Taxonomy and biostratigraphy of new and emended species of Cenozoic deep-water agglutinated foraminifera from the Labrador and North Seas

Deep marine, fine grained sedimentary strata of Maastrichtian through Miocene age in the Labrador and North Sea sedimentary basins are rich in agglutinated benthic foraminifera. Six new taxa have been found in these regions, several of which also extend to other circum-Atlantic Paleogene localities. The new taxa are: Ammomarginulina aubertae, n. sp. (Maastrichtian to Eocene), Adercotryma agterbergi, n. sp. (middle Eocene to lower Oligocene), Reticulophragmoides jarvisi (Thalmann) emended herein (Paleocene to lower Oligocene), Reticulophragmoides sp. 5 (Oligocene to Miocene), and Spiroplectammina navarroana Cushman emended herein (Maastrichtian to lower middle Eocene). The last occurrences of these taxa are important elements in the high-resolution probabilistic biozonations for the Labrador and North Sea basins

On Pebble Automata for Data Languages with Decidable Emptiness Problem

In this paper we study a subclass of pebble automata (PA) for data languages for which the emptiness problem is decidable. Namely, we introduce the so-called top view weak PA. Roughly speaking, top view weak PA are weak PA where the equality test is performed only between the data values seen by the two most recently placed pebbles. The emptiness problem for this model is decidable. We also show that it is robust: alternating, nondeterministic and deterministic top view weak PA have the same recognition power. Moreover, this model is strong enough to accept all data languages expressible in Linear Temporal Logic with the future-time operators, augmented with one register freeze quantifier.Comment: An extended abstract of this work has been published in the proceedings of the 34th International Symposium on Mathematical Foundations of Computer Science (MFCS) 2009}, Springer, Lecture Notes in Computer Science 5734, pages 712-72

Modern agglutinated Foraminifera from the Hovgård Ridge, Fram Strait, west of Spitsbergen: evidence for a deep bottom current

Deep-water agglutinated foraminifera on the crest of the Hovgård Ridge, west of Spitsbergen, consist mostly of large tubular astrorhizids. At a boxcore station collected from the crest of Hovgård Ridge at a water depth of 1169 m, the sediment surface was covered with patches of large (1 mm diameter) tubular forms, belonging mostly to the species Astrorhiza crassatina Brady, with smaller numbers of Saccorhiza, Hyperammina, and Psammosiphonella. Non-tubular species consisted mainly of opportunistic forms, such as Psammosphaera and Reophax. The presence of large suspension-feeding tubular genera as well as opportunistic forms point to the presence of deep currents at this locality that are strong enough to disturb the benthic fauna. This is confirmed by data obtained from sediment echosounding, which exhibit lateral variation in relative sedimentation rates within the Pleistocene sedimentary drape covering the ridge, indicative of winnowing in a south-easterly direction

An automaton over data words that captures EMSO logic

We develop a general framework for the specification and implementation of systems whose executions are words, or partial orders, over an infinite alphabet. As a model of an implementation, we introduce class register automata, a one-way automata model over words with multiple data values. Our model combines register automata and class memory automata. It has natural interpretations. In particular, it captures communicating automata with an unbounded number of processes, whose semantics can be described as a set of (dynamic) message sequence charts. On the specification side, we provide a local existential monadic second-order logic that does not impose any restriction on the number of variables. We study the realizability problem and show that every formula from that logic can be effectively, and in elementary time, translated into an equivalent class register automaton

A label-free, quantitative assay of amyloid fibril growth based on intrinsic fluorescence.

Kinetic assay of seeded growth: The graph shows the variation in intrinsic fluorescence intensity of amyloid fibrils. Fluorescence increases during the seeded aggregation of α-synuclein seeds with α-synuclein monomeric protein (blue curve) but not when α-synuclein seeds are incubated with β-synuclein monomeric protein (black curve), thus showing that no seeded growth occurred in this case

Bounded Model Checking for Probabilistic Programs

In this paper we investigate the applicability of standard model checking approaches to verifying properties in probabilistic programming. As the operational model for a standard probabilistic program is a potentially infinite parametric Markov decision process, no direct adaption of existing techniques is possible. Therefore, we propose an on-the-fly approach where the operational model is successively created and verified via a step-wise execution of the program. This approach enables to take key features of many probabilistic programs into account: nondeterminism and conditioning. We discuss the restrictions and demonstrate the scalability on several benchmarks

Direct observation of heterogeneous amyloid fibril growth kinetics via two-color super-resolution microscopy.

The self-assembly of normally soluble proteins into fibrillar amyloid structures is associated with a range of neurodegenerative disorders, such as Parkinson's and Alzheimer's diseases. In the present study, we show that specific events in the kinetics of the complex, multistep aggregation process of one such protein, α-synuclein, whose aggregation is a characteristic hallmark of Parkinson's disease, can be followed at the molecular level using optical super-resolution microscopy. We have explored in particular the elongation of preformed α-synuclein fibrils; using two-color single-molecule localization microscopy we are able to provide conclusive evidence that the elongation proceeds from both ends of the fibril seeds. Furthermore, the technique reveals a large heterogeneity in the growth rates of individual fibrils; some fibrils exhibit no detectable growth, whereas others extend to more than ten times their original length within hours. These large variations in the growth kinetics can be attributed to fibril structural polymorphism. Our technique offers new capabilities in the study of amyloid growth dynamics at the molecular level and is readily translated to the study of the self-assembly of other nanostructures

Persistence and Uncertainty in the Academic Career

Understanding how institutional changes within academia may affect the overall potential of science requires a better quantitative representation of how careers evolve over time. Since knowledge spillovers, cumulative advantage, competition, and collaboration are distinctive features of the academic profession, both the employment relationship and the procedures for assigning recognition and allocating funding should be designed to account for these factors. We study the annual production n_{i}(t) of a given scientist i by analyzing longitudinal career data for 200 leading scientists and 100 assistant professors from the physics community. We compare our results with 21,156 sports careers. Our empirical analysis of individual productivity dynamics shows that (i) there are increasing returns for the top individuals within the competitive cohort, and that (ii) the distribution of production growth is a leptokurtic "tent-shaped" distribution that is remarkably symmetric. Our methodology is general, and we speculate that similar features appear in other disciplines where academic publication is essential and collaboration is a key feature. We introduce a model of proportional growth which reproduces these two observations, and additionally accounts for the significantly right-skewed distributions of career longevity and achievement in science. Using this theoretical model, we show that short-term contracts can amplify the effects of competition and uncertainty making careers more vulnerable to early termination, not necessarily due to lack of individual talent and persistence, but because of random negative production shocks. We show that fluctuations in scientific production are quantitatively related to a scientist's collaboration radius and team efficiency.Comment: 29 pages total: 8 main manuscript + 4 figs, 21 SI text + fig

Nanoscopic insights into seeding mechanisms and toxicity of α-synuclein species in neurons.

New strategies for visualizing self-assembly processes at the nanoscale give deep insights into the molecular origins of disease. An example is the self-assembly of misfolded proteins into amyloid fibrils, which is related to a range of neurodegenerative disorders, such as Parkinson's and Alzheimer's diseases. Here, we probe the links between the mechanism of α-synuclein (AS) aggregation and its associated toxicity by using optical nanoscopy directly in a neuronal cell culture model of Parkinson's disease. Using superresolution microscopy, we show that protein fibrils are taken up by neuronal cells and act as prion-like seeds for elongation reactions that both consume endogenous AS and suppress its de novo aggregation. When AS is internalized in its monomeric form, however, it nucleates and triggers the aggregation of endogenous AS, leading to apoptosis, although there are no detectable cross-reactions between externally added and endogenous protein species. Monomer-induced apoptosis can be reduced by pretreatment with seed fibrils, suggesting that partial consumption of the externally added or excess soluble AS can be significantly neuroprotective.We thank Dr Q. Jeng and Dr A. Stephens for technical assistance and Dr J. Skepper for TEM imaging. This work was funded by grants from the U.K. Medical Research Council (MR/K015850/1 and MR/K02292X/1), Alzheimer’s Research UK (ARUK-EG2012A-1), U.K. Engineering and Physical Sciences Research Council (EPSRC) (EP/H018301/1) and the Wellcome Trust (089703/Z/09/Z). D.P. wishes to acknowledge support from the Swiss National Science Foundation and the Wellcome Trust through personal fellowships. A.K.B thanks Magdalene College, Cambridge and the Leverhulme Trust for support.This is the author accepted manuscript. The final version is available from the National Academy of Sciences via http://dx.doi.org/10.1073/pnas.1516546113