Space-Time Clustering and Correlations of Major Earthquakes

Earthquake occurrence in nature is thought to result from correlated elastic stresses, leading to clustering in space and time. We show that occurrence of major earthquakes in California correlates with time intervals when fluctuations in small earthquakes are suppressed relative to the long term average. We estimate a probability of less than 1% that this coincidence is due to random clustering.Comment: 5 pages, 3 figures. Submitted to PR

Senescence in vitro and ionising radiations—the human diploid fibroblast model

The influence of ionising radiations on ageing is still controversial. Since Hayflick established the concept that diploid cells have finite lifespan in vitro, human diploid fibroblast (HDF) cultures have been recognised as a potent experimental model for cytogerontological investigations. In this study HDF cultures in phase II were exposed to acute irradiation with either X-rays on fast neutrons. The replicative potentials and labelling indices with [3H]thymidine were measured post irradiation until the cultures ceased growth in phase III. Cell mortality was measured by cloning. The apparent loss in replicative potential of irradiated mass cultures was wholly attributable to the loss of viable clonogenic cells. The current concept of precocious clonal senescence in vitro as a late effect of irradiation in clonogenic survivors is not supported by the present experiments. Instead, our results suggest that exposure to a single dose of ionising radiations either causes total replicative incapacitation (killing) of HDF cells and their progeny early after irradiation or leaves their replicative potentials unperturbed

MACiE: exploring the diversity of biochemical reactions

MACiE (which stands for Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms, and can be accessed from http://www.ebi.ac.uk/thornton-srv/databases/MACiE/. This article presents the release of Version 3 of MACiE, which not only extends the dataset to 335 entries, covering 182 of the EC sub-subclasses with a crystal structure available (∼90%), but also incorporates greater chemical and structural detail. This version of MACiE represents a shift in emphasis for new entries, from non-homologous representatives covering EC reaction space to enzymes with mechanisms of interest to our users and collaborators with a view to exploring the chemical diversity of life. We present new tools for exploring the data in MACiE and comparing entries as well as new analyses of the data and new searches, many of which can now be accessed via dedicated Perl scripts

Is EC class predictable from reaction mechanism?

We thank the Scottish Universities Life Sciences Alliance (SULSA) and the Scottish Overseas Research Student Awards Scheme of the Scottish Funding Council (SFC) for financial support.Background: We investigate the relationships between the EC (Enzyme Commission) class, the associated chemical reaction, and the reaction mechanism by building predictive models using Support Vector Machine (SVM), Random Forest (RF) and k-Nearest Neighbours (kNN). We consider two ways of encoding the reaction mechanism in descriptors, and also three approaches that encode only the overall chemical reaction. Both cross-validation and also an external test set are used. Results: The three descriptor sets encoding overall chemical transformation perform better than the two descriptions of mechanism. SVM and RF models perform comparably well; kNN is less successful. Oxidoreductases and hydrolases are relatively well predicted by all types of descriptor; isomerases are well predicted by overall reaction descriptors but not by mechanistic ones. Conclusions: Our results suggest that pairs of similar enzyme reactions tend to proceed by different mechanisms. Oxidoreductases, hydrolases, and to some extent isomerases and ligases, have clear chemical signatures, making them easier to predict than transferases and lyases. We find evidence that isomerases as a class are notably mechanistically diverse and that their one shared property, of substrate and product being isomers, can arise in various unrelated ways. The performance of the different machine learning algorithms is in line with many cheminformatics applications, with SVM and RF being roughly equally effective. kNN is less successful, given the role that non-local information plays in successful classification. We note also that, despite a lack of clarity in the literature, EC number prediction is not a single problem; the challenge of predicting protein function from available sequence data is quite different from assigning an EC classification from a cheminformatics representation of a reaction.Publisher PDFPeer reviewe

Multidecadal variability of potential temperature, salinity, and transport in the eastern subpolar North Atlantic

The Extended Ellett Line (EEL) hydrographic section extends from Scotland to Iceland crossing the Rockall Trough, Hatton-Rockall Basin and Iceland Basin. With 61 full-depth stations at a horizontal resolution of 10 to 50 km, the EEL samples the upper limb of the Atlantic Meridional Overturning Circulation flowing across the Iceland-Scotland Ridge into the Nordic Seas. The Rockall Trough has been sampled nearly four times per year from 1975 to 1996, and the full section annually since 1996. The EEL is an exceptionally long timeseries of deep-ocean temperatures and salinities. This study extends prior work in the Rockall Trough, and examines for the first time 18 year records in the Iceland and Hatton-Rockall Basins. We quantify errors in the timeseries from two sources: observational errors and aliasing. The data quality and annual sampling are suitable for observing interannual to decadal variability because the variability exceeds our error estimates. The upper waters of all 3 basins are cooler/fresher from 1997 to 2001, warmer/more saline 2001 to 2006, and cooler/fresher from 2006 to 2014. A reference level for geostrophic shear is developed heuristically and by comparison with sea-surface altimetry. The mean northward transport in the upper waters is 6.7±3.7 Sv and there is a 6.1±2.5 Sv southward flow below the thermocline. Although the magnitude of the Iceland Basin overturning circulation (4.3±1.9 Sv) is greater than in the Rockall Trough (3.0±3.7 Sv), the variability is greater in the Rockall Trough. We discuss the results in the context of our understanding of drivers of variability

Concorde noise-induced building vibrations: John F. Kennedy International Airport

Outdoor and indoor noise levels resulting from aircraft flyovers and certain nonaircraft events were recorded at eight homesites and a school along with the associated vibration levels in the walls, windows, and floors at these test sites. Limited subjective tests were conducted to examine the human detection and annoyance thresholds for building vibration and rattle caused by aircraft noise. Both vibration and rattle were detected subjectively in several houses for some operations of both the Concorde and subsonic aircraft. Seated subjects more readily detected floor vibrations than wall or window vibrations. Aircraft noise generally caused more window vibrations than common nonaircraft events such as walking and closing doors. Nonaircraft events and aircraft flyovers resulted in comparable wall vibration levels, while floor vibrations were generally greater for nonaircraft events than for aircraft flyovers. The relationship between structural vibration and aircraft noise is linear, with vibration levels being accurately predicted from overall sound pressure levels (OASPL) measured near the structure. Relatively high levels of structural vibration measured during Concorde operations are due more to higher OASPL levels than to unique Concorde-source characteristics

ChemmineR: a compound mining framework for R

Motivation: Software applications for structural similarity searching and clustering of small molecules play an important role in drug discovery and chemical genomics. Here, we present the first open-source compound mining framework for the popularstatistical programming environment R. The integration with a powerful statistical environment maximizes the flexibility, expandability and programmability of the provided analysis functions

Concorde Noise-Induced Building Vibrations, Montgomery County, Maryland

A series of studies are reported to assess the noise induced building vibrations associated with Concorde operations. The levels of induced vibration and associated indoor/outdoor noise levels resulting from aircraft and nonaircraft events in selected homes, historic and other buildings near Dulles International Airport were recorded. The building response resulting from aircraft operations was found to be directly proportional to the overall sound pressure level and approximately independent of the aircraft type. The noise levels and, consequently, the response levels were observed to be higher for the Concorde operations than for the CTOL operations. Furthermore, the vibration could be closely reproduced by playing aircraft noise through a loudspeaker system located near the vibration measurement location. Nonaircraft events such as door closing were again observed to result in higher response levels than those induced by aircraft

Noise-Induced Building Vibrations Caused by Concorde and Conventional Aircraft Operations at Dulles and Kennedy International Airports

Outdoor and indoor noise levels resulting from aircraft flyovers and certain nonaircraft events were recorded, as were the associated vibration levels in the walls, windows, and floors at building test sites. In addition, limited subjective tests were conducted to examine the human detection and annoyance thresholds for building vibration and rattle caused by aircraft noise. Representative peak levels of aircraft noise-induced building vibrations are reported and comparisons are made with structural damage criteria and with vibration levels induced by common domestic events. In addition, results of a pilot study are reported which indicate the human detection threshold for noise-induced floor vibrations