Abstract:
:Recent progress in genomics and experimental biology has brought exponential growth of the biological information available for computational analysis in public genomics databases. However, applying the potentially enormous scientific value of this information to the understanding of biological systems requires computing and data storage technology of an unprecedented scale. The Grid, with its aggregated and distributed computational and storage infrastructure, offers an ideal platform for high-throughput bioinformatics analysis. To leverage this we have developed the Genome Analysis Research Environment (GNARE)--a scalable computational system for the high-throughput analysis of genomes, which provides an integrated database and computational backend for data-driven bioinformatics applications. GNARE efficiently automates the major steps of genome analysis including acquisition of data from multiple genomic databases; data analysis by a diverse set of bioinformatics tools; and storage of results and annotations. High-throughput computations in GNARE are performed using distributed heterogeneous Grid computing resources such as Grid2003, TeraGrid, and the DOE Science Grid. Multi-step genome analysis workflows involving massive data processing, the use of application-specific tools and algorithms and updating of an integrated database to provide interactive web access to results are all expressed and controlled by a "virtual data" model which transparently maps computational workflows to distributed Grid resources. This paper describes how Grid technologies such as Globus, Condor, and the Gryphyn Virtual Data System were applied in the development of GNARE. It focuses on our approach to Grid resource allocation and to the use of GNARE as a computational framework for the development of bioinformatics applications.
journal_name
J Clin Monit Computjournal_title
Journal of clinical monitoring and computingauthors
Sulakhe D,Rodriguez A,D'Souza M,Wilde M,Nefedova V,Foster I,Maltsev Ndoi
10.1007/s10877-005-3463-ysubject
Has Abstractpub_date
2005-10-01 00:00:00pages
361-9issue
4-5eissn
1387-1307issn
1573-2614journal_volume
19pub_type
杂志文章abstract:BACKGROUND:The ventricular stroke work refers to the work done by the left or right ventricle to eject the volume of blood during one cardiac cycle, called stroke volume. Sarnoff and Berglund were one of the first to calculate the stroke work from the pressure volume diagram in 1954. However, they published a wrong uni...
journal_title:Journal of clinical monitoring and computing
pub_type: 杂志文章,评审
doi:10.1007/s10877-010-9234-4
更新日期:2010-06-01 00:00:00
abstract::Central venous pressure (CVP) is an important clinical parameter for physicians but only the absolute CVP value is typically monitored in the intensive care unit (ICU). In this study, we propose a novel mathematical method to present and analyze CVP signals. A total of 44 suitable samples were chosen from a total of 6...
journal_title:Journal of clinical monitoring and computing
pub_type: 杂志文章
doi:10.1007/s10877-016-9882-0
更新日期:2017-06-01 00:00:00
abstract::Perioperative goal-directed therapy is considered to improve patient outcomes after high-risk surgery. The association of compliance with perioperative goal-directed therapy protocols and postoperative outcomes is unclear. The purpose of this study is to determine the effect of protocol compliance on postoperative out...
journal_title:Journal of clinical monitoring and computing
pub_type: 杂志文章
doi:10.1007/s10877-020-00585-w
更新日期:2020-09-12 00:00:00
abstract:OBJECTIVE:It was hypothesized that somato- sensory evoked potentials can be achieved faster by selective averaging during periods of low spontaneous electroen- cephalographic (EEG) activity. We analyzed the components of EEG that decrease the signal-to-noise ratio of somatosensory evoked potential (SEP) recordings duri...
journal_title:Journal of clinical monitoring and computing
pub_type: 杂志文章
doi:10.1007/s10877-009-9188-6
更新日期:2009-08-01 00:00:00
abstract::The recently developed technique for measuring cutaneous mitochondrial oxygen tension (mitoPO2) by means of the Protoporphyrin IX-Triplet State Lifetime Technique (PpIX-TSLT) provides new opportunities for assessing mitochondrial function in vivo. The aims of this work were to study whether cutaneous mitochondrial mea...
journal_title:Journal of clinical monitoring and computing
pub_type: 杂志文章
doi:10.1007/s10877-014-9628-9
更新日期:2015-08-01 00:00:00
abstract::Central venous cannulation is a commonly preformed procedure in many branches of medicine, particularly in anaesthesia and intensive care medicine. The purpose of this study was to compare the landmark-guided technique to the ultrasound-guided technique for internal jugular vein cannulation in cardiovascular surgery p...
journal_title:Journal of clinical monitoring and computing
pub_type: 杂志文章,随机对照试验
doi:10.1007/s10877-014-9585-3
更新日期:2015-02-01 00:00:00
abstract::The Sensmart Model X-100 (Nonin Medical Inc, Plymouth, MN, USA) is a relatively new device that possesses two sets of emitters and detectors and uses near infrared spectroscopy (NIRS) to measure regional cerebral oxygen saturation (rSO2). The value of rSO2 obtained by other NIRS devices is affected by physiological an...
journal_title:Journal of clinical monitoring and computing
pub_type: 杂志文章
doi:10.1007/s10877-020-00567-y
更新日期:2020-07-31 00:00:00
abstract::Near-infrared spectrophotometry assesses cerebral oxygen saturation (ScO2) based on the absorption spectra of oxygenated and deoxygenated hemoglobin, and the translucency of biological tissue, in the near-infrared band. There is increasing evidence that optimising cerebral oxygenation, guided by ScO2, is associated wi...
journal_title:Journal of clinical monitoring and computing
pub_type: 杂志文章
doi:10.1007/s10877-014-9642-y
更新日期:2015-10-01 00:00:00
abstract:OBJECTIVE:To demonstrate the usefulness of rectus femoris muscle MEPs monitoring in a paraparetic neuromuscular scoliosis case. METHODS:Multiple monitoring modalities including SEPs, MEPs and EMG were performed for an anterior and posterior correction surgery for a neuromuscular scoliosis patient with no motor and sen...
journal_title:Journal of clinical monitoring and computing
pub_type: 杂志文章
doi:10.1007/s10877-011-9325-x
更新日期:2012-02-01 00:00:00
abstract::To determine the effect of implementing an algorithm of fluid and blood administration based on continuous monitoring of hemoglobin (SpHb) and PVI (plethysmography variability index) on mortality and transfusion on a whole hospital scale. This single-center quality program compared transfusion at 48 h and mortality at...
journal_title:Journal of clinical monitoring and computing
pub_type: 杂志文章
doi:10.1007/s10877-019-00367-z
更新日期:2020-08-01 00:00:00
abstract::The capnodynamic method is a minimally invasive method continuously calculating effective pulmonary blood flow (COEPBF), equivalent to cardiac output when intra pulmonary shunt flow is low. The capnodynamic equation joined with a ventilator pattern containing cyclic reoccurring expiratory holds, provides breath to bre...
journal_title:Journal of clinical monitoring and computing
pub_type: 杂志文章
doi:10.1007/s10877-017-0021-3
更新日期:2018-04-01 00:00:00
abstract::Univent tube (UT) and EZ-blocker were used for one-lung ventilation (OLV). UT is a single lumen tube with a small separate lumen containing a bronchial blocker. EZ-blocker differs with its unique y-shaped double-cuffed distal end. We aimed to compare these two airway devices effects on airway pressures, oxygenation, v...
journal_title:Journal of clinical monitoring and computing
pub_type: 杂志文章,随机对照试验
doi:10.1007/s10877-017-0028-9
更新日期:2018-04-01 00:00:00
abstract::The use of processed electroencephalography (EEG) using a simple frontal lead system has been made available for assessing the impact of anesthetic medications during surgery. This review discusses the basic principles behind these devices. The foundations of anesthesia monitoring rest on the observations of Guedel wi...
journal_title:Journal of clinical monitoring and computing
pub_type: 杂志文章,评审
doi:10.1007/s10877-006-9044-x
更新日期:2006-12-01 00:00:00
abstract::It remains to be discovered whether a formula predicting the subglottic transverse diameter measured by ultrasound (SGDformula) for the selection of an appropriate endotracheal tube (ETT) for children without congenital heart disease (CHD) is useful for children with CHD. A formula for predicting SGD was established a...
journal_title:Journal of clinical monitoring and computing
pub_type: 杂志文章
doi:10.1007/s10877-018-0203-7
更新日期:2019-08-01 00:00:00
abstract::Closed loop target-control infusion systems using a Bispectral (BIS) signal as an input (TCI Loop) can automatically maintain intravenous anesthesia in a BIS range of 40-60 %. Our purpose was to assess to what extent such a system could decrease anesthesia workload in comparison to the use of a stand alone TCI system ...
journal_title:Journal of clinical monitoring and computing
pub_type: 杂志文章,随机对照试验
doi:10.1007/s10877-013-9453-6
更新日期:2014-02-01 00:00:00
abstract::Continual vital sign assessment on the general care, medical-surgical floor is expected to provide early indication of patient deterioration and increase the effectiveness of rapid response teams. However, there is concern that continual, multi-parameter vital sign monitoring will produce alarm fatigue. The objective ...
journal_title:Journal of clinical monitoring and computing
pub_type: 杂志文章
doi:10.1007/s10877-015-9790-8
更新日期:2016-12-01 00:00:00
abstract:OBJECTIVE:Transcranial Motor Evoked Potentials (TcMEPs) are sometimes used during lumbar spine surgery in order to detect and prevent an intraoperative nerve root injury. Typically, a fixed stimulus is applied, and one monitors for changes in response amplitude from several myotomes. Increased stimulating voltage may o...
journal_title:Journal of clinical monitoring and computing
pub_type: 杂志文章
doi:10.1007/s10877-010-9269-6
更新日期:2010-12-01 00:00:00
abstract::This report presents a method for tracking Motor Evoked Potential (MEP) amplitudes over the course of a case using a moving least squares linear regression (LSMAs). During a case, newly obtained MEP amplitudes are compared to those predicted by a just previous linear regression (least squares moving average or LSMA). ...
journal_title:Journal of clinical monitoring and computing
pub_type: 杂志文章
doi:10.1007/s10877-018-0181-9
更新日期:2019-06-01 00:00:00
abstract:OBJECTIVES:Optimizing cerebral oxygenation is of paramount importance in certain intraoperative situations. There is, however, a paucity of published data pertaining to changes in cerebral oxygenation seen with increases in the inspired fraction of oxygen (FIO2) or end-tidal carbon dioxide (PETCO2) in anesthetized pati...
journal_title:Journal of clinical monitoring and computing
pub_type: 临床试验,杂志文章
doi:10.1007/s10877-010-9265-x
更新日期:2010-12-01 00:00:00
abstract::The effectiveness of two different methods for calculating the arterial occlusion pressure (AOP) to set tourniquet inflation pressures were assessed in patients underwent knee arthroscopy. Eighty patients were included in this study. Tourniquet inflation pressure was set by adding 20 mmHg of safety margin above the AO...
journal_title:Journal of clinical monitoring and computing
pub_type: 杂志文章
doi:10.1007/s10877-019-00366-0
更新日期:2020-08-01 00:00:00
abstract::The American Society of Neurophysiological Monitoring (ASNM) is developing position statements aimed at assisting practitioners and others in making decisions regarding neurophysiological monitoring practice. This paper describes the procedures used in drafting these documents. ...
journal_title:Journal of clinical monitoring and computing
pub_type: 杂志文章
doi:10.1007/s10877-005-9000-1
更新日期:2006-02-01 00:00:00
abstract:OBJECTIVE:Describe reproducibility of a measurement method to investigate deficits in eye-head co-ordination. METHODS:Combined recordings of head and eye rotation using wireless motion sensors and electro-oculography (EOG) were used as an initial step towards a method to quantify eye-head co-ordination deficits. Head ...
journal_title:Journal of clinical monitoring and computing
pub_type: 杂志文章
doi:10.1007/s10877-009-9160-5
更新日期:2009-02-01 00:00:00
abstract::Incident dark field imaging (IDF) is a new generation handheld microscope for bedside visualization and quantification of microcirculatory alterations. IDF is the technical successor of sidestream dark field imaging (SDF), currently the most used device for microcirculatory measurements. In (pre)term neonates the redu...
journal_title:Journal of clinical monitoring and computing
pub_type: 杂志文章
doi:10.1007/s10877-015-9708-5
更新日期:2015-10-01 00:00:00
abstract:OBJECTIVE:To further elucidate temperature related changes in subcortical components of somatosensory evoked potentials (SEP) in intraoperative monitoring. METHODS:Intraoperative monitoring of subcortical median nerve SEP under deep hypothermia is described in a patient undergoing intracranial giant aneurysm surgery. ...
journal_title:Journal of clinical monitoring and computing
pub_type: 杂志文章
doi:10.1023/a:1020792729242
更新日期:2002-04-01 00:00:00
abstract:OBJECTIVES:The application of sighs during baseline ventilation was found to improve alveolar recruitment and oxygenation in patients with acute respiratory distress syndrome (ARDS). The present investigation evaluates if respiratory mechanics can be modified by a sigh. METHODS:Ten consecutive patients with acute lung...
journal_title:Journal of clinical monitoring and computing
pub_type: 临床试验,杂志文章
doi:10.1007/s10877-006-9028-x
更新日期:2006-08-01 00:00:00
abstract::In the present investigation, the data sets of NCD (Non Communicable Diseases) risk factors, a standard report of Saudi Arabia 2005, in collaboration with WHO (World Health Organisation) were employed. The Oracle Data Miner (ODM) tool was used for the analysis and prediction of data. The data sets for different age gr...
journal_title:Journal of clinical monitoring and computing
pub_type: 杂志文章
doi:10.1007/s10877-010-9260-2
更新日期:2010-12-01 00:00:00
abstract:OBJECTIVES:This study was conducted to determine the response time of the Opti-Q continuous cardiac output (CCO) device to a step change in cardiac. DESIGN:Prospective study. SETTING:University hospital animal lab. MODEL:Female sheep. INTERVENTIONS:In ten animals, cardiac output was altered suddenly by opening and ...
journal_title:Journal of clinical monitoring and computing
pub_type: 杂志文章
doi:10.1023/a:1009934112134
更新日期:1999-12-01 00:00:00
abstract::Alarms in the operating room remain a major source of annoyance and confusion. Nearly all alarms result from a transgression of certain alarm limits. We surveyed manufacturers at a major meeting of anesthesiologists for their default alarm limits. We also conducted a mail survey of anesthesiologists in the United Stat...
journal_title:Journal of clinical monitoring and computing
pub_type: 杂志文章
doi:10.1023/a:1009992830942
更新日期:1999-02-01 00:00:00
abstract::With the AnaConDa™ and the MIRUS™ system, volatile anesthetics can be administered for inhalation sedation in intensive care units. Instead of a circle system, both devices use anesthetic reflectors to save on the anesthetic agent. We studied the efficiency of desflurane reflection with both devices using different ti...
journal_title:Journal of clinical monitoring and computing
pub_type: 杂志文章
doi:10.1007/s10877-016-9902-0
更新日期:2018-08-01 00:00:00
abstract::Leakage of inhalational anesthetic gases is an important issue not only to staff health but awareness during general anesthesia. After inhalation of sevoflurane commenced, the audible and visible alarm of our custom-made air monitoring system was activated. The system measured 2-4 ppm of sevoflurane. A thorough search...
journal_title:Journal of clinical monitoring and computing
pub_type: 杂志文章
doi:10.1007/s10877-013-9479-9
更新日期:2013-12-01 00:00:00