The Sequence Read Archive

The combination of significantly lower cost and increased speed of sequencing has resulted in an explosive growth of data submitted into the primary next-generation sequence data archive, the Sequence Read Archive (SRA). The preservation of experimental data is an important part of the scientific record, and increasing numbers of journals and funding agencies require that next-generation sequence data are deposited into the SRA. The SRA was established as a public repository for the next-generation sequence data and is operated by the International Nucleotide Sequence Database Collaboration (INSDC). INSDC partners include the National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EBI) and the DNA Data Bank of Japan (DDBJ). The SRA is accessible at http://www.ncbi.nlm.nih.gov/Traces/sra from NCBI, at http://www.ebi.ac.uk/ena from EBI and at http://trace.ddbj.nig.ac.jp from DDBJ. In this article, we present the content and structure of the SRA, detail our support for sequencing platforms and provide recommended data submission levels and formats. We also briefly outline our response to the challenge of data growth

Archiving next generation sequencing data

Next generation sequencing platforms are producing biological sequencing data in unprecedented amounts. The partners of the International Nucleotide Sequencing Database Collaboration, which includes the National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EBI), and the DNA Data Bank of Japan (DDBJ), have established the Sequence Read Archive (SRA) to provide the scientific community with an archival destination for next generation data sets. The SRA is now accessible at http://www.ncbi.nlm.nih.gov/Traces/sra from NCBI, at http://www.ebi.ac.uk/ena from EBI and at http://www.ddbj.nig.ac.jp/sub/trace_sra-e.html from DDBJ. Users of these resources can obtain data sets deposited in any of the three SRA instances. Links and submission instructions are provided

Versatile and open software for comparing large genomes

The newest version of MUMmer easily handles comparisons of large eukaryotic genomes at varying evolutionary distances, as demonstrated by applications to multiple genomes. Two new graphical viewing tools provide alternative ways to analyze genome alignments. The new system is the first version of MUMmer to be released as open-source software. This allows other developers to contribute to the code base and freely redistribute the code. The MUMmer sources are available at

Interannual variability of Alexandrium fundyense abundance and shellfish toxicity in the Gulf of Maine

Author Posting. © The Authors, 2005. This is the author's version of the work. It is posted here by permission of Elsevier B. V. for personal use, not for redistribution. The definitive version was published in Deep Sea Research Part II: Topical Studies in Oceanography 52 (2005): 2843-2855, doi:10.1016/j.dsr2.2005.06.020.Six years of oceanographic surveys of Alexandrium fundyense concentrations in the Gulf of Maine are combined with shellfish toxicity records from coastal monitoring stations to assess covariations of these quantities on seasonal to interannual time scales. Annual mean gulf-wide cell abundance varies by less than one order of magnitude during the time interval examined (1993-2002). Fluctuations in gulf-wide annual mean cell abundance and shellfish toxicity are not related in a consistent manner. This suggests that interannual variations in toxicity may be regulated by transport and delivery of offshore cell populations, rather than the absolute abundance of the source populations themselves.We gratefully acknowledge the support of the US ECOHAB Program, sponsored by NOAA, NSF, EPA, NASA, and ONR

Fall‐Associated Difficulty with Activities of Daily Living in Functionally Independent Individuals Aged 65 to 69 in the United States: A Cohort Study

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/96257/1/jgs12071.pd

Age-related differences in adaptation during childhood: The influences of muscular power production and segmental energy flow caused by muscles

Acquisition of skillfulness is not only characterized by a task-appropriate application of muscular forces but also by the ability to adapt performance to changing task demands. Previous research suggests that there is a different developmental schedule for adaptation at the kinematic compared to the neuro-muscular level. The purpose of this study was to determine how age-related differences in neuro-muscular organization affect the mechanical construction of pedaling at different levels of the task. By quantifying the flow of segmental energy caused by muscles, we determined the muscular synergies that construct the movement outcome across movement speeds. Younger children (5-7 years; n = 11), older children (8-10 years; n = 8), and adults (22-31 years; n = 8) rode a stationary ergometer at five discrete cadences (60, 75, 90, 105, and 120 rpm) at 10% of their individually predicted peak power output. Using a forward dynamics simulation, we determined the muscular contributions to crank power, as well as muscular power delivered to the crank directly and indirectly (through energy absorption and transfer) during the downstroke and the upstroke of the crank cycle. We found significant age × cadence interactions for (1) peak muscular power at the hip joint [Wilks' Lambda = 0.441, F(8,42) = 2.65, p = 0.019] indicating that at high movement speeds children produced less peak power at the hip than adults, (2) muscular power delivered to the crank during the downstroke and the upstroke of the crank cycle [Wilks' Lambda = 0.399, F(8,42) = 3.07, p = 0.009] indicating that children delivered a greater proportion of the power to the crank during the upstroke when compared to adults, (3) hip power contribution to limb power [Wilks' Lambda = 0.454, F(8,42) = 2.54, p = 0.023] indicating a cadence-dependence of age-related differences in the muscular synergy between hip extensors and plantarflexors. The results demonstrate that in spite of a successful performance, children construct the task of pedaling differently when compared to adults, especially when they are pushed to their performance limits. The weaker synergy between hip extensors and plantarflexors suggests that a lack of inter-muscular coordination, rather than muscular power production per se, is a factor that limits children's performance ranges

Radiometric Stability of the SABER Instrument

The SABER instrument on the National Aeronautics and Space Administration Thermosphere‐Ionosphere‐Mesosphere Energetics and Dynamics satellite continues to provide a long‐term record of Earth\u27s stratosphere, mesosphere, and lower thermosphere. The SABER data are being used to examine long‐term changes and trends in temperature, water vapor, and carbon dioxide. A tacit, central assumption of these analyses is that the SABER instrument radiometric calibration is not changing with time; that is, the instrument is stable. SABER stratospheric temperatures and those derived from Global Positioning System Radio Occultation measurements are compared to examine SABER\u27s stability. Global Positioning System Radio Occultation measurements are inherently stable due to the accuracy and traceability of the measured phase delay rate to the Système Internationale definition of the second. Differences in global annual mean SABER and COSMIC lower stratospheric temperatures show little significant change with time in the 11 years spanning 2007–2017. From this analysis we infer that SABER temperatures are stable to better than 0.1 to 0.2 K per decade

Clinical validation of a novel postural support device for hospitalized sub-acute post stroke wheelchair users

Purpose: We present a novel wheelchair posture support device (WPSD) and its clinical validation. The device was developed in order to assure correct sitting posture and to reduce the time spent by caregivers for re-positioning of hospitalized, wheelchair-bound, post-acute stroke patients. Method: The device was validated with 16 subjects during a period of 5 days in which use of the device was compared with regular care practice. Results: The device was used for the five consecutive days in 69% of patients, while for 6% it was not suitable; 25% did not complete the 5 days for reasons unrelated to the device. Caregivers needed to re-position the patients that used the device for the full 5 days (n=11) on an average 52% less often when using the device, as compared to regular practice. Furthermore, the device was rated as usable and functional by the caregivers while significantly reducing perception of trunk and shoulder pain in patients during its use. Conclusions: The newly designed WPSD is a valuable system for the improvement of medical assistance to wheelchair-bound post-stroke patients by reducing pain and number of re-positioning manoeuvres. The WPSD might be applicable to any group of patients who need posture control in either wheelchair or common chair with arms support.The FIK initiative; funding the development of the Varstiff material technology. Fundaci on Bot ın’s ‘‘Mind the Gap’’ program co-funding the design process of the WPSD. Spherium Biomed co-funding the study with the WPSD