New approach for regional crop yield gap analysis in the Borujen Plain, Iran

This study was performed to analyze the regional crop yield gap for potential and water-limited production situations in the cold-semiarid climate at Borujen basin, Iran. Experimental data were used for model calibration and evaluation of WOFOST as a crop growth simulation model. WOFOST divides wheat growth into three key development stages: 1) emergence, 2) flowering and 3) physiological maturity. The length of growth period and phenology was calibrated using the field experiments results. In general, simulated results matched well with the measured parameters in the calibration procedure. Calibrated results of WOFOST model are linked to a geographic information system, in order, to get easier their presentation and also to contribute to identification of hotspots for interventions aimed at yield improvements. Finally, the results of quantitative analysis (yield estimation in different wheat cropping systems) performed on four different agro-ecological zones, include: 1) yield gaps = 4.2 to 6.2 Mg/ha, 2) yield gaps = 3 to 3.6 Mg/ha, 3) yield gaps < 2.4 Mg/ha, and 4) is unsuitable area. This yield gap between potential and rainfed production system is due to rainfall period during spring when temperature is not a limiting factor for wheat growth. Borujen Basin has semiarid climatic conditions with cold winter and winter precipitation. For the sake of it, temperature was a decisive factor during rainfall seasons, limiting the crop growth period. This study demonstrates that WOFOST model can be used to analyze cropping systems and accurately simulate regional wheat yields in cold semi arid climates.Key words: GIS, yield gaps, wheat, suitability, WOFOST

Emergence of hexatic and long-range herringbone order in two-dimensional smectic liquid crystals : A Monte Carlo study

Using a high resolution Monte Carlo simulation technique based on multi-histogram method and cluster-algorithm, we have investigated critical properties of a coupled XY model, consists of a six-fold symmetric hexatic and a three-fold symmetric herringbone field, in two dimensions. The simulation results demonstrate a series of novel continues transitions, in which both long-range hexatic and herringbone orderings are established simultaneously. It is found that the specific-heat anomaly exponents for some regions in coupling constants space are in excellent agreement with the experimentally measured exponents extracted from heat-capacity data near the smecticA-hexaticB transition of two-layer free standing film

The Distance Precision Matrix: computing networks from non-linear relationships

Motivation: Full-order partial correlation, a fundamental approach for network reconstruction, e.g. in the context of gene regulation, relies on the precision matrix (the inverse of the covariance matrix) as an indicator of which variables are directly associated. The precision matrix assumes Gaussian linear data and its entries are zero for pairs of variables that are independent given all other variables. However, there is still very little theory on network reconstruction under the assumption of non-linear interactions among variables. Results: We propose Distance Precision Matrix, a network reconstruction method aimed at both linear and non-linear data. Like partial distance correlation, it builds on distance covariance, a measure of possibly non-linear association, and on the idea of full-order partial correlation, which allows to discard indirect associations. We provide evidence that the Distance Precision Matrix method can successfully compute networks from linear and non-linear data, and consistently so across different datasets, even if sample size is low. The method is fast enough to compute networks on hundreds of nodes. Availability: An R package DPM is available at https://github.molgen.mpg.de/ghanbari/DPM. Supplementary information: Supplementary data are available at Bioinformatics online

Decreased expression of fecal miR-4478 and miR-1295b-3p in early-stage colorectal cancer

BACKGROUND: Colorectal cancer (CRC) is a major cause of cancer-related deaths world-wide. Detection of molecular markers in stool samples is a promising strategy for CRC screening. MicroRNAs (miRNAs) are short, non-coding RNA molecules that are commonly dysregulated in neoplasia. OBJECTIVE: The objective of this study was to evaluate the fecal miRNAs differentiation between early-stage CRC patients and healthy subjects. METHODS: Stool samples were collected from 40 patients with early stage (I, II) CRC and 16 healthy controls. RNA was extracted from all samples using miRNAeasy Mini Kits. MiRNA microarray expression profiling was performed with Agilent's miRNA Microarray system on 12 CRC and 8 normal stool samples. The expression levels of miR-4478 and miR-1295b-3p were determined by the SYBR Green miScript PCR system. RESULTS: In profiling study, we found 215 down-regulated miRNAs in CRC group. Furthermore, in validation study we found that the expression levels of fecal miR-4487 and miR-1295b-3p were significantly decreased in CRC patients compared to healthy controls. CONCLUSIONS: The expression of miR-4478 and miR-1295b-3p were significantly diminished in stool samples of CRC patients with early stage (I, II) in comparison with normal group. These miRNAs maybe use as potential non-invasive molecular markers for CRC diagnosis, but further studies are needed. © 2015 - IOS Press and the authors. All rights reserved

Downregulation of plasma MiR-142-3p and MiR-26a-5p in patients with colorectal carcinoma

Background: Colorectal cancer is one of the most commonly diagnosed cancers and cancer- related death worldwide. Identification of new specific biomarkers could be helpful to detection of this malignancy. Altered plasma microRNA expression has been identified in many cancers, including colorectal cancer. Objectives: The main objective of this study was to identify the circulating microRNAs with the most expression changes in colorectal cancer patients compared with neoplasm free healthy individuals. Materials and Methods: MicroRNA expression profiling was performed on plasma samples of 37 colorectal cancer patients and 8 normal subjects using microRNA microarray. Quantitative real-time reverse transcription polymerase chain reaction was used to validate the two selected altered microR NAs. Plasma samples from 61 colorectal cancer patients and 24 normal subjects were used in our validation study. Results: In profiling study we found a panel of six plasma microRNAs with significant downregulation. MicroRNA-142-3p and microRNA-26a-5p were selected and validated by polymerase chain reaction. Our results demonstrated that expression levels of plasma microRNA-142-3p and microRNA-26a-5p were significantly downregulated in patients with colorectal cancer when compared to control group. Conclusions: Our findings suggest that downregulation of plasma microRNA-142-3p and microRNA-26a-5p might serve as novel noninvasive biomarkers in the diagnosis of colorectal cancer, although more studies are needed to highlight the theoretical strengths. © 2015, Iranian Journal of Cancer Prevention