Shrinkage prediction of seed-voxel brain connectivity using resting state fMRI.

Resting-state functional magnetic resonance imaging (rs-fMRI) is used to investigate synchronous activations in spatially distinct regions of the brain, which are thought to reflect functional systems supporting cognitive processes. Analyses are often performed using seed-based correlation analysis, allowing researchers to explore functional connectivity between data in a seed region and the rest of the brain. Using scan-rescan rs-fMRI data, we investigate how well the subject-specific seed-based correlation map from the second replication of the study can be predicted using data from the first replication.

Mutation in xyloglucan 6-xylosytransferase results in abnormal root hair development in Oryza sativa.

Root hairs are important for nutrient uptake, anchorage, and plant-microbe interactions. From a population of rice (Oryza sativa) mutagenized by ethyl methanesulfonate (EMS), a short root hair2 (srh2) mutant was identified. In hydroponic culture, srh2 seedlings were significantly reduced in root hair length.

Oxygen deficit alleviates phosphate overaccumulation toxicity in OsPHR2 overexpression plants.

Overexpression of OsPHR2 increases phosphate (Pi) uptake and causes overaccumulation of Pi in rice plants, which is toxic to rice plants when they are grown in media with a sufficient Pi supply. The toxicity that results from OsPHR2 overexpression can be significantly relieved by growing the plants in a waterlogged paddy field. A comparison of the Pi uptake and growth status of OsPHR2-overexpression plants (PHR2-Oe plants) grown in paddy fields or in a laboratory setting in aerated or stagnant hydroponic conditions indicated that the oxygen limitation that is present in paddy fields and in stagnant rice culture solutions inhibits the Pi overaccumulation toxicity of PHR2-Oe plants by reducing their Pi uptake.

RNA-seq analysis identifies an intricate regulatory network controlling cluster root development in white lupin.

Background: Highly adapted plant species are able to alter their root architecture to improve nutrient uptake and thrive in environments with limited nutrient supply. Cluster roots (CRs) are specialised structures of dense lateral roots formed by several plant species for the effective mining of nutrient rich soil patches through a combination of increased surface area and exudation of carboxylates. White lupin is becoming a model-species allowing for the discovery of gene networks involved in CR development.

Large-scale production and evaluation of marker-free rice IR64 expressing phytoferritin genes.

Biofortification of rice ( L.) using a transgenic approach to increase the amount of iron in the grain is proposed as a low-cost, reliable, and sustainable solution to help developing countries combat anemia. In this study, we generated and evaluated a large number of rice or soybean ferritin over-accumulators in rice mega-variety IR64, including marker-free events, by introducing soybean or rice ferritin genes into the endosperm for product development.

Simultaneous transcriptional profiling of bacteria and their host cells.

We developed an RNA-Seq-based method to simultaneously capture prokaryotic and eukaryotic expression profiles of cells infected with intracellular bacteria. As proof of principle, this method was applied to Chlamydia trachomatis-infected epithelial cell monolayers in vitro, successfully obtaining transcriptomes of both C. trachomatis and the host cells at 1 and 24 hours post-infection.

Spatio-temporal transcript profiling of rice roots and shoots in response to phosphate starvation and recovery.

Using rice (Oryza sativa) as a model crop species, we performed an in-depth temporal transcriptome analysis, covering the early and late stages of Pi deprivation as well as Pi recovery in roots and shoots, using next-generation sequencing. Analyses of 126 paired-end RNA sequencing libraries, spanning nine time points, provided a comprehensive overview of the dynamic responses of rice to Pi stress. Differentially expressed genes were grouped into eight sets based on their responses to Pi starvation and recovery, enabling the complex signaling pathways involved in Pi homeostasis to be untangled.

Rice DB: an Oryza Information Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis.

Omics research in Oryza sativa (rice) relies on the use of multiple databases to obtain different types of information to define gene function. We present Rice DB, an Oryza information portal that is a functional genomics database, linking gene loci to comprehensive annotations, expression data and the subcellular location of encoded proteins. Rice DB has been designed to integrate the direct comparison of rice with Arabidopsis (Arabidopsis thaliana), based on orthology or 'expressology', thus using and combining available information from two pre-eminent plant models.

Quantifying the reliability of image replication studies: the image intraclass correlation coefficient (I2C2).

This article proposes the image intraclass correlation (I2C2) coefficient as a global measure of reliability for imaging studies. The I2C2 generalizes the classic intraclass correlation (ICC) coefficient to the case when the data of interest are images, thereby providing a measure that is both intuitive and convenient. Drawing a connection with classical measurement error models for replication experiments, the I2C2 can be computed quickly, even in high-dimensional imaging studies.

Normalization and extraction of interpretable metrics from raw accelerometry data.

We introduce an explicit set of metrics for human activity based on high-density acceleration recordings from a hip-worn tri-axial accelerometer. These metrics are based on two concepts: (i) Time Active, a measure of the length of time when activity is distinguishable from rest and (ii) AI, a measure of the relative amplitude of activity relative to rest. All measurements are normalized (have the same interpretation across subjects and days), easy to explain and implement, and reproducible across platforms and software implementations.

Spinel/layered heterostructured cathode material for high-capacity and high-rate Li-ion batteries.

Best of both worlds: A heterostructured material is synthesized that comprises a core of layered lithium-rich material and an outer layer of nanospinel material. This spinel/layered heterostructured material maximizes the inherent advantages of the 3D Li(+) insertion/extraction framework of the spinel structure and the high Li(+) storage capacity of the layered structure. The material exhibits super-high reversible capacities, outstanding rate capability and excellent cycling ability.

Improvement of phosphorus efficiency in rice on the basis of understanding phosphate signaling and homeostasis.

Rice is one of the most important cereal crops feeding a large segment of the world's population. Inefficient utilization of phosphate (Pi) fertilizer by the plant in rice production increases cost and pollution. Developing cultivars with improved Pi use efficiency is essential for the sustainability of agriculture.

Screening Chinese soybean genotypes for Agrobacterium-mediated genetic transformation suitability.

The Agrobacterium-mediated transformation system is the most commonly used method in soybean transformation. Screening of soybean genotypes favorable for Agrobacterium-infection and tissue regeneration is the most important step to establish an efficient genetic transformation system. In this study, twenty soybean genotypes that originated from different soybean production regions in China were screened for transient infection, regeneration capacity, and stable transgenic efficiency.

Antagonistic, overlapping and distinct responses to biotic stress in rice (Oryza sativa) and interactions with abiotic stress.

Background: Every year, substantial crop loss occurs globally, as a result of bacterial, fungal, parasite and viral infections in rice. Here, we present an in-depth investigation of the transcriptomic response to infection with the destructive bacterial pathogen Xanthomonas oryzae pv. oryzae(Xoo) in both resistant and susceptible varieties of Oryza sativa.

Effect of heat treatment on lignification of postharvest bamboo shoots (Phyllostachys praecox f. prevernalis.).

In order to evaluate the effects of heat treatment on the quality of postharvest bamboo shoots, the firmness, disease incidence, respiration and ethylene production, ACC synthase (ACS) and ACC oxidase (ACO) activities, lignin and cellulose contents, and the activities of phenylalanine ammonia-lyase (PAL), cinnamyl alcohol dehydrogenase (CAD) and peroxidase (POD) were examined during storage at 20°C after heat treatment at 45°C for 5h. Heat treatment inhibited disease incidence and respiration, retarded ethylene production, and decreased ACS and ACO activities in bamboo shoots. Furthermore, heat treatment significantly delayed the rise in the activities of PAL, CAD and POD, which were associated with the inhibition of the synthesis of lignin and the delayed tissue lignification.

Overexpression of OsPAP10a, a root-associated acid phosphatase, increased extracellular organic phosphorus utilization in rice.

Phosphorus (P) deficiency is a major limitation for plant growth and development. Among the wide set of responses to cope with low soil P, plants increase their level of intracellular and secreted acid phosphatases (APases), which helps to catalyze inorganic phosphate (Pi) hydrolysis from organo-phosphates. In this study we characterized the rice (Oryza sativa) purple acid phosphatase 10a (OsPAP10a).

Functional characterization of the rice SPX-MFS family reveals a key role of OsSPX-MFS1 in controlling phosphate homeostasis in leaves.

• Proteins possessing the SPX domain are found in several proteins involved in inorganic phosphate (Pi) transport and signalling in yeast and plants. Although the functions of several SPX-domain protein subfamilies have recently been uncovered, the role of the SPX-MFS subfamily is still unclear. • Using quantitative RT-PCR analysis, we studied the regulation of SPX-MFS gene expression by the central regulator, OsPHR2 and Pi starvation.

Identification of OsbHLH133 as a regulator of iron distribution between roots and shoots in Oryza sativa.

Iron (Fe) is an essential micronutrient element for plant growth. Regulation of Fe-deficiency signalling networks is one of the many functions reported for basic helix-loop-helix (bHLH) transcription factors in plants. In the present study, OsbHLH133 was found to be induced by Fe-deficiency conditions in Oryza sativa.

The emerging importance of the SPX domain-containing proteins in phosphate homeostasis.

Plant growth and development are strongly influenced by the availability of nutrients in the soil solution. Among them, phosphorus (P) is one of the most essential and most limiting macro-elements for plants. In the environment, plants are often confronted with P starvation as a result of extremely low concentrations of soluble inorganic phosphate (Pi) in the soil.

Phosphate homeostasis in the yeast Saccharomyces cerevisiae, the key role of the SPX domain-containing proteins.

In the yeast Saccharomyces cerevisiae, a working model for nutrient homeostasis in eukaryotes, inorganic phosphate (Pi) homeostasis is regulated by the PHO pathway, a set of phosphate starvation induced genes, acting to optimize Pi uptake and utilization. Among these, a subset of proteins containing the SPX domain has been shown to be key regulators of Pi homeostasis. In this review, we summarize the recent progresses in elucidating the mechanisms controlling Pi homeostasis in yeast, focusing on the key roles of the SPX domain-containing proteins in these processes, as well as describing the future challenges and opportunities in this fast-moving field.

[Feasibility of unilateral or bilateral nerve-sparing radical hysterectomy in patients with cervical cancer and evaluation of the post-surgery recovery of the bladder and rectal function].

Objective: To investigate the feasibility of unilateral or bilateral nerve-sparing radical hysterectomy and evaluate the recovery of bladder and bowel function postoperatively.

Methods: From August 2008 to October 2009, sixty-one patients with cervical cancer stage Ib1 to IIa underwent radical hysterectomy (33 cases) and nerve-sparing radical hysterectomy (28 cases). Unilateral nerve-sparing radical hysterectomy was performed in 10 patients, and bilateral nerve-sparing radical hysterectomy (BNS) was performed in 18 patients.

Identification of rice purple acid phosphatases related to phosphate starvation signalling.

Purple acid phosphatases (PAPs) are a family of metallo-phosphoesterases involved in a variety of physiological functions, especially phosphate deficiency adaptations in plants. We identified 26 putative PAP genes by a genome-wide analysis of rice (Oryza sativa), 24 of which have isolated EST sequences in the dbEST database. Amino acid sequence analysis revealed that 25 of these genes possess sets of metal-ligating residues typical of known PAPs.

Ethylene is involved in the regulation of iron homeostasis by regulating the expression of iron-acquisition-related genes in Oryza sativa.

Plants employ two distinct strategies to obtain iron (Fe) from the soil. In Strategy I but not Strategy II plants, Fe limitation invokes ethylene production which regulates Fe deficiency responses. Oryza sativa (rice) is the only graminaceous plant described that possesses a Strategy I-like system for iron uptake as well as the classic Strategy II system.

Identification of a novel iron regulated basic helix-loop-helix protein involved in Fe homeostasis in Oryza sativa.

Background: Iron (Fe) is the most limiting micronutrient element for crop production in alkaline soils. A number of transcription factors involved in regulating Fe uptake from soil and transport in plants have been identified. Analysis of transcriptome data from Oryza sativa grown under limiting Fe conditions reveals that transcript abundances of several genes encoding transcription factors are altered by Fe availability.

[Association between endometrial cancer and metabolic syndrome].

Objective: To study the association between endometrioid uterine carcinomas and metabolic syndrome (MS).

Methods: A retrospective study was conducted on 123 patients who were admitted in Department of Gynecology Oncology, Zhejiang Cancer Hospital (study group) and 90 healthy women (control group) with matching age from Jan. 2005 to Mar.