NCBI GEO: archive for functional genomics data sets—10 years on

A decade ago, the Gene Expression Omnibus (GEO) database was established at the National Center for Biotechnology Information (NCBI). The original objective of GEO was to serve as a public repository for high-throughput gene expression data generated mostly by microarray technology. However, the research community quickly applied microarrays to non-gene-expression studies, including examination of genome copy number variation and genome-wide profiling of DNA-binding proteins. Because the GEO database was designed with a flexible structure, it was possible to quickly adapt the repository to store these data types. More recently, as the microarray community switches to next-generation sequencing technologies, GEO has again adapted to host these data sets. Today, GEO stores over 20 000 microarray- and sequence-based functional genomics studies, and continues to handle the majority of direct high-throughput data submissions from the research community. Multiple mechanisms are provided to help users effectively search, browse, download and visualize the data at the level of individual genes or entire studies. This paper describes recent database enhancements, including new search and data representation tools, as well as a brief review of how the community uses GEO data. GEO is freely accessible at http://www.ncbi.nlm.nih.gov/geo/

Land use change impacts on floods at the catchment scale: Challenges and opportunities for future research

Research gaps in understanding flood changes at the catchment scale caused by changes in forest management, agricultural practices, artificial drainage and terracing are identified. Potential strategies in addressing these gaps are proposed, such as complex systems approaches to link processes across time scales, long-term experiments on physical-chemical-biological process interactions, and a focus on connectivity and patterns across spatial scales. It is suggested that these strategies will stimulate new research that coherently addresses the issues across hydrology, soil and agricultural sciences, forest engineering, forest ecology and geomorphology

Lawson criterion for ignition exceeded in an inertial fusion experiment

For more than half a century, researchers around the world have been engaged in attempts to achieve fusion ignition as a proof of principle of various fusion concepts. Following the Lawson criterion, an ignited plasma is one where the fusion heating power is high enough to overcome all the physical processes that cool the fusion plasma, creating a positive thermodynamic feedback loop with rapidly increasing temperature. In inertially confined fusion, ignition is a state where the fusion plasma can begin "burn propagation" into surrounding cold fuel, enabling the possibility of high energy gain. While "scientific breakeven" (i.e., unity target gain) has not yet been achieved (here target gain is 0.72, 1.37 MJ of fusion for 1.92 MJ of laser energy), this Letter reports the first controlled fusion experiment, using laser indirect drive, on the National Ignition Facility to produce capsule gain (here 5.8) and reach ignition by nine different formulations of the Lawson criterion

Twenty-three unsolved problems in hydrology (UPH) – a community perspective

This paper is the outcome of a community initiative to identify major unsolved scientific problems in hydrology motivated by a need for stronger harmonisation of research efforts. The procedure involved a public consultation through on-line media, followed by two workshops through which a large number of potential science questions were collated, prioritised, and synthesised. In spite of the diversity of the participants (230 scientists in total), the process revealed much about community priorities and the state of our science: a preference for continuity in research questions rather than radical departures or redirections from past and current work. Questions remain focussed on process-based understanding of hydrological variability and causality at all space and time scales. Increased attention to environmental change drives a new emphasis on understanding how change propagates across interfaces within the hydrological system and across disciplinary boundaries. In particular, the expansion of the human footprint raises a new set of questions related to human interactions with nature and water cycle feedbacks in the context of complex water management problems. We hope that this reflection and synthesis of the 23 unsolved problems in hydrology will help guide research efforts for some years to come

Expression of IFITM1 in chronic myeloid leukemia patients

Cataloged from PDF version of article.We investigated the peripheral blood gene expression profile of interferon induced transmembrane protein 1 (IFITM1) in sixty chronic myeloid leukemia (CML) patients classified according to new prognostic score (NPS). IFITM1 is a component of a multimeric complex involved in the trunsduction of antiproliferative and cell adhesion signals. Expression level of IFITM1 was found significantly different between the high- and low-risk groups (P = 9.7976 x 10(-11)) by real-time reverse transcription polymerase chain reaction (RT-PCR). Higher IFITM1 expression correlated with improved survival (P = 0.01). These results indicate that IFITM1 expression profiling could be used for molecular classification of CML, which may also predict survival. (C) 2004 Elsevier Ltd. All rights reserved

Spatial variability in the isotopic composition of water in small catchments and its effect on hydrograph separation

Hydrograph separation is a widely applied technique that uses the stable isotopes of water (²H and 18O) or other tracers to quantify the contribution of different water sources to streamflow. For its successful application it is critical to adequately characterize these sources (end‐members). In most small catchment studies, water samples are collected from end‐members at one or a few locations that are assumed to be representative for the entire catchment. We tested this assumption by reviewing 148 papers that used the stable isotopes of water to investigate hydrological processes in catchments up to 10 km². We assessed the typical spatial variability in the isotopic composition of different hydrological compartments when they were sampled at five or more locations across a catchment. The median reported spatial variability was largest for snowmelt and soil water, followed by throughfall and shallow groundwater. To determine how this spatial variability might affect isotope‐based hydrograph separation results, we used three‐component hydrograph separation for two real rainfall‐runoff events and a synthetic rainfall‐runoff event and adjusted the isotopic composition of the end‐members (throughfall, soil water, and shallow groundwater) by the median observed spatial variability. The estimated maximum contributions of the three components differed by up to 26% from the reference scenario. This suggests that caution is needed when interpreting hydrograph separation results if they are based on samples taken at one or only a few locations. Above all, these results show that the assumption of negligible spatial variability may not be valid for small catchments