In this paper, we apply flexible data-driven analysis methods on large-scale mass transit data to identify areas for improvement in the engineering and operation of urban rail systems. Specifically, we use data from automated fare collection (AFC) and automated vehicle location (AVL) systems to obtain a more precise characterisation of the drivers of journey time variance on the London Underground, and thus an improved understanding of delay. Total journey times are decomposed via a probabilistic assignment algorithm, and semiparametric regression is undertaken to disentangle the effects of passenger-specific travel characteristics from network-related factors. For total journey times, we find that network characteristics, primarily train speeds and headways, represent the majority of journey time variance. However, within the typically twice as onerous access and egress time components, passenger-level heterogeneity is more influential. On average, we find that intra-passenger heterogeneity represents 6% and 19% of variance in access and egress times, respectively, and that inter-passenger effects have a similar or greater degree of influence than static network characteristics. The analysis shows that while network-specific characteristics are the primary drivers of journey time variance in absolute terms, a nontrivial proportion of passenger-perceived variance would be influenced by passenger-specific characteristics. The findings have potential applications related to improving the understanding of passenger movements within stations, for example, the analysis can be used to assess the relative way-finding complexity of stations, which can in turn guide transit operators in the targeting of potential interventions.

The Neotoma Paleoecology Database is a community-curated data resource that supports interdisciplinary global change research by enabling broad-scale studies of taxon and community diversity, distributions, and dynamics during the large environmental changes of the past. By consolidating many kinds of data into a common repository, Neotoma lowers costs of paleodata management, makes paleoecological data openly available, and offers a high-quality, curated resource. Neotoma’s distributed scientific governance model is flexible and scalable, with many open pathways for participation by new members, data contributors, stewards, and research communities. The Neotoma data model supports, or can be extended to support, any kind of paleoecological or paleoenvironmental data from sedimentary archives. Data additions to Neotoma are growing and now include >3.8 million observations, >17,000 datasets, and >9200 sites. Dataset types currently include fossil pollen, vertebrates, diatoms, ostracodes, macroinvertebrates, plant macrofossils, insects, testate amoebae, geochronological data, and the recently added organic biomarkers, stable isotopes, and specimen-level data. Multiple avenues exist to obtain Neotoma data, including the Explorer map-based interface, an application programming interface, the neotoma R package, and digital object identifiers. As the volume and variety of scientific data grow, community-curated data resources such as Neotoma have become foundational infrastructure for big data science.

Radio emission from astrophysical transients allows us to derive calorimetry of kinetic feedback and detailed imaging in ways that are not possible at other wavelengths, and as such it forms an important part of the multi-messenger follow-ups of these events. The field is burgeoning, with a renaissance of interest in accretion, stellar explosions and jetted supernovæ, alongside newer classes of phenomena such as fast radio bursts and tidal disruption events. The purpose of this workshop was to discuss the infrastructure and techniques for detecting, identifying and probing radio transients, with a particular focus on how best to exploit transient alerts from multi-messenger facilities. We examined the type of transient alerts those facilities will broadcast, and methods for following them up, such as rapid-response triggering and shadowing. In break-out groups, participants chose a science question related to a particular radio transient type or class and discussed whether the planned transient strategies and observing techniques on the Square Kilometre Array will be adequate to address the particular question. The classes they chose included fast radio bursts, supernovæ, cataclysmic variable and unknown transients. Any proposed adaptation or suggestion was relayed to a panel of experts for further discussion. The second part of the workshop concentrated on the application of long baseline interferometry for detecting and measuring radio transients.

Advances in DNA sequencing, based on fluorescent microscopy, have transformed many areas of biological research. However, only relatively short molecules can be sequenced by these technologies. Dramatic improvements in genomic research will require accurate sequencing of long (>10,000 base-pairs), intact DNA molecules. Our approach directly visualizes the sequence of DNA molecules using electron microscopy. This report represents the first identification of DNA base pairs within intact DNA molecules by electron microscopy. By enzymatically incorporating modified bases, which contain atoms of increased atomic number, direct visualization and identification of individually labeled bases within a synthetic 3,272 base-pair DNA molecule and a 7,249 base-pair viral genome have been accomplished. This proof of principle is made possible by the use of a dUTP nucleotide, substituted with a single mercury atom attached to the nitrogenous base. One of these contrast-enhanced, heavy-atom-labeled bases is paired with each adenosine base in the template molecule and then built into a double-stranded DNA molecule by a template-directed DNA polymerase enzyme. This modification is small enough to allow very long molecules with labels at each A-U position. Image contrast is further enhanced by using annular dark-field scanning transmission electron microscopy (ADF-STEM). Further refinements to identify additional base types and more precisely determine the location of identified bases would allow full sequencing of long, intact DNA molecules, significantly improving the pace of complex genomic discoveries.

Atrioventricular septal defect with common atrioventricular junction is a relatively common congenital cardiac malformation. It sometimes presents challenging surgical problems, especially when seen in combination with tetralogy of Fallot. We describe herein our current concepts regarding surgical repair of atrioventricular septal defect with and without tetralogy, discussing indications for surgery, timing, technical aspects, and outcomes.

Four ponies were each inoculated with a different serotype of African horse sickness virus (AHSV) which had been passaged through cell culture in order to achieve attenuation. Three of the ponies died suddenly after showing mild clinical signs, the fourth pony remained clinically normal and was killed at day 38. Infectious AHSV was isolated from blood samples collected at intervals from all four ponies. Positive antigen ELISA reactions were only observed with blood samples from two of the ponies on the two days preceding death. Specific AHSV antibodies were detected by ELISA in serum samples from the other two ponies although one eventually died. African horse sickness viral antigens were detected by ELISA in post-mortem tissue samples collected from all four ponies. No infectious virus could be detected in tissue samples taken post-mortem from the pony which survived African horse sickness (AHS) infection. In the event of a suspected outbreak of AHS it is recommended that sera and heparinized blood should be tested for specific antibodies and AHSV antigen respectively. When available, post-mortem tissues, including spleen, heart, lung and liver, should also be tested for AHSV antigen. Although the ELISA used for the detection of AHSV antigen is highly sensitive and specific, negative ELISA results should be confirmed by virus isolation attempts.

A competition enzyme-linked immunosorbent assay (ELISA) has been developed for the rapid identification and quantification of antibodies against African horse sickness (AHS) in sera from solipeds. The data showed the ELISA to be sensitive, specific and reliable.

More than 1600 sera from 37 different countries were examined and results compared with those obtained by agar gel immuno-diffusion (AGID) tests. In no case did any of 775 sera from countries where AHS has never been reported and where AHS vaccines are not used, record an ELISA titre greater than 4. A titre equal to or greater than 8 was considered positive. Using this criterion, 96·3% of sera tested in both assays were in agreement. Doubtful results by AGID (1·7%) were clearly defined in terms of positivity and negativity by ELISA.

This ELISA is suited for the rapid laboratory confirmation of AHS and should be considered as a replacement for the traditional AGID test.

In this paper we study a model problem describing the movement of a glacier under Glen's flow law and investigated by Colinge and Rappaz [Colinge and Rappaz, ESAIM: M2AN33 (1999) 395–406]. We establish error estimates for finite element approximation using the results of Chow [Chow, SIAM J. Numer. Analysis29 (1992) 769–780] and Liu and Barrett [Liu and Barrett, SIAM J. Numer. Analysis33 (1996) 98–106] and give an analysis of the convergence of the successive approximations used in [Colinge and Rappaz, ESAIM: M2AN33 (1999) 395–406]. Supporting numerical convergence studies are carried out and we also demonstrate the numerical performance of an a posteriori error estimator in adaptive mesh refinement computation of the problem.

It has been an underlying assumption in many studies that near-surface layers imaged by ground-penetrating radar (GPR) can be interpreted as depositional markers or isochrones. It has been shown that GPR layers can be approximately reproduced from the measured electrical properties of ice, but these material layers are generally narrower and more closely spaced than can be resolved by typical GPR systems operating in the range 50−400 MHz. Thus GPR layers should be interpreted as interference patterns produced from closely spaced and potentially discontinuous material layers, and should not be assumed to be interpretable as precise markers of isochrones. We present 100 MHz GPR data from Lyddan Ice Rise, Antarctica, in which near-surface (<50 m deep) layers are clearly imaged. The growth of the undulations in these layers with depth is approximately linear, implying that, rather than resulting from a pattern of vertical strain rate, they do correspond to some pattern of snowfall variation. Furthermore, comparison of the GPR layers with snow-stake measurements suggests that around 80% of the rms variability in mean annual accumulation is present in the GPR layers. The observations suggest that, at least in this case, the GPR layers do approximate isochrones, and that patterns of snow accumulation over Lyddan Ice Rise are dominated by extremely persistent spatial variations with only a small residual spatial variability. If this condition is shown to be widely applicable it may reduce the period required for measurements of surface elevation change to be taken as significant indications of mass imbalance.

It is not known if the ruminant animal gastrointestinal tract (GIT) can oxidise essential amino acids (AA) other than leucine. Therefore, the oxidation of four essential AA (leucine, lysine, methionine and phenylalanine), supplied systemically as labelled 1-13C forms, was monitored across the mesenteric-drained viscera (MDV; small intestine) and portal-drained viscera (PDV; total GIT), as part of a 4×4 Latin square design, in four wether sheep (35–45 kg) fed at 1·4 × maintenance. Oxidation was assessed primarily by appearance of 13CO2, corrected for sequestration of [13C]bicarbonate. The GIT contributed 25 % (P<0·001) and 10 % (P<0·05) towards whole-body AA oxidation for leucine and methionine respectively. This reduced net appearance across the PDV by 23 and 11 % respectively. The contribution of MDV metabolism to total PDV oxidation was 40 % for leucine and 60 % for methionine. There was no catabolism of systemic lysine or phenylalanine across the GIT. Production and exchange of secondary metabolites (e.g. 4-methyl-2-oxo-pentanoate, homocysteine, 2-aminoadipate) across the GIT was also limited. Less AA appeared across the PDV than MDV (P<0·001), indicative of use by tissues such as the forestomach, large intestine, spleen and pancreas. The PDV: MDV net appearance ratios varied (P<0·001) between AA, e.g. phenylalanine (0·81), lysine (0·71), methionine (0·67), leucine (0·56), histidine (0·71), threonine (0·63) and tryptophan (0·48). These differences probably reflect incomplete re-absorption of endogenous secretions and, together with the varied oxidative losses measured, will alter the pattern of AA net supply to the rest of the animal.