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The realistic rendering of woven and knitted fabrics has posed significant challenges throughout many years. Previously, fiber‐based micro‐appearance models have achieved considerable success in attaining high levels of realism. However, rendering such models remains complex due to the intricate internal scatterings of hundreds of fibers within a yarn, requiring vast amounts of memory and time to render. In this paper, we introduce a new framework to capture aggregated appearance by tracing many light paths through the underlying fiber geometry. We then employ lightweight neural networks to accurately model the aggregated BSDF, which allows for the precise modeling of a diverse array of materials while offering substantial improvements in speed and reductions in memory. Furthermore, we introduce a novel importance sampling scheme to further speed up the rate of convergence. We validate the efficacy and versatility of our framework through comparisons with preceding fiber‐based shading models as well as the most recent yarn‐based model. [ABSTRACT FROM AUTHOR]

Differentiable rasterization changes the standard formulation of primitive rasterization — by enabling gradient flow from a pixel to its underlying triangles — using distribution functions in different stages of rendering, creating a "soft" version of the original rasterizer. However, choosing the optimal softening function that ensures the best performance and convergence to a desired goal requires trial and error. Previous work has analyzed and compared several combinations of softening. In this work, we take it a step further and, instead of making a combinatorial choice of softening operations, parameterize the continuous space of common softening operations. We study meta‐learning tunable softness functions over a set of inverse rendering tasks (2D and 3D shape, pose and occlusion) so it generalizes to new and unseen differentiable rendering tasks with optimal softness. [ABSTRACT FROM AUTHOR]

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Objective: Family history (FH) provides insights into the effects of shared genomic susceptibilities, environments and behaviors, making it a potentially valuable risk assessment tool for chronic diseases. We assessed whether coronary heart disease (CHD) risk assessment is improved when FH information is added to other clinical information recommended in guidelines. Methods: We applied logistic regression analyses to cross-sectional data originally obtained from a UK study of women who delivered a live-born infant between 1951 and 1970. We developed 3 models: Model 1 included only the covariates in a guideline applicable to the population, Model 2 added FH to Model 1, and Model 3 included a fuller range of risk factors. For each model, its ability to discriminate between study subjects with and those without CHD was evaluated and its impact on risk classification examined using the net reclassification index. Results: FH was an independent risk factor for CHD (odds ratio = 1.7, 95% confidence interval = 1.26-2.47) and improved discrimination beyond guideline-defined clinical factors (p < 0.0006). However, the difference in the area under the curve of 2.8% and the extent of patient reclassification resulting from the inclusion of FH were small (p = 0.11). Conclusion: While FH were a significant independent risk factor for CHD, it added little to risk factors typically included in guidelines. © 2013 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

Background: Measures of insulin resistance (IR)/sensitivity (IS) are emerging tools to identify metabolic-associated fatty liver disease (MAFLD). However, the comprehensive assessment of the performance of various indicators is limited. Moreover, the utility of measures of IR/IS in detecting liver fibrosis remains unclear., Aims: To evaluate the predictive ability of seventeen IR/IS and two beta cell function indices to identify MAFLD and liver fibrosis., Methods: A cross-sectional study was conducted on individuals aged 25-75 years. Transient elastography was used to estimate liver stiffness and controlled attenuation parameter. The following measures were computed: homeostatic model assessment (HOMA/HOMA2) for IR, IS, and beta cell function; QUICKI; Bennett index; glucose/insulin; FIRI; McAuley index; Reynaud index; SPISE index; TyG; TyG-BMI; TyG-WC; TyG-WHtR; TG/HDL; and METS-IR. Subgroup analyses were performed according to age, gender, diabetes status, and body weight., Results: A total of 644 individuals were included in our analysis. MAFLD and significant liver fibrosis were detected in 320 (49.7%) and 80 (12.4%) of the participants, respectively. All measures of IR/IS identified MAFLD and liver fibrosis. However, TyG-WC, TyG-BMI, and TyG-WHtR were the top three indicators that identified MAFLD. Measures that include insulin level in their mathematical calculation, namely, Raynaud index, HOMA-IR, HOMA 2-IR, FIRI, and QUICKI had the best performance in identifying liver fibrosis in the entire population, as well as among the study subgroups., Conclusions: TyG-WC, TyG-BMI, and TyG-WHtR were the best predictors of MAFLD. Insulin-based measures had better performances in the detection of advanced fibrosis. This was independent of age, gender, obesity, or diabetes status., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

A new bio-inspired metaheuristic algorithm named the Pufferfish Optimization Algorithm (POA), that imitates the natural behavior of pufferfish in nature, is introduced in this paper. The fundamental inspiration of POA is adapted from the defense mechanism of pufferfish against predators. In this defense mechanism, by filling its elastic stomach with water, the pufferfish becomes a spherical ball with pointed spines, and as a result, the hungry predator escapes from this threat. The POA theory is stated and then mathematically modeled in two phases: (i) exploration based on the simulation of a predator's attack on a pufferfish and (ii) exploitation based on the simulation of a predator's escape from spiny spherical pufferfish. The performance of POA is evaluated in handling the CEC 2017 test suite for problem dimensions equal to 10, 30, 50, and 100. The optimization results show that POA has achieved an effective solution with the appropriate ability in exploration, exploitation, and the balance between them during the search process. The quality of POA in the optimization process is compared with the performance of twelve well-known metaheuristic algorithms. The simulation results show that POA provides superior performance by achieving better results in most of the benchmark functions in order to solve the CEC 2017 test suite compared to competitor algorithms. Also, the effectiveness of POA to handle optimization tasks in real-world applications is evaluated on twenty-two constrained optimization problems from the CEC 2011 test suite and four engineering design problems. Simulation results show that POA provides effective performance in handling real-world applications by achieving better solutions compared to competitor algorithms.

In this paper, a new bio-inspired metaheuristic algorithm called the Lyrebird Optimization Algorithm (LOA) that imitates the natural behavior of lyrebirds in the wild is introduced. The fundamental inspiration of LOA is the strategy of lyrebirds when faced with danger. In this situation, lyrebirds scan their surroundings carefully, then either run away or hide somewhere, immobile. LOA theory is described and then mathematically modeled in two phases: (i) exploration based on simulation of the lyrebird escape strategy and (ii) exploitation based on simulation of the hiding strategy. The performance of LOA was evaluated in optimization of the CEC 2017 test suite for problem dimensions equal to 10, 30, 50, and 100. The optimization results show that the proposed LOA approach has high ability in terms of exploration, exploitation, and balancing them during the search process in the problem-solving space. In order to evaluate the capability of LOA in dealing with optimization tasks, the results obtained from the proposed approach were compared with the performance of twelve well-known metaheuristic algorithms. The simulation results show that LOA has superior performance compared to competitor algorithms by providing better results in the optimization of most of the benchmark functions, achieving the rank of first best optimizer. A statistical analysis of the performance of the metaheuristic algorithms shows that LOA has significant statistical superiority in comparison with the compared algorithms. In addition, the efficiency of LOA in handling real-world applications was investigated through dealing with twenty-two constrained optimization problems from the CEC 2011 test suite and four engineering design problems. The simulation results show that LOA has effective performance in handling optimization tasks in real-world applications while providing better results compared to competitor algorithms.

In this paper, a new bio-inspired metaheuristic algorithm named the Kookaburra Optimization Algorithm (KOA) is introduced, which imitates the natural behavior of kookaburras in nature. The fundamental inspiration of KOA is the strategy of kookaburras when hunting and killing prey. The KOA theory is stated, and its mathematical modeling is presented in the following two phases: (i) exploration based on the simulation of prey hunting and (ii) exploitation based on the simulation of kookaburras' behavior in ensuring that their prey is killed. The performance of KOA has been evaluated on 29 standard benchmark functions from the CEC 2017 test suite for the different problem dimensions of 10, 30, 50, and 100. The optimization results show that the proposed KOA approach, by establishing a balance between exploration and exploitation, has good efficiency in managing the effective search process and providing suitable solutions for optimization problems. The results obtained using KOA have been compared with the performance of 12 well-known metaheuristic algorithms. The analysis of the simulation results shows that KOA, by providing better results in most of the benchmark functions, has provided superior performance in competition with the compared algorithms. In addition, the implementation of KOA on 22 constrained optimization problems from the CEC 2011 test suite, as well as 4 engineering design problems, shows that the proposed approach has acceptable and superior performance compared to competitor algorithms in handling real-world applications.

Introduction: Nonalcoholic fatty liver disease (NAFLD) frequently coexists with type 2 diabetes mellitus (T2DM) and synergistically contributes to the development of atherosclerosis. Flow-mediated dilation (FMD) is a commonly used noninvasive test for assessing endothelial function. The main objective of this study was to explore FMD in patients with T2DM with and without NAFLD., Methods: In this cross-sectional study, conducted on people with T2DM, NAFLD was defined as controlled attenuation parameter (CAP) score > 302 dB/m. Endothelial dysfunction was detected when arterial FMD of brachial artery was equal or less than 0.7%. Regression analyses were applied to assess factors associated with impaired FMD., Result: A total of 147 patients (72 with NAFLD and 75 without NAFLD) were included in the final analysis. Patients with NAFLD were more likely to develop FMD ≤ 7% (77.8% vs. 58.7%, P = 0.01). In multivariate analysis, NAFLD (OR = 2.581, 95% CI (1.18-5.62), P = 0.017) and hypertension (HTN) (OR = 3.114, 95% CI (1.31-7.35), P = 0.010) were associated with an increased risk of impaired FMD. However, female sex was associated with a decreased risk of impaired FMD (OR = 0.371, 95% CI (0.15-0.87), P = 0.024)., Conclusion: NAFLD is associated with endothelial dysfunction in people with T2DM. This risk is comparable with the risk imposed by HTN, highlighting the importance of screening and management of NAFLD in these patients., (© 2023. BioMed Central Ltd., part of Springer Nature.)

In this research article, we uphold the principles of the No Free Lunch theorem and employ it as a driving force to introduce an innovative game-based metaheuristic technique named Golf Optimization Algorithm (GOA). The GOA is meticulously structured with two distinctive phases, namely, exploration and exploitation, drawing inspiration from the strategic dynamics and player conduct observed in the sport of golf. Through comprehensive assessments encompassing fifty-two objective functions and four real-world engineering applications, the efficacy of the GOA is rigorously examined. The results of the optimization process reveal GOA's exceptional proficiency in both exploration and exploitation strategies, effectively striking a harmonious equilibrium between the two. Comparative analyses against ten competing algorithms demonstrate a clear and statistically significant superiority of the GOA across a spectrum of performance metrics. Furthermore, the successful application of the GOA to the intricate energy commitment problem, considering network resilience, underscores its prowess in addressing complex engineering challenges. For the convenience of the research community, we provide the MATLAB implementation codes for the proposed GOA methodology, ensuring accessibility and facilitating further exploration.

Air pollution particulate matter (PM) is a world risk factor that the effects of long-term exposure to these factors in terms of damage to cardiovascular and pulmonary function are well known, but little is known comparatively about the effects of PM on emotional and cognitive processes. Exposure to PM can adversely affect the central nervous system (CNS) by inflammatory pathways and activation of reactive oxygen species (ROS) associated with urban air pollution PM. Therefore, we investigated whether prolonged exposure to diesel exhaust particles (DEPs) affects hippocampal inflammatory cytokines and emotional and cognition responses. Male mice were exposed to DEPs for 6 and 12 weeks. DEP-exposed mice indicated more disorders in depressive-like responses and spatial memory and learning than in control groups. Pro-inflammatory cytokine expression in tge hippocampus was increased among mice exposed to DEPs. The number of activated microglia increased in the dentate gyrus (DG) and CA1 regions of the hippocampus in DEP-exposed mice. These results show that chronic exposure to DEPs can alter neurobehavioral and impair cognition. Generally, these findings reaffirm the importance of protecting from exposure to ambient PM2.5 and also advance our understanding of the toxic actions of air pollution nanoparticles., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Air pollution exposure is among the most prevalent reasons for environmentally-induced oxidative stress and inflammation, both of which are involved in the development and progression of central nervous system (CNS) diseases. Ultrafine particles (UFPs) plays an important role in global air pollution and the diesel exhaust particles (DEPs) are the most important component in this regard. There are more than 40 toxic air pollutants in diesel exhaust (DE), which is one of the main constituents of an environmental pollutant and including particulate matter (PM) especially UFPs. Thus, in this study, adult female and male NMRI mice were exposed to DEPs (350-400 μg/m 3 ) for 14 weeks (6 h per day and 5 days per week). After 14 weeks of exposure, expression of pro-inflammatory cytokines (IL-1α, IL-1β, IL-6, TNF-α), nNOS, HO1, NR2A, and NR2B and malondialdehyde (MDA) level were analyzed in various brain regions such as the hippocampus (HI) and olfactory bulb (OB). Exposure to DEPs caused neuroinflammation and oxidative stress in female and male mice. That these effects observed in females were less pronounced than in male mice. The male mice emerged to be more susceptible significantly than the female mice to induced neuroinflammation following DEPs exposure. Also, our findings indicate that long term exposure to DEPs results in altered expression of hippocampal NMDA receptor subunits, and suggests that gender can play important role in the modulating susceptibility to neurotoxicity induced by DEPs exposure., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Optimization seeks to find inputs for an objective function that result in a maximum or minimum. Optimization methods are divided into exact and approximate (algorithms). Several optimization algorithms imitate natural phenomena, laws of physics, and behavior of living organisms. Optimization based on algorithms is the challenge that underlies machine learning, from logistic regression to training neural networks for artificial intelligence. In this paper, a new algorithm called two-stage optimization (TSO) is proposed. The TSO algorithm updates population members in two steps at each iteration. For this purpose, a group of good population members is selected and then two members of this group are randomly used to update the position of each of them. This update is based on the first selected good member at the first stage, and on the second selected good member at the second stage. We describe the stages of the TSO algorithm and model them mathematically. Performance of the TSO algorithm is evaluated for twenty-three standard objective functions. In order to compare the optimization results of the TSO algorithm, eight other competing algorithms are considered, including genetic, gravitational search, grey wolf, marine predators, particle swarm, teaching-learning-based, tunicate swarm, and whale approaches. The numerical results show that the new algorithm is superior and more competitive in solving optimization problems when compared with other algorithms.

It has been demonstrated that sub-chronic exposure to air pollution containing nanoscale (˂100 nm) diesel exhaust particles (DEPs) may lead to excessive oxidative stress and neuro-inflammation in adult male mice. Hereby, we investigated the effects of DEPs on hippocampus-dependent spatial learning and neuro-inflammation and memory-related gene expression in male mice. In this study, we divided 48 adult NMRI male mice into control group VS. three exposure groups. Mice were exposed to 300-350 μg/m 3 DEPs for 2, 5, and 7 h daily for 12 weeks. The Morris Water Maze (MWM) and Elevated Plus Maze device were used to examine anxiety, spatial memory and learning, respectively. The mRNAs expression of pro-inflammatory cytokines, N-methyl-D-aspartate (NMDA) receptor subunits, and glutaminase were studied in hippocampus (HI) by real-time RT-PCR. Besides, malondialdehyde (MDA) tests were used to determine the state of oxidative stress. After 5 and 7 h. of DEPs exposure, mRNA expression of NR2A and NR3B IL1α, IL1β, TNFα, NMDA receptor subunits and MDA levels increased significantly ( P  < 0.05). Also, DEPs exposed mice for 2, 5, and 7 h. showed diminished entrance into open arms with short time spent there. Indeed, 5 and 7 h/day exposed mice required a longer time to reach the hidden platform. Sub-chronic exposure to DEPs increased oxidative stress markers, neuroinflammation, anxiety, impaired spatial learning and memory., Competing Interests: Competing interestsThe authors declared that they have no competing interests., (© Springer Nature Switzerland AG 2021.)

Micro-appearance models have brought unprecedented fidelity and details to cloth rendering. Yet, these models neglect fabric mechanics: when a piece of cloth interacts with the environment, its yarn and fiber arrangement usually changes in response to external contact and tension forces. Since subtle changes of a fabric's microstructures can greatly affect its macroscopic appearance, mechanics-driven appearance variation of fabrics has been a phenomenon that remains to be captured. We introduce a mechanics-aware model that adapts the microstructures of cloth yarns in a physics-based manner. Our technique works on two distinct physical scales: using physics-based simulations of individual yarns, we capture the rearrangement of yarn-level structures in response to external forces. These yarn structures are further enriched to obtain appearance-driving fiber-level details. The cross-scale enrichment is made practical through a new parameter fitting algorithm for simulation, an augmented procedural yarn model coupled with a custom-design regression neural network. We train the network using a dataset generated by joint simulations at both the yarn and the fiber levels. Through several examples, we demonstrate that our model is capable of synthesizing photorealistic cloth appearance in a mechanically plausible way.

Objective: To provide an understanding of the role of common genetic variations in colorectal cancer (CRC) risk, we report an updated field synopsis and comprehensive assessment of evidence to catalogue all genetic markers for CRC (CRCgene2)., Design: We included 869 publications after parallel literature review and extracted data for 1063 polymorphisms in 303 different genes. Meta-analyses were performed for 308 single nucleotide polymorphisms (SNPs) in 158 different genes with at least three independent studies available for analysis. Scottish, Canadian and Spanish data from genome-wide association studies (GWASs) were incorporated for the meta-analyses of 132 SNPs. To assess and classify the credibility of the associations, we applied the Venice criteria and Bayesian False-Discovery Probability (BFDP). Genetic associations classified as 'positive' and 'less-credible positive' were further validated in three large GWAS consortia conducted in populations of European origin., Results: We initially identified 18 independent variants at 16 loci that were classified as 'positive' polymorphisms for their highly credible associations with CRC risk and 59 variants at 49 loci that were classified as 'less-credible positive' SNPs; 72.2% of the 'positive' SNPs were successfully replicated in three large GWASs and the ones that were not replicated were downgraded to 'less-credible' positive (reducing the 'positive' variants to 14 at 11 loci). For the remaining 231 variants, which were previously reported, our meta-analyses found no evidence to support their associations with CRC risk., Conclusion: The CRCgene2 database provides an updated list of genetic variants related to CRC risk by using harmonised methods to assess their credibility., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2020. Re-use permitted under CC BY. Published by BMJ.)

The cause of colorectal cancer (CRC) is multifactorial, involving both genetic variants and environmental risk factors. We systematically searched the MEDLINE, EMBASE, China National Knowledge Infrastructure (CNKI) and Wanfang databases from inception to December 2016, to identify systematic reviews and meta-analyses of observational studies that investigated gene-environment (G×E) interactions in CRC risk. Then, we critically evaluated the cumulative evidence for the G×E interactions using an extension of the Human Genome Epidemiology Network's Venice criteria. Overall, 15 articles reporting systematic reviews of observational studies on 89 G×E interactions, 20 articles reporting meta-analyses of candidate gene- or single-nucleotide polymorphism-based studies on 521 G×E interactions, and 8 articles reporting 33 genome-wide G×E interaction analyses were identified. On the basis of prior and observed scores, only the interaction between rs6983267 (8q24) and aspirin use was found to have a moderate overall credibility score as well as main genetic and environmental effects. Though 5 other interactions were also found to have moderate evidence, these interaction effects were tenuous due to the lack of main genetic effects and/or environmental effects. We did not find highly convincing evidence for any interactions, but several associations were found to have moderate strength of evidence. Our conclusions are based on application of the Venice criteria which were designed to provide a conservative assessment of G×E interactions and thus do not include an evaluation of biological plausibility of an observed joint effect., (© 2018 The Authors. International Journal of Cancer published by John Wiley & Sons Ltd on behalf of UICC.)

Background: Asthma is a multifactorial syndrome that threatens the health of children. Body mass index (BMI) might be one of the potential factors but the evidence is controversial. The aim of this study is to perform a comprehensive meta-analysis to investigate the association between asthma and BMI., Methods: Electronic databases including, Web of Science, Pubmed, Scopus, Science Direct, ProQuest, up to April 2017, were searched by two researchers independently. The keywords "asthma, body mass index, obesity, overweight, childhood and adolescence" were used. Random and fixed effects models were applied to obtain the overall odds ratios (ORs) and standardized mean difference (SMD). Heterogeneity between the studies was examined using I 2 and Cochrane Q statistics., Results: After reviewing 2511 articles, 16 studies were eligible for meta-analysis according to inclusion/exclusion criteria. A meta-analysis from 11 case-control studies revealed OR of asthma and overweight as OR = 1.64; (95% Confidence Interval (CI): 1.13-2.38) and from 14 case-control studies, OR for asthma and obesity was OR = 1.92 (95% CI: 1.39-2.65), which indicated that risk of asthma in overweight and obese children and adolescence was significantly higher (1.64 and 1.92 times) than that of individuals with (p-value < 0.01 for underweight/normal weight in both cases). Furthermore, there was a significant relationship between asthma and BMI > 85 percentile according to SMD SMD = 0.21; (95%CI: 0.03-0.38; p-value = 0.021)., Conclusions: The results showed a significant relationship between BMI (obesity/overweight) and asthma among children and adolescents. It is important to study the confounding factors that affect the relationship between asthma and BMI in future epidemiological researches.

Background: Low back pain (LBP) as a musculoskeletal disorder is one of the most common occupational injuries in nurses but there isn't any valid measure of the prevalence of LBP in Iranian nursing. In order to increase the power and improve the estimates of the prevalence of LBP in Iranian nurses, a comprehensive meta-analysis was carried out. A summary measure of all studies conducted in this field was found and distributions of LBP were evaluated based on different variables., Methods: Inclusion criteria included articles with prevalence of LBP in Iranian nurses, who had at least six months of work experience without any trauma, injuries to spine, or any underlying disease. The keywords"prevalence, low back pain, nurses", and "Iran" were used as part of this search. Databases such as Pubmed, Web of Science, Science direct, Scopus, IranMedex, Irandoc, Magiran, SID, CIVILICA, IMEMR and Google scholar were searched up to and including 15 June 2016. For data extraction a form was designed that included the following variables: Author names, province, sample size, age, gender, marital status, work experience, body mass index, job type, smoking status, work schedule, year of publication, type of standard questionnaire, prevalence of LBP, studies' quality score and climate classifications. Data analysis was carried out using fixed and random effects model. Heterogeneity between studies was assessed by using the I 2 and Q tests., Results: In all 1250 articles were identified and 22 articles with 9347 participants met the inclusion criteria for meta-analyses after filtering. The prevalence of low back pain during their working life and during the last year, was estimated at 63% (95% Confidence Interval (CI): 57.4-68.5) and 61.2% (95% CI: 55.7-66.7) respectively. The prevalence rate of this disorder was 58.7% (95% CI: 35.8-81.7) and 60.4% (95% CI: 52.2-68.6) among men and women respectively. Furthermore, prevalence's of LBP were 59.5% in wards nurses, 50.3% in operating room technicians, and 39.4% in aid nurses., Conclusions: The results showed the high prevalence of LBP injury in nurses, especially female nurses. The effect of musculoskeletal disorders such as LBP may be reduced by considering proper observation of the principles of ergonomics in the workplace, performing physical examinations on a regular basis, identifying risk factors in the advancement of musculoskeletal disorders and then trying to fix them.

Objective: Although accumulating evidence suggests harmful effects of waterpipe smoking, there is limited information about its direct association with chronic diseases, notably cancer. We provide an up-to-date systematic review and meta-analysis of the association between waterpipe smoking and cancer., Data Sources: Systematic search of articles indexed in main biomedical databases: Pubmed, EmBase, Google Scholar and Web of Science, published between 1962 and September 2014. Search keywords included a combination of waterpipe or hookah, sheesha, nargile, hubble-bubble, goza or gaylan, and cancer., Study Selection: Focus on observational studies (cohort, case-control, cross-sectional) that evaluated the association between waterpipe smoking and cancer. Studies with mixed exposures excluded., Data Extraction: Two investigators independently extracted data and reached consensus on all items., Data Synthesis: 13 case-control studies met the inclusion criteria and were considered for meta-analysis. The methodological quality of included studies was assessed using the Newcastle-Ottawa Scale (NOS). Meta-analysis revealed a positive association between waterpipe smoking and lung cancer (OR=4.58 (2.61 to 8.03); I 2 =44.67%), and oesophageal cancer (OR=3.63 (1.39 to 9.44); I 2 =94.49%). The majority of studies had a NOS score of 5-6 or 7, indicating 'fair' or 'good' quality, respectively., Conclusions: Our findings support a positive association between waterpipe smoking and cancer risk. However, high-quality studies with standardised exposure measurements are needed to clarify the contribution of waterpipe smoking to chronic diseases. More investments in initiatives for surveillance, intervention and regulatory policy for waterpipe smoking are urgently warranted., (Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.)

Background: Low penetrance genetic variants, primarily single nucleotide polymorphisms, have substantial influence on colorectal cancer (CRC) susceptibility. Most CRCs develop from colorectal adenomas (CRA). Here we report the first comprehensive field synopsis that catalogues all genetic association studies on CRA, with a parallel online database [http://www.chs.med.ed.ac.uk/CRAgene/]., Methods: We performed a systematic review, reviewing 9750 titles, and then extracted data from 130 publications reporting on 181 polymorphisms in 74 genes. We conducted meta-analyses to derive summary effect estimates for 37 polymorphisms in 26 genes. We applied the Venice criteria and Bayesian False Discovery Probability (BFDP) to assess the levels of the credibility of associations., Results: We considered the association with the rs6983267 variant at 8q24 as 'highly credible', reaching genome-wide statistical significance in at least one meta-analysis model. We identified 'less credible' associations (higher heterogeneity, lower statistical power, BFDP > 0.02) with a further four variants of four independent genes: MTHFR c.677C>T p.A222V (rs1801133), TP53 c.215C>G p.R72P (rs1042522), NQO1 c.559C>T p.P187S (rs1800566), and NAT1 alleles imputed as fast acetylator genotypes. For the remaining 32 variants of 22 genes for which positive associations with CRA risk have been previously reported, the meta-analyses revealed no credible evidence to support these as true associations., Conclusions: The limited number of credible associations between low penetrance genetic variants and CRA reflects the lower volume of evidence and associated lack of statistical power to detect associations of the magnitude typically observed for genetic variants and chronic diseases. The CRA gene database provides context for CRA genetic association data and will help inform future research directions., (© The Author 2015; all rights reserved. Published by Oxford University Press on behalf of the International Epidemiological Association.)

Enzymatic deamination of cytidines in DNA is an intrinsic component of antibody maturation and retroviral resistance, but can also be a source of HIV drug resistance and cancer-causing mutations. Here, we developed a high-throughput method based on high resolution melt (HRM) analysis called HyperHRM that can screen genomic DNA for rare hypermutated proviral sequences and accurately quantify the number of C-to-T or G-to-A mutations in each sequence. We demonstrate the effectiveness of the approach by profiling in parallel the intensity of the DNA mutator activity of all seven human APOBEC3 proteins on the near full-length sequence of HIV-1 and the Moloney murine leukemia virus. Additionally, HRM was successfully used to identify hypermutated proviral sequences in peripheral blood mononuclear cells from an HIV-1 patient. These results exemplify the effectiveness of HRM-based approaches for hypermutation quantification and for the detection of hypermutated DNA sequences potentially associated with disease or retroviral drug resistance., (© 2013 Elsevier Inc. All rights reserved.)

Background: Colorectal cancer is a major global public health problem, with approximately 950,000 patients newly diagnosed each year. We report the first comprehensive field synopsis and creation of a parallel publicly available and regularly updated database (CRCgene) that catalogs all genetic association studies on colorectal cancer (http://www.chs.med.ed.ac.uk/CRCgene/)., Methods: We performed two independent systematic reviews, reviewing 10&emsp14;145 titles, then collated and extracted data from 635 publications reporting on 445 polymorphisms in 110 different genes. We carried out meta-analyses to derive summary effect estimates for 92 polymorphisms in 64 different genes. For assessing the credibility of associations, we applied the Venice criteria and the Bayesian False Discovery Probability (BFDP) test., Results: We consider 16 independent variants at 13 loci (MUTYH, MTHFR, SMAD7, and common variants tagging the loci 8q24, 8q23.3, 11q23.1, 14q22.2, 1q41, 20p12.3, 20q13.33, 3q26.2, 16q22.1, and 19q13.1) to have the most highly credible associations with colorectal cancer, with all variants except those in MUTYH and 19q13.1 reaching genome-wide statistical significance in at least one meta-analysis model. We identified less-credible (higher heterogeneity, lower statistical power, BFDP >0.2) associations with 23 more variants at 22 loci. The meta-analyses of a further 20 variants for which associations have previously been reported found no evidence to support these as true associations., Conclusion: The CRCgene database provides the context for genetic association data to be interpreted appropriately and helps inform future research direction.

Research on analyzing microarray data has focused on the problem of identifying differentially expressed genes to the neglect of the problem of how to integrate evidence that a gene is differentially expressed with information on the extent of its differential expression. Consequently, researchers currently prioritize genes for further study either on the basis of volcano plots or, more commonly, according to simple estimates of the fold change after filtering the genes with an arbitrary statistical significance threshold. While the subjective and informal nature of the former practice precludes quantification of its reliability, the latter practice is equivalent to using a hard-threshold estimator of the expression ratio that is not known to perform well in terms of mean-squared error, the sum of estimator variance and squared estimator bias. On the basis of two distinct simulation studies and data from different microarray studies, we systematically compared the performance of several estimators representing both current practice and shrinkage. We find that the threshold-based estimators usually perform worse than the maximum-likelihood estimator (MLE) and they often perform far worse as quantified by estimated mean-squared risk. By contrast, the shrinkage estimators tend to perform as well as or better than the MLE and never much worse than the MLE, as expected from what is known about shrinkage. However, a Bayesian measure of performance based on the prior information that few genes are differentially expressed indicates that hard-threshold estimators perform about as well as the local false discovery rate (FDR), the best of the shrinkage estimators studied. Based on the ability of the latter to leverage information across genes, we conclude that the use of the local-FDR estimator of the fold change instead of informal or threshold-based combinations of statistical tests and non-shrinkage estimators can be expected to substantially improve the reliability of gene prioritization at very little risk of doing so less reliably. Since the proposed replacement of post-selection estimates with shrunken estimates applies as well to other types of high-dimensional data, it could also improve the analysis of SNP data from genome-wide association studies.

Motivation: Measurements of gene expression over time enable the reconstruction of transcriptional networks. However, Bayesian networks and many other current reconstruction methods rely on assumptions that conflict with the differential equations that describe transcriptional kinetics. Practical approximations of kinetic models would enable inferring causal relationships between genes from expression data of microarray, tag-based and conventional platforms, but conclusions are sensitive to the assumptions made., Results: The representation of a sufficiently large portion of genome enables computation of an upper bound on how much confidence one may place in influences between genes on the basis of expression data. Information about which genes encode transcription factors is not necessary but may be incorporated if available. The methodology is generalized to cover cases in which expression measurements are missing for many of the genes that might control the transcription of the genes of interest. The assumption that the gene expression level is roughly proportional to the rate of translation led to better empirical performance than did either the assumption that the gene expression level is roughly proportional to the protein level or the Bayesian model average of both assumptions., Availability: http://www.oisb.ca points to R code implementing the methods (R Development Core Team 2004)., Supplementary Information: http://www.davidbickel.com.