bluuebunny/crossref_metadata_2025_split huggingface dataset:
THE IMPACT OF GEOGRAPHIC ORIGIN ON SENSORY PROPERTIES OF VITIS VINIFERA CV. MENCÍA
Authors: VILANOVA MAR , SOTO BEATRIZ 
Published: January 2006

ABSTRACT The objective of this study was to establish the aromatic descriptors that identify the aroma of young Mencía wines from different geographic areas of Ribeira Sacra Appellation of Origin Controlled in Galicia (NW Spain). Initially, 36 attributes were identified. A multivariate analysis was carried out to evaluate this possible differentiation between the Mencía wines according to production area. Principal component analysis of sensory data permitted the differentiation among geographic areas. The wines differed significantly for seven sensory attributes. The wines from Chantada and Ribeira do Miño were characterized by higher intensities of metallic and bread odors, while Amandi and Quiroga‐Bibei by balsamic, apple and phenolic characters. The wines from Ribeira do Sil exhibited a toasting character and the lactic character was present in all wines except those from Ribeira do Sil.
Detection of venous invasion in surgical specimens of colorectal carcinoma: the efficacy of various types of tissue blocks: Table 1
Authors: Sternberg A , Mizrahi A , Amar M , Groisman G 
Published: January 2006

Background:Venous invasion (VI) is an important prognosis predictor after colorectal carcinoma (CRC) resection, enabling more accurate staging and influencing postoperative management.Aims:To assess/compare various tissue block types (perpendicular, tangential, across mesentery (AM), from major vessels or lymph nodes (LNs)) for VI detection in CRC.Methods:Fifty two CRCs (51 colectomies, one polypectomy) were studied. Tumours were measured, surface area calculated, and colorectum and bowel wall sites recorded. Weigert’s staining for elastin facilitated VI detection. VI sites, type, and amount were recorded. Ratios of relative yield of tissue block types to their frequency were calculated.Results:Average numbers of tissue blocks/colectomy specimen were: perpendicular, 10.2; tangential, 9.1; AM, 3.3; from major vessels, 2.1. Average number of LNs examined was 16.47. VI was detected in 22 tumours. Overall, VI was detected in 16 perpendicular, seven tangential, five AM, and two LN blocks. VI was detected in eight, two, one, and three tumours in perpendicular, tangential, LN, and AM blocks alone, respectively. In seven tumours, VI was identified in multiple tissue block types. The average number of blocks obtained was 39.7, 42.1, and 38 from all tumours, VI positive, and VI negative tumours, respectively (p = 0.0497). Efficacy to detect VI was 2.151, 2.088, 1.092, 0.172, and 0 for AM, perpendicular, tangential, LN, and mesenteric vessel blocks, respectively.Conclusions:VI was identified most frequently and in eight cases only in perpendicular blocks. However, extramural VI was detected in six tumours only in blocks cut tangentially, AM, or from harvested LNs. Hence, all these types of blocks should be submitted routinely and scanned for VI.
cDNA microarray analysis of cancer associated gene expression profiles in malignant peripheral nerve sheath tumours
Authors: Karube K , Nabeshima K , Ishiguro M , Harada M , Iwasaki H 
Published: January 2006

Background:Malignant peripheral nerve sheath tumour (MPNST) is a highly aggressive malignancy that arises within peripheral nerves, and is associated with poor prognosis. Little is known about the underlying biology of MPNST, especially the mechanisms involved in cell proliferation, invasion, or escape from apoptosis.Aims:To identify genes differentially expressed in MPNST compared with benign tumours, such as neurofibromas and schwannomas, by means of cDNA microarray analysis.Methods:Six MPNST cases and five benign cases (three schwannomas and two neurofibromas) were analysed.Results:Six genes (keratin 18, survivin, tenascin C, adenosine deaminase, collagen type VIa3, and collagen type VIIa1) were significantly upregulated in MPNST, whereas one gene, insulin-like growth factor binding protein 6, was downregulated in MPNST. Survivin and tenascin C expression was validated by reverse transcription polymerase chain reaction. Immunohistochemistry confirmed upregulation of survivin in MPNST at the protein level in six of eight cases compared with benign tumours. Tenascin C was also expressed at the invasive front and tumorous stroma in all MPNST cases. MPNST cells expressed tenascin C in four of nine cases.Conclusions:Survivin and tenascin C may be associated with the malignant potential of MPNST and could be considered as potential therapeutic targets.
An audit of thrombophilia screens: results from the National Pathology Alliance benchmarking review
Authors: Lyons S , Galloway M J , Osgerby J , Hanley J 
Published: January 2006

Aims:The National Pathology Alliance benchmarking review has completed six years of data collection and analysis of the workload and organisation of haematology laboratories in the UK. This study audits national practice of routine thrombophilia screening against the current standards, as set out in the British committee for standards in haematology (BCSH) guidelines on investigation of heritable thrombophilia.Methods:Each laboratory completed a standard data collection questionnaire about the number of routine thrombophilia assays performed each year. Information was collected on which thrombophilia tests were performed as part of a routine thrombophilia screen. These results were then compared against the BCSH guidelines on investigation of heritable thrombophilia.Results:Of the 57 National Health Service trusts that submitted data for review in 2002/2003, 47 performed a routine thrombophilia screen. Ten laboratories complied with the guidelines but 37 laboratories did not.Conclusion:There was variation in practice in the tests used in routine thrombophilia screens. There is evidence that some laboratories deviate from what may be regarded as “evidence based practice”. The lack of compliance with the guidelines was in general associated with the performance of additional tests not recommended in the guideline. In a minority of laboratories, a clinically significant diagnosis would be missed by the failure to include one or more tests in a thrombophilia screen.
Twenty year review of histopathological findings in enucleated/eviscerated eyes
Authors: Saeed M U , Chang B Y P , Khandwala M , Shivane A G , Chakrabarty A 
Published: January 2006

Background/Aims:To evaluate the need for routine histopathological analysis of enucleated/eviscerated eyes and changes in indications for eye removal.Methods:Retrospective review of all enucleation/evisceration histopathology reports over 20 years. Clinical history was correlated with pathological findings. Two 10 year periods (1984–93, 1994–2003) were compared to detect changes in indications for eye removal.Results:In total, 285 histopathology results were traced from 1984 to 2003; 161 and 124 were evisceration and enucleation specimens, respectively. Glaucoma, malignant melanoma, trauma, and retinal detachment were the most frequent diagnoses 1984–1993. Ocular trauma was the most frequent diagnosis 1994–2003, followed by phthisis bulbi and endophthalmitis. Three cases were diagnosed as metastatic carcinoma; all were suspected preoperatively. A fourth case was a diagnostic surprise: adenocarcinoma found in an eye removed for pain and phthisis. Comparison of two 10 year periods showed a decrease in the number of enucleations/eviscerations, perhaps reflecting a decrease in the number of specimens sent. A preference for eviscerations was evident over the 20 years.Conclusion:The number of eyes removed and histologically analysed decreased in the period 1994 to 2003, perhaps because of better treatment options, allowing globe preservation. There was a significant shift in the diagnosis in the two time periods, and a preference for evisceration in both. Only one diagnostic surprise was discovered (0.35%). This study does not support the need to send all globes/contents for histopathological examination. However, because of the one unexpected finding, it is recommended where the examination is incomplete or the history of visual loss is unclear.
Proangiogenic Effects of Protease-Activated Receptor 2 Are Tumor Necrosis Factor-α and Consecutively Tie2 Dependent
Authors: Zhu Tang , Sennlaub Florian , Beauchamp Martin Hervé , Fan Li , Joyal Jean Sebastian , Checchin Daniella , Nim Satra , Lachapelle Pierre , Sirinyan Mirna , Hou Xin , Bossolasco Michela , Rivard Georges-Etienne , Heveker Nikolaus , Chemtob Sylvain 
Published: January 2006

Objective—Angiogenesis is essential physiologically in growth and pathologically in tumor development, chronic inflammatory disorders, and proliferative retinopathies. Activation of protease-activated receptor 2 (PAR2) leads to a proangiogenic response, but its mechanisms have yet to be specifically described. Here, we investigated the mode of action of PAR2 in retinal angiogenesis.Methods and Results—PAR2-activating peptide, SLIGRL, increased retinal angiogenesis associated with an induction of vascular endothelial growth factor and angiopoetin-2 and most notably tie2 in the retina in vivo as well as in cultured neuroretinal endothelial cells. SLIGRL also induced release of the proinflammatory and angiogenic mediator tumor necrosis factor-α (TNF-α) via the MEK/extracellular signal-regulated kinase (ERK) (MEK/ERK) pathway in these endothelial cells. TNF-α, in turn, elicited tie2 expression by activating the MEK/ERK pathway. PAR2-evoked tie2 expression, endothelium proliferation (in vitro), and retinal neovascularization (in vivo) were abrogated by selective TNF-α blockers (neutralizing antibody infliximab and soluble TNF-α receptor-Fc fusion protein etanercept) as well as the MEK inhibitor PD98059.Conclusion—The proangiogenic properties of PAR2 are intertwined with its proinflammatory effects, such that in retinal vasculature, they depend on TNF-α and subsequent induction of tie2 via the MEK/ERK pathway.
Angiotensin II Attenuates Endothelium-Dependent Responses in the Cerebral Microcirculation Through Nox-2–Derived Radicals
Authors: Girouard Helene , Park Laibaik , Anrather Josef , Zhou Ping , Iadecola Costantino 
Published: January 2006

Objective—Angiotensin II (Ang II) exerts deleterious effect on the cerebral circulation through production of reactive oxygen species (ROS). However, the enzymatic source of the ROS has not been defined. We tested the hypothesis that Ang II impairs endothelium-dependent responses in the cerebral microcirculation through ROS generated in cerebrovascular cells by the enzyme NADPH oxidase.Methods and Results—Cerebral blood flow (CBF) was monitored by laser Doppler flowmetry in anesthetized mice equipped with a cranial window. Ang II (0.25±0.02 μg/kg per minute for 30 to 45 minutes) attenuated the CBF increase produced by the endothelium-dependent vasodilators acetylcholine (−42±5%;P<0.05), bradykinin (−53±5%;P<0.05), and A23187 (−43±4%;P<0.05), and induced cerebrovascular ROS production, assessed by hydroethidine fluoromicrography. These actions of Ang II were prevented by losartan, by the ROS scavenger Mn(III) tetrakis (4-benzoic acid) porphyrin chloride (100 μmol/L), or by the NADPH oxidase peptide inhibitor gp91ds-tat (1 μmol/L), and were not observed in mice lacking the NADPH oxidase subunit gp91phox(nox-2).Conclusions—Ang II impairs the endothelial regulation of the cerebral microcirculation through AT1 receptor-mediated cerebrovascular oxidative stress. The source of the ROS is a nox-2-containing NADPH oxidase. These effects of Ang II could threaten the cerebral blood supply and contribute to the increased susceptibility to stroke and dementia associated with hypertension.
Rapid TNFR1-dependent lymphocyte depletion in vivo with a selective chemical inhibitor of IKKβ
Authors: Nagashima Kumiko , Sasseville Vito G. , Wen Danyi , Bielecki Andrew , Yang Hua , Simpson Chris , Grant Ethan , Hepperle Michael , Harriman Gerry , Jaffee Bruce , Ocain Tim , Xu Yajun , Fraser Christopher C. 
Published: January 2006

AbstractThe transcription factor NF-κB plays a central role in regulating inflammation and apoptosis, making it a compelling target for drug development. We identified a small molecule inhibitor (ML120B) that specifically inhibits IKKβ, an Ikappa-B kinase that regulates NF-κB. IKKβ and NF-κB are required in vivo for prevention of TNFα-mediated apoptosis. ML120B sensitized mouse bone marrow progenitors and granulocytes, but not mature B cells to TNFα killing in vitro, and induced apoptosis in vivo in the bone marrow and spleen within 6 hours of a single oral dose. In vivo inhibition of IKKβ with ML120B resulted in depletion of thymocytes and B cells in all stages of development in the bone marrow but did not deplete granulocytes. TNF receptor–deficient mouse thymocytes and B cells were resistant to ML120B-induced depletion in vivo. Surprisingly, surviving bone marrow granulocytes expressed TNFR1 and TNFR2 after dosing in vivo with ML120B. Our results show that inhibition of IKKβ with a small molecule in vivo leads to rapid TNF-dependent depletion of T and B cells. This observation has several implications for potential use of IKKβ inhibitors for the treatment of inflammatory disease and cancer.
Loss of NAD(H) from swollen yeast mitochondria
Authors: Bradshaw Patrick C , Pfeiffer Douglas R 
Published: January 2006

Abstract

Background
The mitochondrial electron transport chain oxidizes matrix space NADH as part of the process of oxidative phosphorylation. Mitochondria contain shuttles for the transport of cytoplasmic NADH reducing equivalents into the mitochondrial matrix. Therefore for a long time it was believed that NAD(H) itself was not transported into mitochondria. However evidence has been obtained for the transport of NAD(H) into and out of plant and mammalian mitochondria. Since Saccharomyces cerevisiae mitochondria can directly oxidize cytoplasmic NADH, it remained questionable if mitochondrial NAD(H) transport occurs in this organism.

Results
NAD(H) was lost more extensively from the matrix space of swollen than normal, condensed isolated yeast mitochondria from Saccharomyces cerevisiae. The loss of NAD(H) in swollen organelles caused a greatly decreased respiratory rate when ethanol or other matrix space NAD-linked substrates were oxidized. Adding NAD back to the medium, even in the presence of a membrane-impermeant NADH dehydrogenase inhibitor, restored the respiratory rate of swollen mitochondria oxidizing ethanol, suggesting that NAD is transported into the matrix space. NAD addition did not restore the decreased respiratory rate of swollen mitochondria oxidizing the combination of malate, glutamate, and pyruvate. Therefore the loss of matrix space metabolites is not entirely specific for NAD(H). However, during NAD(H) loss the mitochondrial levels of most other nucleotides were maintained. Either hypotonic swelling or colloid-osmotic swelling due to opening of the yeast mitochondrial unspecific channel (YMUC) in a mannitol medium resulted in decreased NAD-linked respiration. However, the loss of NAD(H) from the matrix space was not mediated by the YMUC, because YMUC inhibitors did not prevent decreased NAD-linked respiration during swelling and YMUC opening without swelling did not cause decreased NAD-linked respiration.

Conclusion
Loss of endogenous NAD(H) from isolated yeast mitochondria is greatly stimulated by matrix space expansion. NAD(H) loss greatly limits NAD-linked respiration in swollen mitochondria without decreasing the NAD-linked respiratory rate in normal, condensed organelles. NAD addition can totally restore the decreased respiration in swollen mitochondria. In live yeast cells mitochondrial swelling has been observed prior to mitochondrial degradation and cell death. Therefore mitochondrial swelling may stimulate NAD(H) transport to regulate metabolism during these conditions.
CoSMoS: Conserved Sequence Motif Search in the proteome
Authors: Liu Xiao I , Korde Neeraj , Jakob Ursula , Leichert Lars I 
Published: January 2006

Abstract

Background
With the ever-increasing number of gene sequences in the public databases, generating and analyzing multiple sequence alignments becomes increasingly time consuming. Nevertheless it is a task performed on a regular basis by researchers in many labs.

Results
We have now created a database called CoSMoS to find the occurrences and at the same time evaluate the significance of sequence motifs and amino acids encoded in the whole genome of the model organism Escherichia coli K12. We provide a precomputed set of multiple sequence alignments for each individual E. coli protein with all of its homologues in the RefSeq database. The alignments themselves, information about the occurrence of sequence motifs together with information on the conservation of each of the more than 1.3 million amino acids encoded in the E. coli genome can be accessed via the web interface of CoSMoS.

Conclusion
CoSMoS is a valuable tool to identify highly conserved sequence motifs, to find regions suitable for mutational studies in functional analyses and to predict important structural features in E. coli proteins.
m-Calpain is required for preimplantation embryonic development in mice
Authors: Dutt Previn , Croall Dorothy E , Arthur J Simon C , De Veyra Teresa , Williams Karen , Elce John S , Greer Peter A 
Published: January 2006

Abstract

Background
μ-calpain and m-calpain are ubiquitously expressed proteases implicated in cellular migration, cell cycle progression, degenerative processes and cell death. These heterodimeric enzymes are composed of distinct catalytic subunits, encoded by Capn1 (μ-calpain) or Capn2 (m-calpain), and a common regulatory subunit encoded by Capn4. Disruption of the mouse Capn4 gene abolished both μ-calpain and m-calpain activity, and resulted in embryonic lethality, thereby suggesting essential roles for one or both of these enzymes during mammalian embryogenesis. Disruption of the Capn1 gene produced viable, fertile mice implying that either m-calpain could compensate for the loss of μ-calpain, or that the loss of m-calpain was responsible for death of Capn4
-/- mice.

Results
To distinguish between the alternatives described above, we deleted an essential coding region in the mouse Capn2 gene in embryonic stems cells and transmitted this mutant allele through the mouse germline. Breeding of heterozygous animals failed to produce homozygous mutant live offspring or implanted embryos. A nested PCR genotyping protocol was established, and homozygous preimplantation mutant embryos were detected at the morula but not at the blastocyts stage.

Conclusion
We conclude that homozygous disruption of the Capn2 gene results in pre-implantation embryonic lethality between the morula and blastocyst stage. This establishes that μ-calpain and m-calpain have distinct functions, and that m-calpain is vital for development of the preimplantation murine embryo.
Colour variation in red grapevines (Vitis vinifera L.): genomic organisation, expression of flavonoid 3'-hydroxylase, flavonoid 3',5'-hydroxylase genes and related metabolite profiling of red cyanidin-/blue delphinidin-based anthocyanins in berry skin
Authors: Castellarin Simone D , Di Gaspero Gabriele , Marconi Raffaella , Nonis Alberto , Peterlunger Enrico , Paillard Sophie , Adam-Blondon Anne-Francoise , Testolin Raffaele 
Published: January 2006

AbstractBackgroundStructural genes of the phenyl-propanoid pathway which encode flavonoid 3'- and 3',5'-hydroxylases (F3'H and F3'5'H) have long been invoked to explain the biosynthesis of cyanidin- and delphinidin-based anthocyanin pigments in the so-called red cultivars of grapevine. The relative proportion of the two types of anthocyanins is largely under genetic control and determines the colour variation among red/purple/blue berry grape varieties and their corresponding wines.ResultsGene fragments ofVvF3'HandVvF3'5'H, that were isolated fromVitis vinifera'Cabernet Sauvignon' using degenerate primers designed on plant homologous genes, translated into 313 and 239 amino acid protein fragments, respectively, with up to 76% and 82% identity to plant CYP75 cytochrome P450 monooxygenases. Putative function was assigned on the basis of sequence homology, expression profiling and its correlation with metabolite accumulation at ten different ripening stages. At the onset of colour transition, transcriptional induction ofVvF3'HandVvF3'5'Hwas temporally coordinated with the beginning of anthocyanin biosynthesis, the expression being 2-fold and 50-fold higher, respectively, in red berries versus green berries. The peak ofVvF3'5'Hexpression was observed two weeks later concomitantly with the increase of the ratio of delphinidin-/cyanidin-derivatives. The analysis of structural genomics revealed that two copies ofVvF3'Hare physically linked on linkage group no. 17 and several copies ofVvF3'5'Hare tightly clustered and embedded into a segmental duplication on linkage group no. 6, unveiling a high complexity when compared to other plant flavonoid hydroxylase genes known so far, mostly in ornamentals.ConclusionWe have shown that genes encoding flavonoid 3'- and 3',5'-hydroxylases are expressed in any tissues of the grape plant that accumulate flavonoids and, particularly, in skin of ripening red berries that synthesise mostly anthocyanins. The correlation between transcript profiles and the kinetics of accumulation of red/cyanidin- and blue/delphinidin-based anthocyanins indicated thatVvF3'HandVvF3'5'Hexpression is consistent with the chromatic evolution of ripening bunches. Local physical maps constructed around theVvF3'HandVvF3'5'Hloci should help facilitate the identification of the regulatory elements of each isoform and the future manipulation of grapevine and wine colour through agronomical, environmental and biotechnological tools.
Simultaneous detection of Fusarium culmorum and F. graminearum in plant material by duplex PCR with melting curve analysis
Authors: Brandfass Christoph , Karlovsky Petr 
Published: January 2006

Abstract

Background
Fusarium head blight (FHB) is a disease of cereal crops, which has a severe impact on wheat and barley production worldwide. Apart from reducing the yield and impairing grain quality, FHB leads to contamination of grain with toxic secondary metabolites (mycotoxins), which pose a health risk to humans and livestock. The Fusarium species primarily involved in FHB are F. graminearum and F. culmorum. A key prerequisite for a reduction in the incidence of FHB is an understanding of its epidemiology.

Results
We describe a duplex-PCR-based method for the simultaneous detection of F. culmorum and F. graminearum in plant material. Species-specific PCR products are identified by melting curve analysis performed in a real-time thermocycler in the presence of the fluorescent dye SYBR Green I. In contrast to multiplex real-time PCR assays, the method does not use doubly labeled hybridization probes.

Conclusion
PCR with product differentiation by melting curve analysis offers a cost-effective means of qualitative analysis for the presence of F. culmorum and F. graminearum in plant material. This method is particularly suitable for epidemiological studies involving a large number of samples.