ArrayInitiative - a tool that simplifies creating custom Affymetrix CDFs

<p>Abstract</p> <p>Background</p> <p>Probes on a microarray represent a frozen view of a genome and are quickly outdated when new sequencing studies extend our knowledge, resulting in significant measurement error when analyzing any microarray experiment. There are several bioinformatics approaches to improve probe assignments, but without in-house programming expertise, standardizing these custom array specifications as a usable file (e.g. as Affymetrix CDFs) is difficult, owing mostly to the complexity of the specification file format. However, without correctly standardized files there is a significant barrier for testing competing analysis approaches since this file is one of the required inputs for many commonly used algorithms. The need to test combinations of probe assignments and analysis algorithms led us to develop ArrayInitiative, a tool for creating and managing custom array specifications.</p> <p>Results</p> <p>ArrayInitiative is a standalone, cross-platform, rich client desktop application for creating correctly formatted, custom versions of manufacturer-provided (default) array specifications, requiring only minimal knowledge of the array specification rules and file formats. Users can import default array specifications, import probe sequences for a default array specification, design and import a custom array specification, export any array specification to multiple output formats, export the probe sequences for any array specification and browse high-level information about the microarray, such as version and number of probes. The initial release of ArrayInitiative supports the Affymetrix 3' IVT expression arrays we currently analyze, but as an open source application, we hope that others will contribute modules for other platforms.</p> <p>Conclusions</p> <p>ArrayInitiative allows researchers to create new array specifications, in a standard format, based upon their own requirements. This makes it easier to test competing design and analysis strategies that depend on probe definitions. Since the custom array specifications are easily exported to the manufacturer's standard format, researchers can analyze these customized microarray experiments using established software tools, such as those available in Bioconductor.</p

Comparison of statistical downscaling methods for climate change impact analysis on precipitation-driven drought

General circulation models (GCMs) are the primary tools for evaluating the possible impacts of climate change; however, their results are coarse in temporal and spatial dimensions. In addition, they often show systematic biases compared to observations. Downscaling and bias correction of climate model outputs is thus required for local applications. Apart from the computationally intensive strategy of dynamical downscaling, statistical downscaling offers a relatively straightforward solution by establishing relationships between small- and large-scale variables. This study compares four statistical downscaling methods of bias correction (BC), the change factor of mean (CFM), quantile perturbation (QP) and an event-based weather generator (WG) to assess climate change impact on drought by the end of the 21st century (2071–2100) relative to a baseline period of 1971–2000 for the weather station of Uccle located in Belgium. A set of drought-related aspects is analysed, i.e. dry day frequency, dry spell duration and total precipitation. The downscaling is applied to a 28-member ensemble of Coupled Model Intercomparison Project Phase 6 (CMIP6) GCMs, each forced by four future scenarios of SSP1–2.6, SSP2–4.5, SSP3–7.0 and SSP5–8.5. A 25-member ensemble of CanESM5 GCM is also used to assess the significance of the climate change signals in comparison to the internal variability in the climate. A performance comparison of the downscaling methods reveals that the QP method outperforms the others in reproducing the magnitude and monthly pattern of the observed indicators. While all methods show a good agreement on downscaling total precipitation, their results differ quite largely for the frequency and length of dry spells. Using the downscaling methods, dry day frequency is projected to increase significantly in the summer months, with a relative change of up to 19 % for SSP5–8.5. At the same time, total precipitation is projected to decrease significantly by up to 33 % in these months. Total precipitation also significantly increases in winter, as it is driven by a significant intensification of extreme precipitation rather than a dry day frequency change. Lastly, extreme dry spells are projected to increase in length by up to 9 %.</p

Quantitative peritumoral magnetic resonance imaging fingerprinting improves machine learning-based prediction of overall survival in colorectal cancer

Aim: To investigate magnetic resonance imaging (MRI)-based peritumoral texture features as prognostic indicators of survival in patients with colorectal liver metastasis (CRLM). Methods: From 2007–2015, forty-eight patients who underwent MRI within 3 months prior to initiating treatment for CRLM were identified. Clinicobiological prognostic variables were obtained from electronic medical records. Ninety-four metastatic hepatic lesions were identified on T1-weighted post-contrast images and volumetrically segmented. A total of 112 radiomic features (shape, first-order, texture) were derived from a 10 mm region surrounding each segmented tumor. A random forest model was applied, and performance was tested by receiver operating characteristic (ROC). Kaplan-Meier analysis was utilized to generate the survival curves. Results: Forty-eight patients (male:female = 23:25, age 55.3 years ± 18 years) were included in the study. The median lesion size was 25.73 mm (range 8.5–103.8 mm). Microsatellite instability was low in 40.4% (38/94) of tumors, with Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) mutation detected in 68 out of 94 (72%) tumors. The mean survival was 35 months ± 21 months, and local disease progression was observed in 35.5% of patients. Univariate regression analysis identified 42 texture features [8 first order, 5 gray level dependence matrix (GLDM), 5 gray level run time length matrix (GLRLM), 5 gray level size zone matrix (GLSZM), 2 neighboring gray tone difference matrix (NGTDM), and 17 gray level co-occurrence matrix (GLCM)] independently associated with metastatic disease progression (P < 0.03). The random forest model achieved an area under the curve (AUC) of 0.88. Conclusions: MRI-based peritumoral heterogeneity features may serve as predictive biomarkers for metastatic disease progression and patient survival in CRLM

In Vitro and in Vivo Effectiveness of Carvacrol, Thymol and Linalool against Leishmania infantum

Background: One of the most important causative agents of visceral leishmaniasis (VL) is Leishmania infantum, which is mainly spread by Phlebotomus and Lutzomyia sandflies in the Old and New World, respectively. Novel and effective drugs to manage this neglected vector-borne disease are urgently required. In this study, we evaluated the toxicity of carvacrol, thymol and linalool, three common essential oil constituents, on amastigotes and promastigotes of L. infantum. Methods: in vitro experiments were performed by 24 h MTT assay. Carvacrol, thymol and linalool at concentrations ranging from 1.3 to 10 µg/mL were tested on promastigotes of L. infantum. For in vivo test, two groups of hamsters (Mesocricetus auratus) received 100 mg/kg of body weight/day of carvacrol and thymol as intraperitoneal injection on day 7 post-infection, followed by a 48 h later injection. The third group was treated with the glucantime as standard drug (500 mg/kg) and the last group (control) just received normal saline. On the 16th day, the number of parasites and histopathological changes in liver and spleen were investigated. Results: 24 h MTT assay showed promising antileishmanial activity of thymol and carvacrol, with IC50 values of 7.2 (48 µM) and 9.8 µg/mL (65 µM), respectively. Linalool at all concentrations did not affect L. infantum promastigote viability. In vivo toxicity data of carvacrol and thymol showed that the former at 100 mg/kg was the safest and most effective treatment with little side effects on the liver. Conclusions: Overall, thymol and carvacrol are highly promising candidates for the development of effective and safe drugs in the fight against VL

Evaluation of onlay island flap technique in shallow urethral plate hypospadiasis

Background: Hypospadias is one of the most common congenital genital anomalies in males that necessitates to be operated early in infancy (when 6 to 9 months old). On the other hand, hypospadias is a challenging field of pediatric urology with multiple reconstruction techniques. A perfect hypospadias repair is supposed to return urethral continuity with sufficient caliber, eradicate phallus curvature, and supply an acceptable appearance with low complications. Objectives: This study aimed to evaluate the outcomes of using onlay island flap technique in the repair of hypospadias with shallow urethral plate. Patients and Methods: In this prospective study within June 2012 to December 2013, we performed onlay island flap procedure to repair hypospadias with shallow urethral plate measuring less than 6 millimeter. This technique was selected for all types of hypospadiasis except subcoronal type. Nesbit�s dorsal plication procedure was established for chordee. In cases with very small glans, urethroplasty was performed without glansplasty. Results: Twenty three patients with mean age of 30 (range 10 -60) months underwent onlay island flap repair; all had a shallow urethral plate < 6 mm, 3 had a very small glans, and 18 had chordee. Meatus was located in distal shaft in 5 cases, mid shaft in 8, proximal in 6 and penoscrotal type in 4 patients. Chordee was corrected with Nesbit�s dorsal plication in 16 cases. Complications were: meatal stenosis in 2 cases and urethrocutaneous fistula in 2 patients, all of which were repaired surgically. Mean follow up time was 13 (3 -20) months. All cases that had glansplasty have excellent esthetic appearance. Conclusions: This technique offers acceptable results regarding meatal stenosis, urethrocutaneous fistula and esthetic outcome. © 2016, Growth & Development Research Center

Mass screening of different rice genotypes to rice striped stem borer, Chilo suppressalis Walker (Lep.: Pyralidae), under the field condition

In this study, a total of 98 Iranian and exotic rice genotypes were tested for their resistance to the Striped Stem Borer, Chilo suppressalis, under field conditions in Rice Research Institute of Iran, Mazandaran branch, Amol. The experiment was carried out in a randomized complete blocks design and three replications. At the reproductive stage, five whole plants per plot were randomly selected and cut off at the base, and percent of white head, number of larvae per hill, plant height, stem diameter, and tiller number per hill were measured. The rice genotypes Novator, G2-Gan74, Estrella, Rashtline-1, and IR72860, had the lowest amount of percent of white head, with means of 1.6%, 2.7%, 2.3%, 2.8%, and 3.2%, respectively, and the genotypes IR72-B, Iranian-New-Hybrid, Fars promising line, IR64-MutantW, IR50 had the highest amount of percent of white head with means of 43.5%, 43.4%, 37.6%, 35.8 %, and 34.8%, respectively. Moreover, genotypes Novator, Estrella and G2-Gan74 had the lowest mean larvae per a whole plant (0.1, 0.1 and 0.2, respectively), while genotypes Chinese-Hybrid1, IR72-B, and Binam had the highest mean larvae per a whole plant, with means of 10.3, 9.7, and 8.9, respectively. Rasht-Line-1 had the lowest mean plant height (74.4 cm), Fars promising line had the lowest mean number of tillers per hill (9.13), and Iranian New-Hybrid had the lowest mean stem diameter (4.44 mm). On the other hand, the Tarom-ARG2 genotypes had the highest mean plant height (138.26 cm), Sahel had the highest mean number of tillers per hill (17.6), and Dorfak had the highest mean stem diameter (12.72 mm).There were significant correlations between percent white head and the number of larvae per a whole plant, and between percent white head and number of tillers per hill, but there no significant correlations was found with plant height and stem diameter. The rice genotypes were grouped on Ward’s clustering procedure into two main clusters, totally four sub-cluster. The rice genotypes such as Novator, Estrella, Rashtline-1 were found to be less sensitive to Chilo suppressalis. Also, in this study, 19 rice genotypes including Novator, Estrella, G2-Gan74, Rashtline-1, Shirodi, Nemat, IR64-Mutant-F3076, MashhadDomsiah/Neda, {(A78.1/LocalAbiji)/(khazar/Tarom)} were recognized as resistant genotypes at field condition. Some of them can be tested in further experiments

Dynamics of polymer film formation during spin coating

Standard models explaining the spin coating of polymer solutions generally fail to describe the early stages of film formation, when hydrodynamic forces control the solution behavior. Using in situ light scattering alongside theoretical and semi-empirical models, it is shown that inertial forces (which initially cause a vertical gradient in the radial solvent velocity within the film) play a significant role in the rate of thinning of the solution. The development of thickness as a function of time of a solute-free liquid (toluene) and a blend of polystyrene and poly(methyl methacrylate) cast from toluene were fitted to different models as a function of toluene partial pressure. In the case of the formation of the polymer blend film, a concentration-dependent (Huggins) viscosity formula was used to account for changes in viscosity during spin coating. A semi-empirical model is introduced, which permits calculation of the solvent evaporation rate and the temporal evolution of the solute volume fraction and solution viscosity