Large-scale Oscillation of Structure-Related DNA Sequence Features in Human Chromosome 21

Human chromosome 21 is the only chromosome in human genome that exhibits oscillation of (G+C)-content of cycle length of hundreds kilobases (500 kb near the right telomere). We aim at establishing the existence of similar periodicity in structure-related sequence features in order to relate this (G+C)% oscillation to other biological phenomena. The following quantities are shown to oscillate with the same 500kb periodicity in human chromosome 21: binding energy calculated by two sets of dinucleotide-based thermodynamic parameters, AA/TT and AAA/TTT bi-/tri-nucleotide density, 5'-TA-3' dinucleotide density, and signal for 10/11-base periodicity of AA/TT or AAA/TTT. These intrinsic quantities are related to structural features of the double helix of DNA molecules, such as base-pair binding, untwisting/unwinding, stiffness, and a putative tendency for nucleosome formation.Comment: submitted to Physical Review

SeeBridge Next Generation Bridge Inspection: Overview, Information Delivery Manual and Model View Definition

Innovative solutions for rapid and intelligent survey and assessment methods are required in maintenance, repair, retrofit and rebuild of enormous numbers of bridges in service throughout the world. Motivated by this need, a next-generation integrated bridge inspection system, called SeeBridge, has been proposed. An Information Delivery Manual (IDM) was compiled to specify the technical components, activities and information exchanges in the SeeBridge process, and a Model View Definition (MVD) was prepared to specify the data exchange schema to serve the IDM. The MVD was bound to the IFC4 Add2 data schema standard. The IDM and MVD support research and development of the system by rigorously defining the information and data that structure bridge engineers' knowledge. The SeeBridge process is mapped, parts of the data repositories are presented, and the future use of the IDM is discussed. The development underlines the real potential for automated inspection of infrastructure at large, because it demonstrates that the hurdles in the way of automated acquisition of detailed and semantically rich models of existing infrastructure are computational in nature, not instrumental, and are surmountable with existing technologies

TRANSFAC(®) and its module TRANSCompel(®): transcriptional gene regulation in eukaryotes

The TRANSFAC(®) database on transcription factors, their binding sites, nucleotide distribution matrices and regulated genes as well as the complementing database TRANSCompel(®) on composite elements have been further enhanced on various levels. A new web interface with different search options and integrated versions of Match™ and Patch™ provides increased functionality for TRANSFAC(®). The list of databases which are linked to the common GENE table of TRANSFAC(®) and TRANSCompel(®) has been extended by: Ensembl, UniGene, EntrezGene, HumanPSD™ and TRANSPRO™. Standard gene names from HGNC, MGI and RGD, are included for human, mouse and rat genes, respectively. With the help of InterProScan, Pfam, SMART and PROSITE domains are assigned automatically to the protein sequences of the transcription factors. TRANSCompel(®) contains now, in addition to the COMPEL table, a separate table for detailed information on the experimental EVIDENCE on which the composite elements are based. Finally, for TRANSFAC(®), in respect of data growth, in particular the gain of Drosophila transcription factor binding sites (by courtesy of the Drosophila DNase I footprint database) and of Arabidopsis factors (by courtesy of DATF, Database of Arabidopsis Transcription Factors) has to be stressed. The here described public releases, TRANSFAC(®) 7.0 and TRANSCompel(®) 7.0, are accessible under

Double sign reversal of the vortex Hall effect in YBa2Cu3O7-delta thin films in the strong pinning limit of low magnetic fields

Measurements of the Hall effect and the resistivity in twinned YBa2Cu3O7-delta thin films in magnetic fields B oriented parallel to the crystallographic c-axis and to the twin boundaries reveal a double sign reversal of the Hall coefficient for B below 1 T. In high transport current densities, or with B tilted off the twin boundaries by 5 degrees, the second sign reversal vanishes. The power-law scaling of the Hall conductivity to the longitudinal conductivity in the mixed state is strongly modified in the regime of the second sign reversal. Our observations are interpreted as strong, disorder-type dependent vortex pinning and confirm that the Hall conductivity in high temperature superconductors is not independent of pinning.Comment: 4 pages, 4 figure

Reading, Trauma and Literary Caregiving 1914-1918: Helen Mary Gaskell and the War Library

This article is about the relationship between reading, trauma and responsive literary caregiving in Britain during the First World War. Its analysis of two little-known documents describing the history of the War Library, begun by Helen Mary Gaskell in 1914, exposes a gap in the scholarship of war-time reading; generates a new narrative of "how," "when," and "why" books went to war; and foregrounds gender in its analysis of the historiography. The Library of Congress's T. W. Koch discovered Gaskell's ground-breaking work in 1917 and reported its successes to the American Library Association. The British Times also covered Gaskell's library, yet researchers working on reading during the war have routinely neglected her distinct model and method, skewing the research base on war-time reading and its association with trauma and caregiving. In the article's second half, a literary case study of a popular war novel demonstrates the extent of the "bitter cry for books." The success of Gaskell's intervention is examined alongside H. G. Wells's representation of textual healing. Reading is shown to offer sick, traumatized and recovering combatants emotional and psychological caregiving in ways that she could not always have predicted and that are not visible in the literary/historical record

The state-of-the-art determination of urinary nucleosides using chromatographic techniques “hyphenated” with advanced bioinformatic methods

Over the last decade metabolomics has gained increasing popularity and significance in life sciences. Together with genomics, transcriptomics and proteomics, metabolomics provides additional information on specific reactions occurring in humans, allowing us to understand some of the metabolic pathways in pathological processes. Abnormal levels of such metabolites as nucleosides in the urine of cancer patients (abnormal in relation to the levels observed in healthy volunteers) seem to be an original potential diagnostic marker of carcinogenesis. However, the expectations regarding the diagnostic value of nucleosides may only be justified once an appropriate analytical procedure has been applied for their determination. The achievement of good specificity, sensitivity and reproducibility of the analysis depends on the right choice of the phases (e.g. sample pretreatment procedure), the analytical technique and the bioinformatic approach. Improving the techniques and methods applied implies greater interest in exploration of reliable diagnostic markers. This review covers the last 11 years of determination of urinary nucleosides conducted with the use of high-performance liquid chromatography in conjunction with various types of detection, sample pretreatment methods as well as bioinformatic data processing procedures

Simultaneous quantification of 12 different nucleotides and nucleosides released from renal epithelium and in human urine samples using ion-pair reversed-phase HPLC

Nucleotides and nucleosides are not only involved in cellular metabolism but also act extracellularly via P1 and P2 receptors, to elicit a wide variety of physiological and pathophysiological responses through paracrine and autocrine signalling pathways. For the first time, we have used an ion-pair reversed-phase high-performance liquid chromatography ultraviolet (UV)-coupled method to rapidly and simultaneously quantify 12 different nucleotides and nucleosides (adenosine triphosphate, adenosine diphosphate, adenosine monophosphate, adenosine, uridine triphosphate, uridine diphosphate, uridine monophosphate, uridine, guanosine triphosphate, guanosine diphosphate, guanosine monophosphate, guanosine): (1) released from a mouse renal cell line (M1 cortical collecting duct) and (2) in human biological samples (i.e., urine). To facilitate analysis of urine samples, a solid-phase extraction step was incorporated (overall recovery rate ? 98 %). All samples were analyzed following injection (100 ?l) into a Synergi Polar-RP 80 Å (250 × 4.6 mm) reversed-phase column with a particle size of 10 ?m, protected with a guard column. A gradient elution profile was run with a mobile phase (phosphate buffer plus ion-pairing agent tetrabutylammonium hydrogen sulfate; pH 6) in 2-30 % acetonitrile (v/v) for 35 min (including equilibration time) at 1 ml min(-1) flow rate. Eluted compounds were detected by UV absorbance at 254 nm and quantified using standard curves for nucleotide and nucleoside mixtures of known concentration. Following validation (specificity, linearity, limits of detection and quantitation, system precision, accuracy, and intermediate precision parameters), this protocol was successfully and reproducibly used to quantify picomolar to nanomolar concentrations of nucleosides and nucleotides in isotonic and hypotonic cell buffers that transiently bathed M1 cells, and urine samples from normal subjects and overactive bladder patients

Turkish D-light : accentuating heritage values with daylight

Historic buildings have their own cultural identity, which is often related to their aesthetic qualities such as period characteristics (geometry, size, colour, form and shape), materials and construction. Daylight is one of the primary elements contributing to the distinctiveness of the visual environment of many historic buildings, but is rarely considered as one of the components that shape the character of a building when adaptive preservation schemes of historical buildings are planned. Many historic buildings were originally designed to accommodate activities different to their new use and preserving the quality of daylight that originally contributed to their visual identity is a challenging task. Maintaining the ‘day-lit appearance’ of a building can be particularly problematic if the building is to be used as a museum or a gallery owing to the artefacts’ conservation requirements. This work investigated the opportunities of maintaining the original ambient conditions of renovated historical buildings while meeting the required daylight levels of the proposed new use. The study utilised an annual daylight simulation method and hourly weather data to preserve daylight conditions in renovated historic buildings. The model was piloted in a Turkish bathhouse situated in Bursa, Turkey, that is currently under renovation. The simulation model produces 4483 hourly values of daylight illuminance for a period of a whole year using the computer program Radiance. It is concluded that daylight characteristics should be taken into account when developing a renovation scheme. With increasing pressure on valuing historic buildings in many parts of the world, the work reported here should be beneficial to those concerned with the conservation and adaptive reuse of historic buildings. The study findings could also be useful to those interested in predicting potential energy savings by combining daylighting and electric lighting in historic buildings