Stratigraphic Architecture of Deep Sea Depositional Systems in the Southern Tyrrhenian Sea: Some Examples in the Ischia and Stromboli Volcanic Islands (Southern Italy)

The stratigraphic architecture of deep sea depositional systems has been discussed in detail. Some examples in Ischia and Stromboli volcanic islands (Southern Tyrrhenian sea, Italy) are here shown and discussed. The submarine slope and base of slope depositional systems represent a major component of marine and lacustrine basin fills, constituting primary targets for hydrocarbon exploration and development. The slope systems are characterized by seven seismic facies building blocks, including the turbiditic channel fills, the turbidite lobes, the sheet turbidites, the slide, slump and debris flow sheets, lobes and tongues, the fine-grained turbidite fills and sheets, the contourite drifts and finally, the hemipelagic drapes and fills. Sparker profiles offshore Ischia are presented. New seismo-stratigraphic evidence on buried volcanic structures and overlying Quaternary deposits of the eastern offshore of the Ischia Island are here discussed to highlight the implications on marine geophysics and volcanology. Regional seismic sections in the Ischia offshore across buried volcanic structures and debris avalanche and debris flow deposits are here presented and discussed. Deep sea depositional systems in the Ischia Island are well developed in correspondence to the Southern Ischia canyon system. The canyon system engraves a narrow continental shelf from Punta Imperatore to Punta San Pancrazio, being limited southwestwards from the relict volcanic edifice of the Ischia bank. While the eastern boundary of the canyon system is controlled by extensional tectonics, being limited from a NE-SW trending (counter-Apenninic) normal fault, its western boundary is controlled by volcanism, due to the growth of the Ischia volcanic bank. Submarine gravitational instabilities also acted in relationships to the canyon system, allowing for the individuation of large scale creeping at the sea bottom and hummocky deposits already interpreted as debris avalanche deposits. High resolution seismic data (Subbottom Chirp) coupled to high resolution Multibeam bathymetry collected in the frame of the Stromboli geophysical experiment aimed at recording seismic active data and tomography of the Stromboli Island are here presented. A new detailed swath bathymetry of Stromboli Island is here shown and discussed to reconstruct an up-to-date morpho-bathymetry and marine geology of the area, compared to volcanologic setting of the Aeolian volcanic complex. The Stromboli DEM gives information about the submerged structure of the volcano, particularly about the volcano-tectonic and gravitational processes involving the submarine flanks of the edifice. Several seismic units have been identified around the volcanic edifice and interpreted as volcanic acoustic basement pertaining to the volcano and overlying slide chaotic bodies emplaced during its complex volcano-tectonic evolution. They are related to the eruptive activity of Stromboli, mainly poliphasic and to regional geological processes involving the geology of the Aeolian Arc.

Prediction of Phosphorylation Sites from Protein Sequences

Phosphorylation is amongst the most crucial and well-studied post-translational modifications. It is involved in multiple cellular processes which makes phosphorylation prediction vital for understanding protein functions. However, wet-lab techniques are labour and time intensive. Thus, computational tools are required for efficiency. This project aims to provide a novel way to predict phosphorylation sites from protein sequences by adding flexibility and Sezerman Grouping amino acid similarity measure to previous methods, as discovering new protein sequences happens at a greater rate than determining protein structures. The predictor – NOPAY - relies on Support Vector Machines (SVMs) for classification. The features include amino acid encoding, amino acid grouping, predicted secondary structure, predicted protein disorder, predicted protein flexibility, solvent accessibility, hydrophobicity and volume. As a result, we have managed to improve phosphorylation prediction accuracy for Homo sapiens by 3% and 6.1% for Mus musculus. Sensitivity at 99% specificity was also increased by 6% for Homo sapiens and for Mus musculus by 5% on independent test sets. In this study, we have managed to increase phosphorylation prediction accuracy for Homo sapiens and Mus musculus. When there is enough data, future versions of the software may also be able to predict other organisms.

Molecular analysis of RNA1 and RNA2 sequences from a betanodavirus isolated from giant grouper (Epinephelus lanceolatus) in Australia

Betanodavirus infections have a significant impact through direct losses and trade restrictions for aquaculture sectors in Australia. The giant grouper, Epinephelus lanceolatus, is a high-value, fast-growing species with significant aquaculture potential. With subacute to chronic mortalities reported from a commercial aquaculture facility in northern Queensland, the viral nervous necrosis in the affected fish was confirmed using a RT-qPCR followed by virus isolation using the SSN-1 cell line. The RNA1 and RNA2 segments were sequenced and nucleotide sequences were compared with betanodavirus sequences from GenBank. Phylogenetic analysis revealed that both these sequences clustered with sequences representing red spotted grouper nervous necrosis virus genotype and showed high sequence identity to virus sequences affecting other grouper species. This is the first report confirming infection by betanodavirus in E. lanceolatus from Australia with successful isolation of the virus in a cell culture system, and analysis of nearly full length RNA1 and RNA2 sequences.

The pianosa contourite depositional system (northern Tyrrhenian sea): drift morphology and plio-quaternary stratigraphic evolution

The Pianosa Contourite Depositional System (CDS) is located in the Corsica Trough (Northern Tyrrhenian Sea), a confined basin dominated by mass transport and contour currents in the eastern flank and by turbidity currents in the western flank. The morphologic and stratigraphic characterisation of the Pianosa CDS is based on multibeam bathymetry, seismic reflection data (multi-channel high resolution mini GI gun, single-channel sparker and CHIRP), sediment cores and ADCP data. The Pianosa CDS is located at shallow to intermediate water depths (170 to 850 m water depth) and is formed under the influence of the Levantine Intermediate Water (LIW). It is 120 km long, has a maximum width of 10 km and is composed of different types of muddy sediment drifts: plastered drift, separated mounded drift, sigmoid drift and multicrested drift. The reduced tectonic activity in the Corsica Trough since the early Pliocene permits to recover a sedimentary record of the contourite depositional system that is only influenced by climate fluctuations. Contourites started to develop in the Middle-Late Pliocene, but their growth was enhanced since the Middle Pleistocene Transition (0.7–0.9 Ma). Although the general circulation of the LIW, flowing northwards in the Corsica Trough, remained active all along the history of the system, contourite drift formation changed, controlled by sediment influx and bottom current velocity. During periods of sea level fall, fast bottom currents often eroded the drift crest in the middle and upper slope. At that time the proximity of the coast to the shelf edge favoured the formation of bioclastic sand deposits winnowed by bottom currents. Higher sediment accumulation of mud in the drifts occurred during periods of fast bottom currents and high sediment availability (i.e. high activity of turbidity currents), coincident with periods of sea level low-stands. Condensed sections were formed during sea level high-stands, when bottom currents were more sluggish and the turbidite system was disconnected, resulting in a lower sediment influx.

Detecting Motifs in System Call Sequences

The search for patterns or motifs in data represents an area of key interest to many researchers. In this paper we present the Motif Tracking Algorithm, a novel immune inspired pattern identification tool that is able to identify unknown motifs which repeat within time series data. The power of the algorithm is derived from its use of a small number of parameters with minimal assumptions. The algorithm searches from a completely neutral perspective that is independent of the data being analysed and the underlying motifs. In this paper the motif tracking algorithm is applied to the search for patterns within sequences of low level system calls between the Linux kernel and the operating system’s user space. The MTA is able to compress data found in large system call data sets to a limited number of motifs which summarise that data. The motifs provide a resource from which a profile of executed processes can be built. The potential for these profiles and new implications for security research are highlighted. A higher level system call language for measuring similarity between patterns of such calls is also suggested.

Contribuição para o conhecimento da geologia do Grupo das Beiras (CXG) na região do Caramulo-Buçaco, Portugal Central

O presente trabalho ocupa-se do estudo do Complexo Xisto-Grauváquico ante-ordovícico (Grupo das Beiras) na região do Caramulo-Buçaco (centro de Portugal). Em termos geológicos, a área estudada pertence à Zona Centro Ibérica e encontra-se limitada a N pelo granito do Caramulo, a S pela bacia meso-cenozóica de Arganil, a W pelo sinclinal paleozóico do Buçaco e pela bacia meso-cenozóica ocidental portuguesa e a E pelo sinclinal paleozóico de Arganil e pelo plutonito granítico de Tábua-Santa Comba Dão; no seio da área estudada encontra-se a bacia meso-cenozóica de Mortágua. Com base nas características litológicas e estruturais distinguem-se no Complexo Xisto Grauváquico 4 grandes conjuntos litológicos concordantes entre si, designados de Unidades I, II, III e IV, que se desenvolvem da base para o topo de N para S. A Unidade I situa-se a N da região. O seu limite inferior é desconhecido, e o superior posiciona-se no último conjunto arenoso com potência decamétrica. É constituída por xistos cinzentos e negros com intercalações de arenitos de espessura não superior a 100 metros e de extensão lateral quilométrica. Apresenta uma espessura mínima de 1000 m. A Unidade II apresenta consideravelmente menor proporção de material arenoso intercalado entre os pelitos comparativamente à unidade inferior. É caracterizada por apresentar um predomínio de material silto-argiloso e escassos níveis arenosos com potência não superior à dezena de metros e escassa continuidade lateral. Cartograficamente esta unidade constitui uma franja alargada de orientação próxima a E-W. Apresenta uma espessura aproximada de 1500 m. A Unidade III é caracterizada pela presença de conjuntos arenosos com extensão lateral quilométrica e espessura de várias dezenas de metros, separados por material silto-argiloso. Os limites inferior e superior estão situados respectivamente abaixo e acima dos principais conjuntos arenosos. Esta unidade apresenta uma espessura máxima estimada na ordem dos 2000 m. A Unidade IV, que é a unidade superior, apresenta um predomínio pelítico, com escassas intercalações de conjuntos arenosos. O seu limite inferior encontra-se no topo do último conjunto arenoso da Unidade III. Apresenta uma espessura mínima de 500 m. As características sedimentológicas das 4 unidades indicam uma sedimentação num ambiente de plataforma externa siliciclástica aberta, com a construção de barras e por vezes sujeita à acção de tempestades, com sucessivos períodos de superficialização e profundização numa bacia de sedimentação bastante subsidente. Em termos estruturais, para além duma deformação pré-ordovícica, que é comprovada pelo forte mergulho e dispersão da orientação dos eixos da 1ª fase varisca e da lineação de intersecção L1, a área estudada foi principalmente afectada pela Orogenia Varisca. A 1ª fase de deformação varisca (F1) gerou dobras com superfícies axiais e xistosidade associada (S1) de direcção WNW-ESE, e forte pendor para NNE. Estas dobras D1 apresentam comprimentos de onda que nunca chegam a ser quilométricos, desenvolvendo-se um grande flanco inverso denunciando a presença de uma antiforma para NNE e uma sinforma para SSW. A 2ª fase de deformação varisca (F2) actuou na parte nordeste da área estudada e é caracterizada por ter gerado dobras de comprimento de onda quilométrico, com planos axiais e xistosidade associada S2 de direcção NW-SE, subverticais ou a pender fortemente para NE. Embora com alguma dispersão, as lineações de intersecção L2 e os eixos das dobras D2 apresentam maioritariamente forte pendor para E. A direcção e tipos de estruturas da F2 sugerem uma correlação com a terceira fase definida em vários pontos da Zona Centro Ibérica e estreitamente relacionada com as intrusões graníticas. Do ponto de vista petrológico, distinguem-se várias rochas sedimentares (pelitos e arenitos) todas elas sujeitas a metamorfismo que não ultrapassa a fácies dos xistos verdes. Dentro das rochas sedimentares mais grosseiras, há a destacar a presença de arenitos vulcânicos cuja composição denuncia, não muito afastados da bacia sedimentar, a presença de aparelhos vulcânicos que estariam em actividade durante a sedimentação. Foram analisadas isotopicamente 27 amostras de metapelitos colhidas em 5 locais diferentes de forma a abranger quase toda a área estudada. Os dados isotópicos de quatro destes locais de amostragem forneceram isócronas Rb-Sr, em rocha total, com valores da ordem dos 400-440 Ma. O granito do Caramulo, datado pela isócrona Rb-Sr em amostras de rocha total, forneceu uma idade de 326±12Ma. As idades modelo Sm-Nd (manto empobrecido) de 5 amostras de metapelitos estão compreendidas entre 1.35 e 1.25 Ga. Este período de tempo pode ser considerado como correspondendo à época de diferenciação mantélica da crusta que deu lugar à maioria das áreas fonte dos metapelitos.

An investigation of Hebbian phase sequences as assembly graphs

Hebb proposed that synapses between neurons that fire synchronously are strengthened, forming cell assemblies and phase sequences. The former, on a shorter scale, are ensembles of synchronized cells that function transiently as a closed processing system; the latter, on a larger scale, correspond to the sequential activation of cell assemblies able to represent percepts and behaviors. Nowadays, the recording of large neuronal populations allows for the detection of multiple cell assemblies. Within Hebb's theory, the next logical step is the analysis of phase sequences. Here we detected phase sequences as consecutive assembly activation patterns, and then analyzed their graph attributes in relation to behavior. We investigated action potentials recorded from the adult rat hippocampus and neocortex before, during and after novel object exploration (experimental periods). Within assembly graphs, each assembly corresponded to a node, and each edge corresponded to the temporal sequence of consecutive node activations. The sum of all assembly activations was proportional to firing rates, but the activity of individual assemblies was not. Assembly repertoire was stable across experimental periods, suggesting that novel experience does not create new assemblies in the adult rat. Assembly graph attributes, on the other hand, varied significantly across behavioral states and experimental periods, and were separable enough to correctly classify experimental periods (Naïve Bayes classifier; maximum AUROCs ranging from 0.55 to 0.99) and behavioral states (waking, slow wave sleep, and rapid eye movement sleep; maximum AUROCs ranging from 0.64 to 0.98). Our findings agree with Hebb's view that assemblies correspond to primitive building blocks of representation, nearly unchanged in the adult, while phase sequences are labile across behavioral states and change after novel experience. The results are compatible with a role for phase sequences in behavior and cognition.

Geological Evolution of Coastal and Marine Environments off the Campania Continental Shelf Through Marine Geological Mapping - The Example of the Cilento Promontory

The geological evolution of coastal and marine environments offshore the Cilento Promontory through marine geological mapping is discussed here. The marine geological map n. 502 “Agropoli,” located offshore the Cilento Promontory (southern Italy), is described and put in regional geologic setting. The study area covers water depths ranging between 30 and 200 m isobaths. The geologic map has been constructed in the frame of a research program financed by the National Geological Survey of Italy (CARG Project), finalized to the construction of an up-to-date cartography of the Campania region. Geological and geophysical data on the continental shelf and slope offshore the southern Campania region have been acquired in an area bounded northward by the Gulf of Salerno and southward by the Gulf of Policastro. A high-resolution multibeam bathymetry has permitted the construction of a digital elevation model (DEM). Sidescan sonar profiles have also been collected and interpreted, and their merging with bathymetric data has allowed for the realization of the base for the marine geologic cartography. The calibration of geophysical data has been attempted through sea-bottom samples. The morpho-structures and the seismic sequences overlying the outcrops of acoustic basement reported in the cartographic representation have been studied in detail using single-channel seismics. The interpretation of seismic profiles has been a support for the reconstruction of the stratigraphic and structural setting of the Quaternary continental shelf successions and the outcrops of rocky acoustic basement in correspondence to the Licosa Cape morphostructural high. These areas result from the seaward prolongation of the stratigraphic and structural units, widely cropping out in the surrounding emerged sector of the Cilento Promontory. The cartographic approach is based on the recognition of laterally coeval depositional systems, interpreted in the frame of system tracts of the Late Quaternary depositional sequence.

Depositional conditions on an alluvial fan at the turn of the Weichselian to the Holocene – a case study in the Żmigród Basin, southwest Poland

Presented are the results of research into the fluvio-aeolian sedimentary succession at the site of Postolin in the Żmigród Basin, southwest Poland. Based on lithofacies analysis, textural analysis, Thermoluminescence and Infrared-Optical Stimulated Luminescence dating and GIS analysis, three lithofacies units were recognised and their stratigraphic suc- cession identified: 1) the lower unit was deposited during the Pleni-Weichselian within a sand-bed braided river fun- ctioning under permafrost conditions within the central part of the alluvial fan; 2) the middle unit is the result of aeolian deposition and fluvial redeposition on the surface of the fan during long-term permafrost and progressive decrease of humidity of the climate at the turn of the Pleni- to the Late Weichselian; 3) the upper unit accumulated following the development of longitudinal dunes at the turn of the Late Weichselian to the Holocene; the development of dunes was interrupted twice by the form being stabilised by vegetation and soil development.

AnnoTALE: Bioinformatics tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences

Transcription activator-like effectors (TALEs) are virulence factors, produced by the bacterial plant-pathogen Xanthomonas, that function as gene activators inside plant cells. Although the contribution of individual TALEs to infectivity has been shown, the specific roles of most TALEs, and the overall TALE diversity in Xanthomonas spp. is not known. TALEs possess a highly repetitive DNA-binding domain, which is notoriously difficult to sequence. Here, we describe an improved method for characterizing TALE genes by the use of PacBio sequencing. We present 'AnnoTALE', a suite of applications for the analysis and annotation of TALE genes from Xanthomonas genomes, and for grouping similar TALEs into classes. Based on these classes, we propose a unified nomenclature for Xanthomonas TALEs that reveals similarities pointing to related functionalities. This new classification enables us to compare related TALEs and to identify base substitutions responsible for the evolution of TALE specificities. © 2016, Nature Publishing Group. All rights reserved.

Added value of diffusion-weighted MRI in detection of cervical cancer recurrence compared with morphologic and dynamic contrast-enhanced MRI sequences

PURPOSE We aimed to evaluate the added value of diffusion-weighted imaging (DWI) to standard magnetic resonance imaging (MRI) for detecting post-treatment cervical cancer recurrence. The detection accuracy of T2-weighted (T2W) images was compared with that of T2W MRI combined with either dynamic contrast-enhanced (DCE) MRI or DWI. METHODS Thirty-eight women with clinically suspected uterine cervical cancer recurrence more than six months after treatment completion were examined with 1.5 Tesla MRI including T2W, DCE, and DWI sequences. Disease was confirmed histologically and correlated with MRI findings. The diagnostic performance of T2W imaging and its combination with either DCE or DWI were analyzed. Sensitivity, positive predictive value, and accuracy were calculated. RESULTS Thirty-six women had histologically proven recurrence. The accuracy for recurrence detection was 80% with T2W/DCE MRI and 92.1% with T2W/DWI. The addition of DCE sequences did not significantly improve the diagnostic ability of T2W imaging, and this sequence combination misclassified two patients as falsely positive and seven as falsely negative. The T2W/DWI combination revealed a positive predictive value of 100% and only three false negatives. CONCLUSION The addition of DWI to T2W sequences considerably improved the diagnostic ability of MRI. Our results support the inclusion of DWI in the initial MRI protocol for the detection of cervical cancer recurrence, leaving DCE sequences as an option for uncertain cases.

A Visual Analytics Approach to Comparing Cohorts of Event Sequences

Sequences of timestamped events are currently being generated across nearly every domain of data analytics, from e-commerce web logging to electronic health records used by doctors and medical researchers. Every day, this data type is reviewed by humans who apply statistical tests, hoping to learn everything they can about how these processes work, why they break, and how they can be improved upon. To further uncover how these processes work the way they do, researchers often compare two groups, or cohorts, of event sequences to find the differences and similarities between outcomes and processes. With temporal event sequence data, this task is complex because of the variety of ways single events and sequences of events can differ between the two cohorts of records: the structure of the event sequences (e.g., event order, co-occurring events, or frequencies of events), the attributes about the events and records (e.g., gender of a patient), or metrics about the timestamps themselves (e.g., duration of an event). Running statistical tests to cover all these cases and determining which results are significant becomes cumbersome. Current visual analytics tools for comparing groups of event sequences emphasize a purely statistical or purely visual approach for comparison. Visual analytics tools leverage humans' ability to easily see patterns and anomalies that they were not expecting, but is limited by uncertainty in findings. Statistical tools emphasize finding significant differences in the data, but often requires researchers have a concrete question and doesn't facilitate more general exploration of the data. Combining visual analytics tools with statistical methods leverages the benefits of both approaches for quicker and easier insight discovery. Integrating statistics into a visualization tool presents many challenges on the frontend (e.g., displaying the results of many different metrics concisely) and in the backend (e.g., scalability challenges with running various metrics on multi-dimensional data at once). I begin by exploring the problem of comparing cohorts of event sequences and understanding the questions that analysts commonly ask in this task. From there, I demonstrate that combining automated statistics with an interactive user interface amplifies the benefits of both types of tools, thereby enabling analysts to conduct quicker and easier data exploration, hypothesis generation, and insight discovery. The direct contributions of this dissertation are: (1) a taxonomy of metrics for comparing cohorts of temporal event sequences, (2) a statistical framework for exploratory data analysis with a method I refer to as high-volume hypothesis testing (HVHT), (3) a family of visualizations and guidelines for interaction techniques that are useful for understanding and parsing the results, and (4) a user study, five long-term case studies, and five short-term case studies which demonstrate the utility and impact of these methods in various domains: four in the medical domain, one in web log analysis, two in education, and one each in social networks, sports analytics, and security. My dissertation contributes an understanding of how cohorts of temporal event sequences are commonly compared and the difficulties associated with applying and parsing the results of these metrics. It also contributes a set of visualizations, algorithms, and design guidelines for balancing automated statistics with user-driven analysis to guide users to significant, distinguishing features between cohorts. This work opens avenues for future research in comparing two or more groups of temporal event sequences, opening traditional machine learning and data mining techniques to user interaction, and extending the principles found in this dissertation to data types beyond temporal event sequences.

Lower Aptian Comparative Stratigraphy of the Basco-Cantabrian Region (Spain) and Eastern Cordillera (Colombia): implications for local factors in the depositional record of Oceanic Anoxic Event 1a (OAE-1a)

An important episode of carbon sequestration, Oceanic Anoxic Event 1a (OAE-1a), characterizes the Lower Aptian worldwide, and is mostly known from deeper-water settings. The present work of two Lower Aptian deposits, Madotz (N Spain) and Curití Quarry (Colombia), is a multiproxy study that includes fossil assemblages, microfacies, X-ray diffraction bulk and clay mineralogy, elemental analyses (major, minor, trace elements), Rock-Eval pyrolysis, biomarkers, inorganic and organic carbon content, and stable carbon isotopes. The results provide baseline evidence of the local and global controlling environmental factors influencing OAE-1a in shallow-water settings. The data also improve our general understanding of the conditions under which organic-carbon-rich deposits accumulate. The sequence at Madotz includes four intervals (Unit 1; Subunits 2a, 2b and 2c) that overlap the times prior to, during and after the occurrence of OAE-1a. The Lower Unit 1(3m thick) is essentially siliciclastic, and Subunit 2a (20m) contains Urgonian carbonate facies that document abruptly changing platform conditions prior to OAE-1a. Subunit 2b (24.4 m) is a mixed carbonate-siliciclastic facies with orbitolinid-rich levels that coincides with OAE-1a δ13C stages C4-C6, and is coeval with the upper part of the Deshayesites forbesi ammonite zone. Levels with pyrite and the highest TOC values (0.4-0.97%), interpreted as accumulating under suboxic conditions, and are restricted to δ13C stages C4 and C5. The best development of the suboxic facies is at the level representing the peak of the transgression. Subunit 2c, within δ13C stage C7, shows a return of the Urgonian facies. The 23.35-m section at Curití includes a 6.3-m interval at the base of the Paja Formation dominated by organic-rich marlstones and shales lacking benthic fossils and bioturbation, with TOC values as high as 8.84%. The interval overlies a level containing reworked and phosphatized assemblages of middle Barremian to lowest Aptian ammonites. The range of values and the overall pattern of the δ13Corg (-22.05‰ to -20.47‰) in the 6.3m-interval is comparable with Lower Aptian δ13C stage C7. Thus, conditions of oxygen depletion at this site also occurred after Oceanic Anoxic Event-1a, which developed between carbon isotope stages C3 and C6. Both sites, Madotz and Curití, attest to the importance of terrigenous and nutrient fluxes in increasing OM productivity that led to episodic oxygen deficiency.