Sampling information, length measurements, DNA alignments, models and phylogenetics trees for Oithona similis s.l.

Traditionally, many small-sized copepod species are considered to be widespread, bipolar or cosmopolitan. However, these large-scale distribution patterns need to be re-examined in view of increasing evidence of cryptic and pseudo-cryptic speciation in pelagic copepods. Here, we present a phylogeographic study of Oithona similis s.l. populations from the Arctic Ocean, the Southern Ocean and its northern boundaries, the North Atlantic and the Mediterrranean Sea. O. similis s.l. is considered as one of the most abundant species in temperate to polar oceans and acts as an important link in the trophic network between the microbial loop and higher trophic levels such as fish larvae. Two gene fragments were analysed: the mitochondrial cytochrome oxidase c subunit I (COI), and the nuclear ribosomal 28S genetic marker. Seven distinct, geographically delimitated, mitochondrial lineages could be identified, with divergences among the lineages ranging from 8 to 24 %, thus representing most likely cryptic or pseudocryptic species within O. similis s.l. Four lineages were identified within or close to the borders of the Southern Ocean, one lineage in the Arctic Ocean and two lineages in the temperate Northern hemisphere. Surprisingly the Arctic lineage was more closely related to lineages from the Southern hemisphere than to the other lineages from the Northern hemisphere, suggesting that geographic proximity is a rather poor predictor of how closely related the clades are on a genetic level. Molecular clock application revealed that the evolutionary history of O. similis s.l. is possibly closely associated with the reorganization of the ocean circulation in the mid Miocene and may be an example of allopatric speciation in the pelagic zone.

Real-time alert correlation with type graphs

The premise of automated alert correlation is to accept that false alerts from a low level intrusion detection system are inevitable and use attack models to explain the output in an understandable way. Several algorithms exist for this purpose which use attack graphs to model the ways in which attacks can be combined. These algorithms can be classified in to two broad categories namely scenario-graph approaches, which create an attack model starting from a vulnerability assessment and type-graph approaches which rely on an abstract model of the relations between attack types. Some research in to improving the efficiency of type-graph correlation has been carried out but this research has ignored the hypothesizing of missing alerts. Our work is to present a novel type-graph algorithm which unifies correlation and hypothesizing in to a single operation. Our experimental results indicate that the approach is extremely efficient in the face of intensive alerts and produces compact output graphs comparable to other techniques.

Bio-QA-GNN: Reasoning with Language Models and Knowledge Graphs for Interpretable Biomedical Question Answering

Nowadays the idea of injecting world or domain-specific structured knowledge into pre-trained language models (PLMs) is becoming an increasingly popular approach for solving problems such as biases, hallucinations, huge architectural sizes, and explainability lack—critical for real-world natural language processing applications in sensitive fields like bioinformatics. One recent work that has garnered much attention in Neuro-symbolic AI is QA-GNN, an end-to-end model for multiple-choice open-domain question answering (MCOQA) tasks via interpretable text-graph reasoning. Unlike previous publications, QA-GNN mutually informs PLMs and graph neural networks (GNNs) on top of relevant facts retrieved from knowledge graphs (KGs). However, taking a more holistic view, existing PLM+KG contributions mainly consider commonsense benchmarks and ignore or shallowly analyze performances on biomedical datasets. This thesis start from a propose of a deep investigation of QA-GNN for biomedicine, comparing existing or brand-new PLMs, KGs, edge-aware GNNs, preprocessing techniques, and initialization strategies. By combining the insights emerged in DISI's research, we introduce Bio-QA-GNN that include a KG. Working with this part has led to an improvement in state-of-the-art of MCOQA model on biomedical/clinical text, largely outperforming the original one (+3.63\% accuracy on MedQA). Our findings also contribute to a better understanding of the explanation degree allowed by joint text-graph reasoning architectures and their effectiveness on different medical subjects and reasoning types. Codes, models, datasets, and demos to reproduce the results are freely available at: \url{https://github.com/disi-unibo-nlp/bio-qagnn}.

Possibilidades e limites da avaliação da qualidade de vida : análise dos instrumentos WHOQOL e modelos clássicos de qualidade de vida no trabalho = Possibilities and limits of quality of life assessment : analysis of WHOQOL instruments and quality of work life classical models

Universidade Estadual de Campinas . Faculdade de Educação Física

Allometric models for estimating the phytomass of a secondary Atlantic Forest area of southeastern Brazil

The purpose of this study was to develop and validate equations to estimate the aboveground phytomass of a 30 years old plot of Atlantic Forest. In two plots of 100 m², a total of 82 trees were cut down at ground level. For each tree, height and diameter were measured. Leaves and woody material were separated in order to determine their fresh weights in field conditions. Samples of each fraction were oven dried at 80 °C to constant weight to determine their dry weight. Tree data were divided into two random samples. One sample was used for the development of the regression equations, and the other for validation. The models were developed using single linear regression analysis, where the dependent variable was the dry mass, and the independent variables were height (h), diameter (d) and d²h. The validation was carried out using Pearson correlation coefficient, paired t-Student test and standard error of estimation. The best equations to estimate aboveground phytomass were: lnDW = -3.068+2.522lnd (r² = 0.91; s y/x = 0.67) and lnDW = -3.676+0.951ln d²h (r² = 0.94; s y/x = 0.56).

Evaluation of Antiproliferative, Anti-Type 2 Diabetes, and Antihypertension Potentials of Ellagitannins from Strawberries (Fragaria x ananassa Duch.) Using In Vitro Models

Strawberries represent the main source of ellagic acid derivatives in the Brazilian diet, corresponding to more than 50% of all phenolic compounds found in the fruit. There is a particular interest in the determination of the ellagic acid content in fruits because of possible chemopreventive benefits. In the present study, the potential health benefits of purified ellagitannins from strawberries were evaluated in relation to the antiproliferative activity and in vitro inhibition of alpha-amylase, alpha-glucosidase, and angiotensin I-converting enzyme (ACE) relevant for potential management of hyperglycemia and hypertension. Therefore, a comparison among ellagic acid, purified ellagitannins, and a strawberry extract was done to evaluate the possible synergistic effects of phenolics. In relation to the antiproliferative activity, it was observed that ellagic acid had the highest percentage inhibition of cell proliferation. The strawberry extract had lower efficacy in inhibiting the cell proliferation, indicating that in the case of this fruit there is no synergism. Purified ellagitannins had high alpha-amylase and ACE inhibitory activities. However, these compounds had low alpha-glucosidase inhibitory activity. These results suggested that the ellagitannins and ellagic acid have good potential for the management of hyperglycemia and hypertension linked to type 2 diabetes. However, further studies with animal and human models are needed to advance the in vitro assay-based biochemical rationale from this study.

Evaluation of Antihyperglycemia and Antihypertension Potential of Native Peruvian Fruits Using In Vitro Models

Local food diversity and traditional crops are essential for cost-effective management of the global epidemic of type 2 diabetes and associated complications of hypertension. Water and 12% ethanol extracts of native Peruvian fruits such as Lucuma (Pouteria lucuma), Pacae (Inga feuille), Papayita arequipena (Carica pubescens), Capuli (Prunus capuli), Aguaymanto (Physalis peruviana), and Algarrobo (Prosopis pallida) were evaluated for total phenolics, antioxidant activity based on 2, 2-diphenyl-1-picrylhydrazyl radical scavenging assay, and functionality such as in vitro inhibition of alpha-amylase, alpha-glucosidase, and angiotensin I-converting enzyme (ACE) relevant for potential management of hyperglycemia and hypertension linked to type 2 diabetes. The total phenolic content ranged from 3.2 (Aguaymanto) to 11.4 (Lucuma fruit) mg/g of sample dry weight. A significant positive correlation was found between total phenolic content and antioxidant activity for the ethanolic extracts. No phenolic compound was detected in Lucuma (fruit and powder) and Pacae. Aqueous extracts from Lucuma and Algarrobo had the highest alpha-glucosidase inhibitory activities. Papayita arequipena and Algarrobo had significant ACE inhibitory activities reflecting antihypertensive potential. These in vitro results point to the excellent potential of Peruvian fruits for food-based strategies for complementing effective antidiabetes and antihypertension solutions based on further animal and clinical studies.

Antidiabetes and antihypertension potential of commonly consumed carbohydrate sweeteners using in vitro models

Commonly consumed carbohydrate sweeteners derived from sugar cane, palm, and corn (syrups) were investigated to determine their potential to inhibit key enzymes relevant to Type 2 diabetes and hypertension based on the total phenolic content and antioxidant activity using in vitro models. Among sugar cane derivatives, brown sugars showed higher antidiabetes potential than white sugars; nevertheless, no angiotensin I-converting enzyme (ACE) inhibition was detected in both sugar classes. Brown sugar from Peru and Mauritius (dark muscovado) had the highest total phenolic content and 1,1-diphenyl-2-picrylhydrazyl radical scavenging activity, which correlated with a moderate inhibition of yeast alpha-glucosidase without showing a significant effect on porcine pancreatic alpha-amylase activity. In addition, chlorogenic acid quantified by high-performance liquid chromatography was detected in these sugars (128 +/- 6 and 144 +/- 2 mu g/g of sample weight, respectively). Date sugar exhibited high alpha-glucosidase, alpha-amylase, and ACE inhibitory activities that correlated with high total phenolic content and antioxidant activity. Neither phenolic compounds or antioxidant activity was detected in corn syrups, indicating that nonphenolic factors may be involved in their significant ability to inhibit alpha-glucosidase, alpha-amylase, and ACE. This study provides a strong biochemical rationale for further in vivo studies and useful information to make better dietary sweetener choices for Type 2 diabetes and hypertension management.

HR Del REMNANT ANATOMY USING TWO-DIMENSIONAL SPECTRAL DATA AND THREE-DIMENSIONAL PHOTOIONIZATION SHELL MODELS

The HR Del nova remnant was observed with the IFU-GMOS at Gemini North. The spatially resolved spectral data cube was used in the kinematic, morphological, and abundance analysis of the ejecta. The line maps show a very clumpy shell with two main symmetric structures. The first one is the outer part of the shell seen in H alpha, which forms two rings projected in the sky plane. These ring structures correspond to a closed hourglass shape, first proposed by Harman & O'Brien. The equatorial emission enhancement is caused by the superimposed hourglass structures in the line of sight. The second structure seen only in the [O III] and [N II] maps is located along the polar directions inside the hourglass structure. Abundance gradients between the polar caps and equatorial region were not found. However, the outer part of the shell seems to be less abundant in oxygen and nitrogen than the inner regions. Detailed 2.5-dimensional photoionization modeling of the three-dimensional shell was performed using the mass distribution inferred from the observations and the presence of mass clumps. The resulting model grids are used to constrain the physical properties of the shell as well as the central ionizing source. A sequence of three-dimensional clumpy models including a disk-shaped ionization source is able to reproduce the ionization gradients between polar and equatorial regions of the shell. Differences between shell axial ratios in different lines can also be explained by aspherical illumination. A total shell mass of 9 x 10(-4) M(circle dot) is derived from these models. We estimate that 50%-70% of the shell mass is contained in neutral clumps with density contrast up to a factor of 30.

Regional scale analysis of landform configuration with base-level (isobase) maps

Base-level maps (or ""isobase maps"", as originally defined by Filosofov, 1960), express a relationship between valley order and topography. The base-level map can be seen as a ""simplified"" version of the original topographic surface, from which the ""noise"" of the low-order stream erosion was removed. This method is able to identify areas with possible tectonic influence even within lithologically uniform domains. Base-level maps have been recently applied in semi-detail scale (e.g., 1:50 000 or larger) morphotectonic analysis. In this paper, we present an evaluation of the method's applicability in regional-scale analysis (e.g., 1:250 000 or smaller). A test area was selected in northern Brazil, at the lower course of the Araguaia and Tocantins rivers. The drainage network extracted from SRTM30_PLUS DEMs with spatial resolution of approximately 900 m was visually compared with available topographic maps and considered to be compatible with a 1:1,000 000 scale. Regarding the interpretation of regional-scale morphostructures, the map constructed with 2nd and 3rd-order valleys was considered to present the best results. Some of the interpreted base-level anomalies correspond to important shear zones and geological contacts present in the 1:5 000 000 Geological Map of South America. Others have no correspondence with mapped Precambrian structures and are considered to represent younger, probably neotectonic, features. A strong E-W orientation of the base-level lines over the inflexion of the Araguaia and Tocantins rivers, suggest a major drainage capture. A N-S topographic swath profile over the Tocantins and Araguaia rivers reveals a topographic pattern which, allied with seismic data showing a roughly N-S direction of extension in the area, lead us to interpret this lineament as an E-W, southward-dipping normal fault. There is also a good visual correspondence between the base-level lineaments and geophysical anomalies. A NW-SE lineament in the southeast of the study area partially corresponds to the northern border of the Mosquito lava field, of Jurassic age, and a NW-SE lineament traced in the northeastern sector of the study area can be interpreted as the Picos-Santa Ines lineament, identifiable in geophysical maps but with little expression in hypsometric or topographic maps.

Planning and operation of large-scale water distribution systems with preemptive priorities

This paper describes the development of an optimization model for the management and operation of a large-scale, multireservoir water supply distribution system with preemptive priorities. The model considers multiobjectives and hedging rules. During periods of drought, when water supply is insufficient to meet the planned demand, appropriate rationing factors are applied to reduce water supply. In this paper, a water distribution system is formulated as a network and solved by the GAMS modeling system for mathematical programming and optimization. A user-friendly interface is developed to facilitate the manipulation of data and to generate graphs and tables for decision makers. The optimization model and its interface form a decision support system (DSS), which can be used to configure a water distribution system to facilitate capacity expansion and reliability studies. Several examples are presented to demonstrate the utility and versatility of the developed DSS under different supply and demand scenarios, including applications to one of the largest water supply systems in the world, the Sao Paulo Metropolitan Area Water Supply Distribution System in Brazil.

Generation of self-similar Gaussian time series by means of the DWT and DWPT variance maps

Due to the several kinds of services that use the Internet and data networks infra-structures, the present networks are characterized by the diversity of types of traffic that have statistical properties as complex temporal correlation and non-gaussian distribution. The networks complex temporal correlation may be characterized by the Short Range Dependence (SRD) and the Long Range Dependence - (LRD). Models as the fGN (Fractional Gaussian Noise) may capture the LRD but not the SRD. This work presents two methods for traffic generation that synthesize approximate realizations of the self-similar fGN with SRD random process. The first one employs the IDWT (Inverse Discrete Wavelet Transform) and the second the IDWPT (Inverse Discrete Wavelet Packet Transform). It has been developed the variance map concept that allows to associate the LRD and SRD behaviors directly to the wavelet transform coefficients. The developed methods are extremely flexible and allow the generation of Gaussian time series with complex statistical behaviors.

COMPETITION AMONG EUCALYPTUS TREES DEPENDS ON GENETIC VARIATION AND RESOURCE SUPPLY

Genetic variation and environmental heterogeneity fundamentally shape the interactions between plants of the same species. According to the resource partitioning hypothesis, competition between neighbors intensifies as their similarity increases. Such competition may change in response to increasing supplies of limiting resources. We tested the resource partitioning hypothesis in stands of genetically identical (clone-origin) and genetically diverse (seed-origin) Eucalyptus trees with different water and nutrient supplies, using individual-based tree growth models. We found that genetic variation greatly reduced competitive interactions between neighboring trees, supporting the resource partitioning hypothesis. The importance of genetic variation for Eucalyptus growth patterns depended strongly on local stand structure and focal tree size. This suggests that spatial and temporal variation in the strength of species interactions leads to reversals in the growth rank of seed-origin and clone-origin trees. This study is one of the first to experimentally test the resource partitioning hypothesis for intergenotypic vs. intragenotypic interactions in trees. We provide evidence that variation at the level of genes, and not just species, is functionally important for driving individual and community-level processes in forested ecosystems.

Annual and polyetic progression of citrus canker on trees protected with copper sprays

The effects of copper sprays on annual and polyetic progress of citrus canker, caused by Xanthomonas citri subsp. citri, in the presence of the Asian citrus leafminer (Phyllocnistis citrella), were evaluated in a study conducted in a commercial orchard in northwest Parana state, Brazil, where citrus canker is endemic. Nonlinear monomolecular, logistic and Gompertz models were fitted to monthly disease incidence data (proportion of leaves with symptoms) for each treatment for three seasons. The logistic model provided the best estimate of disease progress for all years and treatments evaluated and logistic parameter estimates were used to describe polyetic disease dynamics. Although citrus canker incidence increased during each of the seasons studied, it decreased over the whole study period, more so in copper-treated trees than in water-sprayed controls. Copper treatment reduced disease incidence compared with controls in every year, especially 2004-2005, when incidence was ca. 10-fold higher in controls than in treated plots (estimated asymptote values 0 center dot 82 and 0 center dot 07, respectively). Copper treatment also reduced estimated initial disease incidence and epidemic growth rates every year.

Quantitative Trait Loci Mapping and The Genetic Basis of Heterosis in Maize and Rice

Despite its importance to agriculture, the genetic basis of heterosis is still not well understood. The main competing hypotheses include dominance, overdominance, and epistasis. NC design III is an experimental design that. has been used for estimating the average degree of dominance of quantitative trait 106 (QTL) and also for studying heterosis. In this study, we first develop a multiple-interval mapping (MIM) model for design III that provides a platform to estimate the number, genomic positions, augmented additive and dominance effects, and epistatic interactions of QTL. The model can be used for parents with any generation of selling. We apply the method to two data sets, one for maize and one for rice. Our results show that heterosis in maize is mainly due to dominant gene action, although overdominance of individual QTL could not completely be ruled out due to the mapping resolution and limitations of NC design III. For rice, the estimated QTL dominant effects could not explain the observed heterosis. There is evidence that additive X additive epistatic effects of QTL could be the main cause for the heterosis in rice. The difference in the genetic basis of heterosis seems to be related to open or self pollination of the two species. The MIM model for NC design III is implemented in Windows QTL Cartographer, a freely distributed software.