Data and visual displays in the Journal of Ecology 1996–2016

Scholars in scientific disciplines face unique challenges in the creation of visualizations, especially in publications that require insights derived from analyses to be visually displayed. The literature on visualizations describes different techniques and best practices for the creation of graphs. However, these techniques have not been used to evaluate the impact of visualizations in academic publications. In the field of ecology, as in other scientific fields, graphs are an essential part of journal articles. Little is known about the connections between the kind of data presented and domain in which the researchers conducted their study that together produces the visual graphics. This study focused on articles published in the Journal of Ecology between 1996 and 2016 to explore possible connections between data type, domain, and visualization type. Specifically, this study asked three questions: How many of the graphics published between 1996 and 2016 follow a particular set of recommendations for best practices? What can Pearson correlations reveal about the relationships between type of data, domain of study, and visual displays? Can the findings be examined through an inter-reliability test lens? Out of the 20,080 visualizations assessed, 54% included unnecessary graphical elements in the early part of the study (1996–2010). The most common type of data was univariate (35%) and it was often displayed using line graphs. Twenty-one percent of the articles in the period studied could be categorized under the domain type “single species.” Pearson correlation analysis showed that data type and domain type was positively correlated ( r = 0.08; p ≤ 0.05). Cohen’s kappa for the reliability test was 0.86, suggesting good agreement between the two categories. This study provides evidence that data type and domain types are equally important in determining the type of visualizations found in scientific journals.

A Systematic Review About Use of TensorFlow for Image Classification and Word Embedding in the Brazilian Context

A great deal of data are available on the Internet, and it is possible to extract any type of implicit knowledge using Artificial Intelligence (AI) tools to support decision making. The open-source TensorFlow framework, developed by the Google Brain Team in 2015, is, presently, the most used tool for several AI applications, such as image classification, word embedding, and chatbot development. This paper presents results of a systematic review of the use of the TensorFlow framework for image classification and word embedding applications written in Portuguese language and in the Brazilian context. We used Google Scholar as Academic Search Engine and 90 were retrieved initially. However, just 12 were remained for reading and obtaining of the main information. Title, publication year, used domain, type of application and covered scope were collected from papers retrieved to accelerate studies in the AI area and to disseminate the potential of this framework for emerging challenges.

A heterodimeric SNX4:SNX7 SNX-BAR autophagy complex coordinates ATG9A trafficking for efficient autophagosome assembly

ABSTRACTEfficient mammalian autophagosome biogenesis requires coordinated input from other cellular endomembrane compartments. Such coordination includes the stimulated trafficking to autophagosome assembly sites of the essential autophagy proteins, ATG9 and ATG16L1, via distinct endosomal compartments. Protein trafficking within the endocytic network is directed by a conserved family of sorting nexins (SNXs), with previous studies implicating SNX18 (an SH3 domain-type SNX-BAR protein) in the mobilisation of ATG9A and ATG16L1 from recycling endosomes during autophagy. Using siRNA and CRISPR-Cas9, we demonstrate that a second mammalian SNX-BAR, SNX4, is needed for efficient LC3 lipidation and autophagosome assembly in mammalian cells. SNX-BARs exist as homo- and heterodimers, and we show that SNX4 forms functional heterodimers with either SNX7 or SNX30, and that these associate with tubulovesicular endocytic membranes at steady state. Detailed image-based analysis during the early stages of autophagosome assembly reveal that SNX4:SNX7 is the autophagy-specific heterodimeric SNX-BAR complex, required for efficient recruitment/retention of core autophagy regulators at the nascent isolation membrane. SNX4 partially co-localises with juxtanuclear ATG9A-positive membranes, with our data linking the SNX4 autophagy defect to the mis-trafficking and/or retention of ATG9A in the Golgi region. Together, our findings show that the SNX4:SNX7 heterodimer coordinates ATG9A trafficking within the endocytic network to establish productive autophagosome assembly sites.SUMMARY STATEMENTA heterodimeric SNX4:SNX7 SNX-BAR complex regulates mammalian autophagosome assembly through the control of ATG9 trafficking.

Synthetic inhibitor leads of human tropomyosin receptor kinase A (hTrkA)

New hTrkA kinase domain type 2 inhibitors and mixed type 1/type 2 inhibitor leads disclosed here offers a differential starting point to investigate the disease pathophysiology.

Dynamic rotation of the protruding domain enhances the infectivity of norovirus

Norovirus is the major cause of epidemic nonbacterial gastroenteritis worldwide. Lack of structural information on infection and replication mechanisms hampers the development of effective vaccines and remedies. Here, using cryo-electron microscopy, we show that the capsid structure of murine noroviruses changes in response to aqueous conditions. By twisting the flexible hinge connecting two domains, the protruding (P) domain reversibly rises off the shell (S) domain in solutions of higher pH, but rests on the S domain in solutions of lower pH. Metal ions help to stabilize the latter conformation in this process. Furthermore, in the resting conformation, the cellular receptor CD300lf is readily accessible, and thus infection efficiency is significantly enhanced. Two P domain conformations were also found in the human norovirus GII.3 capsid. These results provide new insights into the infection mechanisms of the non-envelope viruses that function in dramatic environmental changes such as the digestive tract.Significance StatementThe capsid structures of caliciviruses have been reported to be classified into two different types, according to species and genotype. One is the rising P domain type as shown in human norovirus GII.10 and rabbit hemorrhagic disease virus, where the P domain rises from the S domain surface. The other is the resting P domain type as shown in human norovirus GI.1, sapovirus and San Miguel sea lion virus, where the P domain rests upon the S domain. Here, we demonstrate that the P domain of the murine norovirus infectious particles changes reversibly between the rising and resting P domain types in response to aqueous conditions. Our findings provide new insights into the mechanisms of viral infection of caliciviruses.

Domain-type RBF Collocation Methods for Biharmonic Problems

In this paper some meshless, domain-type discretization techniques are investigated in the context of problems modeled by biharmonic equations. These numerical methods use interpolant composed of radial basis functions (RBFs) as well as collocation technique to discretize a continuous mathematical model. To overcome a problem that appears for biharmonic equations, where two boundary conditions are associated with a boundary node, at which typically only one degree of freedom exists, some modifications of the methods are proposed. They are validated by a benchmark problem of bending and free vibration of Kirchhoff plates. Special attention is paid to estimate proper value of the shape parameter included in radial functions to ensure stability of the solution process and high accuracy. The results obtained show the usefulness of the proposed approaches.