The ExPASy (the Expert Protein Analysis System) World Wide Web server (http://www.expasy.org), is provided as a service to the life science community by a multidisciplinary team at the Swiss ...Institute of Bioinformatics (SIB). It provides access to a variety of databases and analytical tools dedicated to proteins and proteomics. ExPASy databases include SWISS-PROT and TrEMBL, SWISS-2DPAGE, PROSITE, ENZYME and the SWISS-MODEL repository. Analysis tools are available for specific tasks relevant to proteomics, similarity searches, pattern and profile searches, post-translational modification prediction, topology prediction, primary, secondary and tertiary structure analysis and sequence alignment. These databases and tools are tightly interlinked: a special emphasis is placed on integration of database entries with related resources developed at the SIB and elsewhere, and the proteomics tools have been designed to read the annotations in SWISS-PROT in order to enhance their predictions. ExPASy started to operate in 1993, as the first WWW server in the field of life sciences. In addition to the main site in Switzerland, seven mirror sites in different continents currently serve the user community.
We present a novel storage-and-access approach for Lagrangian particles in a multiresolution local-timestepping framework for multiphase flow simulations. The proposed method applies a block-particle ...mapping strategy for efficient access of all particles on a specific refinement level while traversing through the multiresolution tree. This allows for extending the local timestepping algorithm with its refinement level-dependent timestep sizes to the evolution of particles, which results in significant speed-up in comparison to standard timestepping. For multi-scale multiphase flow simulations, the particle model is combined with a level-set based multiphase model on a Cartesian grid. To maintain robustness of fluid-state interpolation for particles near the level set-based fluid–fluid interface, WENO-based interpolation is applied which includes both real- and ghost-fluid cells. This enforces the sharp interface property also for interpolated fluid states, and suppresses spurious oscillations in the event of discontinuities.
We validate the particle model with a one-dimensional simulation of a single particle in an air–helium shock tube for one-way coupling, and with two-dimensional simulations of a particle injected in a quiescent domain for the feedback force. Simulations of two-dimensional aerodynamic fragmentation in shear-induced entrainment and Rayleigh–Taylor piercing regimes use Lagrangian particles as sub-grid scale representation of small droplets post-breakup. Finally, three-dimensional massively-parallel simulations of single- and triple-bubble collapse near a wall coated with free-floating particles are presented. The particle cleaning radius of the single-bubble setup agrees reasonably well with experimental reference data. These simulations consider 106 particles and an Eulerian grid with effectively 1012 finite-volume cells at compression rates of more than 90% for the particulate phase. This underlines the advantageous effect of embedding the particles in the multiresolution tree with its spatial and temporal adaptivity, which is necessary for performing such large scale simulations efficiently.
•Efficient multi-scale multiphase framework with multiresolution local-timestepping.•Block-particle mapping for synchronous local integration of particles and cells.•Ghost-fluid based fluid-state interpolation to suppress spurious oscillations.•Massively-parallelized simulations of ultrasound surface cleaning.
Objective
To determine whether World Trade Center (WTC)‐exposure intensity and post‐traumatic stress disorder (PTSD) are associated with subjective cognitive change in rescue/recovery workers.
Method
...The population included 7875 rescue/recovery workers who completed a subjective cognition measure, the Cognitive Function Instrument (CFI), between 3/1/2018 and 2/28/2019 during routine monitoring, indicating whether they had experienced cognitive and functional difficulties in the past year. Higher scores indicated greater self‐perceived cognitive change. Probable PTSD, depression, and alcohol abuse were evaluated by validated mental health screeners. Logistic regression assessed the associations of WTC exposure and current PTSD with top‐quartile (≥2) CFI score, and of early post‐9/11 PTSD with top‐quartile CFI in a subpopulation (N = 6440). Models included demographics, smoking, depression, and alcohol abuse as covariates.
Results
Mean age at CFI completion was 56.7 ± 7.7 (range: 36–81). Participants with high‐intensity WTC exposure had an increased likelihood of top‐quartile CFI score (odds ratioOR vs. low exposure: 1.32, 95%CI: 1.07–1.64), controlling for covariates. Current and early PTSD were both associated with top‐quartile CFI (OR: 3.25, 95%CI: 2.53–4.19 and OR: 1.56, 95%CI: 1.26–1.93) respectively.
Conclusions
High‐intensity WTC exposure was associated with self‐reported cognitive change 17 years later in rescue/recovery workers, as was PTSD. Highly WTC‐exposed subgroups may benefit from additional cognitive evaluation and monitoring of cognition over time.
SWISS-2DPAGE, ten years later Hoogland, Christine; Mostaguir, Khaled; Sanchez, Jean-Charles ...
Proteomics (Weinheim),
August 2004, Letnik:
4, Številka:
8
Journal Article
Recenzirano
The SWISS‐2DPAGE database was established in 1993 and is maintained collaboratively by the Swiss Institute of Bioinformatics (SIB) and the Biomedical Proteomics Research Group (BPRG) of the Geneva ...University Hospital. During these years, SWISS‐2DPAGE underwent constant modification and improvement. Current content includes about 4000 identified spots corresponding to 1200 different protein entries in 36 reference maps from human, mouse, Arabidopsis thaliana, Dictyostelium discoideum, Escherichia coli, Saccharomyces cerevisiae and Staphylococcus aureus origins. With a high level of annotation and integration with other relevant databases, SWISS‐2DPAGE is a reference source in the proteomics world. Queries to SWISS‐2DPAGE database currently reach 1000 hits per day.
In the last ten years, the field of proteomics has expanded at a rapid rate. A range of exciting new technology has been developed and enthusiastically applied to an enormous variety of biological ...questions. However, the degree of stringency required in proteomic data generation and analysis appears to have been underestimated. As a result, there are likely to be numerous published findings that are of questionable quality, requiring further confirmation and/or validation. This manuscript outlines a number of key issues in proteomic research, including those associated with experimental design, differential display and biomarker discovery, protein identification and analytical incompleteness. In an effort to set a standard that reflects current thinking on the necessary and desirable characteristics of publishable manuscripts in the field, a minimal set of guidelines for proteomics research is then described. These guidelines will serve as a set of criteria which editors of PROTEOMICS will use for assessment of future submissions to the Journal.
In recent years, proteomics research has gained importance due to increasingly powerful techniques in protein purification, mass spectrometry and identification, and due to the development of ...extensive protein and DNA databases from various organisms. Nevertheless, current identification methods from spectrometric data have difficulties in handling modifications or mutations in the source peptide. Moreover, they have low performance when run on large databases (such as genomic databases), or with low quality data, for example due to bad calibration or low fragmentation of the source peptide. We present a new algorithm dedicated to automated protein identification from tandem mass spectrometry (MS/MS) data by searching a peptide sequence database. Our identification approach shows promising properties for solving the specific difficulties enumerated above. It consists of matching theoretical peptide sequences issued from a database with a structured representation of the source MS/MS spectrum. The representation is similar to the spectrum graphs commonly used by de novo sequencing software. The identification process involves the parsing of the graph in order to emphazise relevant sections for each theoretical sequence, and leads to a list of peptides ranked by a correlation score. The parsing of the graph, which can be a highly combinatorial task, is performed by a bio‐inspired algorithm called Ant Colony Optimization algorithm.
Effect of smoking cessation on cough reflex sensitivity Dicpinigaitis, P. V; Sitkauskiene, B; Stravinskaite, K ...
European respiratory journal/The European respiratory journal,
10/2006, Letnik:
28, Številka:
4
Journal Article
Recenzirano
Odprti dostop
Recent studies have shown that cigarette smokers have diminished cough reflex sensitivity compared with nonsmokers. The current authors proposed a mechanism of chronic cigarette smoke-induced ...desensitisation of airway cough receptors. To investigate this hypothesis, cough sensitivity to inhaled capsaicin (C5) in chronic smokers was measured both while they were actively smoking and 2, 6, 12 and 24 weeks after smoking cessation. In total, 29 subjects underwent baseline capsaicin challenge while smoking and 2 weeks after smoking cessation. Mean+/-sem log C5 fell from 1.86+/-0.12 to 1.60+/-0.12, demonstrating significant enhancement of cough reflex sensitivity. Of the total, 20, 18 and 14 subjects successfully abstained from smoking for 6, 12 and 24 weeks, respectively. Mean log C5 values after 12 and 24 weeks of smoking cessation were significantly diminished from baseline. In a control group of smokers, mean log C5 did not decrease from baseline after 6, 12 and 24 weeks. Overall, the log C5 profile of the smoking cessation group showed a clear, linearly decreasing trend over time compared with the control group. Even after many years of smoking, cough sensitivity is enhanced as early as 2 weeks after smoking cessation. Given the importance of an intact cough reflex, these changes may provide clinical benefit.
Objectives
We evaluated the use of rocuronium 0.3 mg/kg intravenously (IV) to facilitate tracheal intubation in cats anesthetized for elective ovariohysterectomy.
Methods
Thirty female cats were ...randomly allocated to receive rocuronium 0.3 mg/kg IV or an equal volume of normal saline, following induction of anesthesia with ketamine and midazolam. Thirty seconds after induction, a single investigator, unaware of treatment allocation, attempted tracheal intubation. The number of attempts and the time to complete intubation were measured. Intubating conditions were assessed as acceptable or unacceptable based on a composite score consisting of five different components. Duration of apnea after induction was measured and cases of hemoglobin desaturation (SpO2 <90%) were identified.
Results
Intubation was completed faster (rocuronium 12 s range 8–75 s; saline 60 s range 9–120 s) and with fewer attempts (rocuronium 1 range 1–2; saline 2 range 1–3, both P = 0.006) in cats receiving rocuronium. Unacceptable intubating conditions on the first attempt occurred in 3/15 cats with rocuronium and in 10/15 with saline (P = 0.01). Apnea lasted 4 ± 1.6 mins with rocuronium and 2.3 ± 0.5 mins with saline (P = 0.0007). No cases of desaturation were observed.
Conclusions and relevance
Rocuronium 0.3 mg/kg IV improves intubating conditions compared with saline, and reduces the time and number of attempts to intubate with only a short period of apnea in cats.
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