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Abstract In Southeast Asia (SEA) fastidious fungi of the Ceratobasidium genus are associated with proliferation of sprouts and vascular necrosis in cacao and cassava, crops that were introduced from the tropical Americas to this region. Here, we report the isolation and in vitro culture of a Ceratobasidium sp. isolated from cassava with symptoms of witches’ broom disease (CWBD), a devastating disease of this crop in SEA. The genome characterization using a hybrid assembly strategy identifies the fungus as an isolate of the species C. theobromae, the causal agent of vascular streak dieback of cacao in SEA. Both fungi have a genome size > 31 Mb (G+C content 49%), share > 98% nucleotide identity of the Internal Transcribed Spacer (ITS) and > 94% in genes used for species-level identification. Using RNAscope® we traced the pathogen and confirmed its irregular distribution in the xylem and epidermis along the cassava stem, which explains the obtention of healthy planting material from symptom-free parts of a diseased plant. These results are essential for understanding the epidemiology of CWBD, as a basis for disease management including measures to prevent further spread and minimize the risk of introducing C. theobromae via long-distance movement of cassava materials to Africa and the Americas.

Urban Green Space management requires a multi-dimensional, evidence-based approach to effectively balance social, environmental, and economic objectives. City administrators currently lack a data-driven framework for allocating resources during constraint scenarios, leading to subjective decisions. Existing literature lacks objective solutions for managing city-scale green spaces, each with its distinct characteristics. Another challenge is handling varied spatial scales required for urban applications. This study proposes a novel goal programming-based model for urban green space management wherein multiple benefit objectives, such as conserving sequestered carbon in trees and enhancing quality and accessibility of parks, as well as handling demand constraints on available resources like water and personnel, are included. The proposed method was demonstrated in two cities with diverse conditions, Berlin and Melbourne, and evaluated on various benefit metrics, such as allocated green space units, resources consumed, and goals achieved. The model was analyzed with resource allocation decisions and goals at different spatial scales. The highest benefit achievement and resource allocation were observed when resources were allocated at the sub-district scale with a city-level target. Alternatively, setting targets at the district level provided a more even resource distribution; however, at the cost of reduced overall benefits. Results show that the proposed method increased the total benefits gained while effectively balancing conflicting goals and constraints. Additionally, it allows incorporating the city’s preferences and priorities, offering a scalable solution for informed decision-making in varied urban applications. Depending on data availability, this approach can be scaled to other cities, including additional benefits and resource constraints as required.

Online communication channels provide rich opportunities for public opinion expression, and the act of posting may lead to an internalization of the expressed views. This research investigated whether such self-effects are affected by feedback comments and whether this influence is stronger in social network sites than in anonymous online forums. In an experiment manipulating valence of feedback and the media context, 161 participants were asked to express their opinion on a current topic. Results showed limited effects of feedback: Negative comments tended to reduce internalization among participants with non-extreme prior attitudes, but this was independent from the media context.

Cassava, a vital global food source, faces a threat from Cassava Brown Streak Disease (CBSD). CBSD results from two viruses: Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). These viruses frequently pose challenges to the traditional symptom-based 1-5 phenotyping method due to its limitations in terms of accuracy and objectivity. Quantitative polymerase chain reaction (qPCR) offers precise virus quantification, although high costs hinder its widespread adoption. In this research, we utilized qPCR to measure the viral titer/load of CBSV and UCBSV. The objectives were to evaluate titer variability within the Cycle 2 (C2) population in two different environments, establish connections between viral titers and CBSD severity scores from the 1-5 scoring method, perform Genome-Wide Association Studies (GWAS) to identify genomic regions associated with CBSV and UCBSV titers, and investigate the functional annotated genes. The results demonstrated a significantly higher prevalence of CBSV (50.2%) in clones compared to UCBSV (12.9%) with mixed infections in some cases. Genotypic effects, particularly concerning UCBSV, were significant, with genotype-by-environment effects primarily influencing CBSV titer. GWAS Studies identified genomic regions associated with CBSV and UCBSV titers. Twenty-one SNP markers on chromosomes 10, 13, 17, and 18 exhibited significant associations with CBSV titer, collectively explaining 43.14% of the phenotypic variation. Additionally, 25 SNP markers on chromosomes 1, 2, 4, 5, 8, 11, 12, 13, 16, and 18 were associated with UCBSV titer, and explained 70.71% of the phenotypic variation. No shared genomic regions were identified between CBSV and UCBSV viral titers. Gene ontology analysis also revealed diverse gene functions, especially in transport and catalytic activities. These findings enhance our understanding of virus prevalence, genetics, and molecular functions in cassava plants, offering valuable insights for targeted breeding strategies.

The liturgical professional development project for pastoral workers and clergy in the Diocese of Rottenburg-Stuttgart has been developed in collaboration with the Department of Liturgical Studies at the University of Tübingen. The concept of biographical learning is the innovative element that explores a new type of liturgical formation (Bildung) where the learning content explores the participant’s unique biography of learning, faith development, and theological education and the impact of these on their understanding of the liturgy and their liturgical practice. The learning process aims to equip professional pastoral theologians to reflect on and be responsive to the liturgical–pastoral contexts in which they work. The Department of Liturgical Studies provides the learning structure and context, while the diocese provides the teaching space and enables the participants to attend. The learning outcomes are unrelated to a specific professional or employment structure or associated with a points system, management, or career progression process. The project provides a learning process rather than a program of learning, distinguishing itself from many traditional approaches to liturgical formation. The challenge for the teaching team is to provide the participants with conceptual or theoretical material to reflect on their biographical narrative of theology and then apply this concept of biographical learning in their specific and diverse pastoral contexts. As part of the biographical learning process, participants contribute to “feedback loops” to the diocese and the teaching team. This paper does not address the competency framework for career development, employment assessment, or learning comprehension. All evaluations of professionalism, role attainment, career development, and competency are employment matters and are the purview of the Diocese of Rottenburg-Stuttgart. However, the learning process provides participants with frameworks for self-assessment and feedback loops to evaluate the teaching team, the process, and the content.

The walkability of the built environment has been shown to be critical to the health of residents, and open data have been widely used to assess walkability. However, previous research has focused on the relationship between the built environment and walking behavior rather than perceived walkability, and there is a lack of systematic research on walkability at the urban scale using open data. This paper presents a methodological framework for systematically measuring and assessing perceived walkability at the urban scale, considering general and specific features. The walkability indices are obtained using variables from open data or calculated automatically through machine learning and algorithms to ensure they can be evaluated at a larger urban scale. The proposed method is applied to Harbin, China, to assess the perceived walkability of streets using hundreds of thousands of street view images and points of interest obtained from open data. The results are compared with a subjective evaluation of walkability to validate the proposed method. The results demonstrate that measures of the urban built environment can describe perceived walkability. Thus, the proposed framework shows promise for assessing the walkability of urban spaces, supporting policy proposals, and establishing design guidelines for optimising urban spaces.

Cassava (Manihot esculenta Crantz) is an essential crop with increasing importance for food supply and as raw material for industrial processing. The crop is vegetatively propagated through stem cuttings taken at the end of the growing cycle and its low multiplication rate and the high cost of stem transportation are detrimental to the increasing demand for high-quality cassava planting materials. Rapid multiplication of vegetative propagules of crops comprises tissue culture (TC) and semi-autotroph hydroponics (SAH) that provide cost-effective propagation of plant materials; however, they contrast the need for specific infrastructure, special media and substrates, and trained personnel. Traditional methods such as TC and SAH have shown promise in efficient plant material propagation. Nonetheless, these techniques necessitate specific infrastructure, specialized media and substrates, as well as trained personnel. Moreover, losses during the intermediate nursery and adaptation stages limit the overall effectiveness of these methods. Building upon an earlier report from Embrapa Brazil, which utilized mature buds from cassava for rapid propagation, we present a modified protocol that simplifies the process for wider adoption. Our method involves excising single nodes with attached leaves from immature (green) cassava stems at 2 months after planting (MAP). These nodes are then germinated in pure water, eliminating the need for specific growth substrates and additional treatments. After the initial phase, the rooted sprouts are transferred into soil within 1–8 weeks. The protocol demonstrates a high turnover rate at minimal costs. Due to its simplicity, cost-effectiveness, and robustness, this method holds significant promise as an efficient means of producing cassava planting materials to meet diverse agricultural needs.

Abstract Background Bhendi or okra (Abelmoschus esculentus) is an important crop widely cultivated in the Indian subcontinent. The production of okra in tropical regions is constrained by several abiotic and biotic factors. Among biotic stresses, yellow vein mosaic disease (YVMD), transmitted by the whitefly (Bemisia tabaci Genn.), causes significant production losses. Results Leaves showing symptoms of YVMD were collected from okra plants in the district of Mardan, Pakistan, from which the total nucleic acid was extracted. It was found that the viral genome was 2739 bp in the length and had seven conserved open reading frames, comparable to those of monopartite begomovirus species from the Old World. Nucleotide sequence comparison revealed that the genome has 97.7% identity with bhendi yellow vein mosaic virus (BYVMV). Additionally, alpha- and betasatellite DNA components were amplified and sequenced. The alpha- and betasatellite DNA sequences were 1367 and 1346 nt in length, respectively. Sequence analysis revealed that the alpha- and betasatellite sequences shared 97.9 and 98.7% similarity with cotton leaf curl Multan alphasatellite DNA (CLCuMuA) and croton yellow vein mosaic betasatellite DNA (CroYVMB), respectively. Conclusions Based on the prevailing classification system, the isolate was identified as a variant of BYVMV, CLCuMuA, and CroYVB. Alphasatellite presence in the begomovirus betasatellite complex detected in the present study indicated a recent mobilization into the viral complex infecting okra in this region. The study findings may facilitate the design of new management strategies to protect this valuable crop against begomovirus infection.

The trend to equip information systems with question-answering capabilities raises the design problem of deciding which questions a system should be able to answer. Typical solutions build on mining human conversations or logs from similar systems for question patterns. For the case of questions about geographic places, we present a complementary approach, showing how to derive possible questions from an ontology of spatial information and a classification of place facets. We argue that such an approach reduces the inherent and substantial data bias of current solutions. At a more general level, we provide a novel understanding of spatial questions and their role in designing and using spatial information systems.

Existing question answering systems struggle to answer factoid questions when geospatial information is involved. This is because most systems cannot accurately detect the geospatial semantic elements from the natural language questions, or capture the semantic relationships between those elements. In this paper, we propose a geospatial semantic encoding schema and a semantic graph representation which captures the semantic relations and dependencies in geospatial questions. We demonstrate that our proposed graph representation approach aids in the translation from natural language to a formal, executable expression in a query language. To decrease the need for people to provide explanatory information as part of their question and make the translation fully automatic, we treat the semantic encoding of the question as a sequential tagging task, and the graph generation of the query as a semantic dependency parsing task. We apply neural network approaches to automatically encode the geospatial questions into spatial semantic graph representations. Compared with current template-based approaches, our method generalises to a broader range of questions, including those with complex syntax and semantics. Our proposed approach achieves better results on GeoData201 than existing methods.

Growing cassava in Africa requires resistance against the viruses causing cassava mosaic disease (CMD) and the viruses causing cassava brown streak disease (CBSD). A dominant CMD2 resistance gene from a West African cassava landrace provides strong resistance against the cassava mosaic viruses. However, resistance against cassava brown streak viruses is limited to cassava varieties that show tolerance to the disease. A recently identified cassava germplasm that cannot be infected with cassava brown streak viruses provides a new source of the resistance required to protect cassava from CBSD. We present a synopsis of the status of virus resistance in cassava and report on the research to combine resistance against CBSD and CMD. We improve the lengthy and erratic screening for CBSD resistance by proposing a virus infection and screening protocol for the viruses causing CBSD and CMD, which allows a rapid and precise assessment of cassava resistance under controlled conditions. Using this approach, we classified the virus responses of cassava lines from Africa and South America and identified truly virus-resistant clones that cannot be infected with any of the known viruses causing CBSD even under the most stringent virus infections. A modification of this protocol was used to test seedlings from cassava crosses for resistance against both diseases. A broad-spectrum resistance was identified in a workflow that lasted 9 months from seed germination to the identification of virus resistance. The workflow we propose dramatically reduces the evaluation and selection time required in a classical breeding workflow to reach the advanced field trial stage in only 9 months by conducting selections for virus resistance and plant multiplication in parallel. However, it does not bypass field evaluations; cassava resistance assessment prior to the field limits the evaluation to candidates with virus resistance defined as the absence of symptoms and the absence of the virus. The transfer of our virus screening workflow to cassava breeding programs enhances the efficiency by which resistance against viruses can be selected. It provides a precise definition of the plant’s resistance response and can be used as a model system to tackle resistance in cassava against other diseases.

OpenStreetMap (OSM), with its global coverage and Open Database License, has recently gained popularity. Its quality is adequate for many applications, but since it is crowd-sourced, errors remain an issue. Errors in associated tags of the road network, for example, are impacting routing applications. Particularly road classification errors often lead to false assumptions about capacity, maximum speed, or road quality, possibly resulting in detours for routing applications. This study aims at finding potential classification errors automatically, which can then be checked and corrected by a human expert. We develop a novel approach to detect road classification errors in OSM by searching for disconnected parts and gaps in different levels of a hierarchical road network. Different parameters are identified that indicate gaps in road networks. These parameters are then combined in a rating system to obtain an error probability to suggest possible misclassifications to a human user. The methodology is applied to an exemplar case for the state of New South Wales in Australia. The results demonstrate that (1) more classification errors are found at gaps than at disconnected parts, and (2) the gap search enables the user to find classification errors quickly using the developed rating system that indicates an error probability. In future work, the methodology can be extended to include available tags in OSM for the rating system. The source code of the implementation is available via GitHub.

Abstract Two-component plant defenses such as cyanogenic glucosides are produced by many plant species, but phloem-feeding herbivores have long been thought not to activate these defenses due to their mode of feeding, which causes only minimal tissue damage. Here, however, we report that cyanogenic glycoside defenses from cassava (Manihot esculenta), a major staple crop in Africa, are activated during feeding by a pest insect, the whitefly Bemisia tabaci, and the resulting hydrogen cyanide is detoxified by conversion to beta-cyanoalanine. Additionally, B. tabaci was found to utilize two metabolic mechanisms to detoxify cyanogenic glucosides by conversion to non-activatable derivatives. First, the cyanogenic glycoside linamarin was glucosylated 1–4 times in succession in a reaction catalyzed by two B. tabaci glycoside hydrolase family 13 enzymes in vitro utilizing sucrose as a co-substrate. Second, both linamarin and the glucosylated linamarin derivatives were phosphorylated. Both phosphorylation and glucosidation of linamarin render this plant pro-toxin inert to the activating plant enzyme linamarase, and thus these metabolic transformations can be considered pre-emptive detoxification strategies to avoid cyanogenesis.

During wayfinding pedestrians do not always choose the shortest available route. Instead, route choices are guided by several well-known wayfinding strategies or heuristics. These heuristics minimize cognitive effort and usually lead to satisfactory route choices. Our previous study evaluated the costs of four well-known pedestrian wayfinding heuristics and their variation across nine network morphologies. It was observed that the variation in the cost of these wayfinding heuristics increased with an increase in the irregularity of the network, indicating that people may opt for more diverse heuristics while walking through relatively regular networks, and may prefer specific heuristics in the relatively irregular ones. The study presented here aims to investigate this claim by comparing simulated routes with observed pedestrian trajectories in Beijing and Melbourne, two cities at opposite ends of the regularity spectrum. We found that the values of mean route length and mean Network Hausdorff Distance for walking trips made in Melbourne were consistently lesser than the corresponding values obtained in Beijing. Also, across both the cities, we found that while there was minimal variation in the popularity of heuristics overall, in cases where different heuristics produced dissimilar routes, the shortest leg first strategy and the least angle strategy were more popular.

Promoting public transport depends on adapting effective tools for concurrent monitoring of perceived service quality. Social media feeds, in general, provide an opportunity to ubiquitously look for service quality events, but when applied to confined geographic area such as a transport node, the sparsity of concurrent social media data leads to two major challenges. Both the limited number of social media messages--leading to biased machine-learning--and the capturing of bursty events in the study period considerably reduce the effectiveness of general event detection methods. In contrast to previous work and to face these challenges, this paper presents a hybrid solution based on a novel fine-tuned BERT language model and aspect-based sentiment analysis. BERT enables extracting aspects from a limited context, where traditional methods such as topic modeling and word embedding fail. Moreover, leveraging aspect-based sentiment analysis improves the sensitivity of event detection. Finally, the efficacy of event detection is further improved by proposing a statistical approach to combine frequency-based and sentiment-based solutions. Experiments on a real-world case study demonstrate that the proposed solution improves the effectiveness of event detection compared to state-of-the-art approaches.

Spatial information science contributes to the foundations of sustainable transport development. This article focuses especially on the role that research on human wayfinding and navigation plays when it comes to designing digital connectivity and autonomy in urban transport.

Localization of pedestrians in 3D scene space from single RGB images is critical for various downstream applications. Current monocular approaches employ either the bounding box of pedestrians or the visible parts of their bodies for localization. Both approaches introduce additional error to the location estimation in the case of real-world scenarios – crowded environments with multiple occluded pedestrians. To overcome the limitation, this paper proposes a novel human pose-aware pedestrian localization framework to model poses of occluded pedestrians, where this enables accurate localization in image and ground space. This is done by proposing a light-weight neural network architecture, where this ensures a fast and accurate prediction of missing body parts for downstream applications. Comprehensive experiments on two real-world datasets demonstrate the effectiveness of the framework compared to state-of-the-art in predicting pedestrians missing body parts as well as pedestrian localization.

In a typical data collection process, a surveyed spatial object is annotated upon creation, and is classified based on its attributes. This annotation can also be guided by textual definitions of objects. However, interpretations of such definitions may differ among people, and thus result in subjective and inconsistent classification of objects. This problem becomes even more pronounced if the cultural and linguistic differences are considered. As a solution, this paper investigates the role of topology as the defining characteristic of a class of spatial objects. We propose a data mining approach based on frequent itemset mining to learn patterns in topological relations between objects of a given class and other spatial objects. In order to capture topological relations between more than two (linear) objects, this paper further proposes a refinement of the 9-intersection model for topological relations of line geometries. The discovered topological relations form topological constraints of an object class that can be used for spatial object classification. A case study has been carried out on bridges in the OpenStreetMap dataset for the state of Victoria, Australia. The results show that the proposed approach can successfully learn topological constraints for the class bridge, and that the proposed refined topological model for line geometries outperforms the 9-intersection model in this task.

Map-matching of trajectory data has widespread applications in vehicle tracking, traffic flow analysis, route planning, and intelligent transportation systems. Map-matching algorithms snap a set of trajectory points observed by a satellite navigation system to the most likely route segments of a map. However, due to the unavoidable errors in the recorded trajectory points and the incomplete map data, map-matching algorithms may match points to incorrect segments, leading to map-matching errors. Identification of these map-matching errors in the absence of ground truth can only be achieved by visual inspection and reasoning. Thus, the identification of map-matching errors without ground truth is a time-consuming and mundane task. Although research has focused on improving map-matching algorithms, to our knowledge no attempts have been made to automatically classify and identify the residual map-matching errors. In this work, we propose the first method to automatically identify map-matching errors in the absence of ground truth, i.e., only using the recorded trajectory points and the map-matched route. We have evaluated our method on a public dataset and observed an average accuracy of 91% in automatically identifying map-matching errors, thus helping analysts to significantly reduce manual effort for map-matching quality assurance.

Cruciferous plants in the order Brassicales defend themselves from herbivory using glucosinolates: sulfur-containing pro-toxic metabolites that are activated by hydrolysis to form compounds, such as isothiocyanates, which are toxic to insects and other organisms. Some herbivores are known to circumvent glucosinolate activation with glucosinolate sulfatases (GSSs), enzymes that convert glucosinolates into inactive desulfoglucosinolates. This strategy is a major glucosinolate detoxification pathway in a phloem-feeding insect, the silverleaf whitefly Bemisia tabaci, a serious agricultural pest of cruciferous vegetables. In this study, we identified and characterized an enzyme responsible for glucosinolate desulfation in the globally distributed B. tabaci species MEAM1. In in vitro assays, this sulfatase showed a clear preference for indolic glucosinolates compared with aliphatic glucosinolates, consistent with the greater representation of desulfated indolic glucosinolates in honeydew. B. tabaci might use this detoxification strategy specifically against indolic glucosinolates since plants may preferentially deploy indolic glucosinolates against phloem-feeding insects. In vivo silencing of the expression of the B. tabaci GSS gene via RNA interference led to lower levels of desulfoglucosinolates in honeydew. Our findings expand the knowledge on the biochemistry of glucosinolate detoxification in phloem-feeding insects and suggest how detoxification pathways might facilitate plant colonization in a generalist herbivore.

While tracking-data analytics can be a goldmine for institutions and companies, the inherent privacy concerns also form a legal, ethical and social minefield. We present a study that seeks to understand the extent and circumstances under which tracking-data analytics is undertaken with social licence-that is, with broad community acceptance beyond formal compliance with legal requirements. Taking a University campus environment as a case, we enquire about the social licence for Wi-Fi-based tracking-data analytics. Staff and student participants answered a questionnaire presenting hypothetical scenarios involving Wi-Fi tracking for university research and services. Our results present a Bayesian logistic mixed-effects regression of acceptability judgements as a function of participant ratings on 11 privacy dimensions. Results show widespread acceptance of tracking-data analytics on campus and suggest that trust, individual benefit, data sensitivity, risk of harm and institutional respect for privacy are the most predictive factors determining this acceptance judgement.

Virus-derived siRNAs (vsiRNAs) generated by the host RNA silencing mechanism are effectors of plant’s defense response and act by targeting the viral RNA and DNA in post-transcriptional gene silencing (PTGS) and transcriptional gene silencing (TGS) pathways, respectively. Contrarily, viral suppressors of RNA silencing (VSRs) compromise the host RNA silencing pathways and also cause disease-associated symptoms. In this backdrop, reports describing the modulation of plant gene(s) expression by vsiRNAs via sequence complementarity between viral small RNAs (sRNAs) and host mRNAs have emerged. In some cases, silencing of host mRNAs by vsiRNAs has been implicated to cause characteristic symptoms of the viral diseases. Similarly, viroid infection results in generation of sRNAs, originating from viroid genomic RNAs, that potentially target host mRNAs causing typical disease-associated symptoms. Pathogen-derived sRNAs have been demonstrated to have the propensity to target wide range of genes including host defense-related genes, genes involved in flowering and reproductive pathways. Recent evidence indicates that vsiRNAs inhibit host RNA silencing to promote viral infection by acting as decoy sRNAs. Nevertheless, it remains unclear if the silencing of host transcripts by viral genome-derived sRNAs are inadvertent effects due to fortuitous pairing between vsiRNA and host mRNA or the result of genuine counter-defense strategy employed by viruses to enhance its survival inside the plant cell. In this review, we analyze the instances of such cross reaction between pathogen-derived vsiRNAs and host mRNAs and discuss the molecular insights regarding the process of pathogenesis.

Political disagreements in social media can result in removing (i.e., "unfriending") a person from one's online network. Given that such actions could lead to the (ideological) homogenization of networks, it is pivotal to understand the psychological processes intertwined in unfriending decisions. This requires not only addressing different types of disagreements but also analyzing them in the relational context they occur. This article proposes that political disagreements leading to drastic measures such as unfriending are attributable to more deeply rooted moral dissents. Based on moral foundations theory and relationship regulation research, this work presents empirical evidence from two experiments. In both studies, subjects rated political statements (that violated different moral foundations) with regard to perceived reprehensibility and the likelihood of unfriending the source. Study 1 (N = 721) revealed that moral judgments of a political statement are moderately related to the unfriending decision. Study 2 (N = 822) replicated this finding but indicated that unfriending is less likely when the source of the morally reprehensible statement is relationally close to the unfriender and provides emotional support. This research extends unfriending literature by pointing to morality as a new dimension of analysis and offers initial evidence uncovering the psychological trade-off behind the decision of terminating digital ties. Drawing on this, our findings inform research on the homogenization of online networks by indicating that selective avoidance (in the form of politically motivated unfriending) is conditional upon the relational context and the interpersonal benefits individuals receive therein.

Abstract Following a request from the EU Commission, the Panel on Plant Health performed a categorisation of beet necrotic yellow vein virus (BNYVV), the causal agent of the sugar beet rhizomania disease. The virus is currently listed in Annex III as a protected zone (PZ) quarantine pest of the Commission Implementing Regulation (EU) 2019/2072. The identity of the BNYVV is well established. BNYVV is a soil‐borne virus transmitted by the obligate root plasmodiophorid endoparasite Polymyxa betae. BNYVV is widely distributed in the EU, but is not reported in the following EU PZs: Ireland, France (Brittany), Portugal (Azores), Finland and Northern Ireland. The virus may enter, become established and spread in the PZs via P. betae resting spores with soil and growing media as such or attached to machinery and with roots and tubercles of species other than B. vulgaris and with plants for planting. Introduction of BNYVV would have a negative impact on sugar beet and other beet crops in PZs, because of yield and sugar content reduction. Phytosanitary measures are available to reduce the likelihood of entry and spread in the PZs. Once the virus and its plasmodiophorid vector have entered a PZ, their eradication would be difficult due to the persistence of viruliferous resting spores in the soil. The main knowledge gaps or uncertainties identified concerning the presence of BNYVV in the PZs and the incidence and distribution of BNYVV in Switzerland, a country to which a range of specific requirements do not apply. BNYVV meets all the criteria that are within the remit of EFSA to qualify as a potential protected zone union quarantine pest. Plants for planting are not considered as a main means of spread, and therefore BNYVV does not satisfy all the criteria evaluated by EFSA to qualify as potential Union regulated non‐quarantine pest.

Abstract Following a request from the European Commission, the Panel on Plant Health performed a pest categorisation on tomato leaf curl New Delhi virus (ToLCNDV). ToLCNDV is a well‐defined bipartite Begomovirus species, sometimes associated with satellite molecules. It is transmitted by Bemisia tabaci to a wide range of hosts. ToLCNDV is reported from Estonia, Greece, Italy, Portugal and Spain, with limited distribution. The prevalent strain (ToLCNDV‐ES) in these countries is particularly adapted to cucurbits and is different from isolates reported outside the EU, which are better adapted to solanaceous crops and could therefore pose additional risk for EU agriculture. The virus is regulated under Commission Implementing Regulation (EU) 2019/2072. The main pathway of entry identified is plants for planting of susceptible hosts, even if entry could also occur via commodities carrying viruliferous B. tabaci and possibly by seeds. While establishment and local spread rely on B. tabaci, the virus can also be dispersed over long distances by movement of infected plants for planting. Establishment and spread are limited to regions with ecoclimatic conditions suitable for the establishment of vector populations (southern regions of Europe) or can occur as outbreaks wherever crops are grown under protected cultivation. The main uncertainties associated with this pest categorisation are the distribution and prevalence of ToLCNDV in the EU, the magnitude of the virus impact particularly on hosts different from Cucurbitaceae, and seed transmission. ToLCNDV meets all the criteria evaluated by EFSA to qualify as potential Union Quarantine Pest (QP); conversely, ToLCNDV does not meet the criterion of being widespread in the EU to qualify as a Regulated Non‐Quarantine Pest (RNQP). Should new data show that ToLCNDV is widespread in the EU, the possibility would exist for non‐EU isolates to qualify as QP, while ToLCNDV EU isolates (ToLCNDV‐ES) could qualify as RNQP.

Screening cassava lines for resistance against viruses causing cassava brown streak disease (CBSD) is cumbersome because of the unpredictable and erratic virus infections in the slow plant infection processes that are frequently not associated with distinct leaf symptoms and because of the reliance on the assessment of root necrosis as an indicator of plant resistance/tolerance. The selection of resistant candidates thus extends over several growing cycles and is still associated with uncertainties about the stage of virus infection. To reduce the time for selection of resistant crosses and the uncertainties associated with field screening, we have developed a fast-forward virus screening workflow to assess cassava seedlings from crosses of cassava brown streak- and cassava mosaic virus-resistant parents. After passing through an intensive and precise virus infection routine, cassava seedlings that carried resistance against cassava brown streak and mosaic viruses were identified. Taking the results of 195 seedlings from 18 crossing families together, it became evident that resistance against the viruses causing CBSD is a dominant trait. The protocol developed for virus resistance screening in cassava can be readily adopted. It shifts resistance evaluation from the field to the nursery and replaces the erroneous and lengthy virus infection and screening process with a method of precision and speed.

Place descriptions in everyday communication or in online text provide a rich source of spatial knowledge about places. Such descriptions typically consist of references to places and spatial relationships between them. An important step to utilize such knowledge in information systems is georeferencing the referred places. Beside place name disambiguation, another challenge is that a significant proportion of place references in such descriptions are not official place names indexed by gazetteers, thus cannot be resolved easily. This paper presents a novel approach for georeferencing places from collective descriptions using place graphs, regardless of whether they are referred to by gazetteered names or not. The approach leverages spatial relation models for approximate locating and matching. Different models are proposed and evaluated using several metrics.

Abstract Background Cassava brown streak disease (CBSD) has a viral aetiology and is caused by viruses belonging to the genus Ipomovirus (family Potyviridae), Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). Molecular and serological methods are available for detection, discrimination and quantification of cassava brown streak viruses (CBSVs) in infected plants. However, precise determination of the viral RNA localization in infected host tissues is still not possible pending appropriate methods. Results We have developed an in situ hybridization (ISH) assay based on RNAscope® technology that allows the sensitive detection and localization of CBSV RNA in plant tissues. The method was initially developed in the experimental host Nicotiana rustica and was then further adapted to cassava. Highly sensitive and specific detection of CBSV RNA was achieved without background and hybridization signals in sections prepared from non-infected tissues. The tissue tropism of CBSV RNAs appeared different between N. rustica and cassava. Conclusions This study provides a robust method for CBSV detection in the experimental host and in cassava. The protocol will be used to study CBSV tropism in various cassava genotypes, as well as CBSVs/cassava interactions in single and mixed infections.

Most plant viruses rely on vector transmission for their spread and specific interactions between vector and virus have evolved to regulate this relationship. The whitefly Bemisia tabaci- transmitted cucumber vein yellowing virus (CVYV; genus Ipomovirus, family Potyviridae) is endemic in the Mediterranean Basin, where it causes significant losses in cucurbit crops. In this study, the role of the coat protein (CP) of CVYV for B. tabaci transmission and plant infection was investigated using a cloned and infectious CVYV cDNA and a collection of point and deletion mutants derived from this clone. Whitefly transmission of CVYV was abolished in a deletion mutant lacking amino acids in position 93–105 of the CP. This deletion mutant caused more severe disease symptoms compared to the cDNA clone representing the wild-type (wt) virus and movement efficiency was likewise affected. Two virus mutants carrying a partially restored CP were transmissible and showed symptoms comparable to the wt virus. Collectively, our data demonstrate that the N-terminus of the CVYV CP is a determinant for transmission by the whitefly vector and is involved in plant infection and symptom expression.

Viral diseases are a major constraint to cucurbit production worldwide. In 2014 rainy and dry cropping seasons, cross-sectional surveys were conducted in farmers’ cucurbits fields in six agro-ecological zones (AEZs) of Côte d’Ivoire to assess prevalence and distribution of viral diseases. A total of 757 leaf samples were collected from melon, squash, cucumber, watermelon, gourd calabash, and pumpkin plants showing various virus-like symptoms. Enzyme linked immunosorbent assay (ELISA) using antisera against cucumber mosaic virus (CMV), zucchini yellow mosaic virus (ZYMV), papaya ringspot virus (PRSV), watermelon mosaic virus (WMV) and Moroccan watermelon mosaic virus (MWMV) were performed to detect viruses in the samples collected. Results revealed that viral diseases were prevalent in all the agro-ecological zones, with significantly higher mean prevalence in the dry season (53.6%) than in the rainy season (29.35%). The overall mean disease severity index was also significantly higher in the dry season (47.58%) than in the rainy season (28.17%). CMV, ZYMV and PRSV were found in all AEZs at varying rates between the rainy and dry seasons, whereas WMV and MWMV were not detected. CMV was more prevalent in the dry season (32%) whereas ZYMV was more prevalent in the rainy season (34%). This study has revealed that viruses infecting cucurbits are widespread and occurred in mixed infection which poses a potential threat to cucurbit crops production in Cote d’Ivoire.

On contemporary online news sites, readers are simultaneously exposed to journalistic articles and social reactions toward these messages. Two online experiments (N = 252) addressed whether negative user reactions can attenuate the persuasive influence of the main article, and whether these effects depend on the reputation of the original source. Results showed a selective consideration of user-generated content: Readers took into account comments with high argument quality and ratings of a credible website but did not follow others’ opinions if the comments merely contained subjective evaluations. On less reputable websites, user reactions were less influential. Findings are discussed with regard to the interplay of multiple sources.

Abstract Background Cassava brown streak disease is emerging as the most important viral disease of cassava in Africa, and is consequently a threat to food security. Two distinct species of the genus Ipomovirus (family Potyviridae) cause the disease: Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). To understand the evolutionary relationships among the viruses, 64 nucleotide sequences from the variable P1 gene from major cassava producing areas of east and central-southern Africa were determined. Methods We sequenced an amplicon of the P1 region of 31 isolates from Malawi and Tanzania. In addition to these, 33 previously reported sequences of virus isolates from Uganda, Kenya, Tanzania, Malawi and Mozambique were added to the analysis. Results Phylogenetic analyses revealed three major P1 clades of Cassava brown streak viruses (CBSVs): in addition to a clade of most CBSV and a clade containing all UCBSV, a novel, intermediate clade of CBSV isolates which has been tentatively called CBSV-Tanzania (CBSV-TZ). Virus isolates of the distinctive CBSV-TZ had nucleotide identities as low as 63.2 and 63.7% with other members of CBSV and UCBSV respectively. Conclusions Grouping of P1 gene sequences indicated for distinct sub-populations of CBSV, but not UCBSV. Representatives of all three clades were found in both Tanzania and Malawi.

Three field experiments were conducted to assess the effect of planting date on the incidence of viral diseases and the severity and the susceptibility of the cultivars. Two cultivars of cucumber (Hybrid Tokyo F1 and Poinsett) and one local variety of zucchini (Bolle) were used for the evaluation in May-July 2014, September-November 2014, and February-April 2015. A randomized complete block design with three replications was used for the experiments. Data were collected on disease incidence, severity, and time until first symptoms occurred. Area under severity index progress curve (AUSIPC) and area under disease progress curve (AUDPC) were calculated respectively for disease severity as well as the incidence on each cultivar. The results demonstrate the susceptibility of all cultivars to the tested viral diseases. The effect of planting dates on cultivars was significantly different (P 0.05) in planting date-variety interaction.

Abstract The Panel on Plant Health of EFSA conducted a pest categorisation of 17 viruses of Rubus L. that were previously classified as either non‐EU or of undetermined standing in a previous opinion. These infectious agents belong to different genera and are heterogeneous in their biology. Blackberry virus X, blackberry virus Z and wineberry latent virus were not categorised because of lack of information while grapevine red blotch virus was excluded because it does not infect Rubus. All 17 viruses are efficiently transmitted by vegetative propagation, with plants for planting representing the major pathway for entry and spread. For some viruses, additional pathway(s) are Rubus seeds, pollen and/or vector(s). Most of the viruses categorised here infect only one or few plant genera, but some of them have a wide host range, thus extending the possible entry pathways. Cherry rasp leaf virus, raspberry latent virus, raspberry leaf curl virus, strawberry necrotic shock virus, tobacco ringspot virus and tomato ringspot virus meet all the criteria to qualify as potential Union quarantine pests (QPs). With the exception of impact in the EU territory, on which the Panel was unable to conclude, blackberry chlorotic ringspot virus, blackberry leaf mottle‐associated virus, blackberry vein banding‐associated virus, blackberry virus E, blackberry virus F, blackberry virus S, blackberry virus Y and blackberry yellow vein‐associated virus satisfy all the other criteria to be considered as potential QPs. Black raspberry cryptic virus, blackberry calico virus and Rubus canadensis virus 1 do not meet the criterion of having a potential negative impact in the EU. For several viruses, the categorisation is associated with high uncertainties, mainly because of the absence of data on biology, distribution and impact. Since the opinion addresses non‐EU viruses, they do not meet the criteria to qualify as potential Union regulated non‐quarantine pests.

Abstract Following a request from the EU Commission, the Panel on Plant Health addressed the pest categorisation of the viruses of Ribes L. determined as being either non‐EU or of undetermined standing in a previous EFSA opinion. These infectious agents belong to different genera and are heterogeneous in their biology. Alaska vitivirus 1 and Ribes virus F were excluded from categorisation because these are very poorly characterised viruses. The pest categorisation was completed for seven viruses with clear identity and for which detection methods are available. All these viruses are efficiently transmitted by vegetative propagation techniques, with plants for planting representing the major pathway for long‐distance dispersal and thus considered as the major pathway for entry. Depending on the virus, additional pathway(s) can also be Ribes seeds, pollen and/or vector(s). Most of the viruses categorised here are known to infect only one or few plant genera, but tomato ringspot virus (ToRSV) has a wide host range, thus extending the possible entry pathways. ToRSV meets all the criteria evaluated by EFSA to qualify as potential Union quarantine pest (QP). With the exception of impact in the EU territory, on which the Panel was unable to conclude, Actinidia virus X, blackcurrant leaf chlorosis‐associated virus, blackcurrant leafroll‐associated virus, black currant‐associated rhabdovirus, blackcurrant waikavirus A and Ribes americanum virus A satisfy all the other criteria to be considered as potential Union QPs. For several viruses, especially those recently discovered, the categorisation is associated with high uncertainties mainly because of the absence of data on their biology, distribution and impact. Since this opinion addresses specifically the non‐EU viruses, in general these viruses do not meet the criteria assessed by EFSA to qualify as potential Union regulated non‐quarantine pests.

Abstract Following a request from the EU Commission, the Panel on Plant Health addressed the pest categorisation of the viruses and viroids of Fragaria L. determined as being either non‐EU or of undetermined standing in a previous EFSA opinion. These infectious agents belong to different genera and are heterogeneous in their biology. With the exclusion of strawberry latent virus and strawberry latent C virus for which very limited information exists, the pest categorisation was completed for 12 viruses having acknowledged identities and available detection methods. All these viruses are efficiently transmitted by vegetative propagation techniques, with plants for planting representing the major pathway for long‐distance dispersal and thus considered as the major pathway for entry. Depending on the virus, additional pathway(s) can also be Fragaria seeds, pollen and/or vector(s). Most of the viruses categorised here are known to infect only one or few plant genera, but some of them have a wide host range, thus extending the possible entry pathways. Strawberry chlorotic fleck‐associated virus, strawberry leaf curl virus, strawberry necrotic shock virus, strawberry pallidosis‐associated virus, strawberry vein banding virus (SVBV) and tomato ringspot virus meet all the criteria evaluated by EFSA to qualify as potential Union quarantine pests (QPs). For SVBV, the Panel considered that following its entry and establishment into the EU territory, an impact of uncertain magnitude is expected mainly because a synergistic effect may occur in strawberry in case of mixed infections with viruses already present in the EU. Strawberry crinivirus 3, strawberry crinivirus 4 and strawberry polerovirus 1 meet all criteria for being considered as potential Union QPs, except for the impact in the EU territory, on which the Panel was unable to conclude. Fragaria chiloensis cryptic virus, Fragaria chiloensis latent virus and strawberry pseudo mild yellow edge virus do not meet the criterion of having potential negative impact in the EU. For several viruses, especially those recently discovered, the categorisation is associated with high uncertainties mainly because of the absence of data on their biology, distribution and impact. Since this opinion addresses specifically the non‐EU viruses, in general, these viruses do not meet the criteria assessed by EFSA to qualify as potential Union regulated non‐quarantine pests.

Abstract Following a request from the EU Commission, the Panel on Plant Health addressed the pest categorisation of the viruses and viroids of Prunus L. determined as being either non‐EU or of undetermined standing in a previous EFSA opinion. These infectious agents belong to different genera and are heterogeneous in their biology. With the exclusion of Ilarvirus S1 and Ilarvirus S2, for which very limited information exists, the pest categorisation was completed for 26 viruses and 1 viroid having acknowledged identities and available detection methods. All these viruses are efficiently transmitted by vegetative plant propagation techniques, with plants for planting representing the major pathway for long‐distance dispersal and thus considered as the major pathway for entry. Depending on the virus, additional pathway(s) can also be Prunus seeds, pollen and/or vector(s). Most of the viruses categorised here are known to infect only one or few plant genera, but some of them have a wide host range, thus extending the possible entry pathways. Apple scar skin viroid, American plum line pattern virus, cherry mottle leaf virus, cherry rasp leaf virus, cherry rosette virus, cherry rusty mottle‐associated virus, cherry twisted leaf‐associated virus, peach enation virus, peach mosaic virus, peach rosette mosaic virus, tobacco ringspot virus and tomato ringspot virus meet all the criteria evaluated by EFSA to qualify as potential Union quarantine pests (QPs). With the exception of impact in the EU territory, on which the Panel was unable to conclude, apricot vein clearing virus, Asian prunus virus 1, Asian prunus virus 2, Asian prunus virus 3, Caucasus prunus virus, cherry virus B, Mume virus A, nectarine stem pitting‐associated virus, nectarine virus M, peach chlorotic mottle virus, peach leaf pitting‐associated virus, peach virus D, prunus virus F and prunus virus T satisfy all the other criteria to be considered as potential Union QPs. Prunus geminivirus A does not meet the criterion of having negative impact in the EU. For several viruses, especially those recently discovered, the categorisation is associated with high uncertainties mainly because of the absence of data on their biology, distribution and impact. Since this opinion addresses specifically the non‐EU viruses, in general these viruses do not meet the criteria assessed by EFSA to qualify as potential Union regulated non‐quarantine pests.

Abstract Following a request from the EU Commission, the Panel on Plant Health performed a pest categorisation of 17 viruses and viroids, herein called viruses, of Cydonia Mill., Malus Mill. and Pyrus L. determined as being either non‐EU or of undetermined standing in a previous EFSA opinion. These viruses belong to different genera and are heterogeneous in their biology. They can be detected by available methods and are efficiently transmitted by vegetative propagation techniques, with plants for planting representing a major long‐distance spread mechanism and, potentially, a major entry pathway. Depending on the viruses, additional pathway(s) can also be seed, pollen and/or vector transmission. Most of the viruses categorised here are known to infect only one of few related plant genera, but some of them have a wider host range, thus extending the possible entry pathways. Three viruses (apple necrotic mosaic virus, cherry rasp leaf virus, temperate fruit decay‐associated virus) and one viroid (apple fruit crinkle viroid) satisfy all the criteria to be considered as Union quarantine pests. Five viruses (apple green crinkle‐associated virus, blackberry chlorotic ringspot virus, eggplant mottled crinkle virus, tobacco ringspot virus and tomato ringspot virus) and one viroid (apple scar skin viroid), satisfy the criteria to be considered as Union quarantine pests with the possible exception of being absent from the EU territory or having a restricted presence and being under official control. The remaining six viruses (apple geminivirus, apple latent spherical virus, apple‐associated luteovirus, Pyrus pyrifolia cryptic virus, Pyrus pyrifolia partitivirus 2 and Tulare apple mosaic virus) and one viroid (apple hammerhead viroid) were not found to satisfy one or more of these criteria. The Panel highlights that for several viruses, especially those recently discovered, the categorisation is associated with high uncertainties mainly linked to the absence of data on biology and distribution. Since this opinion addresses specifically the non‐EU viruses, in general these viruses do not meet the criteria assessed by EFSA to qualify as a potential Union regulated non‐quarantine pests.

Abstract The Panel on Plant Health performed a listing of non‐EU viruses and viroids (reported hereinafter as viruses) of Cydonia Mill., Fragaria L., Malus Mill., Prunus L., Pyrus L., Ribes L., Rubus L. and Vitis L. A systematic literature review identified 197 viruses infecting one or more of the host genera under consideration. Viruses were allocated into three categories (i) 86 non‐EU viruses, known to occur only outside the EU or having only limited presence in the EU (i.e. reported in only one or few Member States (MSs), known to have restricted distribution, outbreaks), (ii) 97 viruses excluded at this stage from further categorisation efforts because they have significant presence in the EU (i.e. only reported so far from the EU or known to occur or be widespread in some MSs or frequently reported in the EU), (iii) 14 viruses with undetermined standing for which available information did not readily allow to allocate to one or the other of the two above groups. Comments provided by MSs during consultation phases were integrated in the opinion. The main knowledge gaps and uncertainties of this listing concern (i) the geographic distribution and prevalence of the viruses analysed, in particular when they were recently described; (ii) the taxonomy and biological status of a number of poorly characterised viruses; (iii) the host status of particular plant genera in relation to some viruses. The viruses considered as non‐EU and those with undetermined standing will be categorised in the next steps to answer a specific mandate from the Commission to develop pest categorisations for non‐EU viruses. This list does not imply a prejudice on future needs for a pest categorisation for other viruses which are excluded from the current categorisation efforts.

Abstract Following a request from the EU Commission, the Panel on Plant Health addressed the pest categorisation of the viruses and viroids of Vitis L. determined as being either non‐EU or of undetermined standing in a previous EFSA opinion. These infectious agents belong to different genera and are heterogeneous in their biology. With the exclusion of grapevine virus 101‐14.N.23.9.1/South Africa/2009 for which very limited information exists, the pest categorisation was completed for 30 viruses or viroids having acknowledged identities and available detection methods. All these viruses are efficiently transmitted by vegetative propagation techniques, with plants for planting representing the major pathway for long‐distance dispersal and thus considered as the major pathway for potential entry. Depending on the virus, additional pathway(s) can also be seeds, pollen and/or vector(s). Most of the viruses categorised here are known to infect only one or few plant genera, but some of them have a wide host range, thus extending the possible entry pathways. Grapevine yellow speckle viroid 2, blueberry leaf mottle virus, grapevine Ajinashika virus, grapevine Anatolian ringspot virus, grapevine berry inner necrosis virus, grapevine deformation virus, grapevine fabavirus, grapevine red blotch virus, grapevine stunt virus, grapevine Tunisian ringspot virus, grapevine vein‐clearing virus, temperate fruit decay‐associated virus, peach rosette mosaic virus, tobacco ringspot virus, tomato ringspot virus meet all the criteria evaluated by EFSA to qualify as potential Union quarantine pests (QPs). With the exception of impact for the EU territory, on which the Panel was unable to conclude, blackberry virus S, grapevine geminivirus A, grapevine leafroll‐associated virus 7, grapevine leafroll‐associated virus 13, grapevine satellite virus, grapevine virus E, grapevine virus I, grapevine virus J, grapevine virus S, summer grape enamovirus, summer grape latent virus satisfy all the other criteria to be considered as potential Union QPs. Australian grapevine viroid, grapevine cryptic virus 1, grapevine endophyte endornavirus and wild vitis virus 1 do not meet all the criteria evaluated by EFSA to be regarded as potential Union QPs because they are not known to cause an impact on Vitis. For several viruses, especially those recently discovered, the categorisation is associated with high uncertainties mainly because of the absence of data on their biology, distribution and impact. Since this opinion addresses specifically non‐EU viruses, in general these viruses do not meet the criteria assessed by EFSA to qualify as a potential Union regulated non‐quarantine pests.

Cassava brown streak disease (CBSD) is a severe virus disease of cassava and prevalent in the eastern regions of Africa. The disease is characterized by distinct vein chlorosis and streak symptoms on leaves and stems and necrosis of storage roots. This necrosis can encompass large areas of the root, rendering it inedible so that the entire cassava harvest can be lost. African cassava varieties are susceptible to either of the two viruses causing the disease, cassava brown streak virus (CBSV) and Uganda cassava brown streak virus, and while there are less sensitive varieties, all cassava eventually succumb to the disease. The lack of CBSD resistance in African cassava varieties prompted this search for new sources of virus resistance in the diversity of South American cassava germplasm held in the collection at International Center for Tropical Agriculture, Columbia. Our search for CBSD resistance in South American cassava germplasm accessions revealed that most of the 238 South American cassava lines infected with CBSV established systemic virus infections with moderate to severe disease symptoms on leaves and stems. Fifteen cassava accessions did not become virus infected, remained free of symptoms, and CBSV was undetected by qRT-PCR. When tuberous roots of those lines were examined, necrotic tissue was found in eight lines and CBSV was detected. The remaining seven cassava accessions remained clear of symptoms on all tissues and organs and were virus free. A broad spectrum of virus resistance also including other virus isolates was confirmed for the breeding lines DSC167 and DSC118. While detailed infection experiments with other cassava lines selected for resistance are still ongoing, this indicates that the resistance identified may also hold against a broader diversity of CBSVs. Taken together, we present the results of a comprehensive study on CBSV resistance and susceptibility in cassava germplasm accessions from South America. The virus resistance in cassava germplasm identified provides compelling evidence for the invaluable contribution of germplasm collections to supply the genetic resources for the improvement of our crops.

Public transit is highly promoted worldwide to reduce traffic congestion. An evidence-based planning of stop locations and routes with regard to residential and workplace locations can reduce walking distances to transit and the number of transfers, which can improve service quality of public transport and thus increase ridership. This paper proposes a novel method of identifying residential and workplace locations from smart card data. The proposed method identifies relevant stops first and then refines their catchments to narrow down residential and workplace locations in three steps: defining constraints from the design of the public transport network, movement logic, and land use. In 2017, we tested the method using Beijing smart card data. The results show close to 69% residential locations inference rates and more than 72% workplace locations inference rates. The mean value of inferred areas is approximately 20% of the areas derived by traditional methods. Available data on alighting stops verify the inferred results at least for flat fare systems.

Field surveys were conducted in Greek olive orchards from 2017 to 2020 to collect information on the sanitary status of the trees. Using a high-throughput sequencing approach, viral sequences were identified in total RNA extracts from several trees and assembled to reconstruct the complete genomes of two isolates of a new viral species of the genus Tepovirus (Betaflexiviridae), for which the name olive virus T (OlVT) is proposed. A reverse transcription–polymerase chain reaction assay was developed which detected OlVT in samples collected in olive growing regions in Central and Northern Greece, showing a virus prevalence of 4.4% in the olive trees screened. Sequences of amplified fragments from the movement–coat protein region of OlVT isolates varied from 75.64% to 99.35%. Three olive varieties (Koroneiki, Arbequina and Frantoio) were infected with OlVT via grafting to confirm a graft-transmissible agent, but virus infections remained latent. In addition, cucumber mosaic virus, olive leaf yellowing-associated virus and cherry leaf roll virus were identified.

Cassava brown streak disease (CBSD) is a destructive disease of cassava in Eastern and Central Africa. Because there was no source of resistance in African varieties to provide complete protection against the viruses causing the disease, we searched in South American germplasm and identified cassava lines that did not become infected with the cassava brown streak viruses. These findings motivated further investigations into the mechanism of virus resistance. We used RNAscope® in situ hybridization to localize cassava brown streak virus in cassava germplasm lines that were highly resistant (DSC 167, immune) or that restricted virus infections to stems and roots only (DSC 260). We show that the resistance in those lines is not a restriction of long-distance movement but due to preventing virus unloading from the phloem into parenchyma cells for replication, thus restricting the virus to the phloem cells only. When DSC 167 and DSC 260 were compared for virus invasion, only a low CBSV signal was found in phloem tissue of DSC 167, indicating that there is no replication in this host, while the presence of intense hybridization signals in the phloem of DSC 260 provided evidence for virus replication in companion cells. In neither of the two lines studied was there evidence of virus replication outside the phloem tissues. Thus, we conclude that in resistant cassava lines, CBSV is confined to the phloem tissues only, in which virus replication can still take place or is arrested.

Human motion trajectories, however captured, provide a rich spatiotemporal data source for human activity recognition, and the rich literature in motion trajectory analysis provides the tools to bridge the gap between this data and its semantic interpretation. But activity is an ambiguous term across research communities. For example, in urban transport research activities are generally characterized around certain locations assuming the opportunities and resources are present in that location, and traveling happens between these locations for activity participation, i.e., travel is not an activity, rather a mean to overcome spatial constraints. In contrast, in human-computer interaction (HCI) research and in computer vision research activities taking place "along the way," such as "reading on the bus," are significant for contextualized service provision. Similarly activities at coarser spatial and temporal granularity, e.g., "holidaying in a country," could be recognized in some context or domain. Thus the context prevalent in the literature does not provide a precise and consistent definition of activity, in particular in differentiation to travel when it comes to motion trajectory analysis. Hence in this paper, a thorough literature review studies activity from different perspectives, and develop a common framework to model and reason human behavior flexibly across contexts. This spatio-temporal framework is conceptualized with a focus on modeling activities hierarchically. Three case studies will illustrate how the semantics of the term activity changes based on scale and context. They provide evidence that the framework holds over different domains. In turn, the framework will help developing various applications and services that are aware of the broad spectrum of the term activity across contexts.

All established models in transportation engineering that estimate the numbers of trips between origins and destinations from vehicle counts use some form of a priori knowledge of the traffic. This paper, in contrast, presents a new origin–destination flow estimation model that uses only vehicle counts observed by traffic count sensors; it requires neither historical origin–destination trip data for the estimation nor any assumed distribution of flow. This approach utilises a method of statistical origin–destination flow estimation in computer networks, and transfers the principles to the domain of road traffic by applying transport-geographic constraints in order to keep traffic embedded in physical space. Being purely stochastic, our model overcomes the conceptual weaknesses of the existing models, and additionally estimates travel times of individual vehicles. The model has been implemented in a real-world road network in the city of Melbourne, Australia. The model was validated with simulated data and real-world observations from two different data sources. The validation results show that all the origin–destination flows were estimated with a good accuracy score using link count data only. Additionally, the estimated travel times by the model were close approximations to the observed travel times in the real world.

Recently, deep convolutional neural networks (CNN) have become popular for indoor visual localisation, where the networks learn to regress the camera pose from images directly. However, these approaches perform a 3D image-based reconstruction of the indoor spaces beforehand to determine camera poses, which is a challenge for large indoor spaces. Synthetic images derived from 3D indoor models have been used to eliminate the requirement of 3D reconstruction. A limitation of the approach is the low accuracy that occurs as a result of estimating the pose of each image frame independently. In this article, a visual localisation approach is proposed that exploits the spatio-temporal information from synthetic image sequences to improve localisation accuracy. A deep Bayesian recurrent CNN is fine-tuned using synthetic image sequences obtained from a building information model (BIM) to regress the pose of real image sequences. The results of the experiments indicate that the proposed approach estimates a smoother trajectory with smaller inter-frame error as compared to existing methods. The achievable accuracy with the proposed approach is 1.6 m, which is an improvement of approximately thirty per cent compared to the existing approaches. A Keras implementation can be found in our Github repository.

Virus discovery based on high-throughput sequencing relies on enrichment for virus sequences prior to library preparation to achieve a sufficient number of viral reads. In general, preparations of double-stranded RNA or total RNA preparations treated to remove rRNA are used for sequence enrichment. We used virus-specific antibodies to immunocapture virions from plant sap to conduct cDNA synthesis, followed by library preparation and HTS. For the four potato viruses PLRV, PVY, PVA and PYV, template preparation by virion immunocapture provided a simpler and less expensive method than the enrichment of total RNA by ribosomal depletion. Specific enrichment of viral sequences without an intermediate amplification step was achieved, and this high coverage of sequences across the viral genomes was important to identify rare sequence variations. Using this approach, the first complete genome sequence of a potato yellowing virus isolate (PYV, DSMZ PV-0706) was determined in this study. PYV can be confidently assigned as a distinct species in the genus Ilarvirus.

Background: Sometimes prayer life can be difficult even for very religious persons, who may experience phases of “spiritual dryness”, which may have a negative effect on their well-being. Methods: To address this topic, we analyzed three contrasting groups of persons (religious brothers and sisters (RBS), n = 273; Catholic lay persons (CLP), n = 716; other lay persons (OLP), n = 351) with standardized measures and investigated how often indicators of spiritual dryness were perceived within these groups and how the perception that private prayers go unanswered could be a result of this. Results: Spiritual dryness was highest in RBS compared to RLP and OLP. For RBS, perception of being “spiritually empty” was the best predictor of prayers going unanswered, indicating emotional/spiritual exhaustion, while in OLP, the perception that God is “distant” was the best predictor, indicating that, particularly in this (younger) group, spiritual doubt is of particular relevance. For CLP, feeling that God is distant, feeling abandoned by God, and feeling “spiritually empty” were similarly relevant predictors of feelings that prayers go unanswered. Conclusions: This knowledge may help psychologists/psychotherapists, pastoral workers, and spiritual advisors to differentiate the underlying causes of spiritual dryness (in terms of “discernment”) and thus support persons struggling with God, their faith, and life.

Tospoviruses cause significant losses to a wide range of agronomic and horticultural crops worldwide. The type member, Tomato spotted wilt tospovirus (TSWV), causes systemic infection in susceptible tomato cultivars, whereas its infection is localized in cultivars carrying the Sw-5 resistance gene. The response to TSWV infection in tomato cultivars with or without Sw-5 was determined at the virus small RNA level in the locally infected leaf. Predicted reads were aligned to TSWV reference sequences. The TSWV genome was found to be differentially processed among each of the three-viral genomic RNAs—Large (L), Medium (M) and Small (S)—in the Sw-5(+) compared to Sw-5(−) genotypes. In the Sw-5(+) cultivar, the L RNA had the highest number of viral small-interfering RNAs (vsiRNAs), whereas in the Sw-5(−) cultivar the number was higher in the S RNA. Among the three-viral genomic RNAs, the distribution of hotspots showed a higher number of reads per million reads of vsiRNAs of 21 and 22 nt class at the 5′ and 3′ ends of the L and the S RNAs, with less coverage in the M RNA. In the Sw-5(−) cultivar, the nature of the 5′ nucleotide-end in the siRNAs varied significantly; reads with 5′-adenine-end were most abundant in the mock control, whereas cytosine and uracil were more abundant in the infected plants. No such differences were seen in case of the resistant genotype. Findings provided insights into the response of tomato cultivars to TSWV infection.