Improvements to previous algorithms to predict gene structure and isoform concentrations using Affymetrix Exon arrays

<p>Abstract</p> <p>Background</p> <p>Exon arrays provide a way to measure the expression of different isoforms of genes in an organism. Most of the procedures to deal with these arrays are focused on gene expression or on exon expression. Although the only biological analytes that can be properly assigned a concentration are transcripts, there are very few algorithms that focus on them. The reason is that previously developed summarization methods do not work well if applied to transcripts. In addition, gene structure prediction, i.e., the correspondence between probes and novel isoforms, is a field which is still unexplored.</p> <p>Results</p> <p>We have modified and adapted a previous algorithm to take advantage of the special characteristics of the Affymetrix exon arrays. The structure and concentration of transcripts -some of them possibly unknown- in microarray experiments were predicted using this algorithm. Simulations showed that the suggested modifications improved both specificity (SP) and sensitivity (ST) of the predictions. The algorithm was also applied to different real datasets showing its effectiveness and the concordance with PCR validated results.</p> <p>Conclusions</p> <p>The proposed algorithm shows a substantial improvement in the performance over the previous version. This improvement is mainly due to the exploitation of the redundancy of the Affymetrix exon arrays. An R-Package of SPACE with the updated algorithms have been developed and is freely available.</p

Sampling sufficiency for mechanical properties of wood

Based on most recently published studies, there is a large variability in both the mechanical properties of wood and sample sizes selected to evaluate them. This study aims to define sampling sufficiency for some mechanical properties of wood, which were bending strength, bending modulus, compressive strength, compressive modulus, hardness, and shear strength. The mechanical tests were carried out according to the ASTM D143 on wood samples cut from clonal Eucalyptus planted in southern Brazil. Sampling sufficiency was determined by an intensive computational method based on resampling of original data using Monte Carlo simulations. The experimental tests data conformed to the normal distribution and most of the obtained sufficient sample sizes determined by Monte Carlo simulation were above those sample sizes used in most already published studies. Furthermore, properties related to wood stiffness presented smaller variabilities than their respective properties associated with wood strength, leading to smaller sample sizes for the former cases

Abundancia de Caminicimex Furnarii (Cordero y Vogelsang) (Heteróptera: Cimicidae) en nidos de Golondrina Doméstica Progne Chalybea (Gmelin) (Passeriformes: Hirundinidae)

Se brindan por primera vez datos sobre densidad, estructura poblacional y proporción de sexos de C. furnarii (Cordero y Vogelsang) en nidos de Golondrina Doméstica Progne chalybea (Gmelin). Tres nidos fueron colocados en embudos Berlese para calcular el número y las proporciones relativas de huevos (66,4%), ninfas (11%) y adultos (22,6%). La proporción de sexos se encontró sesgada hacia los machos (1,61). El número de chinches/nido fue elevado y varió entre 210 a 1163; en el menos infestado de los nidos habría entre 30 y 42 chinches/golondrina, y en el más infestado, entre 166 y 233. El ciclo de las chinches está ajustado a largos períodos de inanición antes del regreso de las golondrinas en la siguiente estación reproductiva

Dieta de pichones de cotorra Myiopsitta m. monachus (Aves: Psittacidae) en la Provincia de Buenos Aires

Dieta de pichones de Cotorra Myiopsitta m. monachus (Aves: Psittacidae) en la Provincia de Buenos Aires. El objetivo de este trabajo fue conocer la composición de la dieta aportada por los progenitores a los pichones durante su permanencia en el nido. Se analizaron los buches de 32 pichones de cotorra cuyos nidos fueron sometidos a control químico, procedentes de Gándara, Cañuelas y Villanueva (Provincia de Buenos Aires). Cada buche fue pesado con balanza analítica. Los distintos ítems integrantes de la dieta fueron separados bajo lupa binocular y pesados. La determinación se realizó en base a caracteres morfológicos externos e internos. Se observó que el 99.5% correspondió a componente vegetal, mientras que el componente mineral sólo se encontró representado en un 0.5%. En la fracción vegetal se destacaron cuatro familias siendo Asteracea y Poacea las de mayor porcentaje (96%)

Chronic obstructive pulmonary disease subtypes. transitions over time

Background Although subtypes of chronic obstructive pulmonary disease are recognized, it is unknown what happens to these subtypes over time. Our objectives were to assess the stability of cluster-based subtypes in patients with stable disease and explore changes in clusters over 1 year. Methods Multiple correspondence and cluster analysis were used to evaluate data collected from 543 stable patients included consecutively from 5 respiratory outpatient clinics. Results Four subtypes were identified. Three of them, A, B, and C, had marked respiratory profiles with a continuum in severity of several variables, while the fourth, subtype D, had a more systemic profile with intermediate respiratory disease severity. Subtype A was associated with less dyspnea, better health-related quality of life and lower Charlson comorbidity scores, and subtype C with the most severe dyspnea, and poorer pulmonary function and quality of life, while subtype B was between subtypes A and C. Subtype D had higher rates of hospitalization the previous year, and comorbidities. After 1 year, all clusters remained stable. Generally, patients continued in the same subtype but 28% migrated to another cluster. Together with movement across clusters, patients showed changes in certain characteristics (especially exercise capacity, some variables of pulmonary function and physical activity) and changes in outcomes (quality of life, hospitalization and mortality) depending on the new cluster they belonged to Conclusions Chronic obstructive pulmonary disease clusters remained stable over 1 year. Most patients stayed in their initial subtype cluster, but some moved to another subtype and accordingly had different outcomes

COPD classification models and mortality prediction capacity

Our aim was to assess the impact of comorbidities on existing COPD prognosis scores. Patients and methods: A total of 543 patients with COPD (FEV1 < 80% and FEV1/ FVC <70%) were included between January 2003 and January 2004. Patients were stable for at least 6 weeks before inclusion and were followed for 5 years without any intervention by the research team. Comorbidities and causes of death were established from medical reports or information from primary care medical records. The GOLD system and the body mass index, obstruction, dyspnea and exercise (BODE) index were used for COPD classification. Patients were also classified into four clusters depending on the respiratory disease and comorbidities. Cluster analysis was performed by combining multiple correspondence analyses and automatic classification. Receiver operating characteristic curves and the area under the curve (AUC) were calculated for each model, and the DeLong test was used to evaluate differences between AUCs. Improvement in prediction ability was analyzed by the DeLong test, category-free net reclassification improvement and the integrated discrimination index. Results: Among the 543 patients enrolled, 521 (96%) were male, with a mean age of 68 years, mean body mass index 28.3 and mean FEV1% 55%. A total of 167 patients died during the study follow-up. Comorbidities were prevalent in our cohort, with a mean Charlson index of 2.4. The most prevalent comorbidities were hypertension, diabetes mellitus and cardiovascular diseases. On comparing the BODE index, GOLDABCD, GOLD2017 and cluster analysis for pre-dicting mortality, cluster system was found to be superior compared with GOLD2017 (0.654 vs 0.722, P=0.006), without significant differences between other classification models. When cardiovascular comorbidities and chronic renal failure were added to the existing scores, their prognostic capacity was statistically superior (P<0.001). Conclusion: Comorbidities should be taken into account in COPD management scores due to their prevalence and impact on mortalit

Origin of Small Barriers in Jahn–Teller Systems:Quantifying the Role of 3d–4s Hybridization in the Model System NaCl:Ni⁺

Despite its relevance, the microscopic origin of the energy barrier, B, between the compressed and elongated geometries of Jahn–Teller (JT) systems is not well understood yet because of a lack of quantitative data about its various contributions. Seeking to clear up this matter, we have carried out both periodic and cluster ab initio calculations on the model system NaCl:Ni+. This system is particularly puzzling because, according to experimental data, its barrier is much smaller than that for other d9 and d7 ions in similar lattices. All calculations performed on the model system lead, in fact, to values |B| ≤ 160 cm–1, which are certainly smaller than B = 500 cm–1 derived for NaCl:M2+ (M = Ag, Rh) or B = 1024 cm–1 obtained for KCl:Ag2+. As a salient feature, analysis of calculations carried out as a function of the Qθ (3z2 – r2) coordinate unveils the microscopic origin of the barrier. It is quantitatively proven that the elongated geometry observed for NaCl:Ni+ is due to the 3d–4s vibronic admixture, which is slightly larger than the anharmonicity in the eg JT mode that favors a compressed geometry. The existence of these two competing mechanisms explains the low value of B for the model system, contrary to cases where the complex formed by d9 or d7 ions is elastically decoupled from the host lattice. Although the magnitude of B for NaCl:Ni+ is particularly small, the tunneling splitting, 3Γ, is estimated to be below 9 cm–1, thus explaining why the coherence is easily destroyed by random strains and thus a static JT effect is observed experimentally. As a main conclusion, the barrier in JT systems cannot be understood neglecting the tiny changes of the electronic density involved in small distortions. The present calculations reasonably explain the experimental g tensor of NaCl:Ni+, pointing out that the d–d transitions in NiCl65– are much smaller than those for CuCl64– and the optical electronegativity of Ni+ is only around 1.</p