bluuebunny/crossref_metadata_2025_split huggingface dataset:
PhenomicDB: a multi-species genotype/phenotype database for comparative phenomics
Authors: Kahraman Abdullah , Avramov Andrey , Nashev Lyubomir G. , Popov Dimitar , Ternes Rainer , Pohlenz Hans-Dieter , Weiss Bertram 
Published: September 2004

AbstractSummary: We have created PhenomicDB, a multi-species genotype/phenotype database by merging public genotype/phenotype data from a wide range of model organisms and Homo sapiens. Until now these data were available in distinct organism-specific databases (e.g. WormBase, OMIM, FlyBase and MGI). We compiled this wealth of data into a single integrated resource by coarse-grained semantic mapping of the phenotypic data fields, by including common gene indices (NCBI Gene), and by the use of associated orthology relationships. With its use-case-oriented user interface, PhenomicDB allows scientists to compare and browse known phenotypes for a given gene or a set of genes from different organisms simultaneously.Availability: PhenomicDB has been implemented at Schering AG as described below. A PhenomicDB implementation differing in some technical details has been set up for the public at Metalife AG http://www.phenomicDB.deContact: bertram.weiss@schering.deSupplementary information: database model, semantic mapping table.
Discovery of stable and significant binding motif pairs from PDB complexes and protein interaction datasets
Authors: Li Haiquan , Li Jinyan 
Published: September 2004

AbstractMotivation: Discovery of binding sites is important in the study of protein–protein interactions. In this paper, we introduce stable and significant motif pairs to model protein-binding sites. The stability is the pattern’s resistance to some transformation. The significance is the unexpected frequency of occurrence of the pattern in a sequence dataset comprising known interacting protein pairs. Discovery of stable motif pairs is an iterative process, undergoing a chain of changing but converging patterns. Determining the starting point for such a chain is an interesting problem. We use a protein complex dataset extracted from the Protein Data Bank to help in identifying those starting points, so that the computational complexity of the problem is much released.Results: We found 913 stable motif pairs, of which 765 are significant. We evaluated these motif pairs using comprehensive comparison results against random patterns. Wet-experimentally discovered motifs reported in the literature were also used to confirm the effectiveness of our method.Contact haiquan@i2r.a-star.edu.sgSupplementary information http://sdmc.i2r.a-star.edu.sg/BindingMotifPairs
MAP-O-MAT: internet-based linkage mapping
Authors: Kong X. , Matise T. C. 
Published: September 2004

Abstract
Summary: MAP-O-MAT is a web-based server for automated linkage mapping of human polymorphic DNA markers. MAP-O-MAT facilitates the verification of order and map distances for custom mapping sets using genotype data from the CEPH database, and from the Marshfield, SNP Consortium and Rutgers linkage maps (exclusive to the deCODE genotyping data). The CRI-MAP program is used for likelihood calculations and some mapping algorithms, and physical map positions are provided from the human genome assembly.
Availability: MAP-O-MAT is located at http://compgen.rutgers.edu/mapomat/
Contact: matise@biology.rutgers.edu
Improving genome annotations using phylogenetic profile anomaly detection
Authors: Mikkelsen Tarjei S. , Galagan James E. , Mesirov Jill P. 
Published: September 2004

AbstractMotivation: A promising strategy for refining genome annotations is to detect features that conflict with known functional or evolutionary relationships between groups of genes. Previous work in this area has been focused on investigating the absence of ‘housekeeping’ genes or components of well-studied pathways. We have sought to develop a method for improving new annotations that can automatically synthesize and use the information available in a database of other annotated genomes.Results: We show that a probabilistic model of phylogenetic profiles, trained from a database of curated genome annotations, can be used to reliably detect errors in new annotations. We use our method to identify 22 genes that were missed in previously published annotations of prokaryotic genomes.Availability: The method was evaluated using MATLAB and open source software referenced in this work. Scripts and datasets are available from the authors upon request.Contact: tarjei@broad.mit.edu
SPAAN: a software program for prediction of adhesins and adhesin-like proteins using neural networks
Authors: Sachdeva Gaurav , Kumar Kaushal , Jain Preti , Ramachandran Srinivasan 
Published: September 2004

Abstract
Motivation: The adhesion of microbial pathogens to host cells is mediated by adhesins. Experimental methods used for characterizing adhesins are time-consuming and demand large resources. The availability of specialized software can rapidly aid experimenters in simplifying this problem. We have employed 105 compositional properties and artificial neural networks to develop SPAAN, which predicts the probability of a protein being an adhesin (Pad).
Results: SPAAN had optimal sensitivity of 89% and specificity of 100% on a defined test set and could identify 97.4% of known adhesins at high Pad value from a wide range of bacteria. Furthermore, SPAAN facilitated improved annotation of several proteins as adhesins. Novel adhesins were identified in 17 pathogenic organisms causing diseases in humans and plants. In the severe acute respiratory syndrome (SARS) associated human corona virus, the spike glycoprotein and nsps (nsp2, nsp5, nsp6 and nsp7) were identified as having adhesin-like characteristics. These results offer new lead for rapid experimental testing.
Availability: SPAAN is freely available through ftp://203.195.151.45
Contact: ramu@igib.res.in
tPatternHunter: gapped, fast and sensitive translated homology search
Authors: Kisman Derek , Li Ming , Ma Bin , Wang Li 
Published: September 2004

Abstract
Summary: New ideas, spaced seeds and gapped alignment before 6-frame translation are implemented for translated homology search in tPatternHunter. The new software compares favorably with tBLASTx.
Availability: The software is free to academics at http://www.bioinformaticssolutions.com/downloads/ph-academic/
Contact: bma@csd.uwo.ca
Online synonymous codon usage analyses with the ade4 and seqinR packages
Authors: Charif D. , Thioulouse J. , Lobry J. R. , Perrière G. 
Published: September 2004

Abstract
Summary: Correspondence analysis of codon usage data is a widely used method in sequence analysis, but the variability in amino acid composition between proteins is a confounding factor when one wants to analyse synonymous codon usage variability. A simple and natural way to cope with this problem is to use within-group correspondence analysis. There is, however, no user-friendly implementation of this method available for genomic studies. Our motivation was to provide to the community a Web facility to easily study synonymous codon usage on a subset of data available in public genomic databases.
Availability: Availability through the Pôle Bioinformatique Lyonnais (PBIL) Web server at http://pbil.univ-lyon1.fr/datasets/charif04/ with a demo allowing us to reproduce the figure in the present application note. All underlying software is distributed under a GPL licence.
Contact: http://pbil.univ-lyon1.fr/members/lobry
Expression-based monitoring of transcription factor activity: the TELiS database
Authors: Cole Steve W. , Yan Weihong , Galic Zoran , Arevalo Jesusa , Zack Jerome A. 
Published: September 2004

AbstractMotivation: In microarray studies it is often of interest to identify upstream transcription control pathways mediating observed changes in gene expression. The Transcription Element Listening System (TELiS) combines sequence-based analysis of gene regulatory regions with statistical prevalence analyses to identify transcription-factor binding motifs (TFBMs) that are over-represented among the promoters of up- or down-regulated genes. Efficiency is maximized by decomposing the problem into two steps: (1) a priori compilation of prevalence matrices specifying the number of putative binding sites for a variety of transcription factors in promoters from all genes assayed by a given microarray, and (2) real-time statistical analysis of pre-compiled prevalence matrices to identify TFBMs that are over- or under-represented in promoters of differentially expressed genes. The interlocking JAVA applications namely, PromoterScan and PromoterStats carry out these tasks, and together constitute the TELiS database for reverse inference of transcription factor activity.Results: In two validation studies, TELiS accurately detected in vivo activation of NF-κB and the Type I interferon system by HIV-1 infection and pharmacologic activation of the glucocorticoid receptor in peripheral blood mononuclear cells. The population-based statistical inference underlying TELiS out-performed conventional statistical tests in analytic sensitivity, with parametric studies demonstrating accurate identification of transcription factor activity from as few as 20 differentially expressed genes. TELiS thus provides a simple, rapid and sensitive tool for identifying transcription control pathways mediating observed gene expression dynamics.Availability: http://www.telis.ucla.eduContact: coles@ucla.edu
RAP: a new computer program for de novo identification of repeated sequences in whole genomes
Authors: Campagna Davide , Romualdi Chiara , Vitulo Nicola , Del Favero Micky , Lexa Matej , Cannata Nicola , Valle Giorgio 
Published: September 2004

AbstractMotivation: DNA repeats are a common feature of most genomic sequences. Their de novo identification is still difficult despite being a crucial step in genomic analysis and oligonucleotides design. Several efficient algorithms based on word counting are available, but too short words decrease specificity while long words decrease sensitivity, particularly in degenerated repeats.Results: The Repeat Analysis Program (RAP) is based on a new word-counting algorithm optimized for high resolution repeat identification using gapped words. Many different overlapping gapped words can be counted at the same genomic position, thus producing a better signal than the single ungapped word. This results in better specificity both in terms of low-frequency detection, being able to identify sequences repeated only once, and highly divergent detection, producing a generally high score in most intron sequences.Availability: The program is freely available for non-profit organizations, upon request to the authors.Contact: giorgio.valle@unipd.itSupplementary information: The program has been tested on the Caenorhabditis elegans genome using word lengths of 12, 14 and 16 bases. The full analysis has been implemented in the UCSC Genome Browser and is accessible at http://genome.cribi.unipd.it.
Disordered quasicrystals: diffuse scattering in decagonal Al–Ni–Fe
Authors: Weidner E. , Frey F. , Lei J.-L. , Pedersen B. , Paulmann C. , Morgenroth W. 
Published: September 2004

High-resolution synchrotron data of near-Bragg diffuse scattering from decagonal Al71.5Ni23.5Fe5quasicrystals were recorded. A dominant phasonic origin is ruled out because of the absence of a significantG⊥dependence. An analysis solely in the frame of thermal diffuse scattering (TDS) theory (phonon scattering) showed a good match between experimental and calculated data in the quasiperiodic layers, but with an improbable ratio of elastic constants,c66/c11 = 4.0.In situhigh-temperature measurements up to 1000 K revealed an increase of the intensity distribution perpendicular to the scattering vectorG. Huang diffuse scattering (HDS) arising from quenched local defects has a general appearance that qualitatively reproduces the observed symmetry and anisotropy. An interpretation based on both TDS and HDS contributions is given.
Comparative aspects of the inner root sheath in adult and developing hairs of mammals in relation to the evolution of hairs
Authors: Alibardi Lorenzo 
Published: September 2004

AbstractThe inner root sheath (IRS) allows the exit of hairs through the epidermal surface. The fine structure of monotreme and marsupial IRS and trichohyalin is not known. Using electron microscopy and immunocytochemistry, the localization of trichohyalin and transglutaminase have been studied in monotreme and marsupial hairs, and compared with trichohyalin localization in placental hairs. Trichohyalin in all mammalian species studied here is recognized by a polyclonal antibody against sheep trichohyalin. This generalized immunoreactivity suggests that common epitopes are present in trichohyalin across mammals. In differentiating IRS cells, trichohyalin granules of variable dimensions are composed of an immunolabelled amorphous matrix associated with a network of 10–12‐nm‐thick keratin filaments. Transglutaminase labelling is present among keratin bundles and trichohyalin granules, and in condensed nuclei of terminally differentiating cells of the inner root sheath. The IRS in monotreme hairs is multistratified but lacks a distinguishable Henle layer. Cornification of IRS determines the sculpturing of the fibre cuticle and later shedding from the follicle for the exit of the hair fibre on the epidermal surface. It is hypothesized that the stratification of IRS in Henle, Huxley and IRS cuticle layers is derived from a simpler organization, like that present in the IRS of monotremes. The IRS is regarded as a localized shedding/sloughing layer needed for the exit of hairs without injury to the epidermis. The formation of the IRS during the evolution of mammalian epidermis allowed the physiological exit of hairs produced inside the skin. The peculiar morphogenesis of hairs in possible primitive skins, such as those of the monotremes (mammals with some reptilian characteristics) or the tails of some rodents (a scaled skin), may elucidate the evolution of hairs. In monotreme and rodent tail skin, the dermal papilla remains localized on the proximal side of the hair peg and forms a hair placode with bilateral symmetry. The papilla is progressively surrounded by the down‐growing hair peg until a dermal papilla with radial symmetry is formed. It is speculated that the progressive reduction of the extended dermal papilla of reptilian scales into small and deep papillae of therapsid reptiles produced hairs in mammals.
Hyaline cartilage engineered by chondrocytes in pellet culture: histological, immunohistochemical and ultrastructural analysis in comparison with cartilage explants
Authors: Zhang Zijun , McCaffery J. Michael , Spencer Richard G. S. , Francomano Clair A. 
Published: September 2004

AbstractCartilage engineering is a strategic experimental goal for the treatment of multiple joint diseases. Based on the process of embryonic chondrogenesis, we hypothesized that cartilage could be engineered by condensing chondrocytes in pellet culture and, in the present study, examined the quality of regenerated cartilage in direct comparison with native cartilage. Chondrocytes isolated from the sterna of chick embryos were cultured in pellets (4 × 106 cells per pellet) for 2 weeks. Cartilage explants from the same source were cultured as controls. After 2 weeks, the regenerated cartilage from pellet culture had a disc shape and was on average 9 mm at the longest diameter. The chondrocyte phenotype was stabilized in pellet culture as shown by the synthesis of type II collagen and aggrecan, which was the same intensity as in the explant after 7 days in culture. During culture, chondrocytes also continuously synthesized type IX collagen. Type X collagen was negatively stained in both pellets and explants. Except for fibril orientation, collagen fibril diameter and density in the engineered cartilage were comparable with the native cartilage. In conclusion, hyaline cartilage engineered by chondrocytes in pellet culture, without the transformation of cell phenotypes and scaffold materials, shares similarities with native cartilage in cellular distribution, matrix composition and density, and ultrastructure.
Cardiac anatomy revisited
Authors: Anderson Robert H. , Razavi Reza , Taylor Andrew M. 
Published: September 2004

AbstractIn tomorrow's world of clinical medicine, students will increasingly be confronted by anatomic displays reconstructed from tomographically derived images. These images all display the structure of the various organs in anatomical orientation, this being determined in time‐honoured fashion by describing the individual in the ‘anatomical position’, standing upright and facing the observer. It follows from this approach that all adjectives used to describe the organs should be related to the three orthogonal planes of the body. Unfortunately, at present this convention is not followed for the heart, even though most students are taught that the so‐called ‘right chambers’ are, in reality, in front of their ‘left’ counterparts. Rigorous analysis of the tomographic images already available, along with comparison with dissected hearts displayed in attitudinally correct orientation, calls into question this continuing tendency to describe the heart in terms of its own orthogonal axes, but with the organ positioned on its apex, so that the chambers can artefactually be visualized with the right atrium and right ventricle in right‐sided position. Although adequate for describing functional aspects, such as ‘right‐to‐left’ shunting across intracardiac communications, this convention falls short when used to describe the position of the artery that supplies the diaphragmatic surface of the heart. Currently known as the ‘posterior descending artery’, in reality it is positioned inferiorly, and its blockage produces inferior myocardial infarction. In this review, we extend the concept of describing cardiac structure in attitudinally correct orientation, showing also how access to tomographic images clarifies many aspects of cardiac structure previously considered mysterious and arcane. We use images prepared using new techniques such as magnetic resonance imaging and computerized tomography, and compare them with dissection of the heart made in time‐honoured fashion, along with cartoons to illustrate contentious topics. We argue that there is much to gain by describing the components of the heart as seen in the anatomical position, along with all other organs and structures in the body. We recognize, nonetheless, that such changes will take many years to be put into practice, if at all.
Characterization and species differences in gastric ghrelin cells from mice, rats and hamsters
Authors: Yabuki Akira , Ojima Toshimichi , Kojima Masayasu , Nishi Yoshihiro , Mifune Hiroharu , Matsumoto Mitsuharu , Kamimura Ryozo , Masuyama Taku , Suzuki Syusaku 
Published: September 2004

AbstractGhrelin is a newly identified gastric peptide hormone that has various important functions, including growth‐hormone release and appetite stimulation. Ghrelin‐immunoreactive cells (ghrelin cells) are characterized by X‐type endocrine cells in the rat stomach. In the present study, we analysed ghrelin cells in fundi of stomach from ICR mice and Syrian hamsters immunohistochemically, immunoelectron microscopically and morphometrically, and compared the results with those from Wistar rats. Immunohistochemistry revealed that ghrelin cells were sparsely distributed in the proper gastric glands in all species. The number of ghrelin cells per unit area in hamsters was significantly lower than that in rats. Immunoelectron microscopy detected ghrelin immunolabelling in granules in the X‐type endocrine cells. However, the diameter of granules in the hamsters was significantly smaller than that in the mice and rats. Gastric ghrelin contents were determined by radioimmunoassay, and levels in the hamsters were significantly lower than those in mice and rats. The results from mice were identical to those from rats. In conclusion, gastric ghrelin cells in mice and hamsters are characterized by X‐type endocrine cells, as has been observed in rats. However, the data indicated that gastric ghrelin production was lower in hamster than in mouse or rat.
Investigation of the effects of partial coherence on exit wave reconstruction
Authors: ALLEN L. J. , MCBRIDE W. , O'LEARY N. L. , OXLEY M. P. 
Published: September 2004

SummaryIn a recent work we presented an iterative wave function reconstruction (IWFR) method that reconstructs a wave function from measurements of its amplitude taken as it propagates in free space (a focal series of images). Although the ideal environment for application of the IWFR method is in a coherent imaging system, it has been developed so that it can be applied in a partially coherent imaging system, in particular for a high‐resolution transmission electron microscope using a field‐emission gun. In this paper we investigate the effects of partial coherence on the accuracy of results obtained using the IWFR method. We then show how results obtained under such conditions can be improved by estimating and subtracting components from the amplitude measurements of the wave function that derive from incoherence in the electron beam.
Direct visualization of receptor arrays in frozen‐hydrated sections and plunge‐frozen specimens of E. coli engineered to overproduce the chemotaxis receptor Tsr
Authors: ZHANG P. , BOS E. , HEYMANN J. , GNAEGI H. , KESSEL M. , PETERS P. J. , SUBRAMANIAM S. 
Published: September 2004

SummaryWe have recently reported electron tomographic studies of sections obtained from chemically fixed E. coli cells overproducing the 60‐kDa chemotaxis receptor Tsr. Membrane extracts from these cells prepared in the presence of Tween‐80 display hexagonally close‐packed microcrystalline assemblies of Tsr, with a repeating unit large enough to accommodate six Tsr molecules arranged as trimers of receptor dimers. Here, we report the direct visualization of the Tsr receptor clusters in (i) vitrified cell suspensions of cells overproducing Tsr, prepared by rapid plunge‐freezing, and (ii) frozen‐hydrated sections obtained from cells frozen under high pressure. The frozen‐hydrated sections were generated by sectioning at −150 °C using a diamond knife with a 25° knife angle, with nominal thicknesses ranging from 20 to 60 nm. There is excellent correspondence between the spatial arrangement of receptors in thin frozen‐hydrated sections and the arrangements found in negatively stained membrane extracts and plunge‐frozen cells, highlighting the potential of using frozen‐hydrated sections for the study of macromolecular assemblies within cells under near‐native conditions.