bluuebunny/crossref_metadata_2025_split huggingface dataset:
UV Radiation Inhibits 15-Hydroxyprostaglandin Dehydrogenase Levels in Human Skin: Evidence of Transcriptional Suppression
Authors: Judson Benjamin L. , Miyaki Akira , Kekatpure Vikram D. , Du Baoheng , Gilleaudeau Patricia , Sullivan-Whalen Mary , Mohebati Arash , Nair Sudhir , Boyle Jay O. , Granstein Richard D. , Subbaramaiah Kotha , Krueger James G. , Dannenberg Andrew J. 
Published: July 2010

AbstractElevated levels of prostaglandins (PG) have been detected in the skin following UV radiation (UVR). PGs play an important role in mediating both the acute and the chronic consequences of UVR exposure. UVR-mediated induction of cyclooxygenase-2 (COX-2) contributes to increased PG synthesis. In theory, reduced catabolism might also contribute to increased PG levels. 15-Hydroxyprostaglandin deyhdrogenase (15-PGDH), a tumor suppressor gene, plays a major role in PG catabolism. In this study, we investigated whether UVR exposure suppressed 15-PGDH while inducing COX-2 in keratinocytes and in human skin. UVR exposure caused dose-dependent induction of COX-2, suppression of 15-PGDH, and increased prostaglandin E2 (PGE2) production in HaCaT cells. Exposure to UVR suppressed the transcription of 15-PGDH, resulting in reduced 15-PGDH mRNA, protein, and enzyme activities. UVR exposure induced Slug, a repressive transcription factor that bound to the 15-PGDH promoter. Silencing Slug blocked UVR-mediated downregulation of 15-PGDH. The effects of UVR were also evaluated in the EpiDerm skin model, a three-dimensional model of human epidermis. Here too, COX-2 levels were induced and 15-PGDH levels suppressed following UVR exposure. Next, the effects of UVR were evaluated in human subjects. UVR treatment induced COX-2 while suppressing 15-PGDH mRNA in the skin of 9 of 10 subjects. Collectively, these data suggest that reduced expression of 15-PGDH contributes to the elevated levels of PGs found in the skin following UVR exposure. Possibly, agents that prevent UVR-mediated downregulation of 15-PGDH will affect the acute or the long-term consequences of UVR exposure, including nonmelanoma skin cancer. Cancer Prev Res; 3(9); 1104–11. ©2010 AACR.
The "Real Dispute" in the Southern Bluefin Tuna Case : a Scientific Dispute?
Authors: Foster Caroline E 
Published: July 2010

AbstractOn 4 August 2000 a LOSC Annex VII ad hoc arbitral tribunal issued its award in the Southern Bluefin Tuna case brought by Australia and New Zealand against Japan. It found it had no jurisdiction under the LOSC in respect of the SBT dispute. The decision has been controversial. This paper identifies the idea, prevalent in many parts of the pleadings in the case, that the "real dispute" in the case lay under the 1993 Convention, and discusses the associated idea that the dispute was scientific in character. Questions raised by the scientific issues in the case are explored, including what may constitute good or "best" scientific evidence, the suitability of scientific disputes for international adjudication, the appropriateness of precautionary approaches, the validity of "margins of appreciation", and the most appropriate forms of dispute resolution for cases involving science. The need for greater attention to be devoted to issues raised by the role of science in international dispute resolution may partly explain the strength of the undercurrent in the SBT case which pushed towards the view that there was only one "real dispute", which fell under the 1993 Convention.
An Empirical Test of CAPM—The Case of Indian Stock Market
Authors: Basu Debarati , Chawla Deepak 
Published: July 2010

A deluge of tests have been conducted on asset pricing models in literature, more so on the Capital Asset Pricing Model (CAPM), to ascertain their validity, efficiency and efficacy in different markets in explaining asset prices. Such tests have been either individual in nature wherein any one model has been studied or comparative in nature where one model has been compared with another. Many studies have also resulted in the development of new models or extensions to the existing theory. However, majority of the aforementioned tests have been undertaken in developed markets, resulting in a dearth of such tests in emerging markets like India where the risk–return relationship gains more significance. A growing, emerging market is always less analyzed but more volatile and thus, more interesting. The article, thus, applies the fundamental CAPM theory to India. This study examines 10 portfolios, covering 50 stocks, over a 5-year period—from 1 January 2003 to 1 February 2008—to verify the efficiency and efficacy of the model and finds that CAPM fails completely in the Indian context. The intercept term, which is expected to be zero, is found to be significant for all 10 portfolios. The study also finds a negative relationship between beta and excess returns indicating an inefficient capital market. Moreover, residual variance, representing unsystematic risk, is also found significant in certain cases. Moreover, the regressions show poor explanatory power. Thus, it can be concluded that CAPM is not a suitable descriptor of asset prices in India over the chosen sample period.
How I treat elderly patients with myeloma
Authors: Mehta Jayesh , Cavo Michele , Singhal Seema 
Published: July 2010

AbstractThe clinical approach to older patients with myeloma has to be modified to take into account comorbidities and the likelihood of higher treatment-related toxicity. Individualization of management and adequate supportive therapy are important to obtain the best response while minimizing adverse effects. Corticosteroids, novel agents, conventional cytotoxic agents, and high-dose chemotherapy with autotransplantation (modalities used in younger patients) are also used in older patients, although the elderly undergo transplantation less frequently. The sequential use of active agents singly and in different combinations has improved response rates and survival of all patients with myeloma, including the elderly.
Front-line treatment of acute promyelocytic leukemia with AIDA induction followed by risk-adapted consolidation for adults younger than 61 years: results of the AIDA-2000 trial of the GIMEMA Group
Authors: Lo-Coco Francesco , Avvisati Giuseppe , Vignetti Marco , Breccia Massimo , Gallo Eugenio , Rambaldi Alessandro , Paoloni Francesca , Fioritoni Giuseppe , Ferrara Felicetto , Specchia Giorgina , Cimino Giuseppe , Diverio Daniela , Borlenghi Erika , Martinelli Giovanni , Di Raimondo Francesco , Di Bona Eros , Fazi Paola , Peta Antonio , Bosi Alberto , Carella Angelo M. , Fabbiano Francesco , Pogliani Enrico M. , Petti Maria C. , Amadori Sergio , Mandelli Franco ,   for the Italian GIMEMA Cooperative Group
Published: July 2010

AbstractAfter the identification of discrete relapse-risk categories in patients with acute promyelocytic leukemia (APL) receiving all-trans retinoic and idarubicin (AIDA)–like therapies, the Gruppo Italiano Malattie Ematologiche dell'Adulto (GIMEMA) designed a protocol for newly diagnosed APL (AIDA-2000) in which postremission treatment was risk-adapted. Patients with low/intermediate risk received remission at 3 anthracycline-based consolidation courses, whereas high-risk patients received the same schedule as in the previous, non–risk-adapted AIDA-0493 trial including cytarabine. In addition, all patients in the AIDA-2000 received all-trans retinoic acid (ATRA) for 15 days during each consolidation. After induction, 600 of 636 (94.3%) and 420 of 445 (94.4%) patients achieved complete remission in the AIDA-0493 and AIDA-2000, respectively. The 6-year overall survival and cumulative incidence of relapse (CIR) rates were 78.1% versus 87.4% (P = .001) and 27.7% versus 10.7% (P < .0001). Significantly lower CIR rates for patients in the AIDA-2000 were most evident in the high-risk group (49.7% vs 9.3%, respectively, P < .0001). Our data confirm that anthracycline-based consolidation is at least equally effective as cytarabine-containing regimens for low-/intermediate-risk patients and suggest that a risk-adapted strategy including ATRA for consolidation improves outcome in newly diagnosed APL. Furthermore, our results highlight the role of cytarabine coupled to anthracyclines and ATRA during consolidation in the high-risk group. This trial was registered at www.clinicaltrials.gov as #NCT 001064570.
Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests
Authors: Abby Sophie S , Tannier Eric , Gouy Manolo , Daubin Vincent 
Published: July 2010

Abstract

Background
To understand the evolutionary role of Lateral Gene Transfer (LGT), accurate methods are needed to identify transferred genes and infer their timing of acquisition. Phylogenetic methods are particularly promising for this purpose, but the reconciliation of a gene tree with a reference (species) tree is computationally hard. In addition, the application of these methods to real data raises the problem of sorting out real and artifactual phylogenetic conflict.

Results
We present Prunier, a new method for phylogenetic detection of LGT based on the search for a maximum statistical agreement forest (MSAF) between a gene tree and a reference tree. The program is flexible as it can use any definition of "agreement" among trees. We evaluate the performance of Prunier and two other programs (EEEP and RIATA-HGT) for their ability to detect transferred genes in realistic simulations where gene trees are reconstructed from sequences. Prunier proposes a single scenario that compares to the other methods in terms of sensitivity, but shows higher specificity. We show that LGT scenarios carry a strong signal about the position of the root of the species tree and could be used to identify the direction of evolutionary time on the species tree. We use Prunier on a biological dataset of 23 universal proteins and discuss their suitability for inferring the tree of life.

Conclusions
The ability of Prunier to take into account branch support in the process of reconciliation allows a gain in complexity, in comparison to EEEP, and in accuracy in comparison to RIATA-HGT. Prunier's greedy algorithm proposes a single scenario of LGT for a gene family, but its quality always compares to the best solutions provided by the other algorithms. When the root position is uncertain in the species tree, Prunier is able to infer a scenario per root at a limited additional computational cost and can easily run on large datasets.
Prunier is implemented in C++, using the Bio++ library and the phylogeny program Treefinder. It is available at: http://pbil.univ-lyon1.fr/software/prunier
VIPR: A probabilistic algorithm for analysis of microbial detection microarrays
Authors: Allred Adam F , Wu Guang , Wulan Tuya , Fischer Kael F , Holbrook Michael R , Tesh Robert B , Wang David 
Published: July 2010

Abstract

Background
All infectious disease oriented clinical diagnostic assays in use today focus on detecting the presence of a single, well defined target agent or a set of agents. In recent years, microarray-based diagnostics have been developed that greatly facilitate the highly parallel detection of multiple microbes that may be present in a given clinical specimen. While several algorithms have been described for interpretation of diagnostic microarrays, none of the existing approaches is capable of incorporating training data generated from positive control samples to improve performance.

Results
To specifically address this issue we have developed a novel interpretive algorithm, VIPR (V iral I dentification using a PR obabilistic algorithm), which uses Bayesian inference to capitalize on empirical training data to optimize detection sensitivity. To illustrate this approach, we have focused on the detection of viruses that cause hemorrhagic fever (HF) using a custom HF-virus microarray. VIPR was used to analyze 110 empirical microarray hybridizations generated from 33 distinct virus species. An accuracy of 94% was achieved as measured by leave-one-out cross validation. Conclusions

VIPR outperformed previously described algorithms for this dataset. The VIPR algorithm has potential to be broadly applicable to clinical diagnostic settings, wherein positive controls are typically readily available for generation of training data.
The bovine chemokine receptors and their mRNA abundance in mononuclear phagocytes
Authors: Widdison Stephanie , Siddiqui Nazneen , Easton Victoria , Lawrence Freya , Ashley George , Werling Dirk , Watson Michael , Coffey Tracey J 
Published: July 2010

AbstractBackgroundThe chemokine and chemokine receptor families play critical roles in both the healthy and diseased organism mediating the migration of cells. The chemokine system is complex in that multiple chemokines can bind to one chemokine receptor andvice versa. Although chemokine receptors have been well characterised in humans, the chemokine receptor repertoire of cattle is not well characterised and many sequences are yet to be experimentally validated.ResultsWe have identified and sequenced bovine homologs to all identified functional human chemokine receptors. The bovine chemokine receptors show high levels of similarity to their human counterparts and similar genome arrangements. We have also characterised an additional bovine chemokine receptor, not present in the available genome sequence of humans or the more closely related pigs or horses. This receptor shows the highest level of similarity to CCR1 but shows significant differences in regions of the protein that are likely to be involved in ligand binding and signalling. We have also examined the mRNA abundance levels of all identified bovine chemokine receptors in mononuclear phagocytic cells. Considerable differences were observed in the mRNA abundance levels of the receptors, and interestingly the identified novel chemokine receptor showed differing levels of mRNA abundance to its closest homolog CCR1. The chemokine receptor repertoire was shown to differ between monocytes, macrophages and dendritic cells. This may reflect the differing roles of these cells in the immune response and may have functional consequences for the trafficking of these cellsin vivo.ConclusionsIn summary, we have provided the first characterisation of the complete bovine chemokine receptor gene repertoire including a gene that is potentially unique to cattle. Further study of this receptor and its ligands may reveal a specific role of this receptor in cattle. The availability of the bovine chemokine receptor sequences will allow further characterisation of the function of these genes and will confer wide-reaching benefits to the study of this important aspect of the bovine immune response.
The Protein Disulfide Isomerase gene family in bread wheat (T. aestivum L.)
Authors: d'Aloisio Elisa , Paolacci Anna R , Dhanapal Arun P , Tanzarella Oronzo A , Porceddu Enrico , Ciaffi Mario 
Published: July 2010

Abstract

Background
The Protein Disulfide Isomerase (PDI) gene family encodes several PDI and PDI-like proteins containing thioredoxin domains and controlling diversified metabolic functions, including disulfide bond formation and isomerisation during protein folding. Genomic, cDNA and promoter sequences of the three homoeologous wheat genes encoding the "typical" PDI had been cloned and characterized in a previous work. The purpose of present research was the cloning and characterization of the complete set of genes encoding PDI and PDI like proteins in bread wheat (Triticum aestivum cv Chinese Spring) and the comparison of their sequence, structure and expression with homologous genes from other plant species.

Results
Eight new non-homoeologous wheat genes were cloned and characterized. The nine PDI and PDI-like sequences of wheat were located in chromosome regions syntenic to those in rice and assigned to eight plant phylogenetic groups. The nine wheat genes differed in their sequences, genomic organization as well as in the domain composition and architecture of their deduced proteins; conversely each of them showed high structural conservation with genes from other plant species in the same phylogenetic group. The extensive quantitative RT-PCR analysis of the nine genes in a set of 23 wheat samples, including tissues and developmental stages, showed their constitutive, even though highly variable expression.

Conclusions
The nine wheat genes showed high diversity, while the members of each phylogenetic group were highly conserved even between taxonomically distant plant species like the moss Physcomitrella patens. Although constitutively expressed the nine wheat genes were characterized by different expression profiles reflecting their different genomic organization, protein domain architecture and probably promoter sequences; the high conservation among species indicated the ancient origin and diversification of the still evolving gene family. The comprehensive structural and expression characterization of the complete set of PDI and PDI-like wheat genes represents a basis for the functional characterization of this gene family in the hexaploid context of bread wheat.
Role of the supine lateral radiograph of the spine in vertebroplasty for osteoporotic vertebral compression fracture: a prospective study
Authors: Wu Meng-Huang , Huang Tsung-Jen , Cheng Chin-Chang , Li Yen-Yao , Hsu Robert Wen-Wei 
Published: July 2010

Abstract

Background
Severely collapsed vertebral compression fracture (VCF) is usually considered as a contraindication for vertebroplasty because of critically decreased vertebral height (less than one-third the original height). However, osteoporotic VCF can possess dynamic mobility with intravertebral cleft (IVC), which can be demonstrated on supine lateral radiographs (SuLR) and standing lateral radiographs (StLR). The purposes of this study were to: (1) evaluate the efficacy of SuLR to detect IVCs and assess the intravertebral mobility in VCFs, and (2) evaluate the short-term results of vertebroplasty in severely collapsed VCFs with IVCs.

Methods
We enrolled 37 patients with 40 symptomatic osteoporotic VCFs for vertebroplasty; 11 had severely collapsed VCFs with concurrent IVCs detected on the SuLR, the others had not-severely collapsed VCFs. A preoperative StLR, SuLR, magnetic resonance imaging (MRI), and postoperative StLR were taken from all patients. Radiographs were digitized to calculate vertebral body morphometrics including vertebral height ratio and Cobb's kyphotic angle. The intensity of the patient's pain was assessed by the visual analogue scale (VAS) on the day before operation and 1 day, 1 month, and 4 months after operation. The patient's VAS scores and image measurement results were assessed with the paired t-test and Pearson correlation tests; Mann-Whitney U test was used for VAS subgroup comparison. Significance was defined as p < 0.05.

Results
IVCs in patients with not-severely collapsed VCFs were detected in 21 vertebrae (72.4%) by MRI, in 15 vertebrae (51.7%) by preoperative SuLR, and in 7 vertebrae (24.1%) by preoperative StLR. Using the MRI as a gold standard to detect IVCs, SuLR exhibit a sensitivity of 0.71 as compared to StLR that yield a sensitivity of 0.33. In patients with VCFs with IVCs detected on SuLR, the average of the postoperative restoration in vertebral height ratio was significantly higher than that in those without IVCs (17.1% vs. 6.4%). There was no statistical difference in the VAS score between severely collapsed VCFs with IVCs detected on SuLR and not-severely collapsed VCFs at any follow-up time point.

Conclusions
The SuLR efficiently detects an IVC in VCF, which indicates a better vertebral height correction after vertebroplasty compared to VCF without IVC. Before performing a costly MRI, SuLR can identify more IVCs than StLR in patients with severely collapsed VCFs, whom may become the candidates for vertebroplasty.
Automated assay for screening the enzymatic release of reducing sugars from micronized biomass
Authors: Navarro David , Couturier Marie , Damasceno da Silva Gabriela Ghizzi , Berrin Jean-Guy , Rouau Xavier , Asther Marcel , Bignon Christophe 
Published: July 2010

Abstract

Background
To reduce the production cost of bioethanol obtained from fermentation of the sugars provided by degradation of lignocellulosic biomass (i.e., second generation bioethanol), it is necessary to screen for new enzymes endowed with more efficient biomass degrading properties. This demands the set-up of high-throughput screening methods. Several methods have been devised all using microplates in the industrial SBS format. Although this size reduction and standardization has greatly improved the screening process, the published methods comprise one or more manual steps that seriously decrease throughput. Therefore, we worked to devise a screening method devoid of any manual steps.

Results
We describe a fully automated assay for measuring the amount of reducing sugars released by biomass-degrading enzymes from wheat-straw and spruce. The method comprises two independent and automated steps. The first step is the making of "substrate plates". It consists of filling 96-well microplates with slurry suspensions of micronized substrate which are then stored frozen until use. The second step is an enzymatic activity assay. After thawing, the substrate plates are supplemented by the robot with cell-wall degrading enzymes where necessary, and the whole process from addition of enzymes to quantification of released sugars is autonomously performed by the robot. We describe how critical parameters (amount of substrate, amount of enzyme, incubation duration and temperature) were selected to fit with our specific use. The ability of this automated small-scale assay to discriminate among different enzymatic activities was validated using a set of commercial enzymes.

Conclusions
Using an automatic microplate sealer solved three main problems generally encountered during the set-up of methods for measuring the sugar-releasing activity of plant cell wall-degrading enzymes: throughput, automation, and evaporation losses. In its present set-up, the robot can autonomously process 120 triplicate wheat-straw samples per day. This throughput can be doubled if the incubation time is reduced from 24 h to 4 h (for initial rates measurements, for instance). This method can potentially be used with any insoluble substrate that is micronizable. A video illustrating the method can be seen at the following URL: http://www.youtube.com/watch?v=NFg6TxjuMWU