Visualization and quality assessment of de novo genome assemblies.

Recent technological progress has greatly facilitated de novo genome sequencing. However, de novo assemblies consist in many pieces of contiguous sequence (contigs) arranged in thousands of scaffolds instead of small numbers of chromosomes. Confirming and improving the quality of such assemblies is critical for subsequent analysis. We present a method to evaluate genome scaffolding by aligning independently obtained transcriptome sequences to the genome and visually summarizing the alignments using the Cytoscape software. Applying this method to the genome of the red fire ant Solenopsis invicta allowed us to identify inconsistencies in 7%, confirm contig order in 20% and extend 16% of scaffolds.Scripts that generate tables for visualization in Cytoscape from FASTA sequence and scaffolding information files are publicly available at https://github.com/ksanao/TGNet.

A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network.

BACKGROUND: The nuclear receptors are a large family of eukaryotic transcription factors that constitute major pharmacological targets. They exert their combinatorial control through homotypic heterodimerisation. Elucidation of this dimerisation network is vital in order to understand the complex dynamics and potential cross-talk involved. RESULTS: Phylogeny, protein-protein interactions, protein-DNA interactions and gene expression data have been integrated to provide a comprehensive and up-to-date description of the topology and properties of the nuclear receptor interaction network in humans. We discriminate between DNA-binding and non-DNA-binding dimers, and provide a comprehensive interaction map, that identifies potential cross-talk between the various pathways of nuclear receptors. CONCLUSION: We infer that the topology of this network is hub-based, and much more connected than previously thought. The hub-based topology of the network and the wide tissue expression pattern of NRs create a highly competitive environment for the common heterodimerising partners. Furthermore, a significant number of negative feedback loops is present, with the hub protein SHP [NR0B2] playing a major role. We also compare the evolution, topology and properties of the nuclear receptor network with the hub-based dimerisation network of the bHLH transcription factors in order to identify both unique themes and ubiquitous properties in gene regulation. In terms of methodology, we conclude that such a comprehensive picture can only be assembled by semi-automated text-mining, manual curation and integration of data from various sources.

The effect of nitrogen and sulphur fertilization on yield and quality of kohlrabi (Brassica oleracea, L.)

In a greenhouse pot experiment with kohlrabi, variety Luna, we explored the joint effect of N (0.6 g N per pot = 6 kg of soil) and S in the soil (25-35-45 mg kg-1 of S) on yields, on N, S and NO3- content in tubers and leaves, and on alterations in the amino acids concentration in the tubers. S fertilisation had no effect on tuber yields. The ranges of N content in tubers and leaves were narrow (between 1.42-1.48 % N and 1.21-1.35 % N, respectively) and the effect of S fertilisation was insignificant. S concentration in the tubers ranged between 0.59 and 0.64 % S. S fertilisation had a more pronounced effect on the S concentration in leaf tissues where it increased from 0.50 to 0.58 or to 0.76 % S under the applied dose. The NO3- content was higher in tubers than in leaves. Increasing the S level in the soil significantly reduced NO3- concentrations in the tubers by 42.2-53.6 % and in the leaves by 8.8-21.7 %. Increasing the S content in the soil reduced the concentration of cysteine + methionine by 16-28 %. The values of valine, tyrosine, aspartic acid and serine were constant. In the S0, S1, and S2 treatments the levels of threonine, isoleucine, leucine, arginine, the sum of essential amino acids and alanine decreased from 37 to 9 %. The histidine concentration increased with increasing S fertilisation. S fertilisation of kohlrabi can be recommended to stabilize the yield and reduce the undesirable NO3- contained in the parts used for consumption.

Care complexity, mood, and quality of life in liver pre-transplant patients.

RATIONALE: This study was intended to document the frequency of care complexity in liver transplant candidates, and its association with mood disturbance and poor health-related quality of life (HRQoL). METHODS: Consecutive patients fulfilling inclusion criteria, recruited in three European hospitals, were assessed with INTERMED, a reliable and valid method for the early assessment of bio-psychosocial health risks and needs. Blind to the results, they were also assessed with the Hospital Anxiety and Depression Scale (HADS). HRQoL was documented with the EuroQol and the SF36. Statistical analysis included multivariate and multilevel techniques. RESULTS: Among patients fulfilling inclusion criteria, 60 patients (75.9%) completed the protocol and 38.3% of them were identified as "complex" by INTERMED, but significant between-center differences were found. In support of the working hypothesis, INTERMED scores were significantly associated with all measures of both the SF36 and the EuroQol, and also with the HADS. A one point increase in the INTERMED score results in a reduction in 0.93 points in EuroQol and a 20% increase in HADS score. CONCLUSIONS: INTERMED-measured case complexity is frequent in liver transplant candidates but varies widely between centers. The use of this method captures in one instrument multiple domains of patient status, including mood disturbances and reduced HRQoL.

Socioeconomics status and quality of care in a population-based sample of swiss diabetic patients

Introduction: Low socioeconomic status (SES) is associated with higher prevalence of diabetes and worse outcomes; it has also been shown to be associated with worse quality of care. We aimed to explore the relationship between SES and quality of care in the Swiss context. Methods: We used data from a population-based survey including 519 adult diabetic patients living in the canton of Vaud. Self-reported data on patients' and diabetes characteristics, indicators of process and outcomes of care and quality of life were collected. Dependent variables included 6 processes of care (PoC) received during the last 12 months (HbA1C, lipid, microalbuminuria, fundoscopy, feet examination and influenza vaccination) and selected clinical outcomes (blood pressure, LDL, HbA1C, diabetes-specific (ADDQoL) and generic quality of life (SF-12)). Regression analyses were performed to assess the relationship between education and income, respectively, and quality of care as measured by PoC and clinical outcomes. Adjustment was made for age, gender and comorbidities. Results: Mean age was 64.5 years, 40% were women; 19%, 56% and 25% of the patients reported primary (I), secondary (II) and tertiary (III) education. Fundoscopy was the only PoC significantly associated with education, with III education patients more likely to get the exam than those with primary education (adjOR 1.8, 95% CI 1.0-3.3). Use of composite indicators of PoC showed that compared to patients with primary education, patients with III education were more likely to receive ≥5/6 PoC (adjOR 1.9, 95% CI 1.1-3.4), and that those with II or III education were more likely to receive 4/4 PoC (adjOR 1.9, 95% CI 1.0-3.3; adjOR 2.1, 95% CI 1.1-4.1, respectively). Quality of life was the only clinical outcome significantly associated with education, with II and III education patients reporting better quality of life compared to primary education patients, as measured by the ADDQoL (β 0.6, 95% CI 0.3-1.0, β 0.6, 95% CI 0.2-1.0, respectively) and the physical component score of the SF-12 (β 2.5, 95% CI 0.2-4.8, β 3.6, 95% CI 0.9-6.4, respectively). No associations were found between income and quality of care. Conclusion: Social inequalities have been demonstrated in Switzerland for global health indicators. Our results suggest that similar associations are found when considering quality of care measures in individuals with diabetes, but only for a few indicators.

Intensity correlation functions of dye lasers: Comparison of colored-gain-noise and colored-loss-noise models

The intensity correlation functions C(t) for the colored-gain-noise model of dye lasers are analyzed and compared with those for the loss-noise model. For correlation times ¿ larger than the deterministic relaxation time td, we show with the use of the adiabatic approximation that C(t) values coincide for both models. For small correlation times we use a method that provides explicit expressions of non-Markovian correlation functions, approximating simultaneously short- and long-time behaviors. Comparison with numerical simulations shows excellent results simultaneously for short- and long-time regimes. It is found that, when the correlation time of the noise increases, differences between the gain- and loss-noise models tend to disappear. The decay of C(t) for both models can be described by a time scale that approaches the deterministic relaxation time. However, in contrast with the loss-noise model, a secondary time scale remains for large times for the gain-noise model, which could allow one to distinguish between both models.

Progeny Trial Estimates of Genetic Parameters for Growth and Quality Traits in Scots Pine

Summary

Iron oxides and quality of organic matter in sugarcane harvesting systems

Improvements in working conditions, sustainable production, and competitiveness have led to substantial changes in sugarcane harvesting systems. Such changes have altered a number of soil properties, including iron oxides and organic matter, as well as some chemical properties, such as the maximum P adsorption capacity of the soil. The aim of this study was to characterize the relationship between iron oxides and the quality of organic matter in sugarcane harvesting systems. For that purpose, two 1 ha plots in mechanically and manually harvested fields were used to obtain soil samples from the 0.00-0.25 m soil layer at 126 different points. The mineralogical, chemical, and physical results were subjected to descriptive statistical analyses, such as the mean comparison test, as well as to multivariate statistical and principal component analyses. Multivariate tests allowed soil properties to be classified in two different groups according to the harvesting method: manual harvest with the burning of residual cane, and mechanical harvest without burning. The mechanical harvesting system was found to enhance pedoenvironmental conditions, leading to changes in the crystallinity of iron oxides, an increase in the humification of organic matter, and a relative decrease in phosphorus adsorption in this area compared to the manual harvesting system.

Patterns of failure and outcome in patients with carcinoma of the anal margin.

BACKGROUND: To evaluate the outcome of patients with carcinoma of anal margin in terms of recurrence, survival, and radiation toxicity. METHODS: A series of 45 consecutive patients, with anal margin carcinoma treated between 1983 and 2006 with curative intent at two institutions, was retrospectively analyzed. A surgical excision (close or positive surgical margin in 22 out of 29 patients) was realized before radiotherapy (RT). RT consisted of definitive external beam RT (EBRT) in 36 patients, brachytherapy (BT) alone in two patients, and both BT and EBRT in seven patients. The median total radiation dose was 59.4 Gy (range, 30-74 Gy). RESULTS: The 5-year locoregional control (LRC) rate was 78% [95% confidence interval (CI), 64-93%]. The 5-year disease-specific survival (DSS) and overall survival (OS) rates were respectively 86% (95% CI, 72-99%) and 55% (95% CI, 44-66%). The overall anal conservation rate was 80% for the whole series. There was no significant association between local recurrence and patient age, histological grade, tumor size, T stage, overall treatment time, RT dose, or chemotherapy. Long-term side effects were observed in 15 patients (33%). Only three patients developed grade 3-4 late toxicity (CTCAE/NCI v3.0). Significant relationship was found between dose, and complication rate (48% for dose >or=59.4 Gy versus 8% for dose < 59.4 Gy; P = 0.03). CONCLUSIONS: We conclude that definitive RT and/or BT yield a good local control and disease-specific survival comparable with published data. This study suggests that radiation dose over 59.4 Gy seems to increase treatment-related morbidity.

On the problematic of reserving and stochastic loss models

Abstract Traditionally, the common reserving methods used by the non-life actuaries are based on the assumption that future claims are going to behave in the same way as they did in the past. There are two main sources of variability in the processus of development of the claims: the variability of the speed with which the claims are settled and the variability between the severity of the claims from different accident years. High changes in these processes will generate distortions in the estimation of the claims reserves. The main objective of this thesis is to provide an indicator which firstly identifies and quantifies these two influences and secondly to determine which model is adequate for a specific situation. Two stochastic models were analysed and the predictive distributions of the future claims were obtained. The main advantage of the stochastic models is that they provide measures of variability of the reserves estimates. The first model (PDM) combines one conjugate family Dirichlet - Multinomial with the Poisson distribution. The second model (NBDM) improves the first one by combining two conjugate families Poisson -Gamma (for distribution of the ultimate amounts) and Dirichlet Multinomial (for distribution of the incremental claims payments). It was found that the second model allows to find the speed variability in the reporting process and development of the claims severity as function of two above mentioned distributions' parameters. These are the shape parameter of the Gamma distribution and the Dirichlet parameter. Depending on the relation between them we can decide on the adequacy of the claims reserve estimation method. The parameters have been estimated by the Methods of Moments and Maximum Likelihood. The results were tested using chosen simulation data and then using real data originating from the three lines of business: Property/Casualty, General Liability, and Accident Insurance. These data include different developments and specificities. The outcome of the thesis shows that when the Dirichlet parameter is greater than the shape parameter of the Gamma, resulting in a model with positive correlation between the past and future claims payments, suggests the Chain-Ladder method as appropriate for the claims reserve estimation. In terms of claims reserves, if the cumulated payments are high the positive correlation will imply high expectations for the future payments resulting in high claims reserves estimates. The negative correlation appears when the Dirichlet parameter is lower than the shape parameter of the Gamma, meaning low expected future payments for the same high observed cumulated payments. This corresponds to the situation when claims are reported rapidly and fewer claims remain expected subsequently. The extreme case appears in the situation when all claims are reported at the same time leading to expectations for the future payments of zero or equal to the aggregated amount of the ultimate paid claims. For this latter case, the Chain-Ladder is not recommended.

Organic Matter Fractions and Quality of the Surface Layer of a Constructed and Vegetated Soil After Coal Mining. I - Humic Substances and Chemical Characterization

After open coal mining, soils are “constructed”, which usually contain low levels and quality of organic matter (OM). Therefore, the use of plant species for revegetation and reclamation of degraded areas is essential. This study evaluated the distribution of carbon (C) in the chemical fractions as well as the chemical characteristics and humification degree of OM in a soil constructed after coal mining under cultivation of perennial grasses. The experiment was established in 2003 with the following treatments: Hemarthria altissima (T1), Paspalum notatum (T2), Cynodon dactilon (T3), Urochloa brizantha (T4), bare constructed soil (T5), and natural soil (T6). In 2009, soil samples were collected from the 0.00-0.03 m layer and the total organic carbon stock (TOC) and C stock in the chemical fractions: acid extract (CHCl), fulvic acid (CFA), humic acid (CHA), and humin (CHU) were determined. The humic acid (HA) fraction was characterized by infrared spectroscopy and the laser-induced fluorescence index (ILIF) of OM was also calculated. After six years, differences were only observed in the CHA stocks, which were highest in T1 (0.89 Mg ha-1) and T4 (1.06 Mg ha-1). The infrared spectra of HA in T1, T2 and T4 were similar to T6, with greater contribution of aliphatic organic compounds than in the other treatments. In this way, ILIF decreased in the sequence T5>T3>T4>T1>T2>T6, indicating higher OM humification in T3 and T5 and more labile OM in the other treatments. Consequently, the potential of OM quality recovery in the constructed soil was greatest in treatments T1 and T4.

Organic Matter Fractions and Quality of the Surface Layer of a Constructed and Vegetated Soil After Coal Mining. II - Physical Compartments and Carbon Management Index

Soils constructed after mining often have low carbon (C) stocks and low quality of organic matter (OM). Cover crops are decisive for the recovery process of these stocks, improving the quality of constructed soils. Therefore, the goal of this study was to evaluate the effect of cover crops on total organic C (TOC) stocks, C distribution in physical fractions of OM and the C management index (CMI) of a soil constructed after coal mining. The experiment was initiated in 2003 with six treatments: Hemarthria altissima (T1), Paspalum notatum (T2), Cynodon dactylon (T3), Urochloa brizantha (T4), bare constructed soil (T5), and natural soil (T6). Soil samples were collected in 2009 from the 0.00-0.03 m layer, and the TOC and C stocks in the physical particle size fractions (carbon in the coarse fraction - CCF, and mineral-associated carbon - MAC) and density fractions (free light fraction - FLF; occluded light fraction - OLF, and heavy fraction - HF) of OM were determined. The CMI components: carbon pool index (CPI), lability (L) and lability index (LI) were estimated by both fractionation methods. No differences were observed between TOC, CCF and MAC stocks. The lowest C stocks in FLF and OLF fractions were presented by T2, 0.86 and 0.61 Mg ha-1, respectively. The values of TOC stock, C stock in physical fractions and CMI were intermediate, greater than T5 and lower than T6 in all treatments, indicating the partial recovery of soil quality. As a result of the better adaptation of the species Hemarthria and Brizantha, resulting in greater accumulation of labile organic material, the CPI, L, LI and CMI values were higher in these treatments, suggesting a greater potential of these species for recovery of constructed soils.