The incidence of corpora amylacea (CA) in the optic nerve of patients with Alzheimer's disease

Corpora amylacea (CA) are spherical or ovoid bodies 50-50 microns in diameter. They have been described in normal elderly brain as well as in a number of neurodegenerative disorders. In this study, the incidence of CA in the optic nerves of Alzheimer's disease (AD) patients was compared with normal elderly controls. Samples of optic nerves (MRC Brain Bank, Institute of Psychiatry) were taken from 12 AD patients (age range 69-94 years) and 18 controls (43-82 years). Optic nerves were fixed in 2% buffered glutaraldehyde, post-fixed in osmium tetroxide, embedded in epoxy resin and then sectioned to a thickness of 2 microns. Sections were stained with toluidine blue. CA were present in all of the optic nerves examined. In addition, a number of similarly stained but more irregularly shaped bodies were present. Fewer CA were found in the optic nerves of AD patients compared with controls. By contrast, the number or irregularly shaped bodies was increased in AD. In AD, there may be a preferential decline in the large diameter fibres which may mediate the M-cell pathway. Hence, the decline in the incidence of CA in AD may be associated with a reduction in these fibres. It is also possible that the irregualrly shaped bodies are a degeneration product of the CA.

Computer-aided categorisation and quantification of connectives in English and Arabic (based on newspaper text corpora).

This study presents a detailed contrastive description of the textual functioning of connectives in English and Arabic. Particular emphasis is placed on the organisational force of connectives and their role in sustaining cohesion. The description is intended as a contribution for a better understanding of the variations in the dominant tendencies for text organisation in each language. The findings are expected to be utilised for pedagogical purposes, particularly in improving EFL teaching of writing at the undergraduate level. The study is based on an empirical investigation of the phenomenon of connectivity and, for optimal efficiency, employs computer-aided procedures, particularly those adopted in corpus linguistics, for investigatory purposes. One important methodological requirement is the establishment of two comparable and statistically adequate corpora, also the design of software and the use of existing packages and to achieve the basic analysis. Each corpus comprises ca 250,000 words of newspaper material sampled in accordance to a specific set of criteria and assembled in machine readable form prior to the computer-assisted analysis. A suite of programmes have been written in SPITBOL to accomplish a variety of analytical tasks, and in particular to perform a battery of measurements intended to quantify the textual functioning of connectives in each corpus. Concordances and some word lists are produced by using OCP. Results of these researches confirm the existence of fundamental differences in text organisation in Arabic in comparison to English. This manifests itself in the way textual operations of grouping and sequencing are performed and in the intensity of the textual role of connectives in imposing linearity and continuity and in maintaining overall stability. Furthermore, computation of connective functionality and range of operationality has identified fundamental differences in the way favourable choices for text organisation are made and implemented.

Post-translational modifications and mass spectrometry detection

In this review, we provide a comprehensive bibliographic overview of the role of mass spectrometry and the recent technical developments in the detection of post-translational modifications (PTMs). We briefly describe the principles of mass spectrometry for detecting PTMs and the protein and peptide enrichment strategies for PTM analysis, including phosphorylation, acetylation and oxidation. This review presents a bibliographic overview of the scientific achievements and the recent technical development in the detection of PTMs is provided. In order to ascertain the state of the art in mass spectrometry and proteomics methodologies for the study of PTMs, we analyzed all the PTM data introduced in the Universal Protein Resource (UniProt) and the literature published in the last three years. The evolution of curated data in UniProt for proteins annotated as being post-translationally modified is also analyzed. Additionally, we have undertaken a careful analysis of the research articles published in the years 2010 to 2012 reporting the detection of PTMs in biological samples by mass spectrometry. © 2013 Elsevier Inc.

Extracting significant words from corpora for ontology extraction

We show a new method for term extraction from a domain relevant corpus using natural language processing for the purposes of semi-automatic ontology learning. Literature shows that topical words occur in bursts. We find that the ranking of extracted terms is insensitive to the choice of population model, but calculating frequencies relative to the burst size rather than the document length in words yields significantly different results.

Development of novel mass spectrometry methodology to detect post-translational modifications in oxidative stress and disease

This paper presented at the European Meeting of the Society-for-Free-Radical-Research-Europe 2007, discusses the development of novel mass spectrometry methodology to detect post-translational modifications in oxidative stress and disease.

Evaluating choices:the role of corpora in translation choices and target text assessment

Translation training in the university context needs to train students in the processes, in order to enhance and optimise the product as outcome of these processes. Evaluation of a target text as product has often been accused of being a subjective process, which does not easily lend itself to the type of feedback that could enable students to apply criteria more widely. For students, it often seems as though they make different inappropriate or incorrect choices every time they translate a new text, and the learning process appears unpredictable and haphazard. Within functionalist approaches to translation, with their focus on the target text in terms of functional adequacy to the intended purpose, as stipulated in the translation brief, there are guidelines for text production that can help to develop a more systematic approach not only to text production, but also to translation evaluation. In the context of a focus on user knowledge needs, target language conventions and acceptability, the use of corpora is an indispensable tool for the trainee translator. Evaluation can take place against the student's own reasoned selection process, based on hard evidence, against criteria which currently obtain in the TL and the TL culture. When trainee and evaluator work within the same guidelines, there is more scope for constructive learning and feedback.

Automatic Identification of False Friends in Parallel Corpora: Statistical and Semantic Approach

False friends are pairs of words in two languages that are perceived as similar but have different meanings. We present an improved algorithm for acquiring false friends from sentence-level aligned parallel corpus based on statistical observations of words occurrences and co-occurrences in the parallel sentences. The results are compared with an entirely semantic measure for cross-lingual similarity between words based on using the Web as a corpus through analyzing the words’ local contexts extracted from the text snippets returned by searching in Google. The statistical and semantic measures are further combined into an improved algorithm for identification of false friends that achieves almost twice better results than previously known algorithms. The evaluation is performed for identifying cognates between Bulgarian and Russian but the proposed methods could be adopted for other language pairs for which parallel corpora and bilingual glossaries are available.

Pichia pastoris regulates its gene-specific response to different carbon sources at the transcriptional, rather than the translational, level

Background: The methylotrophic, Crabtree-negative yeast Pichia pastoris is widely used as a heterologous protein production host. Strong inducible promoters derived from methanol utilization genes or constitutive glycolytic promoters are typically used to drive gene expression. Notably, genes involved in methanol utilization are not only repressed by the presence of glucose, but also by glycerol. This unusual regulatory behavior prompted us to study the regulation of carbon substrate utilization in different bioprocess conditions on a genome wide scale. Results: We performed microarray analysis on the total mRNA population as well as mRNA that had been fractionated according to ribosome occupancy. Translationally quiescent mRNAs were defined as being associated with single ribosomes (monosomes) and highly-translated mRNAs with multiple ribosomes (polysomes). We found that despite their lower growth rates, global translation was most active in methanol-grown P. pastoris cells, followed by excess glycerol- or glucose-grown cells. Transcript-specific translational responses were found to be minimal, while extensive transcriptional regulation was observed for cells grown on different carbon sources. Due to their respiratory metabolism, cells grown in excess glucose or glycerol had very similar expression profiles. Genes subject to glucose repression were mainly involved in the metabolism of alternative carbon sources including the control of glycerol uptake and metabolism. Peroxisomal and methanol utilization genes were confirmed to be subject to carbon substrate repression in excess glucose or glycerol, but were found to be strongly de-repressed in limiting glucose-conditions (as are often applied in fed batch cultivations) in addition to induction by methanol. Conclusions: P. pastoris cells grown in excess glycerol or glucose have similar transcript profiles in contrast to S. cerevisiae cells, in which the transcriptional response to these carbon sources is very different. The main response to different growth conditions in P. pastoris is transcriptional; translational regulation was not transcript-specific. The high proportion of mRNAs associated with polysomes in methanol-grown cells is a major finding of this study; it reveals that high productivity during methanol induction is directly linked to the growth condition and not only to promoter strength.

Linguistic Corpora as International Cultural Heritage: The Corpus of Bulgarian and Ukrainian Parallel Texts

The paper relates about our ongoing work on the creation of a corpus of Bulgarian and Ukrainian parallel texts. We discuss some differences in the approaches and the interpretation of some concepts, as well as various problems associated with the construction of our corpus, in particular the occasional ‘nonparallelism’ of original and translated texts. We give examples of the application of the parallel corpus for the study of lexical semantics and note the outstanding role of the corpus in the lexicographic description of Ukrainian and Bulgarian translation equivalents. We draw attention to the importance of creating parallel corpora as objects of national as well as global cultural heritage.

Web-application for Presentation of Bulgarian Language Heritage: Bilingual Digital Corpora and Dictionaries

The paper describes three software packages - the main components of a software system for processing and web-presentation of Bulgarian language resources – parallel corpora and bilingual dictionaries. The author briefly presents current versions of the core components “Dictionary” and “Corpus” as well as the recently developed component “Connection” that links both “Dictionary” and “Corpus”. The components main functionalities are described as well. Some examples of the usage of the system’s web-applications are included.

Targeted mass spectrometry methods for detecting oxidative post-translational modifications

Oxidative post-translational modifications (oxPTMs) can alter the function of proteins, and are important in the redox regulation of cell behaviour. The most informative technique to detect and locate oxPTMs within proteins is mass spectrometry (MS). However, proteomic MS data are usually searched against theoretical databases using statistical search engines, and the occurrence of unspecified or multiple modifications, or other unexpected features, can lead to failure to detect the modifications and erroneous identifications of oxPTMs. We have developed a new approach for mining data from accurate mass instruments that allows multiple modifications to be examined. Accurate mass extracted ion chromatograms (XIC) for specific reporter ions from peptides containing oxPTMs were generated from standard LC-MSMS data acquired on a rapid-scanning high-resolution mass spectrometer (ABSciex 5600 Triple TOF). The method was tested using proteins from human plasma or isolated LDL. A variety of modifications including chlorotyrosine, nitrotyrosine, kynurenine, oxidation of lysine, and oxidized phospholipid adducts were detected. For example, the use of a reporter ion at 184.074 Da/e, corresponding to phosphocholine, was used to identify for the first time intact oxidized phosphatidylcholine adducts on LDL. In all cases the modifications were confirmed by manual sequencing. ApoB-100 containing oxidized lipid adducts was detected even in healthy human samples, as well as LDL from patients with chronic kidney disease. The accurate mass XIC method gave a lower false positive rate than normal database searching using statistical search engines, and identified more oxidatively modified peptides. A major advantage was that additional modifications could be searched after data collection, and multiple modifications on a single peptide identified. The oxPTMs present on albumin and ApoB-100 have potential as indicators of oxidative damage in ageing or inflammatory diseases.

CUBEs: decoupled, compact, and monolithic spatial translational compliant parallel manipulators

This paper deals with the conceptual design of decoupled, compact, and monolithic XYZ compliant parallel manipulators (CPMs): CUBEs. Position spaces of compliant P (P: prismatic) joints are first discussed, which are represented by circles about the translational directions. A design method of monolithic XYZ CPMs is then proposed in terms of both the kinematic substitution method and the position spaces. Three types of monolithic XYZ CPMs are finally designed using the proposed method with the help of three classes of kinematical decoupled 3-DOF (degree of freedom) translational parallel mechanisms (TPMs). These monolithic XYZ CPMs include a 3-PPP XYZ CPM composed of identical parallelogram modules (a previously reported design), a novel 3-PPPR (R: revolute) XYZ CPM composed of identical compliant four-beam modules, and a novel 3-PPPRR XYZ CPM. The latter two monolithic designs also have extended lives. It is shown that the proposed design method can be used to design other decoupled and compact XYZ CPMs by using the concept of position spaces, and the resulting XYZ CPM is the most compact one when the fixed ends of the three actuated compliant P joints thereof overlap.