IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences

IntFOLD is an independent web server that integrates our leading methods for structure and function prediction. The server provides a simple unified interface that aims to make complex protein modelling data more accessible to life scientists. The server web interface is designed to be intuitive and integrates a complex set of quantitative data, so that 3D modelling results can be viewed on a single page and interpreted by non-expert modellers at a glance. The only required input to the server is an amino acid sequence for the target protein. Here we describe major performance and user interface updates to the server, which comprises an integrated pipeline of methods for: tertiary structure prediction, global and local 3D model quality assessment, disorder prediction, structural domain prediction, function prediction and modelling of protein-ligand interactions. The server has been independently validated during numerous CASP (Critical Assessment of Techniques for Protein Structure Prediction) experiments, as well as being continuously evaluated by the CAMEO (Continuous Automated Model Evaluation) project. The IntFOLD server is available at: http://www.reading.ac.uk/bioinf/IntFOLD/

Rapid changes in the redox conditions of the western Tethys Ocean during the early Aptian oceanic anoxic event

The early Aptian (125 to 121 Ma) records an episode of severe environmental change including a major perturbation of the carbon cycle, an oceanic anoxic event (OAE 1a, 122.5 Ma), a platform drowning episode and a biocalcification crisis. We propose to trace changes in the oxygenation state of the ocean during the early Aptian anoxic event using the redox-sensitive trace-element (RSTE) distribution, phosphorus accumulation rates (PARs) and organic-matter characterization in three different basins of the western Tethys. The following sections have been investigated: Gorgo a Cerbara (central Italy) in the Umbria Marche basin, Glaise (SE France) in the Vocontian basin and Cassis/La Bédoule (SE France) located in the Provencal basin. In the Gorgo a Cerbara section, RSTE distributions show a low background level along the main part of the section, contrasted by different maxima in concentrations within the Selli level. In the Glaise section, the Goguel level displays a weak increase in RSTE contents coeval with moderate TOC values. At Cassis/La Bédoule, no significant RSTE enrichments have been observed in sediments equivalent to the Selli level. These differences in the records of the geochemical proxies of the Selli level or its equivalent indicate the deposition under different redox conditions, probably related to the paleogeography. Our data indicate the development of anoxic–euxinic conditions in the deeper part of the Tethys during OAE 1a, whereas in the shallower environments, conditions were less reducing. Moreover, at Gorgo a Cerbara, the Selli level is characterized by rapid changes in the intensity of reducing conditions in the water column. Ocean eutrophication seems to be a major factor in the development and the persistence of anoxia as suggested by the PAR evolution. Higher PAR values at the onset of OAE 1a suggest an increase in nutrient input, whereas the return to lower values through the first part of the OAE 1a interval may be related to the weakened capacity to retain P in the sedimentary reservoir due to bottom-water oxygen depletion. This general pattern is contrasted by the data of Gorgo a Cerbara, where the sediments deposited during the OAE 1a interval show P-enrichments (mainly authigenic P). This is associated with maxima in TOC values and Corg:Ptot ratios, suggesting that a part of the remobilized P was trapped in the sediments and as such prevented from returning to the water column.

Formulaic sequences in native and non-native argumentative writing in German

Whereas there is substantial scholarship on formulaic language in L1 and L2 English, there is less research on formulaicity in other languages. The aim of this paper is to contribute to learner corpus research into formulaic language in native and non-native German. To this effect, a corpus of argumentative essays written by advanced British students of German (WHiG) was compared with a corpus of argumentative essays written by German native speakers (Falko-L1). A corpus-driven analysis reveals a larger number of 3-grams in WHiG than in Falko-L1, which suggests that British advanced learners of German are more likely to use formulaic language in argumentative writing than their native-speaker counterparts. Secondly, by classifying the formulaic sequences according to their functions, this study finds that native speakers of German prefer discourse-structuring devices to stance expressions, whilst British advanced learners display the opposite preferences. Thirdly, the results show that learners of German make greater use of macro-discourse-structuring devices and cautious language, whereas native speakers favour micro-discourse structuring devices and tend to use more direct language. This study increases our understanding of formulaic language typical of British advanced learners of German and reveals how diverging cultural paradigms can shape written native speaker and learner output.

Implications of event attribution for loss and damage policy

The United Nations Framework Convention on Climate Change (UNFCCC) has established the Warsaw International Mechanism (WIM) to deal with loss and damage associated with climate change impacts, including extreme events, in developing countries. It is not yet known whether events will need to be attributed to anthropogenic climate change to be considered under the WIM. Attribution is possible for some extreme events- a climate model assessment can estimate how greenhouse gas emissions have affected the likelihood of their occurrence. Dialogue between scientists and stakeholders is required to establish whether, and how, this science could play a role in the WIM.

The expression of the Cenomanian-Turonian oceanic anoxic event in Tibet

The Gongzha section of Tibet, China is located at the northern margin of the Indian Plate (SE Tethys) and is characterized by hemipelagic grey marls and marly limestones, light grey limestones and silty limestones, but no organic-rich sediments. High-resolution biostratigraphy reveals an expanded Cenomanian–Turonian (CT) boundary interval and the δ13C record includes the main features of the classical positive carbon-isotope excursion that characterizes the CT oceanic anoxic event. The biotic response inferred from the foraminifera suggests that oxic to dysoxic conditions prevailed, except for a short interval marked by peak abundance of Heterohelix that indicates a significantly dysoxic environment during the δ13C “b” peak excursion. The overall decreasing trend in redox-sensitive trace elements (RSTE) during the maximum δ13C excursion confirms the absence of significant longer-lasting anoxia in the Gongzha section. Enrichments in RSTE are linked to phases of increased detrital input. Chemical weathering indices suggest that the upper Cenomanian sediments accumulated under an increasingly hot and humid climate that culminated near the CT boundary. In the early Turonian lower weathering indices suggest a warm, drier climatic regime with reduced continental runoff. Phosphorus mass-accumulation rates show a significant peak at the onset of the positive δ13C excursion, followed by a decrease up to the basal Turonian. This pattern is positively correlated with the long-term decrease in detrital index as also observed in numerous other CT boundary sections (e.g., Eastbourne, Pueblo, and Whadi El Ghaib, Sinaï). Long-term phosphorus accumulation in the Gongzha section is therefore associated with changes in detrital input. The overall decreased detrital input can be explained by the increasingly remote continental sources due to the major transgression at the end of Cenomanian, coupled with changes in continental weathering intensity linked to increasingly more arid climate conditions.

Memory and burstiness in dynamic networks

A discrete-time random process is described, which can generate bursty sequences of events. A Bernoulli process, where the probability of an event occurring at time t is given by a fixed probability x, is modified to include a memory effect where the event probability is increased proportionally to the number of events that occurred within a given amount of time preceding t. For small values of x the interevent time distribution follows a power law with exponent −2−x. We consider a dynamic network where each node forms, and breaks connections according to this process. The value of x for each node depends on the fitness distribution, \rho(x), from which it is drawn; we find exact solutions for the expectation of the degree distribution for a variety of possible fitness distributions, and for both cases where the memory effect either is, or is not present. This work can potentially lead to methods to uncover hidden fitness distributions from fast changing, temporal network data, such as online social communications and fMRI scans.

Second language influence on first language motion event encoding and categorization in Spanish-speaking children learning L2 English

Studies show cross-linguistic differences in motion event encoding, such that English speakers preferentially encode manner of motion more than Spanish speakers, who preferentially encode path of motion. Focusing on native Spanish speaking children (aged 5;00-9;00) learning L2 English, we studied path and manner verb preferences during descriptions of motion stimuli, and tested the linguistic relativity hypothesis by investigating categorization preferences in a non-verbal similarity judgement task of motion clip triads. Results revealed L2 influence on L1 motion event encoding, such that bilinguals used more manner verbs and fewer path verbs in their L1, under the influence of English. We found no effects of linguistic structure on non-verbal similarity judgements, and demonstrate for the first time effects of L2 on L1 lexicalization in child L2 learners in the domain of motion events. This pattern of verbal behaviour supports theories of bilingual semantic representation that postulate a merged lexico-semantic system in early bilinguals.

PETS 2014: dataset and challenge

This paper describes the dataset and vision challenges that form part of the PETS 2014 workshop. The datasets are multisensor sequences containing different activities around a parked vehicle in a parking lot. The dataset scenarios were filmed from multiple cameras mounted on the vehicle itself and involve multiple actors. In PETS2014 workshop, 22 acted scenarios are provided of abnormal behaviour around the parked vehicle. The aim in PETS 2014 is to provide a standard benchmark that indicates how detection, tracking, abnormality and behaviour analysis systems perform against a common database. The dataset specifically addresses several vision challenges corresponding to different steps in a video understanding system: Low-Level Video Analysis (object detection and tracking), Mid-Level Video Analysis (‘simple’ event detection: the behaviour recognition of a single actor) and High-Level Video Analysis (‘complex’ event detection: the behaviour and interaction recognition of several actors).

Tests of sunspot number sequences: 3. Effects of regression procedures on the calibration of historic sunspot data

We use sunspot group observations from the Royal Greenwich Observatory (RGO) to investigate the effects of intercalibrating data from observers with different visual acuities. The tests are made by counting the number of groups RB above a variable cut-off threshold of observed total whole-spot area (uncorrected for foreshortening) to simulate what a lower acuity observer would have seen. The synthesised annual means of RB are then re-scaled to the full observed RGO group number RA using a variety of regression techniques. It is found that a very high correlation between RA and RB (rAB > 0.98) does not prevent large errors in the intercalibration (for example sunspot maximum values can be over 30 % too large even for such levels of rAB). In generating the backbone sunspot number (RBB), Svalgaard and Schatten (2015, this issue) force regression fits to pass through the scatter plot origin which generates unreliable fits (the residuals do not form a normal distribution) and causes sunspot cycle amplitudes to be exaggerated in the intercalibrated data. It is demonstrated that the use of Quantile-Quantile (“Q  Q”) plots to test for a normal distribution is a useful indicator of erroneous and misleading regression fits. Ordinary least squares linear fits, not forced to pass through the origin, are sometimes reliable (although the optimum method used is shown to be different when matching peak and average sunspot group numbers). However, other fits are only reliable if non-linear regression is used. From these results it is entirely possible that the inflation of solar cycle amplitudes in the backbone group sunspot number as one goes back in time, relative to related solar-terrestrial parameters, is entirely caused by the use of inappropriate and non-robust regression techniques to calibrate the sunspot data.

Stakeholder perceptions of event attribution in the loss and damage debate

In 2013 the Warsaw International Mechanism (WIM) for loss and damage (L&D) associated with climate change impacts was established under the United Nations Framework Convention on Climate Change (UNFCCC). For scientists, L&D raises ques- tions around the extent that such impacts can be attributed to anthropogenic climate change, which may generate complex results and be controversial in the policy arena. This is particularly true in the case of probabilistic event attribution (PEA) science, a new and rapidly evolving field that assesses whether changes in the probabilities of extreme events are attributable to GHG emissions. If the potential applications of PEA are to be considered responsibly, dialogue between scientists and policy makers is fundamental. Two key questions are considered here through a literature review and key stakeholder interviews with representatives from the science and policy sectors underpinning L&D. These provided the opportunity for in-depth insights into stakeholders’ views on firstly, how much is known and understood about PEA by those associated with the L&D debate? Secondly, how might PEA inform L&D and wider climate policy? Results show debate within the climate science community, and limited understanding among other stakeholders, around the sense in which extreme events can be attributed to climate change. However, stake- holders do identify and discuss potential uses for PEA in the WIM and wider policy, but it remains difficult to explore precise applications given the ambiguity surrounding L&D. This implies a need for stakeholders to develop greater understandings of alternative conceptions of L&D and the role of science, and also identify how PEA can best be used to support policy, and address associated challenges.

Buckets, baskets and boots: exhibition event at MERL

Launch event part of Universities Week on Monday 9th Co-researchers from Reading College Learners with Learning Difficulties/Disabilities dept will present their Sensory Objects research in the Museum of English Rural Life (MERL)

Towards expressive rule induction on IP network event streams

In order to gain insights into events and issues that may cause errors and outages in parts of IP networks, intelligent methods that capture and express causal relationships online (in real-time) are needed. Whereas generalised rule induction has been explored for non-streaming data applications, its application and adaptation on streaming data is mostly undeveloped or based on periodic and ad-hoc training with batch algorithms. Some association rule mining approaches for streaming data do exist, however, they can only express binary causal relationships. This paper presents the ongoing work on Online Generalised Rule Induction (OGRI) in order to create expressive and adaptive rule sets real-time that can be applied to a broad range of applications, including network telemetry data streams.

A common framework for approaches to extreme event attribution

The extent to which a given extreme weather or climate event is attributable to anthropogenic climate change is a question of considerable public interest. From a scientific perspective, the question can be framed in various ways, and the answer depends very much on the framing. One such framing is a risk-based approach, which answers the question probabilistically, in terms of a change in likelihood of a class of event similar to the one in question, and natural variability is treated as noise. A rather different framing is a storyline approach, which examines the role of the various factors contributing to the event as it unfolded, including the anomalous aspects of natural variability, and answers the question deterministically. It is argued that these two apparently irreconcilable approaches can be viewed within a common framework, where the most useful level of conditioning will depend on the question being asked and the uncertainties involved.