Spatial clustering and common regulatory elements correlate with coordinated gene expression

Many cellular responses to surrounding cues require temporally concerted transcriptional regulation of multiple genes. In prokaryotic cells, a single-input-module motif with one transcription factor regulating multiple target genes can generate coordinated gene expression. In eukaryotic cells, transcriptional activity of a gene is affected by not only transcription factors but also the epigenetic modifications and three-dimensional chromosome structure of the gene. To examine how local gene environment and transcription factor regulation are coupled, we performed a combined analysis of time-course RNA-seq data of TGF-\b{eta} treated MCF10A cells and related epigenomic and Hi-C data. Using Dynamic Regulatory Events Miner (DREM), we clustered differentially expressed genes based on gene expression profiles and associated transcription factors. Genes in each class have similar temporal gene expression patterns and share common transcription factors. Next, we defined a set of linear and radial distribution functions, as used in statistical physics, to measure the distributions of genes within a class both spatially and linearly along the genomic sequence. Remarkably, genes within the same class despite sometimes being separated by tens of million bases (Mb) along genomic sequence show a significantly higher tendency to be spatially close despite sometimes being separated by tens of Mb along the genomic sequence than those belonging to different classes do. Analyses extended to the process of mouse nervous system development arrived at similar conclusions. Future studies will be able to test whether this spatial organization of chromosomes contributes to concerted gene expression.Comment: 30 pages, 9 figures, accepted in PLoS Computational Biolog

On the impact of aggregation on the performance of traffic aware routing

Abstract — This paper investigates the impact of traffic aggregation on the performance of routing algorithms that incorporate traffic information. The focus is on two main issues. Firstly, we explore the relationship between the average performance of the network and the level of granularity at which traffic can be assigned to routes. More specifically, we are interested in how average network performance improves as the ability of the routing protocol to split traffic arbitrarily across multiple paths increases. Secondly, we focus on the impact of traffic aggregation on short-term routing behavior. In particular, we explore the effects of traffic aggregation on traffic variability, which directly affects short-term routing performance. Our analysis is based on traffic traces collected from an operational network. The results of this study provide insights into the cost-performance trade-offs associated with deploying routing protocols that incorporate traffic awareness

What Cross-morphemic Letter Transposition in Derived Nonwords Tells us about Lexical Processing

According to an obligatory decomposition account of polymorphemic word recognition, a nonword that is composed of a real word plus derivational affix (e.g., teachen) should prime its stem (TEACH) to the same extent that a truly suffixed word does (e.g., teacher). The stem will be activated in both cases after the suffix is removed prior to the lexical status of the letter-string being of relevance. Importantly, disruption to the stem and suffix through letter transposition should have the same impact on the nonwords and words, with teacehn and teacehr equally priming TEACH. However, an experiment by Diependaele, Morris, Serota, Bertrand, and Grainger (2013) found that the equivalent priming for nonwords and words only occurred when they were intact. When letters were transposed, only the truly derived words showed priming. Since such a result cannot be handled by an obligatory decomposition account, it is important to replicate it. Therefore, the present study repeated the conditions of Diependaele et al. (2013), along with a nonword condition where the stem was followed by a non-suffix (e.g., teachin or teacihn). It was found that priming was maintained across all conditions regardless of letter transposition, hence maintaining obligatory decomposition as a viable account. However, the findings with the non-suffixed nonwords led to the conclusion that morphological structure does not control decomposition, but rather, has its impact after form-based components of the letter-string have been activated

Anisotropy of graphite optical conductivity

The graphite conductivity is evaluated for frequencies between 0.1 eV, the energy of the order of the electron-hole overlap, and 1.5 eV, the electron nearest hopping energy. The in-plane conductivity per single atomic sheet is close to the universal graphene conductivity $e^2/4\hbar$ and, however, contains a singularity conditioned by peculiarities of the electron dispersion. The conductivity is less in the $c-$direction by the factor of the order of 0.01 governed by electron hopping in this direction.Comment: 3 pages, 3 figure

New Perspectives in Sinographic Language Processing Through the Use of Character Structure

Chinese characters have a complex and hierarchical graphical structure carrying both semantic and phonetic information. We use this structure to enhance the text model and obtain better results in standard NLP operations. First of all, to tackle the problem of graphical variation we define allographic classes of characters. Next, the relation of inclusion of a subcharacter in a characters, provides us with a directed graph of allographic classes. We provide this graph with two weights: semanticity (semantic relation between subcharacter and character) and phoneticity (phonetic relation) and calculate "most semantic subcharacter paths" for each character. Finally, adding the information contained in these paths to unigrams we claim to increase the efficiency of text mining methods. We evaluate our method on a text classification task on two corpora (Chinese and Japanese) of a total of 18 million characters and get an improvement of 3% on an already high baseline of 89.6% precision, obtained by a linear SVM classifier. Other possible applications and perspectives of the system are discussed.Comment: 17 pages, 5 figures, presented at CICLing 201

Liaising the Catalog: Collaborating Across Library Departments to Promote Successful Discoverability through Enhanced Cataloging

Academic libraries are increasingly asked to articulate connections between the work of library staff and student success. This article discusses how a team of librarians participating in CARLI Counts, an immersive professional development program funded by a Laura Bush 21st Century Librarian Grant through the Institute of Museum and Library Services, responded to the lack of research investigating the indirect impact of the work of technical services staff on student learning. An anonymous online survey distributed to library staff of the Consortium of Academic and Research Libraries in Illinois (CARLI) member institutions explored the perceived value of enhanced cataloging in supporting student research. Survey results point to opportunities for communication and collaboration among technical services and public services librarians to improve understanding of enhanced catalog functionality and user needs

HARMONY: a pragmatic cluster randomised controlled trial of a culturally competent systems intervention to prevent and reduce domestic violence among migrant and refugee families in general practice:study protocol

INTRODUCTION: Domestic violence and abuse (DVA) is prevalent, harmful and more dangerous among diaspora communities because of the difficulty accessing DVA services, language and migration issues. Consequently, migrant/refugee women are common among primary care populations, but evidence for culturally competent DVA primary care practice is negligible. This pragmatic cluster randomised controlled trial aims to increase DVA identification and referral (primary outcomes) threefold and safety planning (secondary outcome) among diverse women attending intervention vs comparison primary care clinics. Additionally, the study plans to improve recording of DVA, ethnicity, and conduct process and economic evaluations. METHODS AND ANALYSIS: Recruitment of ≤28 primary care clinics in Melbourne, Australia with high migrant/refugee communities. Eligible clinics need ≥1 South Asian general practitioner (GP) and one of two common software programmes to enable aggregated routine data extraction by GrHanite. Intervention staff undertake three DVA training sessions from a GP educator and bilingual DVA advocate/educator. Following training, clinic staff and DVA affected women 18+ will be supported for 12 months by the advocate/educator. Comparison clinics are trained in ethnicity and DVA data entry and offer routine DVA care. Data extraction of DV identification, safety planning and referral from routine GP data in both arms. Adjusted regression analysis by intention-to-treat by staff blinded to arm. Economic evaluation will estimate cost-effectiveness and cost-utility. Process evaluation interviews and analysis with primary care staff and women will be framed by Normalisation Process Theory to maximise understanding of sustainability. Harmony will be the first primary care trial to test a culturally competent model for the care of diverse women experiencing DVA. ETHICS AND DISSEMINATION: Ethical approval from La Trobe University Human Ethics Committee (HEC18413) and dissemination by policy briefs, journal articles and conference and community presentations. TRIAL REGISTRATION NUMBER: ANZCTR- ACTRN12618001845224; Pre-results

The challenges of statistical patterns of language: the case of Menzerath's law in genomes

The importance of statistical patterns of language has been debated over decades. Although Zipf's law is perhaps the most popular case, recently, Menzerath's law has begun to be involved. Menzerath's law manifests in language, music and genomes as a tendency of the mean size of the parts to decrease as the number of parts increases in many situations. This statistical regularity emerges also in the context of genomes, for instance, as a tendency of species with more chromosomes to have a smaller mean chromosome size. It has been argued that the instantiation of this law in genomes is not indicative of any parallel between language and genomes because (a) the law is inevitable and (b) non-coding DNA dominates genomes. Here mathematical, statistical and conceptual challenges of these criticisms are discussed. Two major conclusions are drawn: the law is not inevitable and languages also have a correlate of non-coding DNA. However, the wide range of manifestations of the law in and outside genomes suggests that the striking similarities between non-coding DNA and certain linguistics units could be anecdotal for understanding the recurrence of that statistical law.Comment: Title changed, abstract and introduction improved and little corrections on the statistical argument

Ab initio identification of transcription start sites in the Rhesus macaque genome by histone modification and RNA-Seq

Rhesus macaque is a widely used primate model organism. Its genome annotations are however still largely comparative computational predictions derived mainly from human genes, which precludes studies on the macaque-specific genes, gene isoforms or their regulations. Here we took advantage of histone H3 lysine 4 trimethylation (H3K4me3)’s ability to mark transcription start sites (TSSs) and the recently developed ChIP-Seq and RNA-Seq technology to survey the transcript structures. We generated 14 013 757 sequence tags by H3K4me3 ChIP-Seq and obtained 17 322 358 paired end reads for mRNA, and 10 698 419 short reads for sRNA from the macaque brain. By integrating these data with genomic sequence features and extending and improving a state-of-the-art TSS prediction algorithm, we ab initio predicted and verified 17 933 of previously electronically annotated TSSs at 500-bp resolution. We also predicted approximately 10 000 novel TSSs. These provide an important rich resource for close examination of the species-specific transcript structures and transcription regulations in the Rhesus macaque genome. Our approach exemplifies a relatively inexpensive way to generate a reasonably reliable TSS map for a large genome. It may serve as a guiding example for similar genome annotation efforts targeted at other model organisms

Synaesthesia in Chinese characters: the role of radical function and position

Grapheme-colour synaesthetes experience unusual colour percepts when they encounter letters and/or digits. Studies of English-speaking grapheme-colour synaesthetes have shown that synaesthetic colours are sometimes triggered by rule-based linguistic mechanisms (e.g., B might be blue). In contrast, little is known about synaesthesia in logographic languages such as Chinese. The current study shows the mechanisms by which synaesthetic speakers of Chinese colour their language. One hypothesis is that Chinese characters might be coloured by their constituent morphological units, known as radicals, and we tested this by eliciting synaesthetic colours for characters while manipulating features of the radicals within them. We found that both the function (semantic vs. phonetic) and position (left vs. right) of radicals influence the nature of the synaesthetic colour generated. Our data show that in Chinese, as in English, synaesthetic colours are influenced by systematic rules, rather than by random associations, and that these rules are based on existing psycholinguistic mechanisms of language processing