The iCrawl Wizard -- Supporting Interactive Focused Crawl Specification

Collections of Web documents about specific topics are needed for many areas of current research. Focused crawling enables the creation of such collections on demand. Current focused crawlers require the user to manually specify starting points for the crawl (seed URLs). These are also used to describe the expected topic of the collection. The choice of seed URLs influences the quality of the resulting collection and requires a lot of expertise. In this demonstration we present the iCrawl Wizard, a tool that assists users in defining focused crawls efficiently and semi-automatically. Our tool uses major search engines and Social Media APIs as well as information extraction techniques to find seed URLs and a semantic description of the crawl intent. Using the iCrawl Wizard even non-expert users can create semantic specifications for focused crawlers interactively and efficiently.Comment: Published in the Proceedings of the European Conference on Information Retrieval (ECIR) 201

Should I Care about Your Opinion? : Detection of Opinion Interestingness and Dynamics in Social Media

In this paper, we describe a set of reusable text processing components for extracting opinionated information from social media, rating it for interestingness, and for detecting opinion events. We have developed applications in GATE to extract named entities, terms and events and to detect opinions about them, which are then used as the starting point for opinion event detection. The opinions are then aggregated over larger sections of text, to give some overall sentiment about topics and documents, and also some degree of information about interestingness based on opinion diversity. We go beyond traditional opinion mining techniques in a number of ways: by focusing on specific opinion-target extraction related to key terms and events, by examining and dealing with a number of specific linguistic phenomena, by analysing and visualising opinion dynamics over time, and by aggregating the opinions in different ways for a more flexible view of the information contained in the documents.EU/27023

Analyzing web archives through topic and event focused sub-collections

Web archives capture the history of the Web and are therefore an important source to study how societal developments have been reflected on the Web. However, the large size of Web archives and their temporal nature pose many challenges to researchers interested in working with these collections. In this work, we describe the challenges of working with Web archives and propose the research methodology of extracting and studying sub-collections of the archive focused on specific topics and events. We discuss the opportunities and challenges of this approach and suggest a framework for creating sub-collections

Variability of Optical Counterparts in the Chandra Galactic Bulge Survey

We present optical lightcurves of variable stars consistent with the positions of X-ray sources identified with the Chandra X-ray Observatory for the Chandra Galactic Bulge Survey. Using data from the Mosaic-II instrument on the Blanco 4m Telescope at CTIO, we gathered time-resolved photometric data on timescales from $\sim2$ hr to 8 days over the $\frac{3}{4}$ of the X-ray survey containing sources from the initial GBS catalog. Among the lightcurve morphologies we identify are flickering in interacting binaries, eclipsing sources, dwarf nova outbursts, ellipsoidal variations, long period variables, spotted stars, and flare stars. $87\%$ of X-ray sources have at least one potential optical counterpart. $24\%$ of these candidate counterparts are detectably variable; a much greater fraction than expected for randomly selected field stars, which suggests that most of these variables are real counterparts. We discuss individual sources of interest, provide variability information on candidate counterparts, and discuss the characteristics of the variable population.Comment: Accepted for publication in the Astrophysical Journal Supplement

Analysis of tissue transglutaminase function in the migration of swiss 3T3 fibroblasts - the active-state conformation of the enzyme does not affect cell motility but is important for its secretion

Increasing evidence suggests that tissue transglutaminase (tTGase; type II) is externalized from cells, where it may play a key role in cell attachment and spreading and in the stabilization of the extracellular matrix (ECM) through protein cross-linking. However, the relationship between these different functions and the enzyme’s mechanism of secretion is not fully understood. We have investigated the role of tTGase in cell migration using two stably transfected fibroblast cell lines in which expression of tTGase in its active and inactive (C277S mutant) states is inducible through the tetracycline-regulated system. Cells overexpressing both forms of tTGase showed increased cell attachment and decreased cell migration on fibronectin. Both forms of the enzyme could be detected on the cell surface, but only the clone overexpressing catalytically active tTGase deposited the enzyme into the ECM and cell growth medium. Cells overexpressing the inactive form of tTGase did not deposit the enzyme into the ECM or secrete it into the cell culture medium. Similar results were obtained when cells were transfected with tTGase mutated at Tyr274 (Y274A), the proposed site for the cis- ,trans peptide bond, suggesting that tTGase activity and/or its tertiary conformation dependent on this bond may be essential for its externalization mechanism. These results indicate that tTGase regulates cell motility as a novel cell-surface adhesion protein rather than as a matrix-cross-linking enzyme. They also provide further important insights into the mechanism of externalization of the enzyme into the extracellular matrix

Gateway vectors for efficient artificial gene assembly in vitro and expression in yeast Saccharomyces cerevisiae

Peer reviewedPublisher PD

Prevalence and orthopedic management of foot and ankle deformities in Charcot Marie Tooth disease

Introduction/Aims: We aimed to determine whether specific severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) vaccines may be associated with acute-onset polyradiculoneuropathy and if they may result in particular clinical presentations. Methods: We retrospectively reviewed records of all persons presenting with acute-onset polyradiculoneuropathy from January 1, 2021, to June 30, 2021, admitted to two Neuroscience centers, of the West and North Midlands, United Kingdom. We compared subjects with previous SARS-CoV2 vaccine exposure with a local cohort of persons with acute-onset polyradiculoneuropathy admitted between 2005 and 2019 and compared admission numbers for the studied time frame with that of the previous 3 years. Results: Of 24 persons with acute-onset polyradiculoneuropathy, 16 (66.7%) presented within 4 weeks after first SARS-CoV2 vaccine. Fourteen had received the AstraZeneca vaccine and one each, the Pfizer and Moderna vaccines. The final diagnosis was Guillain-Barré syndrome (GBS) in 12 and acute-onset chronic inflammatory demyelinating polyneuropathy in 4. Among AstraZeneca vaccine recipients, facial weakness in nine persons (64.3%), bulbar weakness in seven (50%), and the bifacial weakness and distal paresthesias GBS variant in three (21.4%), were more common than in historical controls (P =.01; P =.004, and P =.002, respectively). A 2.6-fold (95% confidence interval: 1.98–3.51) increase in admissions for acute-onset polyradiculoneuropathy was noted during the studied time frame, compared to the same period in the previous 3 years. Discussion: Despite a low risk, smaller than that of SARS-CoV2 infection and its complications, exposure to the first dose of AstraZeneca SARS-CoV2 vaccine may be a risk factor for acute-onset polyradiculoneuropathy, characterized by more common cranial nerve involvement

Fungicide usage is increasing: don’t forget to rotate fungicides

Non-Peer Reviewe

Contrasting roles of condensin I and condensin II in mitotic chromosome formation

© 2012. Published by The Company of Biologists LtdIn vertebrates, two condensin complexes exist, condensin I and condensin II, which have differing but unresolved roles in organizing mitotic chromosomes. To dissect accurately the role of each complex in mitosis, we have made and studied the first vertebrate conditional knockouts of the genes encoding condensin I subunit CAP-H and condensin II subunit CAP-D3 in chicken DT40 cells. Live-cell imaging reveals highly distinct segregation defects. CAP-D3 (condensin II) knockout results in masses of chromatin-containing anaphase bridges. CAP-H (condensin I)-knockout anaphases have a more subtle defect, with chromatids showing fine chromatin fibres that are associated with failure of cytokinesis and cell death. Super-resolution microscopy reveals that condensin-I-depleted mitotic chromosomes are wider and shorter, with a diffuse chromosome scaffold, whereas condensin-II-depleted chromosomes retain a more defined scaffold, with chromosomes more stretched and seemingly lacking in axial rigidity. We conclude that condensin II is required primarily to provide rigidity by establishing an initial chromosome axis around which condensin I can arrange loops of chromatin.This work was supported by an Australian Research Council discovery project [grant number DP110100784 to D.F.H., K.H.A.C. and W.C.E.]; National Health and Medical Research Council (NHMRC) project grants [APP1030358 and 546454]; an NHMRC RD Wright Fellowship to P.K.; an NHMRC Senior Research Fellowship to C.B.W.; an NHMRC Senior Principal Research Fellowship to K.H.A.C.; and by the Victorian Government’s Operational Infrastructure Support Progra

Aggressive aggregation

Among the first steps in a compilation pipeline is the construction of an Intermediate Representation (IR), an in-memory representation of the input program. Any attempt to program optimisation, both in terms of size and running time, has to operate on this structure. There may be one or multiple such IRs, however, most compilers use some form of a Control Flow Graph (CFG) internally. This representation clearly aims at general-purpose programming languages, for which it is well suited and allows for many classical program optimisations. On the other hand, a growing structural difference between the input program and the chosen IR can lose or obfuscate information that can be crucial for effective optimisation. With today’s rise of a multitude of different programming languages, Domain-Specific Languages (DSLs), and computing platforms, the classical machine-oriented IR is reaching its limits and a broader variety of IRs is needed. This realisation yielded, e.g., Multi-Level Intermediate Representation (MLIR), a compiler framework that facilitates the creation of a wide range of IRs and encourages their reuse among different programming languages and the corresponding compilers. In this modern spirit, this dissertation explores the potential of Algebraic Decision Diagrams (ADDs) as an IR for (domain-specific) program optimisation. The data structure remains the state of the art for Boolean function representation for more than thirty years and is well-known for its optimality in size and depth, i.e. running time. As such, it is ideally suited to represent the corresponding classes of programs in the role of an IR. We will discuss its application in a variety of different program domains, ranging from DSLs to machine-learned programs and even to general-purpose programming languages. Two representatives for DSLs, a graphical and a textual one, prove the adequacy of ADDs for the program optimisation of modelled decision services. The resulting DSLs facilitate experimentation with ADDs and provide valuable insight into their potential and limitations: input programs can be aggregated in a radical fashion, at the risk of the occasional exponential growth. With the aggregation of large Random Forests into a single aggregated ADD, we bring this potential to a program domain of practical relevance. The results are impressive: both running time and size of the Random Forest program are reduced by multiple orders of magnitude. It turns out that this ADD-based aggregation can be generalised, even to generaliii purpose programming languages. The resulting method achieves impressive speedups for a seemingly optimal program: the iterative Fibonacci implementation. Altogether, ADDs facilitate effective program optimisation where the input programs allow for a natural transformation to the data structure. In these cases, they have proven to be an extremely powerful tool for the optimisation of a program’s running time and, in some cases, of its size. The exploration of their potential as an IR has only started and deserves attention in future research