Increasing the power of genome wide association studies in natural populations using repeated measures : evaluation and implementation

1. Genomewide association studies (GWAS) enable detailed dissections of the genetic basis for organisms' ability to adapt to a changing environment. In long-term studies of natural populations, individuals are often marked at one point in their life and then repeatedly recaptured. It is therefore essential that a method for GWAS includes the process of repeated sampling. In a GWAS, the effects of thousands of single-nucleotide polymorphisms (SNPs) need to be fitted and any model development is constrained by the computational requirements. A method is therefore required that can fit a highly hierarchical model and at the same time is computationally fast enough to be useful. 2. Our method fits fixed SNP effects in a linear mixed model that can include both random polygenic effects and permanent environmental effects. In this way, the model can correct for population structure and model repeated measures. The covariance structure of the linear mixed model is first estimated and subsequently used in a generalized least squares setting to fit the SNP effects. The method was evaluated in a simulation study based on observed genotypes from a long-term study of collared flycatchers in Sweden. 3. The method we present here was successful in estimating permanent environmental effects from simulated repeated measures data. Additionally, we found that especially for variable phenotypes having large variation between years, the repeated measurements model has a substantial increase in power compared to a model using average phenotypes as a response. 4. The method is available in the R package RepeatABEL. It increases the power in GWAS having repeated measures, especially for long-term studies of natural populations, and the R implementation is expected to facilitate modelling of longitudinal data for studies of both animal and human populations.

Isolation and selection of plant growth-promoting bacteria associated with sugarcane

v. 46, n. 2, p. 149-158, apr./jun. 2016.

Type 2 Diabetes Mellitus: Risk Evaluation and Advice in Undergraduate Students in Ashrafieh, Lebanon

Type 2 diabetes mellitus (T2DM) is a chronic lifestyle disease. It has become evident that T2DM occurs even among the younger age groups.1 In Lebanon, T2DM has a major public health impact through high disease prevalence, significant downstream pathophysiologic effects, and enormous financial liabilities.2

ESTUDIO DE IMPACTO DE INSTRUMENTOS DE EVALUACIÓN Y MEJORA DE CENTROS EDUCATIVOS: Impact study of evaluation and improvement tools of schools

Se estudia la percepción del impacto de la aplicación del sistema de calidad ISO (International Standard Organization). Se aplicaron cuestionarios a los directores y docentes de dos centros con características contrastantes. Uno chico, gratuito, que recibe niños de una zona pobre y de bajos ingresos. El segundo es un centro grande, que recibe niños de zonas de ingresos altos y cobra una cuota alta. Los dos certificaron aspectos parciales con ISO, mostrando estrategias de implementación parecidas. Los resultados son similares y muestran limitados aportes del instrumento a ambos centros, con pocas diferencias entre sí. A la vez coinciden con otros estudios que se reseñan, que encontraron escasos aportes de los sistemas ISO a la mejora educativa, junto con sobrecarga administrativa

Evaluation and comparison of durability of polycyclic aromatic hydrocarbon compounds (PAHs) and its relation to the lipid content in smoked fishes, Silver carp (Hypophthalmichthys molitrix), Rutilus frisii kutum and Herring (Alosa caspia)

Cold smoking method is one of the commonest ways for fish smoking. It is done by the smoke that is the result of burning hard and soft woods is smoking rooms. Smoke includes a number of chemical constructs and its main part is poly aromatic hydrocarbons. More than one hundred kinds of these constructs are recognized in smoke that is produced from saturated hydrocarbons resulted from the solution of the woods Ligno cellulose in high temperature and lack of oxygen conditions. The high poisoning potentials and carcinogenic features sixteen constructs among them are proved and observed on humans. In this research, the PAH compounds were identified and observed in a three month period after smoking and during storing among three types of smoked fishes Silver carp and Caspian sea Sefid and herring. They are the most produced and consumed smoked fish in Iran. To find the relationship between the concentrations of PAH constructs and the amount of lipid in fish, first, the amount of lipid were determined separately in the skin and flesh of 30 samples of each type. The method used was Bligh and Dyer (1959). PAH compounds derivation were made for all skin and flesh samples smoked fish using organic solvents with Soxeleh and the derived samples were injected to gas chromatography (GC) by Hamilton injectors for determining their components quality and their quantity. The height of the used column was 25 meters and its diameter was 0.32 mm with the silica filler, nitrogen gas as carrier and flame ionization detector (FID) that are special for these constructs. For data analysis, Statistical tests were used by computer soft ware identified that the difference in the amount of lipid within the flesh and skin of each species and also among each other is significant. The largest amount was in Herrings flesh and skin, 18.74% in skin and 14.47% in flesh. The least amount in the skin 4.19% and the flesh 3.10% of Sefid. The amount in Silver carp was 13.28%in skin and 8.16% in flesh. The examination of the PAH compounds in smoked fish showed that is carcinogenic compounds; exist in these in these fish with different quantities in each. It seems that its amount is directly related to the amount of their lipid. The amount is different in flesh and skin. One of the most important reasons is the direct content of smoke and the concentration of lipid in tissues of all three types. The maintenance of the smoked fish for three months showed that most of PAH compounds were solved and their density decreased. The changes in density within time in different in each type and in flesh and skin. The amount of their receiving in human through the consumption of the smoked fish depends on the resulted density, the way and the amount of consumption and now we can determine and execute standards for the maximum dosage per day and per month regarding effective factors.

Evaluation and measurement of chromium in sea water in order to remove it with mineral absorbent kaolin for desalination

Today, the use of heavy metals and chemical products industry expanded. The presence of significant amounts of, pollutants in industrial waste water can lead to serious risks to the environment and human health have heavy metals like chromium is one example of the future of salmon knock pond environment. Chromium is an essential element in the diet, but high doses of this element is very dangerous. Hence the use of chemical methods as a tool for the removal of metals from waste water pond be used. The aim of this study was to investigate the mineral kaolin adsorbents for the removal of chromium is water. Thus, the effect of different concentrations of absorbent micro amounts of chromium absorption and variable temperature, pH and electrolytes were studied. During the investigation of spectroscopic instrument (Varian) UV-VIS are used. Comparison of the absorption mechanism of chromium adsorption by the adsorbent with nano-absorbent kaolin kaolin was investigated. According to the studies done in the same conditions of temperature, pH and shaking rate of chromium absorption by nano kaolin kaolin is much more attractive. Therefore, its use as an adsorbent abundant, cheap, accessible, efficient and effective is proposed.

Thermal and exergy analysis for evaluation and optimization of performance of cooling towers for fresh water and seawater

In this study, thermal, exergetic analysis and performance evaluation of seawater and fresh wet cooling tower and the effect of parameters on its performance is investigated. With using of energy and mass balance equations, experimental results, a mathematical model and EES code developed. Due to lack of fresh water, seawater cooling is interesting choice for future of cooling, so the effect of seawater in the range of 1gr/kg to 60gr/kg for salinity on the performance characteristics like air efficiency, water efficiency, output water temperature of cooling tower, flow of the exergy, and the exergy efficiency with comparison with fresh water examined. Decreasing of air efficiency about 3%, increasing of water efficiency about 1.5% are some of these effects. Moreover with formation of fouling the performance of cooling tower decreased about 15% which this phenomena and its effects like increase in output water temperature and tower excess volume has been showed and also accommodate with others work. Also optimization for minimizing cost, maximizing air efficiency, and minimizing exergy destruction has been done, results showed that optimization on minimizing the exergy destruction has been satisfy both minimization of the cost and the maximization of the air efficiency, although it will not necessarily permanent for all inputs and optimizations. Validation of this work is done by comparing computational results and experimental data which showed that the model have a good accuracy.

Are the preference and selection patterns of hermit crabs for gastropod shells species- or site-specific?

Experimental analyses of hermit crabs and their preferences for shells are essential to understand the intrinsic relationship of the crabs' dependence on shells, and may be useful to explain their shell use pattern in nature. The aim of this study was to evaluate the effect of crab species and site on the pattern of shell use, selection, and preference in the south-western Atlantic hermit crabs Pagurus brevidactylus and Pagurus criniticornis, comparing sympatric and allopatric populations. Differently from the traditional approach to evaluate shell preference by simply determining the shell selection pattern (i.e., the number of shells of each type selected), preference was defined (according to [Liszka, D., Underwood, AJ., 1990. An experimental design to determine preferences for gastropod shells by a hermit-crab. J. Exp. Mar. Biol. Ecol., 137(1), 47-62]) by the comparison of the number of crabs changing for a particular shell type when three options were given (Cerithium atratum, Morula nodulosa, and Tegula viridula) with the number of crabs changing for this same type when only this type was offered. The effect of crab species was tested at Cabelo Gordo Beach, where P. brevidacrylus was found occupying shells of C. atratum, M. nodulosa, and T viridula in similar frequencies, whereas P. criniticornis occupied predominantly shells of C atratum. In laboratory experiments the selection patterns of the two hermit-crab species for these three gastropods were different, with P criniticornis selecting mainly shells of C atratum, and R brevidactylus selecting more shells of M. nodulosa. The shell preference was also dependent on crab species, with P. criniticornis showing a clear preference for shells of C atratum, whereas P. brevidactylus did not show a preference for any of the tested shells. The effect of site was tested for the two species comparing data from Cabelo Gordo to Preta (P brevidactylus) and Araca beaches (P. criniticornis). The pattern of shell use, selection, and preference was demonstrated to be dependent on site only for P. brevidactylus. The results also showed that the shell use pattern of P criniticornis can be explained by its preference at both sites, whereas for P. brevidactylus it occurred only at Cabelo Gordo, where the absence of preference was correlated with the similar use of the three gastropod species studied. Finally, the results showed that the shell selection pattern cannot be considered as a measure of shell preference, since it overestimates crab selectivity. (C) 2009 Elsevier B.V. All rights reserved.

Postnatal Evaluation and Outcome of Prenatal Hydronephrosis

Background: Prenatal hydronephrosis (PNH) is dilation in urinary collecting system and is the most frequent neonatal urinary tract abnormality with an incidence of 1% to 5% of all pregnancies. PNH is defined as anteroposterior diameter (APD) of renal pelvis ≥ 4 mm at gestational age (GA) of < 33 weeks and APD ≥ 7 mm at GA of ≥ 33 weeks to 2 months after birth. All patients need to be evaluated after birth by postnatal renal ultrasonography (US). In the vast majority of cases, watchful waiting is the only thing to do; others need medical or surgical therapy. Objectives: There is a direct relationship between APD of renal pelvis and outcome of PNH. Therefore we were to find the best cutoff point APD of renal pelvis which leads to surgical outcome. Patients and Methods: In this retrospective cohort study we followed 200 patients 1 to 60 days old with diagnosis of PNH based on before or after birth ultrasonography; as a prenatal or postnatal detected, respectively. These patients were referred to the nephrology clinic in Zahedan Iran during 2011 to 2013. The first step of investigation was a postnatal renal US, by the same expert radiologist and classifying the patients into 3 groups; normal, mild/moderate and severe. The second step was to perform voiding cystourethrogram (VCUG) for mild/moderate to severe cases at 4 - 6 weeks of life. Tc-diethylene triamine-pentaacetic acid (DTPA) was the last step and for those with normal VCUG who did not show improvement in follow-up examination, US to evaluate obstruction and renal function. Finally all patients with mild/moderate to severe PNH received conservative therapy and surgery was preserved only for progressive cases, obstruction or renal function ≤35%. All patients’ data and radiologic information was recorded in separate data forms, and then analyzed by SPSS (version 22). Results: 200 screened PNH patients with male to female ratio 3.5:1 underwent first postnatal control US, of whom 65% had normal, 18% mild/moderate and 17% severe hydronephrosis. 167 patients had VCUG of whom 20.82% with VUR. 112 patients performed DTPA with following results: 50 patients had obstruction and 62 patients showed no obstructive finding. Finally 54% of 200 patients recovered by conservative therapy, 12.5% by surgery and remaining improved without any surgical intervention. Conclusions: The best cutoff point of anteroposterior renal pelvis diameter that led to surgery was 15 mm, with sensitivity 88% and specificity 74%.

Cooking time of common bean: genetic parameters and selection of elite lines.

The objectives of this study were to investigate the genetic variability and select elite lines for CT, since these lines aggregate essential agronomic traits.

EVALUATION AND MONITORING OF ASH (FRAXINUS SPP.) TOLERANT TO LONG-TERM EMERALD ASH BORER (AGRILUS PLANIPENNIS [COLEOPTERA: BUPRESTIDAE]) EXPOSURE

Invasive insects that successfully establish in introduced areas can significantly alter natural communities. These pests require specific establishment criteria (e.g. host suitability) that, when known, can help quantify potential damage to infested areas. Emerald ash borer (Agrilus planipennis [Coleoptera: Buprestidae]) is an invasive phloem-feeding pest which is responsible for the death of millions of ash trees (Fraxinus spp. L.). Over 200 surviving ash trees were previously identified in the Huron-Clinton Metroparks located in southeast Michigan. Trees were assessed over a four year period and a hierarchical cluster analysis was performed on dieback, vigor, and presence of signs and symptoms, in order to place trees into one of three tolerance groups. The clustering of trees with different responses to emerald ash borer attack suggests that there are different tolerance levels in North American ash trees in southeastern Michigan, and these groups were designated as apparently tolerant, not tolerant and intermediate tolerance. Adult landing rates and evidence of adult emergence were significantly lower in the apparently tolerant group compared with the not tolerant group, but larval survival from eggs placed on trees did not differ between tolerance groups. Therefore, it appears that apparently tolerant trees survive because they are less attractive to adult beetles which results in fewer eggs being laid on them. Trees in the apparently tolerant group remained of higher vigor over the four years of the study. North American ash may survive the emerald ash borer epidemic due to natural variation and inherent resistance regardless of the lack of co-evolutionary history with emerald ash borer.

Exploring Hidden Coherent Feature Groups and Temporal Semantics for Multimedia Big Data Analysis

Thanks to the advanced technologies and social networks that allow the data to be widely shared among the Internet, there is an explosion of pervasive multimedia data, generating high demands of multimedia services and applications in various areas for people to easily access and manage multimedia data. Towards such demands, multimedia big data analysis has become an emerging hot topic in both industry and academia, which ranges from basic infrastructure, management, search, and mining to security, privacy, and applications. Within the scope of this dissertation, a multimedia big data analysis framework is proposed for semantic information management and retrieval with a focus on rare event detection in videos. The proposed framework is able to explore hidden semantic feature groups in multimedia data and incorporate temporal semantics, especially for video event detection. First, a hierarchical semantic data representation is presented to alleviate the semantic gap issue, and the Hidden Coherent Feature Group (HCFG) analysis method is proposed to capture the correlation between features and separate the original feature set into semantic groups, seamlessly integrating multimedia data in multiple modalities. Next, an Importance Factor based Temporal Multiple Correspondence Analysis (i.e., IF-TMCA) approach is presented for effective event detection. Specifically, the HCFG algorithm is integrated with the Hierarchical Information Gain Analysis (HIGA) method to generate the Importance Factor (IF) for producing the initial detection results. Then, the TMCA algorithm is proposed to efficiently incorporate temporal semantics for re-ranking and improving the final performance. At last, a sampling-based ensemble learning mechanism is applied to further accommodate the imbalanced datasets. In addition to the multimedia semantic representation and class imbalance problems, lack of organization is another critical issue for multimedia big data analysis. In this framework, an affinity propagation-based summarization method is also proposed to transform the unorganized data into a better structure with clean and well-organized information. The whole framework has been thoroughly evaluated across multiple domains, such as soccer goal event detection and disaster information management.

Clinical characteristics and selection of treatment modality for patients with vitreomacular traction:real-world implementation of NICE guidance (TA297)

Aim: To investigate the qualitative aspects in patient selection and the quantitative impact of disease burden in real world treatment of vitreomacular traction (VMT) and implementation of the National Institute for Health and Care Excellence (NICE) guidance (TA297). Methods: A monocentric, retrospective review of consecutive patients undergoing optical coherence tomography (OCT) imaging over a 3 month period. Patients with VMT in at least one eye were identified for further data collection on laterality, visual acuity, symptoms, presence of epiretinal membrane, macular hole and treatment selection. Results: A total of 3472 patients underwent OCT imaging with a total of 6878 eyes scanned. Out of 87 patients, 74 patients had unilateral VMT (38 right, 36 left) and 13 patients had bilateral VMT. Eighteen patients with unilateral VMT satisfied NICE criteria of severe sight problems in the affected eye. Eight were managed for a coexisting pathology, one refused treatment, one patient did not attend, two closed spontaneously, and one received ocriplasmin prior to the study start date. Only two patients with unilateral VMT received ocriplasmin and three underwent vitrectomy. Those failing to meet NICE criteria for unilateral VMT were predominantly asymptomatic (n=49) or had coexisting ERM (n=5) or both (n=2). Conclusion: Ocriplasmin provides an alternative treatment for patients with symptomatic VMT. Our data shows that the majority of patients with VMT do not meet NICE TA297 primarily due to lack of symptoms. Those meeting NICE criteria, but not treated, tended to have coexisting macular pathology. Variation in patient selection due to subjective factors not outlined in NICE guidance suggests that real world outcomes of ocriplasmin therapy should be interpreted with caution.