bluuebunny/crossref_metadata_2025_split huggingface dataset:
A systems biology approach to investigate the response of Synechocystis sp. PCC6803 to a high salt environment
Authors: Pandhal Jagroop , Noirel Josselin , Wright Phillip C , Biggs Catherine A 
Published: September 2009

AbstractBackgroundSalt overloading during agricultural processes is causing a decrease in crop productivity due to saline sensitivity. Salt tolerant cyanobacteria share many cellular characteristics with higher plants and therefore make ideal model systems for studying salinity stress. Here, the response of fully adaptedSynechocystissp. PCC6803 cells to the addition of 6% w/v NaCl was investigated using proteomics combined with targeted analysis of transcripts.ResultsIsobaric mass tagging of peptides led to accurate relative quantitation and identification of 378 proteins, and approximately 40% of these were differentially expressed after incubation in BG-11 media supplemented with 6% salt for 9 days. Protein abundance changes were related to essential cellular functional alterations. Differentially expressed proteins involved in metabolic responses were also analysed using the probabilitistic tool Mixed Model on Graphs (MMG), where the role of energy conversion through glycolysis and reducing power through pentose phosphate pathway were highlighted. Temporal RT-qPCR experiments were also run to investigate protein expression changes at the transcript level, for 14 non-metabolic proteins. In 9 out of 14 cases the mRNA changes were in accordance with the proteins.ConclusionSynechocystissp. PCC6803 has the ability to regulate essential metabolic processes to enable survival in high salt environments. This adaptation strategy is assisted by further regulation of proteins involved in non-metabolic cellular processes, supported by transcriptional and post-transcriptional control. This study demonstrates the effectiveness of using a systems biology approach in answering environmental, and in particular, salt adaptation questions inSynechocystissp. PCC6803
Classical sheep scrapie in Great Britain: spatial analysis and identification of environmental and farm-related risk factors
Authors: Stevens Kim B , Del Río Vilas Victor J , Guitián Javier 
Published: September 2009

AbstractBackgroundPrevious studies suggest that the spatial distribution of classical sheep scrapie in Great Britain is uneven and that certain flock characteristics may be associated with occurrence of the disease. However, the existence of areas of high and low disease-risk may also result from differences in the spatial distribution of environmental characteristics. In this study we explored the spatial pattern of classical scrapie in Great Britain between 2002 and 2005 and investigated the association between disease occurrence and various environmental and farm-related risk factors.ResultsExploratory spatial analysis: South Wales was found to have a higher density of scrapie-positive farms than the rest of Great Britain. In addition, a small cluster of high-risk farms was identified in the center of this region in which clustering of scrapie-positive farms occurred up to a distance of approximately 40 km.Spatial modelling: A mixed-effects regression model identified flock-size and soil drainage to be significantly associated with the occurrence of scrapie in England and Wales (area under the curve (AUC) 0.71 ± 0.01, 95% CI 0.68 - 0.74). The predictive risk map based on the estimated association between these factors and disease occurrence showed most of Wales to be at risk of being confirmed positive for scrapie with areas of highest risk in central and south Wales. In England, areas with the highest risk occurred mainly in the north and the midlands.ConclusionThe observed distribution of scrapie in Great Britain exhibited a definite spatial pattern with south Wales identified as an area of high occurrence. In addition both flock (flock size) and environmental variables (soil drainage) were found to be significantly associated with the occurrence of the disease. However, the model's AUC indicated unexplained variation remaining in the model and the source of this variation may lie in farm-level characteristics rather than spatially-varying ones such as environmental factors.
Effect of Genistein on vasculogenic mimicry formation by human uveal melanoma cells
Authors: Cong Rihong , Sun Qingmin , Yang Li , Gu Haijuan , Zeng Ying , Wang Bin 
Published: September 2009

Abstract

Background
Vasculogenic mimicry (VM) was increasingly recognized as a form of aggressive melanoma acquiring blood supply. Genistein had attracted much attention as a potential anticancer agent. Therefore, we examined the effect of Genistein on VM in human uveal melanoma cells.

Methods
VM structure was detected by periodic acid-Schiff (PAS) staining for uveal melanoma C918 cells cultured on the three-dimensional type I collagen gels after exposed to Genistein. We used reverse transcription polymerase chain reaction (RT-PCR) and Western Blot analysis to examine the effect of Genistein on vascular endothelial cadherin (VE-cadherin) mRNA and protein expression. The nude mice models of human uveal melanoma C918 cells were established to assess the number of VM using immunohistochemical and PAS double-staining.

Results
Genistein inhibited the survival of C918 cells in vitro. The ectopic model study showed that VM in tumor tissue sections were significantly reduced by Genistein in vivo. In vitro, the VM structure was found in control, 25 and 50 μM Genistein-treatment groups but not in 100 and 200 μM. RT-PCR and Western Blot showed that 100 and 200 μM concentration of Genistein could significantly decrease VE-cadherin mRNA and protein expression of C918 cells compared with control (P < 0.05). However, the 25 and 50 μM Genistein slightly decreased the VE-cadherin level in vitro (P > 0.05).

Conclusion
Genistein inhibits VM formation of uveal melanoma cells in vivo and in vitro. One possible underlying molecular mechanism by which Genistein could inhibit VM formation of uveal melanoma is related to down-regulation of VE-cadherin.
Advanced glycation end products induce cell cycle arrest and proinflammatory changes in osteoarthritic fibroblast-like synovial cells
Authors: Franke Sybille , Sommer Manfred , Rüster Christiane , Bondeva Tzvetanka , Marticke Julia , Hofmann Gunther , Hein Gert , Wolf Gunter 
Published: September 2009

Abstract
Introduction
Advanced glycation end products (AGEs) have been introduced to be involved in the pathogenesis of osteoarthritis (OA). The influence of AGEs on osteoarthritic fibroblast-like synovial cells (FLS) has been incompletely understood as yet. The present study investigates a potential influence of AGE-modified bovine serum albumin (AGE-BSA) on cell growth, and on the expression of proinflammatory and osteoclastogenic markers in cultured FLS.

Methods
FLS were established from OA joints and stimulated with AGE-BSA. The mRNA expression of p27Kip1, RAGE (receptor for AGEs), nuclear factor kappa B subunit p65 (NFκB p65), tumor necrosis factor alpha (TNF-α, interleukin-6 (IL-6), receptor activator of NFκB ligand (RANKL) and osteoprotegerin was measured by real-time PCR. The respective protein expression was evaluated by western blot analysis or ELISA. NFκB activation was investigated by luciferase assay and electrophoretic mobility shift assay (EMSA). Cell cycle analysis, cell proliferation and markers of necrosis and early apoptosis were assessed. The specificity of the response was tested in the presence of an anti-RAGE antibody.

Results
AGE-BSA was actively taken up into the cells as determined by immunohistochemistry and western blots. AGE-induced p27Kip1 mRNA and protein expression was associated with cell cycle arrest and an increase in necrotic, but not apoptotic cells. NFκB activation was confirmed by EMSAs including supershift experiments. Anti-RAGE antibodies attenuated all AGE-BSA induced responses. The increased expression of RAGE, IL-6 and TNF-α together with NFκB activation indicates AGE-mediated inflammation. The decreased expression of RANKL and osteoprotegerin may reflect a diminished osteoclastogenic potential.

Conclusions
The present study demonstrates that AGEs modulate growth and expression of genes involved in the pathophysiological process of OA. This may lead to functional and structural impairment of the joints.
An intraductal human-in-mouse transplantation model mimics the subtypes of ductal carcinoma in situ
Authors: Behbod Fariba , Kittrell Frances S , LaMarca Heather , Edwards David , Kerbawy Sofia , Heestand Jessica C , Young Evelin , Mukhopadhyay Purna , Yeh Hung-Wen , Allred D Craig , Hu Min , Polyak Kornelia , Rosen Jeffrey M , Medina Daniel 
Published: September 2009

Abstract
Introduction
Human models of noninvasive breast tumors are limited, and the existing in vivo models do not mimic inter- and intratumoral heterogeneity. Ductal carcinoma in situ (DCIS) is the most common type (80%) of noninvasive breast lesions. The aim of this study was to develop an in vivo model whereby the natural progression of human DCIS might be reproduced and studied. To accomplish this goal, the intraductal human-in-mouse (HIM) transplantation model was developed. The resulting models, which mimicked some of the diversity of human noninvasive breast cancers in vivo, were used to show whether subtypes of human DCIS might contain distinct subpopulations of tumor-initiating cells.

Methods
The intraductal models were established by injection of human DCIS cell lines (MCF10DCIS.COM and SUM-225), as well as cells derived from a primary human DCIS (FSK-H7), directly into the primary mouse mammary ducts via cleaved nipple. Six to eight weeks after injections, whole-mount, hematoxylin and eosin, and immunofluorescence staining were performed to evaluate the type and extent of growth of the DCIS-like lesions. To identify tumor-initiating cells, putative human breast stem/progenitor subpopulations were sorted from MCF10DCIS.COM and SUM-225 with flow cytometry, and their in vivo growth fractions were compared with the Fisher's Exact test.

Results
Human DCIS cells initially grew within the mammary ducts, followed by progression to invasion in some cases into the stroma. The lesions were histologically almost identical to those of clinical human DCIS. This method was successful for growing DCIS cell lines (MCF10DCIS.COM and SUM-225) as well as a primary human DCIS (FSK-H7). MCF10DCIS.COM represented a basal-like DCIS model, whereas SUM-225 and FSK-H7 cells were models for HER-2+ DCIS. With this approach, we showed that various subtypes of human DCIS appeared to contain distinct subpopulations of tumor-initiating cells.

Conclusions
The intraductal HIM transplantation model provides an invaluable tool that mimics human breast heterogeneity at the noninvasive stages and allows the study of the distinct molecular and cellular mechanisms of breast cancer progression.
Cardiac effects of induction agents in the septic rat heart
Authors: Zausig York A , Busse Hendrik , Lunz Dirk , Sinner Barbara , Zink Wolfgang , Graf Bernhard M 
Published: September 2009

Abstract
Introduction
The current debate about the side effects of induction agents, e.g. possible adrenal suppression through etomidate, emphasizes the relevance of choosing the correct induction agent in septic patients. However, cardiovascular depression is still the most prominent adverse effect of these agents, and might be especially hazardous in septic patients presenting with a biventricular cardiac dysfunction - or so-called septic cardiomyopathy. Therefore, we tested the dose-response direct cardiac effects of clinically available induction agents in an isolated septic rat heart model.

Methods
A polymicrobial sepsis was induced via cecal ligation and single puncture. Hearts (n = 50) were isolated and randomly assigned to five groups, each receiving etomidate, s(+)-ketamine, midazolam, propofol, or methohexitone at concentrations of 1 × 10-8 to 1 × 10-4 M. Left ventricular pressure, contractility and lusitropy, and coronary flow were measured. Cardiac work, myocardial oxygen delivery, oxygen consumption, and percentage of oxygen extraction were calculated.

Results
All of the induction agents tested showed a dose-dependent depression of cardiac work. Maximal cardiac work dysfunction occurred in the rank order of s(+)-ketamine (-6%) <etomidate (-17%) <methohexitone (-31%) <midazolam (-38%) <propofol (-50%). In addition, propofol showed a maximum decrease in contractility of -38%, a reduction in lusitropy of -44%, and a direct vasodilator effect by increasing coronary flow by +29%.

Conclusions
Overall, this study demonstrates that these tested drugs indeed have differential direct cardiac effects in the isolated septic heart. Propofol showed the most pronounced adverse direct cardiac effects. In contrast, S(+)ketamine showed cardiovascular stability over a wide range of concentrations, and might therefore be a beneficial alternative to etomidate.
A global survey identifies novel upstream components of the Ath5 neurogenic network
Authors: Souren Marcel , Martinez-Morales Juan Ramon , Makri Panagiota , Wittbrodt Beate , Wittbrodt Joachim 
Published: September 2009

Abstract
Background
Investigating the architecture of gene regulatory networks (GRNs) is essential to decipher the logic of developmental programs during embryogenesis. In this study we present an upstream survey approach, termed trans-regulation screen, to comprehensively identify the regulatory input converging on endogenous regulatory sequences.

Results
Our dual luciferase-based screen queries transcriptome-scale collections of cDNAs. Using this approach we study the regulation of Ath5, the central node in the GRN controlling retinal ganglion cell (RGC) specification in vertebrates. The Ath5 promoter integrates the input of upstream regulators to enable the transient activation of the gene, which is an essential step for RGC differentiation. We efficiently identified potential Ath5 regulators that were further filtered for true positives by an in situ hybridization screen. Their regulatory activity was validated in vivo by functional assays in medakafish embryos.

Conclusions
Our analysis establishes functional groups of genes controlling different regulatory phases, including the onset of Ath5 expression at cell-cycle exit and its down-regulation prior to terminal RGC differentiation. These results extent the current model of the GRN controlling retinal neurogenesis in vertebrates.
Thomas Reid on Consciousness and Attention
Authors: Yaffe Gideon 
Published: September 2009

It was common enough in the seventeenth and eighteenth centuries to find philosophers holding the position that for something to be ‘in the mind’ and for that mind to be conscious of it are one and the same thing. The thought is that consciousness is a relation between a mind and a mental entity playing the same role as the relation of inherence found between a substance and qualities belonging to it. What it is, on this view, for something to ‘inhere’ in the mind is for that mind to be conscious of it. Locke was explicit in his acceptance of such a claim, writing, for instance,[T]o be in the Mind, and, never to be perceived, is all one, as to say, any thing is, and is not, in the Mind.
Augustine on Testimony
Authors: King Peter , Ballantyne Nathan 
Published: September 2009

Philosophical work on testimony has flourished in recent years. Testimony roughly involves a source affirming or stating something in an attempt to transfer information to one or more persons. It is often said that the topic of testimony has been neglected throughout most of the history of philosophy, aside from contributions by David Hume (1711-1776) and Thomas Reid (1710-1796). True as this may be, Hume and Reid aren't the only ones who deserve a tip of the hat for recognizing the importance of testimony: Augustine of Hippo (354-430) affirms the place of testimony in human cognition, at least in his later writings.In what follows, we consider three questions raised by Augustine's thinking about testimony: the analytical question of what sources count as testimony (Section I); the epistemological question about the status of testimony-based belief (Section II); and the doxastic question about the circumstances in which it is appropriate to believe on the basis of testimony (Section III).
Can One Get Bivalence from (Tarskian) Truth and Falsity?
Authors: López de sa Dan 
Published: September 2009

According to one understanding of them, Tarskian principles about truth (and falsity) aim to explicate the core of the classical conception of truth (and falsity), as endorsed by Aristotle and others:To say of what is that it is not, or of what is not that it is, is false, while to say of what is that it is, or of what is not that it is not, is true, so that he who says of anything that it is, or that it is not, will say either what is true or what is false. Metaphysics (Book IV.7, 1011ª: 26–8)Timothy Williamson famously offered an argument from these Tarskian principles in favour of bivalence — the contention that whatever says something is either true or false — to the effect that denying bivalence in particular cases classically entails a contradiction. This has played a crucial role in the reception of Williamson's case against the main alternative classical view of the nature of vagueness, supervaluationism, and thus in favor of his own epistemic view.
Probabilistic Chloride Corrosion Service Life Model Validation: Global and Individual Bridge Deck Predictions
Authors: Williamson G. , Weyers R. E. , Sprinkel M. M. 
Published: September 2009

Abstract
Deterioration of steel reinforced concrete bridge decks by chloride induced corrosion in North America is of major concern. Chloride from applications of sodium, calcium, and magnesium chloride during winter maintenance operations initiates corrosion, which subsequently spalls the reinforcing steel cover concrete. Initial service life prediction models were diffusion based deterministic/empirical models, which significantly overestimate service lives. Probabilistic solutions provided more realistic estimates. However, chloride corrosion service life models for reinforced concrete elements have not been sufficiently validated against actual field performance. The objective of this study was to validate a probabilistic model using field survey data from ten bridge decks built in Virginia. Field surveys included damage assessments as the sum of spalls, delaminations, and patches. Damage surveys were conducted initially and 3 years later. Chloride content and clear concrete cover depth surveys were conducted to establish cover depth, surface chloride concentration, and chloride diffusion constant global variations. Validation comparisons were performed considering the ten decks as representative of a construction era and as individual decks. Results demonstrated that the probabilistic model accurately predicts global performance but not individual deck performance. Damage predictions of individual decks were greater than and less than the field assessed condition. Differences ranged from an overestimate of 64 years to an underestimate of 11 years. Underestimates averaged 14 years and overestimates averaged 43 years. The large overestimates of 44, 62, and 64 years occurred for estimated service lives of 80–100 years. Insufficient number of model input parameters of surface chloride and particularly the diffusion constant is the plausible reason for the lack of prediction accuracies for the individual decks.
Chlorine Trifluoride Exposure Testing and Oxidizer Reactivity Results
Authors: VanOmmeren James 
Published: September 2009

Abstract
Chlorine trifluoride (ClF3) was first synthesized in the 1930s and is one of the most oxidizing and reactive halogen fluorides known. In fact, with the exception of elemental fluorine, ClF3 may represent one of the most oxidizing and reactive materials in existence. Active research and commercial use of ClF3 began in the late 1940s, and ClF3 has been utilized in such diverse applications as military weapons usage, rocket fuel oxidant, nuclear fuels processing, oil well rod cutting, mineral analysis, and electronics manufacturing equipment cleaning. Such fluoride compounds present significant toxic, oxidizing, highly reactive, and environmental challenges in their manufacture, delivery, customer use, handling, disposal treatment, and emergency response. Air Products has been the primary manufacturer of ClF3 in North America for about 40 years, and ClF3 represents one of the strongest oxidizing and highest reactivity materials that Air Products handles worldwide. However, little information has been available in public literature or the industry regarding its oxidizing potential and reactivity strength with specific materials it may routinely or accidentally come in contact with. Therefore, Air Products conducted extensive release testing to expose various materials of construction (metals, plastics, and elastomers), building materials, personal protective equipment, and other common materials to both vapor and liquid phase releases of ClF3. This paper discusses the synthesis, hazards, varied uses, and major incidents involving ClF3. For example, one major ClF3 liquid spill accident from the 1960s is discussed where an eyewitness stated, “The concrete was on fire!” The paper details controlled release exposure testing methods Air Products employed, results, and lessons learned regarding improved handling and usage recommendations for ClF3 suppliers and customers. For example, a significant potential hazard was discovered regarding use of a safety shower if a person's clothing was exposed to ClF3 liquid, which caused Air Products to change their Material Safety Data Sheet and Product Safety hazards training.
Fatigue Crack Growth Simulation in Components with Random Defects
Authors: Shirani M. , Härkegård G. 
Published: September 2009

Abstract
The three dimensional distribution of defects within a fatigue specimen cut from a large spheroidal graphite cast iron component has been obtained by X-ray computed tomography. This distribution has been used as input for a fatigue assessment postprocessor for the calculation of fatigue life distribution in cast components.
Predicting Grouted Concrete Masonry Prism Strength
Authors: Thompson JJ , Walloch CT , Thomas RD 
Published: September 2009

The structural performance of masonry is in part influenced by the relative and absolute compressive strength of the units, mortar, and grout. However, during the period immediately following masonry construction, the compressive strength of a given assemblage is often uncertain, as these materials have had insufficient time to fully cure. Further, with a near infinite number of combinations of unit, mortar, and grout strengths, designers have historically had little guidance related to available individual component properties when selecting a specified compressive strength of masonry for design purposes.
In response to these needs, this paper analyzes a database of prism compression tests, which incorporate varying material properties into their construction. Based on the results of the prism tests, a prediction model is proposed that provides a correlation to the unit strength, mortar type, grout strength, and prism configuration to the measured prism compressive strength at varying ages of curing.
The prediction model is based on 14 sets of prisms that were constructed and tested to meaure the influence of age on the strength of grouted masonry prisms. The prisms were all constructed using the same materials and construction methods and were tested at ages of 0, 1, 2, 3, 4, 5, 6, 7, 14, 21, 28, 35, 42, and 56 days following grouting.
Additional 28-day strengths of grouted prisms from other research programs were used to validate the model and to further correlate the influence of mortar type, unit strength, grout strength, and prism configuration on the measured versus predicted prism strength.