Tree View Research Articles

Design, synthesis and biological evaluation of 4-aminoquinoline derivatives as receptor-interacting protein kinase 2 (RIPK2) inhibitors

Receptor-interacting protein kinase 2 (RIPK2) is an essential protein kinase mediating signal transduction by NOD1 and NOD2, which play an important role in regulating immune signalling. In this study, we designed and synthesised a novel series of 4-aminoquinoline-based derivatives as RIPK2 inhibitors. In vitro, compound 14 exhibited high affinity (IC50 = 5.1 ± 1.6 nM) and excellent selectivity to RIPK2 showing in a dendrogram view of the human kinome phylogenetic tree. Bearing favourable lipophilicity and eligible lipophilic ligand efficiency (LipE), compound 14 was selected to investigate cellular anti-inflammatory effect and was identified as a potent inhibitor to reduce the secretion of MDP-induced TNF-α with a dose-dependent manner. Moreover, compound 14 showed moderate stability in human liver microsome. Given these promising results, compound 14 could serve as a favourable inhibitor of RIPK2 for further physiological and biochemical research so as to be used in therapeutic treatment.

NCAlt: Alternatives and Difference Visualizations for Behavior Trees in Game Development Learning

When learning how to develop AI behavior it is common for students to test different ideas before settling on a desired outcome. This functionality is not available in modern behavior tree systems beyond the traditional methods of duplication and conditional execution. We present NCAlt - a visual behavior authoring framework for exploring multiple game AI behaviors. The system also allows selective merging of nodes between multiple behavior tree alternatives and their visual differencing in the game scene and behavior tree views. We present two worked examples which demonstrate how NCAlt can improve the workflow of game development students. We have conducted a user study where NCAlt was compared against NodeCanvas for creating and using alternatives with moderately skilled game development students. Participants rated NCAlt 15% higher than NodeCanvas on the System Usability Scale (SUS). NCAlt was also rated higher on a self-developed questionnaire. We also conducted a semi-structured interview and a detailed longitudinal follow-up and obtained mostly positive feedback for NCAlt. The results suggest NCAlt has a potential to improve the types of workflows with behavior trees that involve exploration for game development students and facilitate learning, as a result. NCAlt was built on top of NodeCanvas - a plugin for the Unity Engine.

Evaluation Strategies on the Thermal Environmental Effectiveness of Street Canyon Clusters: A Case Study of Harbin, China

Urban overheating significantly affects people’s physical and mental health. The addition of street trees is an essential, economical, and effective means by which to mitigate urban heat and optimize the overall thermal environment. Focusing on typical street canyon clusters in Harbin, China, landscape morphology was quantified by streetscape interface measurements (sky view factor, tree view factor, and building view factor). Through ENVI-met simulations, the correlation mechanism between streetscape interface measurements and thermal environment was evaluated, and optimization methods for assessing the thermal environment of urban streets were proposed. The results revealed: (1) The thermal environment optimization efficiency of general street canyon types was greatest when street tree spacing was 12 m. At present, the smaller spacing has not been simulated and may yield better thermal environment results. The average decrease in temperature (Ta), relative humidity (RH) and mean radiant temperature (MRT) was 0.78%, 2.23%, and 30.20%, respectively. (2) Specific street canyon types should adopt precise control strategies of streetscape interface according to their types to achieve the optimal balance between thermal environment optimization and cost. (3) Streetscape interface measurements and thermal environment indexes show quadratic correlation characteristics, and are critical points for further investigation. The conclusions are more specific than previous research findings, which are of great significance for decreasing the urban heat island effect at the block scale, improving residents’ physical and mental health, and improving the urban environment quality.

IOFS-SA: An interactive online feature selection tool for survival analysis

Background:Survival analysis is a primary problem before clinical treatments to cancer patients after their operations. In order to make this kind of analysis simple, many corresponding tools have been proposed. Though these tools are easy to use, there exist still two fatal flaws. One is that sample grouping is commonly empirical and wrongly based on original gene expressions or survival time. The other is that their feature selection methods mostly depend univariate semi-supervised regression or the multivariate one without considering the small sample size compared with the high dimension. Objective:In order to solve the two problems, we design an automatic feature selection web tool which can also satisfy interactive sample grouping. Methods:An automatic feature selection is performed on user-defined data or TCGA data. users can also perform manual feature selection. Then, hierarchical clustering is used and an automatic re-clustering strategy is proposed after interactive risk score split. Kaplan–Meier survival curve and log-rank test are utilized as the measurement. Results:Experimental results on 53 datasets from TCGA demonstrate the effectiveness of our method. The tree view, heat map and scatter map can intuitively display the result of the selected genes to the doctors for further research. Conclusions:This method is suitable for survival analysis of high-dimensional small sample data sets. At the same time, it also provides a platform for researchers to analyze custom data. It solves the problems of the existing web tools and provides an effective feature selection method for survival analysis. Availability:The full code package is freely available and can be downloaded at https://github.com/Yuan-23/IOFS-SA-ecp-data-main, and the online version at https://bioinfor.nefu.edu.cn/IOFS-SA/ is ready for use freely.

Assessing Effects of Urban Greenery on the Regulation Mechanism of Microclimate and Outdoor Thermal Comfort during Winter in China’s Cold Region

A comfortable thermal environment in outdoor spaces is beneficial to people’s physical and mental health in cold conditions during winter. Greenery can improve outdoor thermal comfort (OTC) via microclimates in winter. Multiple methods have been employed to investigate how greenery influences OTC and microclimate. However, the underlying mechanism of how microclimate participates in the regulation of the effect of greenery on OTC is unclear. To examine the mediating effect of microclimate on the relation between greenery and OTC in cold weather during winter, we conducted meteorological measurement and thermal comfort surveys in Zhengzhou, a city in China’s cold region, from 29 to 30 December 2019. Two objective greening indices from different dimensions were extracted at twelve sampling points: (1) the green view index (GVI) from horizontal normal images from people’s perspective, and (2) the tree view factor (TVF) from vertical-upward fisheye images. With microclimatic parameters as the mediators, a comprehensive multi-step mediation analysis was conducted. The regression results revealed that the GVI and TVF were negatively associated with the thermal comfort vote (TCV) (i.e., the more greenery, the less TCV, which means the more comfortable the thermal environment). Our findings show that both GVI and TVF contribute to OTC through different mechanisms in cold climatic conditions during winter. Vegetation in sight revealed by the GVI can directly regulate OTC by affecting people’s mental feelings or other factors. Air temperature (Ta), relative humidity (RH), and wind speed (Va) served as significant partial mediators for the GVI. Moreover, there was a complete mediation for TVF–OTC correlation with Ta, RH, and Va as significant mediators. The mediating effects of microclimate accounted for 81.00% for GVI and 89.02% for TVF, respectively. The GVI is propitious to the study of people’s mental health and landscape preferences, whereas TVF is suitable for studies on microclimate adaptation.

Influence of view factors on intra-urban air temperature and thermal comfort variability in a temperate city

Urban geometry is known to be one of the major factors in explaining the intra-urban temperature variations. A commonly used indicator to describe the urban geometry is the sky view factor. However, the existing studies have shown that the relationship between SVF and urban temperature is quite contradictory. This suggests that a single SVF cannot accurately quantify the urban geometry. For comparison, we here propose to use view factors, including sky, building and tree view factors (SVF, BVF, and TVF, respectively), to accurately quantify the three-dimensional urban geometry. Based on microclimate measurements conducted in Beijing Olympic Park and its surrounding urban environment in Beijing, China, the impact of view factors on intra-urban air temperature and thermal comfort was evaluated. Measurements were conducted along a selected path during hot summer days with clear skies and light winds by mobile traverses. The obtained results showed that SVF was positively correlated with air temperature during the day but negatively correlated with air temperature at night. BVF mainly played a warming role in both daytime and nighttime. Especially at night, BVF was the main geometric warming factor. TVF had a significant cooling effect during the day but did not have a negative effect at night due to reduced SVF. There was a strong point-to-point correlation between SVF and outdoor thermal comfort in the daytime. The mean differences in Mean Radiant Temperature and Physiologically Equivalent Temperature between shaded and unshaded sites were 12.0 °C and 6.8 °C, respectively, which suggested that providing effective shading is extremely important for improving outdoor daytime thermal comfort.

Context-Aware Phylogenetic Trees for Phylogeny-Based Taxonomy Visualization.

Sustained efforts in next-generation sequencing technologies are changing the field of taxonomy. The increase in the number of resolved genomes has made the traditional taxonomy of species antiquated. With phylogeny-based methods, taxonomies are being updated and refined. Although such methods bridge the gap between phylogeny and taxonomy, phylogeny-based taxonomy currently lacks interactive visualization approaches. Motivated by enriching and increasing the consistency of evolutionary and taxonomic studies alike, we propose Context-Aware Phylogenetic Trees (CAPT) as an interactive web tool to support users in exploration- and validation-based tasks. To complement phylogenetic information with phylogeny-based taxonomy, we offer linking two interactive visualizations which compose two simultaneous views: the phylogenetic tree view and the taxonomic icicle view. Thanks to its space-filling properties, the icicle visualization follows the intuition behind taxonomies where different hierarchical rankings with equal number of child elements can be represented with same-sized rectangular areas. In other words, it provides partitions of different sizes depending on the number of elements they contain. The icicle view integrates seven taxonomic rankings: domain, phylum, class, order, family, genus, and species. CAPT enriches the clades in the phylogenetic tree view with context from the genomic data and supports interactive techniques such as linking and brushing to highlight correspondence between the two views. Four different use cases, extracted from the Genome Taxonomy DataBase, were employed to create four scenarios using our approach. CAPT was successfully used to explore the phylogenetic trees as well as the taxonomic data by providing context and using the interaction techniques. This tool is essential to increase the accuracy of categorization of newly identified species and validate updated taxonomies. The source code and data are freely available at https://github.com/ghattab/CAPT.

PhyloCloud: an online platform for making sense of phylogenomic data.

Phylogenomics data have grown exponentially over the last decades. It is currently common for genome-wide projects to generate hundreds or even thousands of phylogenetic trees and multiple sequence alignments, which may also be very large in size. However, the analysis and interpretation of such data still depends on custom bioinformatic and visualisation workflows that are largely unattainable for non-expert users. Here, we present PhyloCloud, an online platform aimed at hosting, indexing and exploring large phylogenetic tree collections, providing also seamless access to common analyses and operations, such as node annotation, searching, topology editing, automatic tree rooting, orthology detection and more. In addition, PhyloCloud provides quick access to tools that allow users to build their own phylogenies using fast predefined workflows, graphically compare tree topologies, or query taxonomic databases such as NBCI or GTDB. Finally, PhyloCloud offers a novel tree visualisation system based on ETE Toolkit v4.0, which can be used to explore very large trees and enhance them with custom annotations and multiple sequence alignments. The platform allows for sharing tree collections and specific tree views via private links, or make them fully public, serving also as a repository of phylogenomic data. PhyloCloud is available at https://phylocloud.cgmlab.org

Identification of Streptomyces spp. from garbage dump soils in Surabaya, Indonesia.

Background and Aim:Streptomyces is a well-known agent of secondary metabolite production. This study aimed to identify Streptomyces spp. from garbage dump soils in Surabaya based on the 16S rRNA gene sequence. Moreover, the structure of new chemical compounds used for treating infectious diseases in humans, animals, and plants was elucidated.Materials and Methods:We isolated Streptomyces spp. from garbage dump soils in Surabaya. In this study, all isolates were characterized according to phenotype, and they were also confirmed by 16S rRNA gene sequence analysis using real-time polymerase chain reaction. Multiple sequence alignment and molecular phylogeny analyses were conducted using the MEGA 5.0 software, and then the TREE VIEW program was used to display the phylogenetic tree. The level of DNA similarity was also evaluated using the basic local alignment search tool (BLAST) program and then compared with nucleotide sequences stored in the GenBank database using National Center for Biotechnology Information BLAST.Results:The eight Streptomyces spp. showed different nucleotide sequence lengths in gel electrophoresis and photography, which is in accordance with the results observed in the phylogenetic tree. New types of Streptomyces spp., Sp-C, Sp-D, Sp-Ep, Sp-G, and Sp-I, were found from the waste heap in Surabaya. Of these, Sp-Ep was very closely related to Streptomyces indonesiasis and Streptomyces nashvillensis. Sp-F was identified as Streptomyces levis strain NRRL B-24299, and Sp-C was identified as Synodontis filamentosus. Sp-D was related to Sida javensis and Staphylococcus roseus. Sp-G was related to Streptomyces roseoviridis strain NBRC 12911 and Streptomyces thermocarboxydovorans strain AT52. Sp-I was related to Streptomyces cangkringensis and Streptomyces asiaticus. Finally, Sp-A was related to Sansevieria laurentii strain LMG 19959.Conclusion:Based on the phylogenetic tree, new strains of Streptomyces isolate, namely, Sp-D, Sp-Ep, Sp-G, and Sp-I, were found in the garbage dump soils of Surabaya. This new strain can produce antibiotics to be used as an alternative to antibiotics; however, further research is needed to confirm the activity.

MOLECULAR ANALYSIS OF FECGH GENE IN HAMDANI SHEEP BREED IN IRAQI KURDISTAN REGION

The objective of this study was to investigate association between FecGH-GDF-9 gene polymorphism and litter size in Hamdani fat-tailed sheep. The genomic DNA was extracted from eighty-seven blood samples of Hamdani ewes. The FecGH-GDF-9 locus was detected by PCRs, and identified DNA genotyped by DNA sequencing. The evaluate several parameters included fertility (%), conception (%), letter size at birth, twining rate (%), triple rate (%), barrenness (%) and productivity (%) were measured and arrived 91.95, 95.40, 1.825, 150, 11.25, 8.05 and 159.77, respectively. The blast tree view results in NCBI blast show Hamdani sheep is more closely to Norway white face sheep, Han sheep and Pelibuey Sheep breeds which have high litter sizes than the Iranian Ghezel sheep. Hamdani ewe’s genome have three changed nucleotides point at 1273 bp (C to G) changed Alanine to Arginine, 1281 bp (A to T) changed lysine to Isoleucine and 1344 bp (C to A) changed Proline to Glutamine. Also three nucleotides deletion were detected at 1279 bp (C), 1283 (T) and 1376 bp (G) position with two inserted nucleotides at 1319 bp (T) and 1357 bp (G) position. The 5'….C/TNAG…3' sequence cite of mutated FecGH locus was detected by Ddel restriction enzyme which have significant effect on litter size in sheep breeds.

The Innate Chronotoxicity hypothesis: an ubiquitous physiological flaw both unnoticed and inevitable. Could circadian rhythm be an evolutionary mismatch?

The aim of this study is to outline a flaw in a com-monly scarcely considered physiological adaptation process, which, unnoticed, can lead to severe pathologies that range from cancer to autoimmunity. This being circadian rhythm (CR) disruption a common factor in the onset of such diseases, an additional objective of this paper is to assess whether or not CR is advantageous for organisms and in which conditions that may be and, if disadvantageous, to measure its chronotoxicity. The term "chronotoxicity" is here intended to denote the degree to which the environment desynchronizes the CR of an organism. An inductive research approach was adopted to integrate, evaluate and interpret the findings of the existing literature to form and verify a new interpretation in the field of research that in this study was named as "Innate Chronotoxicity" (IC) hypothesis. The analysis of the cited literature provided data to derive four empirical assumptions for the attainment of the IC hypothesis, and namely that: the equatorial region is the only area on our planet that is not chronotoxic for humans because its constant LD cycle corresponds to the human organism's internal clock cycle and may therefore correctly entrain the circadian rhythm; chronotoxicity is therefore innate and inevitable considering that the majority of hu-mans live a long way from the equator and the circadian rhythm is a congenital physiological feature of all humans; the circadian rhythm is an evolutionary mismatch since innate chronotoxicity is inherently a disadvantage; IC intensity increases proportionally to the distance a person lives from the equator. Innate chronotoxicity and its causes have remained unnoticed and undetected even to this day, although this study's fin-dings robustly validate the above four assumptions. If this hypothesis is confirmed through further rigorous research, it bears significant implications for the world's healthcare systems, due to the burden placed on them by the estimated population affected and the severity of the resulting related diseases. To entertain further speculation, in the conclusions it is cautiously suggested an expanded view of the circadian pacemaker tree.

Subjective or objective measures of street environment, which are more effective in explaining housing prices?

Houses with better street design are found to relate to a price premium. Prior studies mainly present the street quality using objective indicators like tree counts and distance to parks with land use data, or most recently using the greenery view index extracted from street view imagery (SVI). We argue that objective indicators cannot completely describe people’s sense of a place, as perception is a highly subjective process. We hypothesize that subjective measures using visual surveys could capture more subtle human perceptions, thus providing stronger predictive power to housing prices. However, the role of subjectively measured street design qualities is less known due to the lack of large-scale perception data. To test our hypothesis, we first collected designers’ perceptions on five urban design qualities from pairwise SVIs rankings in Shanghai with an online visual survey. Unlike the mainstream of using generic image features, we followed urban design theory and used rule-based features, i.e., about thirty streetscape elements extracted from SVIs to train machine learning (ML) models to predict subjective perceptions. The predictive power of five qualities versus ten selected individual streetscapes on housing price were compared using the hedonic price model. Besides the standard ordinary least squares (OLS), spatial regression and geographical weighted regression (GWR) were also developed to account for the spatial dependence and heterogeneity effects. We found both subjectively measured design qualities and objective indicators outperformed housing structural attributes in explaining housing price. While the objective view indexes collectively explained more price variances, the five perceptions individually exhibited stronger strength. Third, less-studied perceptions like “human scale” showed stronger strength than commonly studied “safety” and “enclosure”. Fourth, less-studied view indexes like “person” and “fence” outperformed ubiquitous features like trees and buildings. Lastly, prior studies might have resulted in biased estimations due to ignoring the multicollinear issues between the sky, tree and building views. Our study addressed the effectiveness of incorporating subjective perceptions at a micro level to infer housing prices. Correlations between subjective perceptions were strong while that of objective indicators were negligible, therefore subjective perceptions can complement the objective indicators. The findings provide important reference to decision makers when selecting street quality indicators to infer urban design, city planning and community and housing development plans.

Estimation of Mean Radiant Temperature in Urban Canyons Using Google Street View: A Case Study on Seoul

Extreme heat exposure has severe negative impacts on humans, and the issue is exacerbated by climate change. Estimating spatial heat stress such as mean radiant temperature (MRT) is currently difficult to apply at city scale. This study constructed a method for estimating the MRT of street canyons using Google Street View (GSV) images and investigated its large-scale spatial patterns at street level. We used image segmentation using deep learning to calculate the view factor (VF) and project panorama into fisheye images. We calculated sun paths to estimate MRT using panorama images from Google Street View. This paper shows that regression analysis can be used to validate between estimated short-wave, long-wave radiation and the measurement data at seven field measurements in the clear-sky (0.97 and 0.77, respectively). Additionally, we compared the calculated MRT and land surface temperature (LST) from Landsat 8 on a city scale. As a result of investigating spatial patterns of MRT in Seoul, South Korea, we found that a high MRT of street canyons (>59.4 °C) is mainly distributed in open space areas and compact low-rise density buildings where the sky view factor is 0.6–1.0 and the building view factor (BVF) is 0.35–0.5, or west-east oriented street canyons with an SVF of 0.3–0.55. However, high-density buildings (BVF: 0.4–0.6) or high-density tree areas (Tree View Factor, TVF: 0.6–0.99) showed low MRT (<47.6). The mapped MRT results had a similar spatial distribution to the LST; however, the MRT was lower than the LST in low tree density or low-rise high-density building areas. The method proposed in this study is suitable for a complex urban environment consisting of buildings, trees, and streets. This will help decision makers understand spatial patterns of heat stress at the street level.

“Between the Mouth of the Two Rivers”

This contribution offers an anthropological view of holy waters, springs, sacred rivers, and trees in the ancient Mesopotamian religious framework. Water is omnipresent in Mesopotamian myths and rituals, particularly in association with the cosmic Apsû, the primeval source of all waters. The pristine waters flow out through springs in the mountains and form the flowing bodies of rivers. For the Babylonians and Assyrians, rivers and watercourses were sacred and cosmic entities, often worshipped as deities. The Tigris and the Euphrates particularly appeared as river deities, with life-giving, motherly, healing, and judging roles. This essay considers the interrelationships between the Apsû, springs and sacred rivers, and the associated sacred trees, mountains and anthropomorphic deities, to shed new light onto ancient Mesopotamian notions about nature, religion, and the cosmos.

AI Augmented Approach to Identify Shared Ideas from Large Format Public Consultation

Public data, contributed by citizens, stakeholders and other potentially affected parties, are becoming increasingly used to collect the shared ideas of a wider community. Having collected large quantities of text data from public consultation, the challenge is often how to interpret the dataset without resorting to lengthy time-consuming manual analysis. One approach gaining ground is the use of Natural Language Processing (NLP) technologies. Based on machine learning technology applied to analysis of human natural languages, NLP provides the opportunity to automate data analysis for large volumes of texts at a scale that would be virtually impossible to analyse manually. Using NLP toolkits, this paper presents a novel approach for identifying and visualising shared ideas from large format public consultation. The approach analyses grammatical structures of public texts to discover shared ideas from sentences comprising subject + verb + object and verb + object that express public options. In particular, the shared ideas are identified by extracting noun, verb, adjective phrases and clauses from subjects and objects, which are then categorised by urban infrastructure categories and terms. The results are visualised in a hierarchy chart and a word tree using cascade and tree views. The approach is illustrated using data collected from a public consultation exercise called “Share an Idea” undertaken in Christchurch, New Zealand, after the 2011 earthquake. The approach has the potential to upscale public participation to identify shared design values and associated qualities for a wide range of public initiatives including urban planning.

Lipopolysaccharide of Pseudomonas mandelii, Isolated from Antarctica

Representatives of the Pseudomonas mandelii species are able to exist and multiply in places where the temperature is constantly low. The optimum growth temperature for P. mandelii is 25–30°C, although this bacterium can grow at 4°C but not at 37°C. Therefore, P. mandelii is an excellent example of psychrotolerant bacterium which like psychrophilic bacteria is characterized by a number of structural and functional adaptations that facilitate survival at low temperatures. To understand these microorganisms’ role in Antarctica the characterization of its biopolymers is vital. One of these biopolymers is lipopolysaccharide (LPS), composition and structure of which are diagnostically significant. This determines the aim of the work – to isolate lipopolysaccharides from the cells of Antarctic strain of P. mandelii, grown at different temperatures, to characterize them chemically, and to study their functional and biological activity. Methods. The object of the study was Pseudomonas sp. U1, isolated from moss on Galindez Island in Antarctica. Lipopolysaccharides were extracted from dried cells by 45% phenol water solution at 65–68°С by Westphal and Jann method. The amount of carbohydrates was determined by phenol-sulfuric method. Carbohydrate content was determined in accordance to the calibration curve, which was built using glucose as a standard. The content of nucleic acids was determined by Spirin, protein − by Lowry method. Serological activity of LPS was investigated by double immunodiffusion in agar using the method of Ouchterlony. Polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate (SDS-PAAG electrophoresis) was performed according to Laemmli. Results. As a result of phylogenetic analysis (programs ClustalX 2.1, Tree view, Mega v. 6.00) it was shown that the Antarctic bacterial strain Pseudomonas sp. U1 associated with green moss has a 99.4% homology with the type strain from the GenBank database NR024902 P. mandelii CIP 105273T. According to these data and proximity to the corresponding cluster of species, the studied isolate can be identified as P. mandelii. A characteristic feature of LPS isolated from P. mandelii cells, grown at different temperatures (20°C and 4°C) is their heterogeneity. This is evidenced by the data of the monosaccharide composition, electrophoretic distribution, which showed that P. mandelii produces S- and SR-forms of LPS, differed in the length of the O-specific polysaccharide chains. The R-form of LPS is also present, which does not contain an O-specific polysaccharide chains. Structural heterogeneity is also inherent in LPS lipid A. This is evidenced by the data of the fatty acid composition. In LPS grown at 4°C no unsaturated fatty acids were found, while such ones are synthesized in LPS of other bacteria grown in the cold, in response to a decrease in growth temperature. The study of the immunochemical properties of LPS was carried out using polyclonal O-antisera as antibodies, and LPS as antigens indicated that in homologous systems LPS exhibited serological activity. LPS obtained from P. mandelii U1 cells, grown at 20°C, had a complex antigenic composition and gave two clear lines of precipitation at a concentration of 1 mg/mL. LPS obtained from P. mandelii U1 cells, grown at 4°C, gave one line, which indicates their serological homogeneity. Conclusions. For the first time lipopolysaccharides were isolated from cells of P. mandelii U1, grown at 4°C and 20°С. A characteristic feature of these LPS is their heterogeneity. This is evidenced by the data of the monosaccharide and fatty acid composition, electrophoretic distribution, which showed that P. mandelii produces S- and SR-forms of LPS, differed in the length of the O-specific polysaccharide chains. LPS, obtained from cells, grown at different temperatures, are differed by serological activity.

A multilevel approach for assessing the effects of microclimatic urban design on pedestrian thermal comfort: The High Line in New York

Due to global warming and rapid urbanization, the frequency and intensity of extreme heat events in the United States have increased. Particularly for pedestrians, excessive heat has been reported as a critical barrier to walking activity, which, in turn, can deteriorate walkability and urban vitality. By using a multilevel spatial approach, this study investigates the combined effects of microclimatic urban design features on daytime pedestrian thermal comfort. For this purpose, it uses on-site field measurements taken in July 2019 and estimates how different scales of street- and block-scale design factor impact the physiological thermal comfort of pedestrians on the High Line in New York City. Based on the findings, the High Line experiences high thermal stress conditions, with clusters of hot spots particularly in its upper section. In addition, the urban design features at both the street and block scales are highly correlated with estimated pedestrian thermal comfort. Specifically, at the block-scale level, the mean energy budget value largely depends on block density and volume, while at the street-scale level, the height-to-width ratio, tree view factors, and tree canopy cover ratio have a negative linear relationship with absorbed solar radiation. Moreover, the findings indicate that the combination of urban design factors at the street- and block-scale levels significantly impact pedestrian thermal comfort. This study offers practical knowledge and a deeper understanding about climate-sensitive urban designs that are highly resistant to extreme heat events.

GTXplorer: A portal to navigate and visualize the evolutionary information encoded in fold A glycosyltransferases.

Glycosyltransferases (GTs) play a central role in sustaining all forms of life through the biosynthesis of complex carbohydrates. Despite significant strides made in recent years to establish computational resources, databases and tools to understand the nature and role of carbohydrates and related glycoenzymes, a data analytics framework that connects the sequence-structure-function relationships to the evolution of GTs is currently lacking. This hinders the characterization of understudied GTs and the synthetic design of GTs for medical and biotechnology applications. Here, we present GTXplorer as an integrated platform that presents evolutionary information of GTs adopting a GT-A fold in an intuitive format enabling in silico investigation through comparative sequence analysis to derive informed hypotheses about their function. The tree view mode provides an overview of the evolutionary relationships of GT-A families and allows users to select phylogenetically relevant families for comparisons. The selected families can then be compared in the alignment view at the residue level using annotated weblogo stacks of the GT-A core specific to the selected clade, family, or subfamily. All data are easily accessible and can be downloaded for further analysis. GTXplorer can be accessed at https://vulcan.cs.uga.edu/gtxplorer/ or from GitHub at https://github.com/esbgkannan/GTxplorer to deploy locally. By packaging multiple data streams into an accessible, user-friendly format, GTXplorer presents the first evolutionary data analytics platform for comparative glycomics.

Visual Analysis of Economic Decision-Making and Wealth Change under Simulated Situations

<p indent=0mm>For the large-scale high-dimensional and dynamic data generated in economic experiments, a visual analysis method is proposed to explore the experimental data of real-effort tasks under simulated situations based on our cooperation with experimental economics experts. A parallel coordinate-like information diagram is designed to give an overview of the experimental process and individual behaviors. Interactive decision tree view, time-series wealth view, and general decision Sankey view are provided to explore the correlation between participants’ behaviors and wealth change. Further, a visual analysis system integrating the visual designs and data mining models is developed for domain experts to analyze the decision-making behaviors and key factors on the wealth change, and provides evidence for the internal mechanism of poverty generation and cycle deterioration. Case studies and expert feedbacks based on real data verify the effectiveness of our system.

Network Creation Games with Traceroute-Based Strategies

Network creation games have been extensively used as mathematical models to capture the key aspects of the decentralized process that leads to the formation of interconnected communication networks by selfish agents. In these games, each user of the network is identified by a node and selects which link to activate by strategically balancing his/her building cost with his/her usage cost (which is a function of the distances towards the other player in the network to be built). In these games, a widespread assumption is that players have a common and complete information about the evolving network topology. This is only realistic for small-scale networks as, when the network size grows, it quickly becomes impractical for the single users to gather such a global and fine-grained knowledge of the network in which they are embedded. In this work, we weaken this assumption, by only allowing players to have a partial view of the network. To this aim, we borrow three popular traceroute-based knowledge models used in network discovery: (i) distance vector, (ii) shortest-path tree view, and (iii) layered view. We settle many of the classical game theoretic questions in all of the above models. More precisely, we introduce a suitable (and unifying) equilibrium concept which we then use to study the convergence of improving and best response dynamics, the computational complexity of computing a best response, and to provide matching upper and lower bounds to the price of anarchy.