous work and continue to indicate a need for strengthening trial research capacity in Africa

Arabidopsis thaliana PGR7 Encodes a Conserved Chloroplast Protein That Is Necessary for Efficient Photosynthetic Electron Transport

A significant fraction of a plant's nuclear genome encodes chloroplast-targeted proteins, many of which are devoted to the assembly and function of the photosynthetic apparatus. Using digital video imaging of chlorophyll fluorescence, we isolated proton gradient regulation 7 (pgr7) as an Arabidopsis thaliana mutant with low nonphotochemical quenching of chlorophyll fluorescence (NPQ). In pgr7, the xanthophyll cycle and the PSBS gene product, previously identified NPQ factors, were still functional, but the efficiency of photosynthetic electron transport was lower than in the wild type. The pgr7 mutant was also smaller in size and had lower chlorophyll content than the wild type in optimal growth conditions. Positional cloning located the pgr7 mutation in the At3g21200 (PGR7) gene, which was predicted to encode a chloroplast protein of unknown function. Chloroplast targeting of PGR7 was confirmed by transient expression of a GFP fusion protein and by stable expression and subcellular localization of an epitope-tagged version of PGR7. Bioinformatic analyses revealed that the PGR7 protein has two domains that are conserved in plants, algae, and bacteria, and the N-terminal domain is predicted to bind a cofactor such as FMN. Thus, we identified PGR7 as a novel, conserved nuclear gene that is necessary for efficient photosynthetic electron transport in chloroplasts of Arabidopsis

Dynamic metabolic patterns tracking neurodegeneration and gliosis following 26S proteasome dysfunction in mouse forebrain neurons

Metabolite profling is an important tool that may better capture the multiple features of neurodegeneration. With the considerable parallels between mouse and human metabolism, the use of metabolomics in mouse models with neurodegenerative pathology provides mechanistic insight and ready translation into aspects of human disease. Using 400MHz nuclear magnetic resonance spectroscopy we have carried out a temporal region-specifc investigation of the metabolome of neuron-specifc 26S proteasome knockout mice characterised by progressive neurodegeneration and Lewy-like inclusion formation in the forebrain. An early signifcant decrease in N-acetyl aspartate revealed evidence of neuronal dysfunction before cell death that may be associated with changes in brain neuroenergetics, underpinning the use of this metabolite to track neuronal health. Importantly, we show early and extensive activation of astrocytes and microglia in response to targeted neuronal dysfunction in this context, but only late changes in myo-inositol; the best established glial cell marker in magnetic resonance spectroscopy studies, supporting recent evidence that additional early neuroinfammatory markers are needed. Our results extend the limited understanding of metabolite changes associated with gliosis and provide evidence that changes in glutamate homeostasis and lactate may correlate with astrocyte activation and have biomarker potential for tracking neuroinfammation

The DESI survey validation : results from visual inspection of bright galaxies, luminous red galaxies, and emission line galaxies

Funding: TWL was supported by the Ministry of Science and Technology (MOST 111-2112-M-002-015-MY3), the Ministry of Education, Taiwan (MOE Yushan Young Scholar grant NTU-110VV007), National Taiwan University research grants (NTU CC-111L894806, NTU- 111L7318), and NSF grant AST-1911140. DMA acknowledges the Science Technology and Facilities Council (STFC) for support through grant code ST/T000244/1. This research is supported by the Director, Office of Science, Office of High Energy Physics of the U.S. Department of Energy under Contract No. DE–AC02–05CH11231, and by the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility under the same contract; additional support for DESI is provided by the U.S. National Science Foundation, Division of Astronomical Sciences under Contract No. AST-0950945 to the NSF’s National Optical-Infrared Astronomy Research Laboratory; the Science and Technologies Facilities Council of the United Kingdom; the Gordon and Betty Moore Foundation; the Heising-Simons Foundation; the French Alternative Energies and Atomic Energy Commission (CEA); the National Council of Science and Technology of Mexico (CONACYT); the Ministry of Science and Innovation of Spain (MICINN), and by the DESI Member Institutions: https://www.desi.lbl.gov/ collaborating-institutions.The Dark Energy Spectroscopic Instrument (DESI) Survey has obtained a set of spectroscopic measurements of galaxies for validating the final survey design and target selections. To assist these tasks, we visually inspect (VI) DESI spectra of approximately 2,500 bright galaxies, 3,500 luminous red galaxies, and 10,000 emission line galaxies, to obtain robust redshift identifications. We then utilize the VI redshift information to characterize the performance of the DESI operation. Based on the VI catalogs, our results show that the final survey design yields samples of bright galaxies, luminous red galaxies, and emission line galaxies with purity greater than 99%. Moreover, we demonstrate that the precision of the redshift measurements is approximately 10 km/s for bright galaxies and emission line galaxies and approximately 40 km/s for luminous red galaxies. The average redshift accuracy is within 10 km/s for the three types of galaxies. The VI process also helps to improve the quality of the DESI data by identifying spurious spectral features introduced by the pipeline. Finally, we show examples of unexpected real astronomical objects, such as Lyman α emitters and strong lensing candidates, identified by VI. These results demonstrate the importance and utility of visually inspecting data from incoming and upcoming surveys, especially during their early operation phases.Publisher PDFPeer reviewe