The ConSurf web‐sever for the analysis of proteins, RNA, and DNA provides a quick and accurate estimate of the per‐site evolutionary rate among homologues. The analysis reveals functionally important ...regions, such as catalytic and ligand‐binding sites, which often evolve slowly. Since the last report in 2016, ConSurf has been improved in multiple ways. It now has a user‐friendly interface that makes it easier to perform the analysis and to visualize the results. Evolutionary rates are calculated based on a set of homologous sequences, collected using hidden Markov model‐based search tools, recently embedded in the pipeline. Using these, and following the removal of redundancy, ConSurf assembles a representative set of effective homologues for protein and nucleic acid queries to enable informative analysis of the evolutionary patterns. The analysis is particularly insightful when the evolutionary rates are mapped on the macromolecule structure. In this respect, the availability of AlphaFold model structures of essentially all UniProt proteins makes ConSurf particularly relevant to the research community. The UniProt ID of a query protein with an available AlphaFold model can now be used to start a calculation. Another important improvement is the Python re‐implementation of the entire computational pipeline, making it easier to maintain. This Python pipeline is now available for download as a standalone version. We demonstrate some of ConSurf's key capabilities by the analysis of caveolin‐1, the main protein of membrane invaginations called caveolae.
The actual functions of a region may not reflect the intent of the original zoning scheme from planners. To identify the actual urban functional regions, numerous methods have been proposed with ...computational advancement. Specifically, remote sensing by image recognition, geodemographic classification, social sensing with big data and geo-text mining techniques have been widely applied. Points-of-interest (POIs) are one of the most common open-access data type used to extract information pertaining to functional zones. However, previous works have either lost sight or did not make full use of the spatial interactions that can be extracted from POIs due to model limitations in the context of geographical space. In this research, we introduced an approach that detects functional regions at the scale of a neighborhood area (NA) by combining POI data and a simplified Place2vec model, which is theorized from the first law of geography. First, the POI-based spatial context is constructed by using the nearest neighbor approach. Then, we can increase the number of training tuples (tcenter,tcontext) based on the weight derived from the distance between the POI tcenter and POI tcontext. Next, high-dimensional characteristic vectors of the POIs are extracted by using the skip-gram training framework. By summarizing the POI vectors at the NA level, we employ a K-means clustering model to cluster the functional regions. Compared with other probabilistic topic models (PTMs) and Word2vec, the Place2vec-based approach obtained the highest mean reciprocal rank value (MRR-SWP=0.356, MRR-SLC=0.401, MRR-SJC=0.433, and MRR-SLin=0.421) in terms of similarity capturing performance and functional region identification accuracy (OA=0.7424). The research has important implications to urban planning and governance.
•Place2vec model performs better than conventional semantic model in dealing with POI (Point of Interest) similarities.•Place2vec model performs better in terms of functional regions identification than conventional semantic model.•Eight urban functional regions are classified based on Place2vec model and K-means cluster algorithm in this study.
Vision develops rapidly during infancy, yet how visual cortex is organized during this period is unclear. In particular, it is unknown whether functional maps that organize the mature adult visual ...cortex are present in the infant striate and extrastriate cortex. Here, we test the functional maturity of infant visual cortex by performing retinotopic mapping with functional magnetic resonance imaging (fMRI). Infants aged 5–23 months had retinotopic maps, with alternating preferences for vertical and horizontal meridians indicating the boundaries of visual areas V1 to V4 and an orthogonal gradient of preferences from high to low spatial frequencies. The presence of multiple visual maps throughout visual cortex in infants indicates a greater maturity of extrastriate cortex than previously appreciated. The areas showed subtle age-related fine-tuning, suggesting that early maturation undergoes continued refinement. This early maturation of area boundaries and tuning may scaffold subsequent developmental changes.
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•Retinotopic organization of striate and extrastriate visual areas in infancy•Spatial frequency sensitivity varies within and across infant visual areas•Weak developmental change from 5 to 23 months, suggesting early maturation•Possible to identify and interrogate functional regions of interest in human infants
Ellis et al. use fMRI to study how the visual system is organized in human infants. They find evidence for multiple visual maps throughout visual cortex, indicating an earlier maturity of extrastriate cortex than previously appreciated. This nascent organization may be critical for scaffolding subsequent developmental changes in perception.
The rapid expansion of cars as the main transport mode over the last few decades has caused many negative effects mainly in urban areas. Many countries across the world thus want to attract ...passengers back to public transport. One of the most important and useful tools is supporting public transport by creating integrated transport systems (ITS). ITS represent innovative solution for organising urban and regional public transport. ITS are based on the integration of individual transport modes into one interconnected and coordinated system. However, the key question is how they are spatially defined and how they are organised internally. This is a relatively complicated issue as natural population flows, tariff systems, as well as the specifics of the transport infrastructure of the area, must be reflected.
The main aim of the article is to propose the optimal delimitation and internal structure of the integrated transport system in the South Bohemian Region of the Czech Republic. To design the optimal delimitation, we use an innovative method based on utilizing location data from mobile phones, which reliably reflect the population flows. To delimitate the zones of a new integrated transport system we use the CURDS regionalisation algorithm and Smart's interaction measure. We found out substantial disproportion between the current organisation of the public transport system and regular population flows based on mobile positioning data. We suggest adjusting and developing a new integrated transport system which will reflect the current organisation of regular population flows. Finally, we test four versions of micro-regions as a sophisticated basis to define and internally structure the new ITS in the South Bohemian Region.
•We use an innovative approach to delimitate and design the transport integrated system of public transport.•Our approach is based on mobile positioning data as a useful tool to analyse regular population flows within the area.•We have delimited four versions of ITS zones. The most suitable is the version D with 58 self-contained micro-regions.•We suggest using the resulting micro-regions as a sophisticated platform for developing new ITS in the research area.
N,N′-substituted p-phenylenediamines (PPDs) are widely used antioxidants in rubber tires, which could be released and accumulated in road dusts with rubber tires wear. As ozonation product of ...N-(1,3-dimethylbutyl)-N′-phenyl-p-phenylenediamine (6PPD), 6PPD-quinone (6PPD-Q) exhibited higher toxicity to coho salmon. However, studies on their environmental behaviors are still limited. Road dust is the major medium PPDs exist, which significantly affects the levels of PPDs in other mediums, especially surface water and particulate matter. In this study, road dust samples were collected in 55 major cities of China to explore the distribution characteristics of PPDs and 6PPD-Q. The concentrations of total PPDs (ΣPPDs) and 6PPD-Q in urban trunk road dust samples were in the ranges of 7.90–727 and 3.00–349 ng/g, with median concentrations of 68 and 49 ng/g, respectively. 6PPD and 6PPD-Q are the dominant components in most road dusts. The functional region-dependent pollution characteristics of PPDs and 6PPD-Q give the first finding that urban tunnel road was the highly polluted region, followed by urban trunk roads. Suburban road dusts had a lower pollution level. Moreover, the estimated daily intake (EDI) of PPDs and 6PPD-Q for children was much higher than adults.
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•Characteristics of PPDs and 6PPD-Q in road dusts were investigated across China.•6PPD-Q and 6PPD were the dominant components in road dusts.•The median concentration of 6PPD-Q in urban trunk road dusts was 49.4 ng/g.•PPDs and 6PPD-Q showed traffic functional region-dependent differences.•Runoff potential assessment indicate the risk of 6PPD-Q to aquatic organisms.
Accurate qualitative and quantitative information on the characteristics of traffic noise exposure in densely populated urban areas is an important prerequisite for reasonable traffic noise control. ...The primary objective of this study is the development and application of a traffic noise exposure evaluation method based on points of interest (POIs). First, an automatic query arithmetic is used to acquire geospatial information, POIs data, building and network information from the webmap. Second, the attribute matrix of preprocessed POIs for the population is constructed. And the population distribution is obtained by principal component analysis (PCA) of POIs and Gaussian decomposition of demographic data. Then, the modified traffic noise line-source model is applied to calculate the noise distribution considering attenuation among buildings based on measured traffic flow parameters. Finally, with the help of the proposed noise evaluation indicators, and considering the noise function requirements (NFRs, which can be divided into four classes according to different area land-use types), traffic noise evaluation is realized. The proposed method is applied to a typical region with four NFR classes. It is concluded that the characteristics of traffic noise exposure are affected by traffic conditions, buildings, NFR classes and population distribution. And the crowds exposed to noise present aggregation effects, which are usually centered around specific buildings. In addition, POI types which people actives related suffer more serious noise exposure, and exposure is overestimated at low requirement regions without considering crowd distribution of the setting scenario.
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•Principal component analysis distributes population based on Interest Points (POIs).•Traffic, buildings, Function Regions and population comprehensively affects noise exposure.•POI types which people actives related, suffer more serious noise exposure.•Exposure is overestimated at low requirement regions without considering crowd distribution.•Noise exposure presents aggregation effects, and centered on specific buildings.
•A road traffic noise evaluation method for heterogeneous crowds is presented.•Heterogeneous crowd distribution, age and acoustic requirements are considered.•A noise response curve (NRC) is ...established.•The application verified the reasonableness and practicality of the method.
The primary objective of this study is to develop an urban traffic noise exposure evaluation method for differential crowd characteristics, which takes crowd distribution, ages and acoustic requirements into consideration. First, road traffic noise data are simulated using a line-source model, and crowd distribution data are obtained by the decomposition of demographic data based on the different building attraction coefficients of the heterogeneous crowd. Then, the noise response curve (NRC) of the heterogeneous crowd is established with the normalization of subjective feelings of respondents and calibrating the response level of each age group in combination. Finally, with the help of the proposed noise evaluation indicators, and considering the noise function requirements (NFR), the traffic noise evaluation of differential crowd characteristics is realized. The method is applied to a typical scenario, and the results and analysis verified the reasonability and practicability of the method in urban traffic noise exposure evaluation.
Many studies are in an effort to explore urban spatial structure, and urban functional regions have become the subject of increasing attention among planners, engineers and public officials. Attempts ...have been made to identify urban functional regions using high spatial resolution (HSR) remote sensing images and extensive geo-data. However, the research scale and throughput have also been limited by the accessibility of HSR remote sensing data. Recently, big geo-data are becoming increasingly popular for urban studies since research is still accessible and objective with regard to the use of these data. This study aims to build a novel framework to provide an alternative solution for sensing urban spatial structure and discovering urban functional regions based on emerging geo-data – points of interest (POIs) data and an embedding learning method in the natural language processing (NLP) field. We started by constructing the intraurban functional corpus using a center-context pairs-based approach. A word embeddings representation model for training that corpus was used to extract multiprototype vectors in the second step, and the last step aggregated the functional parcels based on an introduced spatial clustering method, hierarchical density-based spatial clustering of applications with noise (HDBSCAN). The clustering results suggested that our proposed framework used in this study is capable of discovering the utilization of urban space with a reasonable level of accuracy. The limitation and potential improvement of the proposed framework are also discussed.
•We proposed a framework to infer urban functional regions using POIs data.•We considered ubiquitous homonymy and polysemy of urban regions based on the NLP model.•We introduced an efficient HDBSCAN clustering method to aggregate the parcel functions.•A case study in intraurban area of Wuhan, China is constructed.
•Spatiotemporal usage patterns of station-free shared bikes are explored.•A topic-based two-stage algorithm is proposed to discover city functional regions.•Region functions are labeled by static POI ...data and dynamic mobility patterns.
Station-free shared bike (SFSB) is a new travel mode that shared bikes are allowed to park in any proper places. It implies that the users are more likely to park the SFSB as close as their destinations. This advantage makes the SFSB data to be an ideal source to understand the land-use distribution. Inspired by the idea in text mining, this paper proposes a topic-based two-stage SFSB data mining algorithm to understand the SFSB user’s travel behavior and to discover city functional regions. A region, a function and human mobility patterns are treated as a document, a topic and words, respectively. Then, a region is represented by a distribution of functions, and a function is featured by a distribution of mobility patterns. The point-of-interest data is combined to annotate the clustered regions to discover the real functions. At last, the proposed method is tested using 14-day SFSB data in Beijing and the results are estimated by the Satellite Map data. The proposed methods and the results can be applied to infer the individual’s travel purpose through functional regions and to improve land-use planning, etc.
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