Ronnie Alves

PALYNOLOGY OF THE MIDDLE MIOCENE–PLIOCENE NOVO REMANSO FORMATION, CENTRAL AMAZONIA, BRAZIL

Abstract. n In order to reassess and amend previously published palynological data drawn from the Novo Remanso Formation, central Amazonia, we revisited the organic-rich samples from their work using systematic and quantitative biostratigraphic analyses, with possible implications in the biodiversity and paleoecological studies of Late Neogene deposits of Amazonia. In the study area, the Novo Remanso Formation is characterized by sandstones and mudstones deposited in a meandering river environment. The palynological assemblage comprises 46 morphotypes, including 21 species of pollen and 25 species of spores. Polypodiisporites usmensis, Retitrescolpites? irregularis and Mauritiidites franciscoi var. franciscoi, typical of lowland freshwater forests and shallow water lakes dominate the assemblage. Also, lower frequencies of Grimsdalea magnaclavata co-occur with Psilatricolporites crassoexinatus, Proteacidites triangulatus, Bombacacidites simpliciriloensis, Pteridaceoisporis gemmatus and Cingulatisporites laevigatus. Based on quantitative biostratigraphic techniques, the Novo Remanso Formation Is assigned a middle Miocene—Pliocene age In our study area. The presence of Elaterosporites klaszii (Albian-Cenomanian) In the Novo Remanso deposits strongly indicates Cretaceous rocks in the source-area, whereas absence of Andine palynomorphs may be indicative of a nearby source area for the deposits during the deposition of the Novo Remanso Formation.

Modern pollen rain as a background for palaeoenvironmental studies in the Serra dos Carajás, southeastern Amazonia

Several alternative interpretations of the pollen records of lake sediments in the Amazonia may arise due to a lack of understanding of the modern environments, mainly related to pollen–vegetation relationship. Therefore, in this work, we studied the modern pollen rain in sediments of the Amendoim Lake, plateaus of the Serra Sul dos Carajás, southeastern Amazonia. This study indicates the predominance of pollen grains from forest formation (ombrophilous forests and capão florestal) over montane savanna in the lake sediments, despite the fact that montane savanna occupies ~90% of the drainage basin. Additionally, these sediments reflect stronger signal of pollen from ombrophilous forests that occur in the slopes of the plateau. Important components of montane savanna such as Vellozia and Cereus were not observed in the modern pollen rain, which may be related to their shorter flowering periods restricted to the beginning of wetter conditions. The absence of Sacoglottis, Trichilia, Clusia, Emmotum, Guapira and Simarouba in the pollen rain is likely associated with different pollination strategy. The occurrence of windblown pollen of Alchornea, Pseudolmedia, Ilex and Cecropia, which are found from low to highlands of the Carajás region, reinforces a regional vegetation signal in sediments. Several plants from the studied site have been improperly described, according to taxonomy and ecology. For example, the current occurrence of Ilex and Styrax in the study site clearly suggests that they cannot be used as indicators of colder palaeoclimate conditions, as previously described. In addition, Poaceae can be found in drier to wetter substrate conditions, and abundance of their pollen grains in lakes can significantly vary according to relief morphology and cannot indicate palaeovegetation openness. Therefore, this work is a good background for further palaeobotany studies for this region.

A Visual-Analytics System for Railway Safety Management

The working environment of railways is challenging and complex and often involves high-risk operations. These operations affect both the company staff and inhabitants of the towns and cities alongside the railway lines. To reduce the employees and publics exposure to risk, railway companies adopt strategies involving trained safety personnel, advanced forms of technology, and special work processes. Nevertheless, unfortunate incidents still occur. To assist railway safety management, researchers developed a visual-analytics system. Using a data analytics workflow, it compiles an incident risk index that processes information about railway incidents. It displays the index on a geographical map, together with socioeconomic information about the associated towns and cities. Feedback on this system suggests that safety engineers and experts can use it to make and communicate decisions.

Pollen morphology of the Poaceae: implications of the palynological and paleoecological records of the southeastern Amazon in Brazil

ABSTRACT A detailed assessment of Poaceae pollen morphology was performed using light and scanning electron microscopy (LM and SEM, respectively), digital image processing and multivariate data analysis of species from the montane savanna (canga vegetation) of the Serra dos Carajas region in the southeastern Amazon to discriminate the lower taxonomic levels and, accordingly, the habitat types of Poaceae. Poaceae pollen are generally stenopalynous monoporate grains with annulate and operculate pores, and distinguishing species by ornamentation using LM is impossible. Under SEM, Poaceae have mainly areolate microechinate/ granulose ornamentation, except for Eragrostis maypurensis (rugulate-microechinate), Andropogon bicornis, Trichanthecium parvifolium and T. polycomum (rugulate granulose), and Rhytachne gonzalezii (microechinate). Digital image processing of ornamentation under SEM coupled with multivariate data analysis allowed for differentiation between the E. maypurensis, R. gonzalezii, A. capillaris, Otachyrium versicolor, Paspalum carinatum and T. polycomum. Distinguishing species of the wet savanna, such as Isachne polygonoides, R. gonzalezii, O. versicolor, P. virgatum, and T. polycomum, from species of the dry savanna can improve paleoecological and paleoclimatic interpretations.

VCloud: adding interactiveness to word clouds for knowledge exploration in large unstructured texts

The identification of relevant information in large text databases is a challenging task. One of the reasons is human beings limitations in handling large volumes of data. A common solution for scavenging data from texts are word clouds. A word cloud illustrates word usage in a document by resizing individual words in documents proportionally to how frequently they appear. Even though word clouds are easy to understand, they are not particularly efficient, because they are static. In addition, the presented information lacks context, i.e., words are not explained and they may lead to radically erroneous interpretations. To tackle these problems we developed VCloud, a tool that allows the user to interact with word clouds, therefore allowing informative and interactive data exploration. Furthermore, our tool also allows one to compare two data sets presented as word clouds. We evaluated VCloud using real data about the evolution of gastritis research through the years. The papers indexed by Pubmed related to this medical context were selected for visualization and data analysis using VCloud. A domain expert explored these visualizations, being able to extract useful information from it. This illustrates how can VCloud be a valuable tool for visual text analytics.

Tally: a scoring tool for boundary determination between repetitive and non-repetitive protein sequences

MOTIVATIONnTandem Repeats (TRs) are abundant in proteins, having a variety of fundamental functions. In many cases, evolution has blurred their repetitive patterns. This leads to the problem of distinguishing between sequences that contain highly imperfect TRs, and the sequences without TRs. The 3D structure of proteins can be used as a benchmarking criterion for TR detection in sequences, because the vast majority of proteins having TRs in sequences are built of repetitive 3D structural blocks. According to our benchmark, none of the existing scoring methods are able to clearly distinguish, based on the sequence analysis, between structures with and without 3D TRs.nnnRESULTSnWe developed a scoring tool called Tally, which is based on a machine learning approach. Tally is able to achieve a better separation between sequences with structural TRs and sequences of aperiodic structures, than existing scoring procedures. It performs at a level of 81% sensitivity, while achieving a high specificity of 74% and an Area Under the Receiver Operating Characteristic Curve of 86%. Tally can be used to select a set of structurally and functionally meaningful TRs from all TRs detected in proteomes. The generated dataset is available for benchmarking purposes.nnnAVAILABILITY AND IMPLEMENTATIONnSource code is available upon request. Tool and dataset can be accessed through our website: http://bioinfo.montp.cnrs.fr/?r=TallynnnCONTACTnandrey.kajava@crbm.cnrs.frnnnSUPPLEMENTARY INFORMATIONnSupplementary data are available at Bioinformatics online.