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The neighbourhood is a basic unit in police work in the city. Throughout the twentieth and twenty-first centuries, theories of crime and place conceptualized the neighbourhood differently; some emphasized sociological aspects, while others focused on physical aspects. Each theory offers different practices for crime reduction and police action strategies in neighbourhoods. This paper shows how the police implement different strategies in a neighbourhood in South Tel Aviv. It argues that the diversity of approaches increases the range and areas of police intervention in the neighbourhood and empowers their control and effect on place. It indicates the dominance of physical and microgeographical approaches over sociological approaches. Methodologically, this paper uses a three-pronged approach: 1. In-depth interviews with police officers and other dominant actors in space; 2. Ethnographic work with the urban police; and 3. Spatial analysis of policework in the neighbourhood. The conclusion discusses the consequences and shortcomings of the current paradigm in policing and suggests three directions as departure points for new thinking on crime and neighbourhoods: rethinking scale; reassessing the subject of concern; and readdressing the entanglement between crime and space. [ABSTRACT FROM AUTHOR]

Prior research reveals the interrelations between gentrification and policing, yet this paper introduces the unheard perspective of the of police on their role in gentrification. The study focuses on South Tel Aviv, which houses immigrants, drug addicts, prostitution and houselessness. It is undergoing massive urban renewal and has become the most policed area in the city. Methodology includes interviews with police officers (N-15), ethnography with urban police and spatial analysis of urban renewal. The paper argues that: 1. Gentrifying a high-crime neighborhood triggers a collision of urban forces and spatial negotiations amid users, institutions, and areas in the city. 2. Police play a significant role in this process and must operate intensive borderwork on various scales, with technology becoming a tool for internal, microgeographical social borderwork. 3. Policing gentrification raises reflexivity among officers regarding their profession, social obligation and position in urban politics. The paper concludes with the concept of policing temporality to describe the role of police in gentrification. [ABSTRACT FROM AUTHOR]

Recent studies demonstrate how violence, social media, and protest intertwine. This article complements this body of knowledge and indicates how social media enables new modes of small-scale protest events and how it is being used by right-wing and middle-class groups to influence urban politics. The article conceptualizes local-digital activism as a particular form of protest that is based on a hybrid framework of action that entangles physical actions in public space with virtual acts of dissent, creating embodied digital activism in specific locales. The key arguments are threefold: (1) local–digital activism initiates a particular framework of action that is embedded in digital culture and can be used by different ideological groups. (2) The approach to place in this type of dissent is central and manifold, with physical and virtual spaces codefining one another. (3) Triggering violent encounters and using violent representations in place is strategic and intentional, a means to expand visibility on digital platforms. Empirically the article analyses two groups in South Tel Aviv, presenting their protest strategies and tactical use of place, digitization, violence, and the body in creating the iconography of the "other in the place." The study is based on geographic and ethnographic work, in-depth interviews (N = 24) with various actors, and social media content analysis (videos = 72, posts = 210). The final discussion addresses the characteristics of local-digital activism and its role in urban political struggles and offers paths for future research. [ABSTRACT FROM AUTHOR]

Aims: Due to the lack of tools evaluating participation of children with ASD in the educational setting, this study aimed to adapt the Structured Preschool Participation Observation (SPO), which assess the participation of preschool children attending mainstream-educational settings to children with ASD attending non-inclusive special education (content validity), to measure its initial psychometric properties (internal reliability, inter-rater reliability), and to describe children's participation characteristics, creating an effective tool to fill this gap. Methods: Content validity was evaluated by 21 experts using questionnaires. Thirty-five children with ASD were observed in their educational setting using the adapted tool (SPO-ASD). Results: Content validity was satisfactory regarding the items and their classification into occupational areas. Moderate to excellent internal consistency (α =.73–.92) and inter-rater reliability (ICC =.61–.95, p<.05) were found for all scales and most areas. Children's participation frequency was high in learning and activities of daily living (ADL), low in play and social participation. Performance level was low in social participation. Enjoyment level was low, and needed assistance in ADL was high. Conclusions: Based on our initial evaluation, the SPO-ASD may be suitable for assessing participation of children with ASD attending special education preschools. Additional studies are needed to more securely establish its psychometric properties. [ABSTRACT FROM AUTHOR]

Viral genomes not only code the protein content, but also include silent, overlapping codes which are important to the regulation of the viral life cycle and affect its evolution. Due to the high density of these codes, their non-modular nature and the complex intracellular processes they encode, the ability of current approaches to decipher them is very limited. We describe the first computational-experimental pipeline for studying the effects of viral silent and non-silent information on its fitness. The pipeline was implemented to study the Porcine Circovirus type 2 (PCV2), the shortest known eukaryotic virus, and includes the following steps: (1) Based on the analyses of 2100 variants of PCV, suspected silent codes were inferred. (2) Five hundred variants of the PCV2 were designed to include various 'smart' silent mutations. (3) Using state of the art synthetic biology approaches, the genomes of these five hundred variants were generated. (4) Competition experiments between the variants were performed in Porcine kidney-15 (PK15) cell-lines. (5) The variant titers were analyzed based on novel next-generation sequencing (NGS) experiments. (6) The features related to the titer of the variants were inferred and their analyses enabled detection of various novel silent functional sequence and structural motifs. Furthermore, we demonstrate that 50 of the silent variants exhibit higher fitness than the wildtype in the analyzed conditions. [ABSTRACT FROM AUTHOR]

This paper is centred on the levels of participation in digital municipal platforms, and its goals are threefold: (1) to assess the normative aspirations and limitations of policy makers and key actors in the municipality with regard to the smart resident idea, with a focus on participation and privacy; (2) to assess and categorise levels of participation in varied social and geographic contexts in the city; and (3) to assess the possible link between participation and privacy practices among users. Empirically, this paper studies the practices of the inhabitants of Tel Aviv-Yafo City, with a focus on the use of digitised services provided by the municipality and the use of the celebrated project 'Digi-Tel' – a digital card that offers to the inhabitants of the city services, discounts, targeted information and benefits around the city. The assessment of the inhabitants' practices is based on a survey that was conducted in four neighbourhoods with different socio-economic, ethnic and geographical characteristics. The survey is supplemented with interviews of prominent figures in the Tel Aviv-Yafo municipality to understand their views on participation and privacy. The paper concludes with a discussion of the varied profiles of the users and non-users of digital platforms in the city, revealing their complex approach to participation in the digital age. [ABSTRACT FROM AUTHOR]

Numerous studies have focused on the global city, the sustainable city, the resilient city, the creative city, and the smart city, analyzing their politics, ideologies, and social implications. However, the literature lacks synthetic analysis that addresses these concepts by juxtaposing them and exploring their similarities and differences. This paper provides synthetic analysis, followed by a discussion of the concepts’ competing and complementary logics of governance and citizenship. The concluding section addresses the importance of taking into account these diverse concepts as political ideas and discusses how these concepts become a prescriptive mix promoted by public officials and private developers. [ABSTRACT FROM AUTHOR]

It is generally believed that introns are not translated; therefore, the potential intronic features that may be related to the translation step (occurring after splicing) have yet to be thoroughly studied. Here, focusing on four fungi, we performed for the first time a comprehensive study aimed at characterizing how translation efficiency is encoded in introns and affects their evolution. By analysing their intronome we provide evidence of selection for STOP codons close to the intronic 50 end, and show that the beginning of introns are selected for significantly high translation, presumably to reduce translation and metabolic costs in cases of non-spliced introns. Ribosomal profiling data analysis in Saccharomyces cerevisiae supports the conjecture that in this organism intron retention frequently occurs, introns are partially translated, and their translation efficiency affects organismal fitness. We show that the reported results are more significant in highly translated and highly spliced genes, but are not associated only with genes with a specific function. We also discuss the potential relation of the reported signals to efficient nonsense-mediated decay due to splicing errors. These new discoveries are supported by population-genetics considerations. In addition, they are contributory steps towards a broader understanding of intron evolution and the effect of silent mutations on gene expression and organismal fitness. [ABSTRACT FROM AUTHOR]

Motivation: Dozens of studies in recent years have demonstrated that codon usage encodes various aspects related to all stages of gene expression regulation. When relevant high-quality large-scale gene expression data are available, it is possible to statistically infer and model these signals, enabling analysing and engineering gene expression. However, when these data are not available, it is impossible to infer and validate such models. Results: In this current study, we suggest Chimera--an unsupervised computationally efficient approach for exploiting hidden high-dimensional information related to the way gene expression is encoded in the open reading frame (ORF), based solely on the genome of the analysed organism. One version of the approach, named Chimera Average Repetitive Substring (ChimeraARS), estimates the adaptability of an ORF to the intracellular gene expression machinery of a genome (host), by computing its tendency to include long substrings that appear in its coding sequences; the second version, named ChimeraMap, engineers the codons of a protein such that it will include long substrings of codons that appear in the host coding sequences, improving its adaptation to a new host's gene expression machinery. We demonstrate the applicability of the new approach for analysing and engineering heterologous genes and for analysing endogenous genes. Specifically, focusing on Escherichia coli, we show that it can exploit information that cannot be detected by conventional approaches (e.g. the CAI--Codon Adaptation Index), which only consider single codon distributions; for example, we report correlations of up to 0.67 for the ChimeraARS measure with heterologous gene expression, when the CAI yielded no correlation. [ABSTRACT FROM AUTHOR]

Motivation: Dozens of studies in recent years have demonstrated that codon usage encodes various aspects related to all stages of gene expression regulation. When relevant high-quality large-scale gene expression data are available, it is possible to statistically infer and model these signals, enabling analysing and engineering gene expression. However, when these data are not available, it is impossible to infer and validate such models. Results: In this current study, we suggest Chimera--an unsupervised computationally efficient approach for exploiting hidden high-dimensional information related to the way gene expression is encoded in the open reading frame (ORF), based solely on the genome of the analysed organism. One version of the approach, named Chimera Average Repetitive Substring (ChimeraARS), estimates the adaptability of an ORF to the intracellular gene expression machinery of a genome (host), by computing its tendency to include long substrings that appear in its coding sequences; the second version, named ChimeraMap, engineers the codons of a protein such that it will include long substrings of codons that appear in the host coding sequences, improving its adaptation to a new host's gene expression machinery. We demonstrate the applicability of the new approach for analysing and engineering heterologous genes and for analysing endogenous genes. Specifically, focusing on Escherichia coli, we show that it can exploit information that cannot be detected by conventional approaches (e.g. the CAI--Codon Adaptation Index), which only consider single codon distributions; for example, we report correlations of up to 0.67 for the ChimeraARS measure with heterologous gene expression, when the CAI yielded no correlation. [ABSTRACT FROM AUTHOR]

Background: Gene expression is a central process in all living organisms. Central questions in the field are related to the way the expression levels of genes are encoded in the transcripts and affect their evolution, and the potential to predict expression levels solely by transcript features. In this study we analyze S. cerevisiae, a model organism with the most abundant relevant cellular and genomic measurements, to evaluate the accuracy in which expression levels can be predicted by different parts of the transcript. To this end, we perform various types of regression analyses based on a total of 5323 features of the transcript. The main advantage of the proposed predictors over previous ones is related to the accurate and comprehensive definitions of the relevant transcript features, which are based on biophysical knowledge of the gene transcription and translation processes, their modeling and evolution. Results: Cross validation analyses of our predictors demonstrate that they achieve a correlation of 0.68/0.68/0.70/ 0.61/0.81 with mRNA levels, ribosomal density, protein levels, proteins per mRNA molecule (PPR), and ribosomal load (RL) respectively (all p-values <10−140). When we consider predictors that are based exclusively on the features related to different parts of the transcript (5’UTR, ORF, 3’UTR), the correlations with protein levels were 0.27/0.71/ 0.25 (all p-values <10−5), suggesting that the information in the UTRs is redundant, and features of the ORF alone yield similar predictions to the ones obtained based on the entire transcript. Conclusions: The reported results demonstrate that in the analyzed model organism the expression levels of a gene are encoded in the transcript. Specifically, the prediction of a large fraction of the variance of the different gene expression steps based on transcript features alone is feasible in S. cerevisiae. We report dozens of novel transcript features related to expression levels predictions, demonstrating how such analyses can aid in understanding the gene expression process and its evolution, and how such predictors can be designed for other organisms in the future. [ABSTRACT FROM AUTHOR]

The accepted model of eukaryotic translation initiation begins with the scanning of the transcript by the pre-initiation complex from the 5′end until an ATG codon with a specific nucleotide (nt) context surrounding it is recognized (Kozak rule). According to this model, ATG codons upstream to the beginning of the ORF should affect translation. We perform for the first time, a genome-wide statistical analysis, uncovering a new, more comprehensive and quantitative, set of initiation rules for improving the cost of translation and its efficiency. Analyzing dozens of eukaryotic genomes, we find that in all frames there is a universal trend of selection for low numbers of ATG codons; specifically, 16–27 codons upstream, but also 5–11 codons downstream of the START ATG, include less ATG codons than expected. We further suggest that there is selection for anti optimal ATG contexts in the vicinity of the START ATG. Thus, the efficiency and fidelity of translation initiation is encoded in the 5′UTR as required by the scanning model, but also at the beginning of the ORF. The observed nt patterns suggest that in all the analyzed organisms the pre-initiation complex often misses the START ATG of the ORF, and may start translation from an alternative initiation start-site. Thus, to prevent the translation of undesired proteins, there is selection for nucleotide sequences with low affinity to the pre-initiation complex near the beginning of the ORF. With the new suggested rules we were able to obtain a twice higher correlation with ribosomal density and protein levels in comparison to the Kozak rule alone (e.g. for protein levels r = 0.7 vs. r = 0.31; p<10−12). [ABSTRACT FROM AUTHOR]

One of the open questions in regulatory genomics is how the efficiency of gene translation is encoded in the coding sequence. Here we analyse recently generated measurements of folding energy in Saccharomyces cerevisiae, showing that genes with high protein abundance tend to have strong mRNA folding (mF; R=0.68). mF strength also strongly correlates with ribosomal density and mRNA levels, suggesting that this relation at least partially pertains to the efficiency of translation elongation, presumably by preventing aggregation of mRNA molecules. [ABSTRACT FROM AUTHOR]

mRNA translation is a fundamental cellular process consuming most of the intracellular energy; thus, it is under extensive evolutionary selection for optimization, and its efficiency can affect the host's growth rate. We describe a generic approach for improving the growth rate (fitness) of any organism by introducing synonymous mutations based on comprehensive computational models. The algorithms introduce silent mutations that may improve the allocation of ribosomes in the cells via the decreasing of their traffic jams during translation respectively. As a result, resources availability in the cell changes leading to improved growth-rate. We demonstrate experimentally the implementation of the method on Saccharomyces cerevisiae: we show that by introducing a few mutations in two computationally selected genes the mutant's titer increased. Our approach can be employed for improving the growth rate of any organism providing the existence of data for inferring models, and with the relevant genomic engineering tools; thus, it is expected to be extremely useful in biotechnology, medicine, and agriculture. [ABSTRACT FROM AUTHOR]

Summary: iMAT is an Integrative Metabolic Analysis Tool, enabling the integration of transcriptomic and proteomic data with genome-scale metabolic network models to predict enzymes' metabolic flux, based on the method previously described by Shlomi et al. The prediction of metabolic fluxes based on high-throughput molecular data sources could help to advance our understanding of cellular metabolism, since current experimental approaches are limited to measuring fluxes through merely a few dozen enzymes.Availability and Implementation: http://imat.cs.tau.ac.il/Contact: zurhadas@post.tau.ac.il; ruppin@post.tau.ac.il; tomersh@cs.technion.ac.ilSupplementary information: Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Summary: The RFMapp is a graphical user interface application based on the RFM (ribosome flow model), enabling the estimation of the translation elongation rates of messenger ribonucleic acids (mRNAs) and the profile of ribosomal densities along the mRNAs, in a computationally efficient way. The RFMapp is based on the approach previously described by Reuveni et al., and unlike other traditional approaches in the field, which are mainly related to the genes' mean codon translation efficiency, the RFM additionally considers the codon order, the ribosomes' size and their order. Thus, it has been shown that RFM outperforms traditional predictors when analyzing both heterologous and endogenous genes.Availability and implementation: Distributable cross-platform application and guideline are available for download at: http://www.cs.tau.ac.il/∼tamirtul/RFM_Installers/install.htmContact: tamirtul@post.tau.ac.il [ABSTRACT FROM AUTHOR]

Alternative transcription and translation initiation multiply the number of protein isoforms in subcellular compartments without increasing the gene copy number. The Lon protease modulates protein quality control in plant organelles. Herein we show that Lon1 and Lon4 proteases evolved complementary subsets of regulatory components for dual-targeting to mitochondria and chloroplasts.Cellular homeostasis relies on components of protein quality control including chaperones and proteases. In bacteria and eukaryotic organelles, Lon proteases play a critical role in removing irreparably damaged proteins and thereby preventing the accumulation of deleterious degradation-resistant aggregates. Gene expression, live-cell imaging, immunobiochemical, and functional complementation approaches provide conclusive evidence for Lon1 dual-targeting to chloroplasts and mitochondria. Dual-organellar deposition of Lon1 isoforms depends on both transcriptional regulation and alternative translation initiation via leaky ribosome scanning from the first AUG sequence context that deviates extensively from the optimum Kozak consensus. Organelle-specific Lon1 targeting results in partial complementation of Arabidopsis lon1-1 mutants, whereas full complementation is solely accomplished by dual-organellar targeting. Both the optimal and non-optimal AUG sequence contexts are functional in yeast and facilitate leaky ribosome scanning complementing the pim1 phenotype when the mitochondrial presequence is used. Bioinformatic search identified a limited number of Arabidopsis genes with Lon1-type dual-targeting sequence organization. Lon4, the paralog of Lon1, has an ambiguous presequence likely evolved from the twin presequences of an ancestral Lon1-like gene, generating a single dual-targeted protein isoform. We postulate that Lon1 and its subfunctional paralog Lon4 evolved complementary subsets of transcriptional and posttranscriptional regulatory components responsive to environmental cues for dual-organellar targeting. [ABSTRACT FROM PUBLISHER]