bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative analyses of genotype dependent expressed sequence tags and stress-responsive transcriptome of chickpea wilt illustrate predicted and unexpected genes and novel regulators of plant immunity
Authors: Ashraf Nasheeman , Ghai Deepali , Barman Pranjan , Basu Swaraj , Gangisetty Nagaraju , Mandal Mihir K , Chakraborty Niranjan , Datta Asis , Chakraborty Subhra 
Published: September 2009

AbstractBackgroundThe ultimate phenome of any organism is modulated by regulated transcription of many genes. Characterization of genetic makeup is thus crucial for understanding the molecular basis of phenotypic diversity, evolution and response to intra- and extra-cellular stimuli. Chickpea is the world's third most important food legume grown in over 40 countries representing all the continents. Despite its importance in plant evolution, role in human nutrition and stress adaptation, very little ESTs and differential transcriptome data is available, let alone genotype-specific gene signatures. Present study focuses onFusariumwilt responsive gene expression in chickpea.ResultsWe report 6272 gene sequences of immune-response pathway that would provide genotype-dependent spatial information on the presence and relative abundance of each gene. The sequence assembly led to the identification of aCaUnigene set of 2013 transcripts comprising of 973 contigs and 1040 singletons, two-third of which represent new chickpea genes hitherto undiscovered. We identified 209 gene families and 262 genotype-specific SNPs. Further, several novel transcription regulators were identified indicating their possible role in immune response. The transcriptomic analysis revealed 649 non-cannonical genes besides many unexpected candidates with known biochemical functions, which have never been associated with pathostress-responsive transcriptome.ConclusionOur study establishes a comprehensive catalogue of the immune-responsive root transcriptome with insight into their identity and function. The development, detailed analysis ofCaEST datasets and global gene expression by microarray provide new insight into the commonality and diversity of organ-specific immune-responsive transcript signatures and their regulated expression shaping the species specificity at genotype level. This is the first report on differential transcriptome of an unsequenced genome during vascular wilt.
Reversal of oncogene transformation and suppression of tumor growth by the novel IGF1R kinase inhibitor A-928605
Authors: Pappano William N , Jung Paul M , Meulbroek Jonathan A , Wang Yi-Chun , Hubbard Robert D , Zhang Qian , Grudzien Meagan M , Soni Niru B , Johnson Eric F , Sheppard George S , Donawho Cherrie , Buchanan Fritz G , Davidsen Steven K , Bell Randy L , Wang Jieyi 
Published: September 2009

AbstractBackgroundThe insulin-like growth factor (IGF) axis is an important signaling pathway in the growth and survival of many cell and tissue types. This pathway has also been implicated in many aspects of cancer progression from tumorigenesis to metastasis. The multiple roles of IGF signaling in cancer suggest that inhibition of the pathway might yield clinically effective therapeutics.MethodsWe describe A-928605, a novel pyrazolo [3,4-d]pyrimidine small molecule inhibitor of the receptor tyrosine kinases (IGF1R and IR) responsible for IGF signal transduction. This compound was first tested for its activity and selectivity via conventionalin vitrokinome profiling and cellular IGF1R autophosphorylation. Additionally, cellular selectivity and efficacy of A-928605 were analyzed in an IGF1R oncogene-addicted cell line by proliferation, signaling and microarray studies. Finally,in vivoefficacy of A-928605 was assessed in the oncogene-addicted cell line and in a neuroblastoma model as a single agent as well as in combination with clinically approved therapeutics targeting EGFR in models of pancreatic and non-small cell lung cancers.ResultsA-928605 is a selective IGF1R inhibitor that is able to abrogate activation of the pathway bothin vitroandin vivo. This novel compound dosed as a single agent is able to produce significant growth inhibition of neuroblastoma xenograftsin vivo. A-928605 is also able to provide additive effects when used in combination with clinically approved agents directed against EGFR in non-small cell lung and human pancreatic tumor models.ConclusionThese results suggest that a selective IGF1R inhibitor such as A-928605 may provide a useful clinical therapeutic for IGF pathway affected tumors and warrants further investigation.
Meta-analysis of glioblastoma multiforme versus anaplastic astrocytoma identifies robust gene markers
Authors: Dreyfuss Jonathan M , Johnson Mark D , Park Peter J 
Published: September 2009

AbstractBackgroundAnaplastic astrocytoma (AA) and its more aggressive counterpart, glioblastoma multiforme (GBM), are the most common intrinsic brain tumors in adults and are almost universally fatal. A deeper understanding of the molecular relationship of these tumor types is necessary to derive insights into the diagnosis, prognosis, and treatment of gliomas. Although genomewide profiling of expression levels with microarrays can be used to identify differentially expressed genes between these tumor types, comparative studies so far have resulted in gene lists that show little overlap.ResultsTo achieve a more accurate and stable list of the differentially expressed genes and pathways between primary GBM and AA, we performed a meta-analysis using publicly available genome-scale mRNA data sets. There were four data sets with sufficiently large sample sizes of both GBMs and AAs, all of which coincidentally used human U133 platforms from Affymetrix, allowing for easier and more precise integration of data. After scoring genes and pathways within each data set, we combined the statistics across studies using the nonparametric rank sum method to identify the features that differentiate GBMs and AAs. We found >900 statistically significant probe sets after correction for multiple testing from the >22,000 tested. We also used the rank sum approach to select >20 significant Biocarta pathways after correction for multiple testing out of >175 pathways examined. The most significant pathway was the hypoxia-inducible factor (HIF) pathway. Our analysis suggests that many of the most statistically significant genes work together in aHIF1A/VEGF-regulated network to increase angiogenesis and invasion in GBM when compared to AA.ConclusionWe have performed a meta-analysis of genome-scale mRNA expression data for 289 human malignant gliomas and have identified a list of >900 probe sets and >20 pathways that are significantly different between GBM and AA. These feature lists could be utilized to aid in diagnosis, prognosis, and grade reduction of high-grade gliomas and to identify genes that were not previously suspected of playing an important role in glioma biology. More generally, this approach suggests that combined analysis of existing data sets can reveal new insights and that the large amount of publicly available cancer data sets should be further utilized in a similar manner.
Innate immune response during Yersinia infection: critical modulation of cell death mechanisms through phagocyte activation
Authors: Bergsbaken Tessa , Cookson Brad T 
Published: September 2009

Abstract
Review of infected macrophages undergoing pyroptosis as a host-healthy alternative to apoptosis.
Yersinia pestis, the etiological agent of plague, is one of the most deadly pathogens on our planet. This organism shares important attributes with its ancestral progenitor, Yersinia pseudotuberculosis, including a 70-kb virulence plasmid, lymphotropism during growth in the mammalian host, and killing of host macrophages. Infections with both organisms are biphasic, where bacterial replication occurs initially with little inflammation, followed by phagocyte influx, inflammatory cytokine production, and tissue necrosis. During infection, plasmid-encoded attributes facilitate bacterial-induced macrophage death, which results from two distinct processes and corresponds to the inflammatory crescendo observed in vivo: Naïve cells die by apoptosis (noninflammatory), and later in infection, activated macrophages die by pyroptosis (inflammatory). The significance of this redirected cell death for the host is underscored by the importance of phagocyte activation for immunity to Yersinia and the protective role of pyroptosis during host responses to anthrax lethal toxin and infections with Francisella, Legionella, Pseudomonas, and Salmonella. The similarities of Y. pestis and Y. pseudotuberculosis, including conserved, plasmid-encoded functions inducing at least two distinct mechanisms of cell death, indicate that comparative studies are revealing about their critical pathogenic mechanism(s) and host innate immune responses during infection. Validation of this idea and evidence of similar interactions with the host immune system are provided by Y. pseudotuberculosis-priming, cross-protective immunity against Y. pestis. Despite these insights, additional studies indicate much remains to be understood concerning effective host responses against Yersinia, including chromosomally encoded attributes that also contribute to bacterial evasion and modulation of innate and adaptive immune responses.
Autonomous three-dimensional tracking for reconfigurable active-vision-based object recognition
Authors: de Ruiter H , Mackay M , Benhabib B 
Published: September 2009

Recognition algorithms would significantly benefit from object images acquired from preferential view points, e.g. unobstructed frontal views or complementary views. Active-vision systems, which are dynamically reconfigurable in an online mode, have been suggested in the literature as effective solutions for achieving this objective, namely, relocating cameras to obtain optimal visibility for a given situation. To obtain optimal visibility of an object of interest (OI), however, that OI's three-dimensional (3D) position and orientation (i.e. six degree-of-freedom pose) must be tracked in real time. Thus, this paper presents such an autonomous, real-time, six degree-of-freedom pose tracking system for a priori unknown objects. The proposed tracking method autonomously (a) selects the OI, (b) builds its approximate 3D model and uses this model to (c) track it in real time. As will be shown in this paper, via experimental results, the output of the proposed modeller can be effectively used by an active-vision system to relocate its cameras for effective preferential image acquisition. In the examples included herein, it will be noted that object visibility data obtained via camera reconfiguration based on the authors' ‘approximate’ tracking method are comparable with those obtainable based on ‘perfect’ OI tracking.
Process value analysis for business process re-engineering
Authors: Borgianni Y , Cascini G , Rotini F 
Published: September 2009

Two decades of studies about business process re-engineering have proposed several strategies for the reorganization of a production process aimed at costs saving and waste reduction. Nevertheless, there is still a substantial lack of suitable means to measure if and how much the production phases contribute to deliver value, i.e. satisfaction, to the end user. The present paper proposes a methodology aimed at supporting business process re-engineering activities by taking into account the impact each phase of a process has on the value perceived by the customers. The methodology swivels on process value analysis, that is performed through the evaluation of both the customer perceived benefits originated from the process phases, and the resources spent in the same phases. On the basis of customer satisfaction requirements, guidelines are defined in order to identify both process evolution strategies and resource reorganization activities allowing the market competitiveness of products and/or services that the process sells to be preserved and improved.The methodology has been applied to a case study in the field of the Italian footwear industry in order to assess its efficiency.
A New Polymorph of Layered LiCoO2
Authors: Komaba Shinichi , Yabuuchi Naoaki , Kawamoto Yuta 
Published: September 2009

Abstract
A new polymorph of layered LiCoO2 was prepared from OP4-LixNayCoO2 by ion exchange. Structural analysis by synchrotron X-ray diffraction revealed that the new polymorph of LiCoO2 is O4-type LiCoO2 whose structure corresponds to intergrowth of O2- and O3-type LiCoO2. It was also confirmed that the O4-type LiCoO2 shows electrochemical activity and different reversible voltage in aprotic lithium cells in comparison to those of O2- and O3-type LiCoO2, which are well-known electrode materials as polymorphs of LiCoO2.
Theoretical Study of the Iron Sulfur Cluster-free Hydrogenase (Hmd): What is the Active Center of Hmd?
Authors: Nakatani Naoki , Nakao Yoshihide , Sato Hirofumi , Sakaki Shigeyoshi 
Published: September 2009

Abstract
The DFT computational geometry and CO stretching frequency of the active center of iron sulfur cluster free hydrogenase (Hmd) indicate that the active site contains low-spin Fe(II) center coordinated with two COs, cysteine, either acylpyridone and water or acylpyridinol and hydroxide.
Adsorption of Trimethylphosphine Oxide Molecules from the Gas Phase to Probe Surface Acidity by Solid-state NMR
Authors: Hayashi Shigenobu 
Published: September 2009

Abstract
Trimethylphosphine oxide (TMPO) molecules were adsorbed on H-type mordenite to probe the surface acidity by solid-state NMR. We found that dichloromethane was coadsorbed when it was used as a solvent. To avoid the effect of the solvent, TMPO was adsorbed from the gas phase, and we have obtained 1H and 31P magic-angle-spinning (MAS) NMR spectra of TMPO-adsorbed H-type mordenite without the effect of the solvent.
Self-assembled Three-dimensional Hierarchical BiVO4 Microspheres from Nanoplates: Malic Acid-assisted Hydrothermal Synthesis and Photocatalytic Activities
Authors: Ma Dekun , Wang Shun , Cai Ping , Jiang Jinglu , Yang Dongpeng , Huang Shaoming 
Published: September 2009

Abstract
Self-assembled three-dimensional (3D) hierarchical BiVO4 microspheres from nanoplates have been first synthesized by a facile malic acid-assisted hydrothermal route on a large scale. In the present hydrothermal system, malic acid played key roles in controlling the morphology and quality of the resultant products. The as-synthesized 3D hierarchical BiVO4 microspheres exhibited good photocatalytic activity in degradation of Rhodamine B (RhB) under Xe-lamp light irradiation.
Comparing progression of non-functioning pituitary adenomas in hypopituitarism patients with and without long-term GH replacement therapy
Authors: Olsson D S , Buchfelder M , Schlaffer S , Bengtsson B-Å , Jakobsson K-E , Johannsson G , Nilsson A G 
Published: September 2009

ObjectiveAn important safety issue with GH replacement therapy (GHRT) in hypopituitary patients with a history of a pituitary adenoma is the risk for tumour recurrence or enlargement.DesignCase–control study.Subjects and methodsWe studied tumour progression rate in 121 patients with hypopituitarism on the basis of non-functioning pituitary adenomas (NFPA) receiving long-term GHRT. A group of 114 NFPA patients not receiving GHRT who were matched in terms of duration of follow-up, gender, age, age at diagnosis and radiotherapy status were used as a control population. The average duration of GHRT was 10±4 years (range 2–17).ResultsIn patients with a known residual adenoma, 63% had no detectable enlargement of tumour during the study. In patients who had no visible residual tumour prior to GHRT, 90% did not suffer from recurrence. In total, the 10-year tumour progression-free survival rate in patients with NFPA receiving GHRT was 74%. In the control population not receiving GHRT, the 10-year progression-free survival rate was 70%. Radiotherapy as part of the initial tumour treatment reduced the rate of tumour progression in both GHRT and non-GHRT patients to a similar extent.ConclusionsThe rate of tumour progression was similar in this large group of GHRT patients and the control population not receiving GHRT. Our results provide further support that long-term use of GH replacement in hypopituitarism may be considered safe in patients with residual pituitary adenomas.
Soluble CTLA-4 receptor an immunological marker of Graves' disease and severity of ophthalmopathy is associated with CTLA-4 Jo31 and CT60 gene polymorphisms
Authors: Daroszewski Jacek , Pawlak Edyta , Karabon Lidia , Frydecka Irena , Jonkisz Anna , Slowik Miroslaw , Bolanowski Marek 
Published: September 2009

ObjectiveGraves' disease (GD) is an autoimmune disorder with genetic and environmental background. CTLA-4 is a candidate gene for thyroid autoimmunity. Increased serum levels of soluble CTLA-4 (sCTLA-4) were found in some autoimmune diseases.AimThe aim of the study was to evaluate the relation between sCTLA-4 level and clinical manifestation of Graves' ophthalmopathy (GO), thyroid status, and CTLA-4 gene polymorphisms.DesignSerum sCTLA-4 concentrations were determined in 93 GO patients and 93 healthy controls. In the GO group, CTLA-4 gene was genotyped in five polymorphic sites: g.319C>T, c.49A>G, CT60 by means of PRC-RFLP, Jo31, and g.*642AT(8_33) by means of minisequencing assay.ResultsSerum sCTLA-4 level was significantly higher in the GO group than in controls (median: 7.94 vs 0.00 ng/ml, P=0.000001). This level was higher in severe than in nonsevere GO (median: 10.3 vs 5.6 ng/ml, P=0.01). sCTLA-4 concentration was related neither to the activity of GO nor to thyroid function. Elevated sCTLA-4 levels were observed in carriers Jo31[G] allele (genotype GG+GT) as compared with subjects with an absence of the [G] allele (TT genotype; median: 9.18 vs 4.0 ng/ml, P=0.02). Also patients possessing CT60[G] allele (genotype GG+GA) had higher serum sCTLA-4 levels than subjects who lack the [G] allele (AA genotype; median: 8.73 vs 2.28 ng/ml, P=0.03).ConclusionsIt was shown for the first time that increased serum concentration of sCTLA-4 correlate with the severity of GO. Genetic variation in the CTLA-4 gene region in GD patients at least partially determines the level of sCTLA-4.
Facial expressions in various emotional states in congenitally blind and sighted subjects
Authors: Peleg Gili , Katzir Gadi , Peleg Ofer , Kamara Michal , Brodsky Leonid , Hel-Or Hagit , Keren Daniel , Nevo Eviatar 
Published: September 2009

Most of the studies comparing facial expressions of born blind and sighted persons that have been carried out up until now have involved children as subjects. Various studies claimed that the quantity and quality of facial expressions of congenitally blind persons deteriorate with increasing age. Here, we compared facial expressions of born blind and sighted individuals using adults predominantly. Facial expressions were documented in an individual interview inducing such emotions as think-concentrate, sadness, anger, disgust, joy, and surprise.Common characteristics found amongst studied individuals were: similar repertoires*of movements over the entire interview, high-frequency and high-repertoire proportion of facial movements in concentration, sadness, and anger relative to those in disgust, joy, and surprise, similar distributions of a cumulative repertoire proportion of facial movements, and also common behavioral profiles of frequencies of facial movements in the emotional states discussed. Similar displays of eyebrow movements were found as well in concentration, sadness, and anger.Our study indicates that most tested characteristics of facial movements are common to born blind and sighted subjects, except for different cumulative mean frequencies in different emotional states, which is possibly related to the lack of visual feedback in born blind persons.Our study substantiates the hypothesis that facial expressions are innate and have important cues in the evolution of social communication.
Host-parasite relationships between Porichthys porosissimus (Pisces) and cestode larvae of the Scolex group
Authors: Guagliardo S. , Tanzola D. , Schwerdt C. , Galeano N. 
Published: September 2009

Abstract
Larvae of tetraphyllidean cestodes have been recorded in several species of marine teleosts. However, little is known on parasite-host interactions. In view of this, the present study aims at i) determining the localization sites of a larval type, belonging to the Scolex group, in the digestive tract mucose; ii) describing the anatomo-pathological features of the larval lesions produced; and iii) evaluating the potential effect of parasite intensity on the body condition of the host. Our findings reveal that parasitic charges were more intense in the second portion of the digestive tract. In the area of contact between the parasite and the epithelium a compressive atrophy of the cells was observed with a marked lowering and disappearance of the epithelial layer. The condition factor of the samples analyzed was significantly affected by infection intensity, thus revealing an adverse effect on the growth and physical condition of the host.
Communities of metazoan parasites of two fishes of the Proterorhinus genus (Actinopterygii: Gobiidae)
Authors: Kvach Yuriy , Oğuz Mehmet 
Published: September 2009

Abstract
Metazoan parasite communities of two gobiids, Proterorhinus marmoratus and P. semilunaris, which are common small-sized fishes native for the Black Sea basin, were studied. The parasite component community of P. marmoratus is represented by 11 species (one monogenean, one cestode, five digeneans, two nematodes, and two acanthocephalans). P. semilunaris had 5 species (one monogenean, one cestode, one digenean, one nematode, and one acanthocephalan). Acanthocephaloides propinquus has a great tendency to join the infracommunity. The differences between the parasite component communities of two Proterorhinus gobies are explained by different quality of habitats and available intermediate hosts. The component community of parasites of P. marmoratus is formed by brackish-water and marine parasite species, and that of P. semilunaris consists of limnetic parasite species. The euryhaline G. proterorhini is the only parasite species found in both P. marmoratus and P. semilunaris. In both species of gobiids, the main abundant parasite species (A. propinquus in P. marmoratus and Nicolla skrjabini in P. semilunaris) infest the host by feeding on crustaceans.
The helminth community of the agile frog, Rana dalmatina Bonaparte, 1839 (Anura: Ranidae) collected from Northwest of Turkey
Authors: Düşen S. , Uğurtaş İ. , Aydoğdu A. , Oğuz M. 
Published: September 2009

Abstract
A total of 33 agile frogs (Rana dalmatina) were collected from 7 localities in Edirne, Bursa and Adapazarı Provinces (Northwest of Turkey), between 1987–2007 and examined for the first time for helminths. R. dalmatina harbored one species of Monogenea (Polystoma sp.), 3 species of Digenea (Diplodiscus subclavatus, Pleurogenoides medians, and Pleurogenes claviger), 4 species of Nematoda (Rhabdias bufonis, Oswaldocruzia filiformis, Cosmocerca ornata, and Oxysomatium brevicaudatum) and one species of Acanthocephala (Acanthocephalus ranae). All helminths represent new host records for Rana dalmatina in Turkey.