bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatio‐Temporal Development of Axonopathy in Canine Intervertebral Disc Disease as a Translational Large Animal Model for Nonexperimental Spinal Cord Injury
Authors: Bock Patricia , Spitzbarth Ingo , Haist Verena , Stein Veronika M. , Tipold Andrea , Puff Christina , Beineke Andreas , Baumgärtner Wolfgang 
Published: July 2012

AbstractSpinal cord injury (SCI) represents a devastating central nervous system disease that still lacks sufficient therapies. Here, dogs are increasingly recognized as a preclinical animal model for the development of future therapies. The aim of this study was a detailed characterization of axonopathy in canine intervertebral disc disease, which produces a mixed contusive and compressive injury and functions as a spontaneous translational animal model for human SCI. The results revealed an early occurrence of ultrastructurally distinct axonal swelling. Immunohistochemically, enhanced axonal expression of β‐amyloid precursor protein, non‐phosphorylated neurofilament (n‐NF) and growth‐associated protein‐43 was detected in the epicenter during acute canine SCI. Indicative of a progressive axonopathy, these changes showed a cranial and caudally accentuated spatial progression in the subacute disease phase. In canine spinal cord slice cultures, immunoreactivity of axons was confined to n‐NF. Real‐time quantitative polymerase chain reaction of naturally traumatized tissue and slice cultures revealed a temporally distinct dysregulation of the matrix metalloproteinases (MMP)‐2 and MMP‐9 with a dominating expression of the latter. Contrasting to early axonopathy, diminished myelin basic protein immunoreactivity and phagocytosis were delayed. The results present a basis for assessing new therapies in the canine animal model for translational research that might allow partial extrapolation to human SCI.
Saproxylic beetle tolerance to habitat fragmentation induced by salvage logging in a boreal mixed‐cover burn
Authors: Saint‐Germain Michel , Drapeau Pierre , Hibbert Annie 
Published: July 2012

Abstract

Saproxylic insect assemblages associated with burned forests are generally abundant and species rich, consisting of a mix of pyrophilous and secondary, opportunistic species depending on time elapsed since disturbance. Life‐history traits associated with each group suggest that they may respond differentially to habitat fragmentation caused by salvage logging, with pyrophilous species having a much higher dispersal potential.
In a 2‐year‐old burn highly fragmented by pre‐ and post‐fire logging, we sampled saproxylic beetles in coniferous and broadleaf burned residual stands along a gradient of spatial context including intensity of fragmentation and isolation from source habitat using Lindgren multiple‐funnels traps.
Beetle assemblages differed in composition between coniferous and broadleaf burned stands, with secondary users dominating the latter. Pyrophilous species increased in abundance with distance from the edge and avoided unburned patches within the fire. Secondary users did not respond negatively to fragmentation or isolation of burned habitats, with one exception, the alleculid
Isomira quadristriata (Couper), being overall diverse and abundant throughout the study area regardless of salvage logging prevalence.
No deleterious effects of isolation were thus detected in the occurrence patterns of secondary users, even up to 8 km from the edge. Our results suggest that older burns, especially those having some broadleaf cover, are intensively used by non‐pyrophilous saproxylic species usually associated with dead wood in green forests and may contribute to maintain broader saproxylic assemblages than originally thought, especially when considering the importance of dead wood volume pulses associated with fire in boreal forests.
Sphingosine‐1‐phosphate modulates expression of vascular endothelial growth factor in human articular chondrocytes: a possible new role in arthritis
Authors: Masuko Kayo , Murata Minako , Beppu Moroe , Nakamura Hiroshi , Kato Tomohiro , Yudoh Kazuo 
Published: July 2012

AbstractAimAlthough sphingosine‐1‐phosphate (S1P) is suggested to have an important role in arthritis, its function in chondrocytes remains unknown. In contrast, vascular endothelial growth factor (VEGF) has been speculated to contribute to the pathogenesis of osteoarthritis (OA), most likely by regulating angiogenesis. We here investigated the in vitro effect of S1P on VEGF expression in human articular chondrocytes from OA patients.MethodsHuman articular cartilage samples were obtained from patients with OA under informed consent. Chondrocytes were isolated by an enzymatic procedure, grown in monolayer culture, and then stimulated with S1P in the presence or absence of mitogen‐activated protein kinase (MAPK) inhibitors or the Gi protein inhibitor pertussis toxin (PTX). VEGF expression and secretion in culture supernatants were analyzed using real‐time polymerase chain reaction and enzyme‐linked immunosorbent assay.ResultsAlthough S1P did not enhance basal secretion of matrix metalloproteinase (MMP)‐1 and MMP‐13, it stimulated VEGF expression in human articular chondrocytes, both at the messenger RNA and protein levels. MAPK inhibitors SB203580 and PD98059 were not effective at suppressing VEGF induction; rather, blocking extracellular signal‐regulated kinase (ERK) MAPK enhanced VEGF expression. The Gi protein inhibitor PTX partially attenuated S1P‐induced VEGF secretion.ConclusionOur results suggest that S1P may contribute to the regulation of VEGF expression in human chondrocytes. S1P may therefore play a unique role in the pathophysiology of OA by regulating VEGF expression in chondrocytes.
Development and evaluation of ForestGrowth‐SRCa process‐based model for short rotation coppice yield and spatial supply reveals poplar uses water more efficiently than willow
Authors: Tallis Matthew J. , Casella Eric , Henshall Paul A. , Aylott Matthew J. , Randle Timothy J. , Morison James I. L. , Taylor Gail 
Published: July 2012

AbstractWoody biomass produced from short rotation coppice (SRC) poplar (Populusspp.) and willow (Salixspp.) is a bioenergy feedstock that can be grown widely across temperate landscapes and its use is likely to increase in future. Process‐based models are therefore required to predict current and future yield potential that are spatially resolved and can consider new genotypes and climates that will influence future yield. The development of a process‐based model forSRCpoplar and willow, ForestGrowth‐SRC, is described and the ability of the model to predictSRCyield and water use efficiency (WUE) was evaluated. ForestGrowth‐SRCwas parameterized from a process‐based model, ForestGrowth for high forest. The new model predicted annual above ground yield well for poplar (r2 = 0.91,RMSE = 1.46 ODT ha−1 yr−1) and willow (r2 = 0.85,RMSE = 1.53 ODT ha−1 yr−1), when compared with measured data from seven sites in contrasting climatic zones across theUnited Kingdom. Average modelled yields for poplar and willow were 10.3 and 9.0 ODT ha−1 yr−1, respectively, and interestingly, the model predicted a higherWUEfor poplar than for willow: 9.5 and 5.5 g kg−1respectively. Using regional mapped climate and soil inputs, modelled and measured yields for willow compared well (r2 = 0.58,RMSE = 1.27 ODT ha−1 yr−1), providing the firstUKmap ofSRCyield, from a process‐based model. We suggest that the model can be used for predicting current and futureSRCyields at a regional scale, highlighting important species and genotype choices with respect to water use efficiency and yield potential.
Cerebral haemorrhage in a pregnant Standardbred mare with Evan's syndrome
Authors: Väänänen L. , Sihvo H.‐K. , Hewetson M. 
Published: July 2012

SummaryA 3‐year‐old pregnant Standardbred mare was treated at the University of Helsinki Equine Teaching Hospital for severe idiopathic immune‐mediated thrombocytopenia and haemolytic anaemia (Evan's syndrome). Despite initial improvement with supportive care and immunosuppressive doses of corticosteroids and azathioprine, the mare died from a fatal cerebral haemorrhage on Day 21 of treatment.
CellMiner: A Web-Based Suite of Genomic and Pharmacologic Tools to Explore Transcript and Drug Patterns in the NCI-60 Cell Line Set
Authors: Reinhold William C. , Sunshine Margot , Liu Hongfang , Varma Sudhir , Kohn Kurt W. , Morris Joel , Doroshow James , Pommier Yves 
Published: July 2012

AbstractHigh-throughput and high-content databases are increasingly important resources in molecular medicine, systems biology, and pharmacology. However, the information usually resides in unwieldy databases, limiting ready data analysis and integration. One resource that offers substantial potential for improvement in this regard is the NCI-60 cell line database compiled by the U.S. National Cancer Institute, which has been extensively characterized across numerous genomic and pharmacologic response platforms. In this report, we introduce a CellMiner (http://discover.nci.nih.gov/cellminer/) web application designed to improve the use of this extensive database. CellMiner tools allowed rapid data retrieval of transcripts for 22,379 genes and 360 microRNAs along with activity reports for 20,503 chemical compounds including 102 drugs approved by the U.S. Food and Drug Administration. Converting these differential levels into quantitative patterns across the NCI-60 clarified data organization and cross-comparisons using a novel pattern match tool. Data queries for potential relationships among parameters can be conducted in an iterative manner specific to user interests and expertise. Examples of the in silico discovery process afforded by CellMiner were provided for multidrug resistance analyses and doxorubicin activity; identification of colon-specific genes, microRNAs, and drugs; microRNAs related to the miR-17-92 cluster; and drug identification patterns matched to erlotinib, gefitinib, afatinib, and lapatinib. CellMiner greatly broadens applications of the extensive NCI-60 database for discovery by creating web-based processes that are rapid, flexible, and readily applied by users without bioinformatics expertise. Cancer Res; 72(14); 3499–511. ©2012 AACR.
Modelling occurrence and duration of building drainage discharge loads from random and intermittent appliance flushes
Authors: Mui KW , Wong LT 
Published: July 2012

Building drainage demands are assumed random and intermittent. The existing Hunter-based models have been developed to aid in the sizing of pipes for instantaneous demands but not to predict the occurrence and duration of such demands. This paper proposes a time series model to determine the occurrence and duration of drainage demand, which are greater than some predefined flow rates due to a number of appliances that discharge randomly and intermittently with variable flow rates. While the duration is resolved using the time series data for simultaneous demands, the occurrence together with the time-dependent flow rate is quantified via Monte Carlo simulation based on occupant usage patterns and appliance discharge profiles derived from appliance flushes at the base of the main vertical stack. The applicability of this model is demonstrated with example discharges from a number of water closet (WC) cisterns with reduced flush volume. Practical application: This study will help designers determine the duration and occurrence of drainage demand due to a number of appliances that discharge randomly and intermittently with variable flow rates.
Comparative genomics of Shiga toxin encoding bacteriophages
Authors: Smith Darren L , Rooks David J , Fogg Paul CM , Darby Alistair C , Thomson Nick R , McCarthy Alan J , Allison Heather E 
Published: July 2012

Abstract

Background
Stx bacteriophages are responsible for driving the dissemination of Stx toxin genes (stx) across their bacterial host range. Lysogens carrying Stx phages can cause severe, life-threatening disease and Stx toxin is an integral virulence factor. The Stx-bacteriophage vB_EcoP-24B, commonly referred to as Ф24B, is capable of multiply infecting a single bacterial host cell at a high frequency, with secondary infection increasing the rate at which subsequent bacteriophage infections can occur. This is biologically unusual, therefore determining the genomic content and context of Ф24B compared to other lambdoid Stx phages is important to understanding the factors controlling this phenomenon and determining whether they occur in other Stx phages.

Results
The genome of the Stx2 encoding phage, Ф24B was sequenced and annotated. The genomic organisation and general features are similar to other sequenced Stx bacteriophages induced from Enterohaemorrhagic Escherichia coli (EHEC), however Ф24B possesses significant regions of heterogeneity, with implications for phage biology and behaviour. The Ф24B genome was compared to other sequenced Stx phages and the archetypal lambdoid phage, lambda, using the Circos genome comparison tool and a PCR-based multi-loci comparison system.

Conclusions
The data support the hypothesis that Stx phages are mosaic, and recombination events between the host, phages and their remnants within the same infected bacterial cell will continue to drive the evolution of Stx phage variants and the subsequent dissemination of shigatoxigenic potential.
Transposable elements in phytopathogenic Verticillium spp.: insights into genome evolution and inter- and intra-specific diversification
Authors: Amyotte Stefan G , Tan Xiaoping , Pennerman Kayla , del Mar Jimenez-Gasco Maria , Klosterman Steven J , Ma Li-Jun , Dobinson Katherine F , Veronese Paola 
Published: July 2012

Abstract

Background

Verticillium dahliae (Vd) and Verticillium albo-atrum (Va) are cosmopolitan soil fungi causing very disruptive vascular diseases on a wide range of crop plants. To date, no sexual stage has been identified in either microorganism suggesting that somatic mutation is a major force in generating genetic diversity. Whole genome comparative analysis of the recently sequenced strains VdLs.17 and VaMs.102 revealed that non-random insertions of transposable elements (TEs) have contributed to the generation of four lineage-specific (LS) regions in VdLs.17.

Results
We present here a detailed analysis of Class I retrotransposons and Class II “cut-and-paste” DNA elements detected in the sequenced Verticillium genomes. We report also of their distribution in other Vd and Va isolates from various geographic origins. In VdLs.17, we identified and characterized 56 complete retrotransposons of the Gypsy-, Copia- and LINE-like types, as well as 34 full-length elements of the “cut-and-paste” superfamilies Tc1/mariner, Activator and Mutator. While Copia and Tc1/mariner were present in multiple identical copies, Activator and Mutator sequences were highly divergent. Most elements comprised complete ORFs, had matching ESTs and showed active transcription in response to stress treatment. Noticeably, we found evidences of repeat-induced point mutation (RIP) only in some of the Gypsy retroelements. While Copia-, Gypsy- and Tc1/mariner-like transposons were prominent, a large variation in presence of the other types of mobile elements was detected in the other Verticillium spp. strains surveyed. In particular, neither complete nor defective “cut-and-paste” TEs were found in VaMs.102.

Conclusions
Copia-, Gypsy- and Tc1/mariner-like transposons are the most wide-spread TEs in the phytopathogens V. dahliae and V. albo-atrum. In VdLs.17, we identified several retroelements and “cut-and-paste” transposons still potentially active. Some of these elements have undergone diversification and subsequent selective amplification after introgression into the fungal genome. Others, such as the ripped Copias, have been potentially acquired by horizontal transfer. The observed biased TE insertion in gene-rich regions within an individual genome (VdLs.17) and the “patchy” distribution among different strains point to the mobile elements as major generators of Verticillium intra- and inter-specific genomic variation.
Deep ancestry of mammalian X chromosome revealed by comparison with the basal tetrapod Xenopus tropicalis
Authors: Mácha Jaroslav , Teichmanová Radka , Sater Amy K , Wells Dan E , Tlapáková Tereza , Zimmerman Lyle B , Krylov Vladimír 
Published: July 2012

Abstract

Background
The X and Y sex chromosomes are conspicuous features of placental mammal genomes. Mammalian sex chromosomes arose from an ordinary pair of autosomes after the proto-Y acquired a male-determining gene and degenerated due to suppression of X-Y recombination. Analysis of earlier steps in X chromosome evolution has been hampered by the long interval between the origins of teleost and amniote lineages as well as scarcity of X chromosome orthologs in incomplete avian genome assemblies.

Results
This study clarifies the genesis and remodelling of the Eutherian X chromosome by using a combination of sequence analysis, meiotic map information, and cytogenetic localization to compare amniote genome organization with that of the amphibian Xenopus tropicalis. Nearly all orthologs of human X genes localize to X. tropicalis chromosomes 2 and 8, consistent with an ancestral X-conserved region and a single X-added region precursor. This finding contradicts a previous hypothesis of three evolutionary strata in this region. Homologies between human, opossum, chicken and frog chromosomes suggest a single X-added region predecessor in therian mammals, corresponding to opossum chromosomes 4 and 7. A more ancient X-added ancestral region, currently extant as a major part of chicken chromosome 1, is likely to have been present in the progenitor of synapsids and sauropsids. Analysis of X chromosome gene content emphasizes conservation of single protein coding genes and the role of tandem arrays in formation of novel genes.

Conclusions
Chromosomal regions orthologous to Therian X chromosomes have been located in the genome of the frog X. tropicalis. These X chromosome ancestral components experienced a series of fusion and breakage events to give rise to avian autosomes and mammalian sex chromosomes. The early branching tetrapod X. tropicalis’ simple diploid genome and robust synteny to amniotes greatly enhances studies of vertebrate chromosome evolution.
Extensive remodeling of the Pseudomonas syringae pv. avellanae type III secretome associated with two independent host shifts onto hazelnut
Authors: O’Brien Heath E , Thakur Shalabh , Gong Yunchen , Fung Pauline , Zhang Jianfeng , Yuan Lijie , Wang Pauline W , Yong Choseung , Scortichini Marco , Guttman David S 
Published: July 2012

AbstractBackgroundHazelnut (Corylus avellana) decline disease in Greece and Italy is caused by the convergent evolution of two distantly related lineages ofPseudomonas syringaepv.avellanae(Pav). We sequenced the genomes of threePavisolates to determine if their convergent virulence phenotype had a common genetic basis due to either genetic exchange between lineages or parallel evolution.ResultsWe found little evidence for horizontal transfer (recombination) of genes betweenPavlineages, but two large genomic islands (GIs) have been recently acquired by one of the lineages. Evolutionary analyses of the genes encoding type III secreted effectors (T3SEs) that are translocated into host cells and are important for both suppressing and eliciting defense responses show that the twoPavlineages have dramatically different T3SE profiles, with only two shared putatively functional T3SEs. OnePavlineage has undergone unprecedented secretome remodeling, including the acquisition of eleven new T3SEs and the loss or pseudogenization of 15, including five of the six core T3SE families that are present in the otherPavlineage. Molecular dating indicates that divergence within both of thePavlineages predates their observation in the field. This suggest that bothPavlineages have been cryptically infecting hazelnut trees or wild relatives for many years, and that the emergence of hazelnut decline in the 1970s may have been due to changes in agricultural practice.ConclusionsThese data show that divergent lineages ofP. syringaecan converge on identical disease etiology on the same host plant using different virulence mechanisms and that dramatic shifts in the arsenal of T3SEs can accompany disease emergence.
Relationship between serum uric acid and internal carotid resistive index in hypertensive women: a cross-sectional study
Authors: Cipolli José Alexandre Addeo , Ferreira-Sae Maria Carolina , Martins Rafael Prado , Pio-Magalhães José Alexandre , Bellinazzi Vera Regina , Matos-Souza José Roberto , Junior Wilson Nadruz 
Published: July 2012

Abstract

Background
The impact of serum uric acid (SUA) on arteries of hypertensive subjects remains to be fully established. This study investigated the relationship between SUA and carotid structural and hemodynamic parameters in hypertensive men and women.

Methods
Three hundred and thirty eight patients (207 women and 131 men) were cross-sectionally evaluated by clinical, laboratory, hemodynamic and carotid ultrasound analysis. Common carotid diameters, circumferential wall tensions, Young’s Elastic Modulus, Stiffness Index, Arterial Compliance and intima-media thickness (IMT) were determined. Internal carotid artery resistive index (ICRI), a hemodynamic measure that reflects local vascular impedance and microangiopathy, was also assessed.

Results
Univariate analysis showed no significant correlation of SUA with carotid diameters, elasticity/stiffness indexes, IMT and circumferential wall tensions in both genders. Conversely, SUA correlated with ICRI (r = 0.34; p < 0.001) in women, but not in men, and hyperuricemic women presented higher ICRI than normouricemic ones (0.684 ± 0.007 vs. 0.649 ± 0.004; p < 0.001). Stepwise and logistic regression analyses adjusted for potential confounding factors showed that ICRI was independently associated with SUA and hyperuricemia in women.

Conclusions
This study demonstrated that SUA was associated with ICRI in hypertensive women, suggesting that there might gender-related differences in the relationship between SUA and vascular damage in subjects with systemic hypertension.
Identification of 3 novel VHL germ-line mutations in Danish VHL patients
Authors: Dandanell Mette , Friis-Hansen Lennart , Sunde Lone , Nielsen Finn C , Hansen Thomas v O 
Published: July 2012

Abstract

Background
von Hippel-Lindau (VHL) disease is a hereditary cancer syndrome in which the patients develop retinal and central nervous system hemangioblastomas, pheochromocytomas and clear-cell renal tumors. The autosomal dominant disease is caused by mutations in the VHL gene.

Methods

VHL mutational analysis was carried out by sequencing of the coding sequence and by multiplex ligation-dependent probe amplification analysis. The functional consequence of the variants was investigated using in silico prediction tools.

Results
A total of 289 probands suspected of having VHL syndrome have been screened for mutations in the VHL gene. Twenty-six different VHL mutations were identified in 36 families including one in-frame duplication, two frame-shift mutations, four nonsense mutations, twelve missense mutations, three intronic mutations and four large genomic rearrangements. Three of these mutations (c.319 C > T, c.342_343dupGGT and c.520_521dupAA) were novel.

Conclusions
In this study we report the VHL germ-line mutations found in Danish families. We found three novel VHL mutations where two were classified as pathogenic and the latter was classified as a variant of unknown significance. Together, our findings contribute to the interpretation of the potential pathogenicity of VHL germ-line mutations.