An algorithm for efficient constrained mate selection

<p>Abstract</p> <p>Background</p> <p>Mate selection can be used as a framework to balance key technical, cost and logistical issues while implementing a breeding program at a tactical level. The resulting mating lists accommodate optimal contributions of parents to future generations, in conjunction with other factors such as progeny inbreeding, connection between herds, use of reproductive technologies, management of the genetic distribution of nominated traits, and management of allele/genotype frequencies for nominated QTL/markers.</p> <p>Methods</p> <p>This paper describes a mate selection algorithm that is widely used and presents an extension that makes it possible to apply constraints on certain matings, as dictated through a group mating permission matrix.</p> <p>Results</p> <p>This full algorithm leads to simpler applications, and to computing speed for the scenario tested, which is several hundred times faster than the previous strategy of penalising solutions that break constraints.</p> <p>Conclusions</p> <p>The much higher speed of the method presented here extends the use of mate selection and enables implementation in relatively large programs across breeding units.</p

Thin film composite membranes with regulated crossover and water migration for long-life aqueous redox flow batteries.

Redox flow batteries (RFBs) are promising for large-scale long-duration energy storage owing to their inherent safety, decoupled power and energy, high efficiency, and longevity. Membranes constitute an important component that affects mass transport processes in RFBs, including ion transport, redox-species crossover, and the net volumetric transfer of supporting electrolytes. Hydrophilic microporous polymers, such as polymers of intrinsic microporosity (PIM), are demonstrated as next-generation ion-selective membranes in RFBs. However, the crossover of redox species and water migration through membranes are remaining challenges for battery longevity. Here, a facile strategy is reported for regulating mass transport and enhancing battery cycling stability by employing thin film composite (TFC) membranes prepared from a PIM polymer with optimized selective-layer thickness. Integration of these PIM-based TFC membranes with a variety of redox chemistries allows for the screening of suitable RFB systems that display high compatibility between membrane and redox couples, affording long-life operation with minimal capacity fade. Thickness optimization of TFC membranes further improves cycling performance and significantly restricts water transfer in selected RFB systems

Thin Film Composite Membranes with Regulated Crossover and Water Migration for Long-Life Aqueous Redox Flow Batteries

Redox flow batteries (RFBs) are promising for large-scale long-duration energy storage owing to their inherent safety, decoupled power and energy, high efficiency, and longevity. Membranes constitute an important component that affects mass transport processes in RFBs, including ion transport, redox-species crossover, and the net volumetric transfer of supporting electrolytes. Hydrophilic microporous polymers, such as polymers of intrinsic microporosity (PIM), are demonstrated as next-generation ion-selective membranes in RFBs. However, the crossover of redox species and water migration through membranes are remaining challenges for battery longevity. Here, a facile strategy is reported for regulating mass transport and enhancing battery cycling stability by employing thin film composite (TFC) membranes prepared from a PIM polymer with optimized selective-layer thickness. Integration of these PIM-based TFC membranes with a variety of redox chemistries allows for the screening of suitable RFB systems that display high compatibility between membrane and redox couples, affording long-life operation with minimal capacity fade. Thickness optimization of TFC membranes further improves cycling performance and significantly restricts water transfer in selected RFB systems

A detailed clinical and molecular survey of subjects with nonsyndromic USH2A retinopathy reveals an allelic hierarchy of disease-causing variants.

Defects in USH2A cause both isolated retinal disease and Usher syndrome (ie, retinal disease and deafness). To gain insights into isolated/nonsyndromic USH2A retinopathy, we screened USH2A in 186 probands with recessive retinal disease and no hearing complaint in childhood (discovery cohort) and in 84 probands with recessive retinal disease (replication cohort). Detailed phenotyping, including retinal imaging and audiological assessment, was performed in individuals with two likely disease-causing USH2A variants. Further genetic testing, including screening for a deep-intronic disease-causing variant and large deletions/duplications, was performed in those with one likely disease-causing change. Overall, 23 of 186 probands (discovery cohort) were found to harbour two likely disease-causing variants in USH2A. Some of these variants were predominantly associated with nonsyndromic retinal degeneration ('retinal disease-specific'); these included the common c.2276 G>T, p.(Cys759Phe) mutation and five additional variants: c.2802 T>G, p.(Cys934Trp); c.10073 G>A, p.(Cys3358Tyr); c.11156 G>A, p.(Arg3719His); c.12295-3 T>A; and c.12575 G>A, p.(Arg4192His). An allelic hierarchy was observed in the discovery cohort and confirmed in the replication cohort. In nonsyndromic USH2A disease, retinopathy was consistent with retinitis pigmentosa and the audiological phenotype was variable. USH2A retinopathy is a common cause of nonsyndromic recessive retinal degeneration and has a different mutational spectrum to that observed in Usher syndrome. The following model is proposed: the presence of at least one 'retinal disease-specific' USH2A allele in a patient with USH2A-related disease results in the preservation of normal hearing. Careful genotype-phenotype studies such as this will become increasingly important, especially now that high-throughput sequencing is widely used in the clinical setting.European Journal of Human Genetics advance online publication, 4 February 2015; doi:10.1038/ejhg.2014.283

Self-rated health in Pakistan: results of a national health survey

BACKGROUND: Self-rated health (SRH) is a robust predictor of mortality. In UK, migrants of South Asian descent, compared to native Caucasian populations, have substantially poorer SRH. Despite its validation among migrant South Asian populations and its popularity in developed countries as a useful public health tool, the SRH scale has not been used at a population level in countries in South Asia. We determined the prevalence of and risk factors for poor/fair SRH among individuals aged ≥15 years in Pakistan (n = 9442). METHODS: The National Health Survey of Pakistan was a cross-sectional population-based survey, conducted between 1990 and 1994, of 18 135 individuals aged 6 months and above; 9442 of them were aged ≥15 years. Our main outcome was SRH which was assessed using the question: "Would you say your health in general is excellent, very good, good, fair, or poor?" SRH was dichotomized into poor/fair, and good (excellent, very good, or good). RESULTS: Overall 65.1% respondents – 51.3 % men vs. 77.2 % women – rated their health as poor/fair. We found a significant interaction between sex and age (p < 0.0001). The interaction was due to the gender differences only in the ages 15–19 years, whereas poor/fair SRH at all older ages was more prevalent among women and increased at the same rate as it did among men. We also found province of dwelling, low or middle SES, literacy, rural dwelling and current tobacco use to be independently associated with poor/fair SRH. CONCLUSION: This is the first study reporting on poor/fair SRH at a population-level in a South Asian country. The prevalence of poor/fair health in Pakistan, especially amongst women, is one of the worst ever reported, warranting immediate attention. Further research is needed to explain why women in Pakistan have, at all ages, poorer SRH than men

Bordetella pertussis Autotransporter Vag8 Binds Human C1 Esterase Inhibitor and Confers Serum Resistance

Bordetella pertussis employs numerous strategies to evade the immune system, including the ability to resist killing via complement. Previously we have shown that B. pertussis binds a complement regulatory protein, C1 esterase inhibitor (C1inh) to its surface in a Bvg-regulated manner (i.e. during its virulence phase), but the B. pertussis factor was not identified. Here we set out to identify the B. pertussis C1inh-binding factor. Using a serum overlay assay, we found that this factor migrates at approximately 100 kDa on an SDS-PAGE gel. To identify this factor, we isolated proteins of approximately 100 kDa from wild type strain BP338 and from BP347, an isogenic Bvg mutant that does not bind C1inh. Using mass spectrometry and bioinformatics, we identified the autotransporter protein Vag8 as the putative C1inh binding protein. To prove that Vag8 binds C1inh, vag8 was disrupted in two different B. pertussis strains, namely BP338 and 18–323, and the mutants were tested for their ability to bind C1inh in a surface-binding assay. Neither mutant strain was capable of binding C1inh, whereas a complemented strain successfully bound C1inh. In addition, the passenger domain of Vag8 was expressed and purified as a histidine-tagged fusion protein and tested for C1inh-binding in an ELISA assay. Whereas the purified Vag8 passenger bound C1inh, the passenger domain of BrkA (a related autotransporter protein) failed to do so. Finally, serum assays were conducted to compare wild type and vag8 mutants. We determined that vag8 mutants from both strains were more susceptible to killing compared to their isogenic wild type counterparts. In conclusion, we have discovered a novel role for the previously uncharacterized protein Vag8 in the immune evasion of B. pertussis. Vag8 binds C1inh to the surface of the bacterium and confers serum resistance

Endothelin receptor antagonist and airway dysfunction in pulmonary arterial hypertension

<p>Abstract</p> <p>Background</p> <p>In idiopathic pulmonary arterial hypertension (IPAH), peripheral airway obstruction is frequent. This is partially attributed to the mediator dysbalance, particularly an excess of endothelin-1 (ET-1), to increased pulmonary vascular and airway tonus and to local inflammation. Bosentan (ET-1 receptor antagonist) improves pulmonary hemodynamics, exercise limitation, and disease severity in IPAH. We hypothesized that bosentan might affect airway obstruction.</p> <p>Methods</p> <p>In 32 IPAH-patients (19 female, WHO functional class II (n = 10), III (n = 22); (data presented as mean ± standard deviation) pulmonary vascular resistance (11 ± 5 Wood units), lung function, 6 minute walk test (6-MWT; 364 ± 363.7 (range 179.0-627.0) m), systolic pulmonary artery pressure, sPAP, 79 ± 19 mmHg), and NT-proBNP serum levels (1427 ± 2162.7 (range 59.3-10342.0) ng/L) were measured at baseline, after 3 and 12 months of oral bosentan (125 mg twice per day).</p> <p>Results and Discussion</p> <p>At baseline, maximal expiratory flow at 50 and 25% vital capacity were reduced to 65 ± 25 and 45 ± 24% predicted. Total lung capacity was 95.6 ± 12.5% predicted and residual volume was 109 ± 21.4% predicted. During 3 and 12 months of treatment, 6-MWT increased by 32 ± 19 and 53 ± 69 m, respectively; p < 0.01; whereas sPAP decreased by 7 ± 14 and 10 ± 19 mmHg, respectively; p < 0.05. NT-proBNP serum levels tended to be reduced by 123 ± 327 and by 529 ± 1942 ng/L; p = 0.11). There was no difference in expiratory flows or lung volumes during 3 and 12 months.</p> <p>Conclusion</p> <p>This study gives first evidence in IPAH, that during long-term bosentan, improvement of hemodynamics, functional parameters or serum biomarker occur independently from persisting peripheral airway obstruction.</p

Intracellular directed evolution of proteins from combinatorial libraries based on conditional phage replication

Directed evolution is a powerful tool to improve the characteristics of biomolecules. Here we present a protocol for the intracellular evolution of proteins with distinct differences and advantages in comparison with established techniques. These include the ability to select for a particular function from a library of protein variants inside cells, minimizing undesired coevolution and propagation of nonfunctional library members, as well as allowing positive and negative selection logics using basally active promoters. A typical evolution experiment comprises the following stages: (i) preparation of a combinatorial M13 phagemid (PM) library expressing variants of the gene of interest (GOI) and preparation of the Escherichia coli host cells; (ii) multiple rounds of an intracellular selection process toward a desired activity; and (iii) the characterization of the evolved target proteins. The system has been developed for the selection of new orthogonal transcription factors (TFs) but is capable of evolving any gene—or gene circuit function—that can be linked to conditional M13 phage replication. Here we demonstrate our approach using as an example the directed evolution of the bacteriophage λ cI TF against two synthetic bidirectional promoters. The evolved TF variants enable simultaneous activation and repression against their engineered promoters and do not cross-react with the wild-type promoter, thus ensuring orthogonality. This protocol requires no special equipment, allowing synthetic biologists and general users to evolve improved biomolecules within ~7 weeks

How does study quality affect the results of a diagnostic meta-analysis?

Background: The use of systematic literature review to inform evidence based practice in diagnostics is rapidly expanding. Although the primary diagnostic literature is extensive, studies are often of low methodological quality or poorly reported. There has been no rigorously evaluated, evidence based tool to assess the methodological quality of diagnostic studies. The primary objective of this study was to determine the extent to which variations in the quality of primary studies impact the results of a diagnostic meta-analysis and whether this differs with diagnostic test type. A secondary objective was to contribute to the evaluation of QUADAS, an evidence-based tool for the assessment of quality in diagnostic accuracy studies. Methods: This study was conducted as part of large systematic review of tests used in the diagnosis and further investigation of urinary tract infection (UTI) in children. All studies included in this review were assessed using QUADAS, an evidence-based tool for the assessment of quality in systematic reviews of diagnostic accuracy studies. The impact of individual components of QUADAS on a summary measure of diagnostic accuracy was investigated using regression analysis. The review divided the diagnosis and further investigation of UTI into the following three clinical stages: diagnosis of UTI, localisation of infection, and further investigation of the UTI. Each stage used different types of diagnostic test, which were considered to involve different quality concerns. Results: Many of the studies included in our review were poorly reported. The proportion of QUADAS items fulfilled was similar for studies in different sections of the review. However, as might be expected, the individual items fulfilled differed between the three clinical stages. Regression analysis found that different items showed a strong association with test performance for the different tests evaluated. These differences were observed both within and between the three clinical stages assessed by the review. The results of regression analyses were also affected by whether or not a weighting (by sample size) was applied. Our analysis was severely limited by the completeness of reporting and the differences between the index tests evaluated and the reference standards used to confirm diagnoses in the primary studies. Few tests were evaluated by sufficient studies to allow meaningful use of meta-analytic pooling and investigation of heterogeneity. This meant that further analysis to investigate heterogeneity could only be undertaken using a subset of studies, and that the findings are open to various interpretations. Conclusion: Further work is needed to investigate the influence of methodological quality on the results of diagnostic meta-analyses. Large data sets of well-reported primary studies are needed to address this question. Without significant improvements in the completeness of reporting of primary studies, progress in this area will be limited