bluuebunny/crossref_metadata_2025_split huggingface dataset:
Non-parametric quantification of protein lysate arrays
Authors: Hu Jianhua , He Xuming , Baggerly Keith A. , Coombes Kevin R. , Hennessy Bryan T.J. , Mills Gordon B. 
Published: June 2007

AbstractMotivation: Proteins play a crucial role in biological activity, so much can be learned from measuring protein expression and post-translational modification quantitatively. The reverse-phase protein lysate arrays allow us to quantify the relative expression levels of a protein in many different cellular samples simultaneously. Existing approaches to quantify protein arrays use parametric response curves fit to dilution series data. The results can be biased when the parametric function does not fit the data.Results: We propose a non-parametric approach which adapts to any monotone response curve. The non-parametric approach is shown to be promising via both simulation and real data studies; it reduces the bias due to model misspecification and protects against outliers in the data. The non-parametric approach enables more reliable quantification of protein lysate arrays.Availability: Code to implement the proposed method in the statistical package R is available at: http://odin.mdacc.tmc.edu/jhu/lysatearray-analysis/Contact: jhu@mdanderson.orgSupplementary information: Supplementary data are available at Bioinformatics online.
A Higher Plant Δ8 Sphingolipid Desaturase with a Preference for (Z)-Isomer Formation Confers Aluminum Tolerance to Yeast and Plants
Authors: Ryan Peter R. , Liu Qing , Sperling Petra , Dong Bei , Franke Stefan , Delhaize Emmanuel 
Published: June 2007

Abstract
Three plant cDNA libraries were expressed in yeast (Saccharomyces cerevisiae) and screened on agar plates containing toxic concentrations of aluminum. Nine cDNAs were isolated that enhanced the aluminum tolerance of yeast. These cDNAs were constitutively expressed in Arabidopsis (Arabidopsis thaliana) and one cDNA from the roots of Stylosanthes hamata, designated S851, conferred greater aluminum tolerance to the transgenic seedlings. The protein predicted to be encoded by S851 showed an equally high similarity to Δ6 fatty acyl lipid desaturases and Δ8 sphingolipid desaturases. We expressed other known Δ6 desaturase and Δ8 desaturase genes in yeast and showed that a Δ6 fatty acyl desaturase from Echium plantagineum did not confer aluminum tolerance, whereas a Δ8 sphingobase desaturase from Arabidopsis did confer aluminum tolerance. Analysis of the fatty acids and sphingobases of the transgenic yeast and plant cells demonstrated that S851 encodes a Δ8 sphingobase desaturase, which leads to the accumulation of 8(Z/E)-C18-phytosphingenine and 8(Z/E)-C20-phytopshingenine in yeast and to the accumulation of 8(Z/E)-C18-phytosphingenine in the leaves and roots of Arabidopsis plants. The newly formed 8(Z/E)-C18-phytosphingenine in transgenic yeast accounted for 3 mol% of the total sphingobases with a 8(Z):8(E)-isomer ratio of approximately 4:1. The accumulation of 8(Z)-C18-phytosphingenine in transgenic Arabidopsis shifted the ratio of the 8(Z):8(E) isomers from 1:4 in wild-type plants to 1:1 in transgenic plants. These results indicate that S851 encodes the first Δ8 sphingolipid desaturase to be identified in higher plants with a preference for the 8(Z)-isomer. They further demonstrate that changes in the sphingolipid composition of cell membranes can protect plants from aluminum stress.
Long-Term Response toward Inorganic Carbon Limitation in Wild Type and Glycolate Turnover Mutants of the Cyanobacterium Synechocystis sp. Strain PCC 6803
Authors: Eisenhut Marion , von Wobeser Eneas Aguirre , Jonas Ludwig , Schubert Hendrik , Ibelings Bas W. , Bauwe Hermann , Matthijs Hans C.P. , Hagemann Martin 
Published: June 2007

Abstract
Concerted changes in the transcriptional pattern and physiological traits that result from long-term (here defined as up to 24 h) limitation of inorganic carbon (Ci) have been investigated for the cyanobacterium Synechocystis sp. strain PCC 6803. Results from reverse transcription-polymerase chain reaction and genome-wide DNA microarray analyses indicated stable up-regulation of genes for inducible CO2 and HCO3 − uptake systems and of the rfb cluster that encodes enzymes involved in outer cell wall polysaccharide synthesis. Coordinated up-regulation of photosystem I genes was further found and supported by a higher photosystem I content and activity under low Ci (LC) conditions. Bacterial-type glycerate pathway genes were induced by LC conditions, in contrast to the genes for the plant-like photorespiratory C2 cycle. Down-regulation was observed for nitrate assimilation genes and surprisingly also for almost all carboxysomal proteins. However, for the latter the observed elongation of the half-life time of the large subunit of Rubisco protein may render compensation. Mutants defective in glycolate turnover (ΔglcD and ΔgcvT) showed some transcriptional changes under high Ci conditions that are characteristic for LC conditions in wild-type cells, like a modest down-regulation of carboxysomal genes. Properties under LC conditions were comparable to LC wild type, including the strong response of genes encoding inducible high-affinity Ci uptake systems. Electron microscopy revealed a conspicuous increase in number of carboxysomes per cell in mutant ΔglcD already under high Ci conditions. These data indicate that an increased level of photorespiratory intermediates may affect carboxysomal components but does not intervene with the expression of majority of LC inducible genes.
Solution structure of the general transcription factor 2I domain in mouse TFII‐I protein
Authors: Doi‐Katayama Yukiko , Hayashi Fumiaki , Inoue Makoto , Yabuki Takashi , Aoki Masaaki , Seki Eiko , Matsuda Takayoshi , Kigawa Takanori , Yoshida Mayumi , Shirouzu Mikako , Terada Takaho , Hayashizaki Yoshihide , Yokoyama Shigeyuki , Hirota Hiroshi 
Published: June 2007

AbstractThe general transcription factor TFII‐I, with the corresponding gene name GTF2I, is an unusual transcriptional regulator that associates with both basal and signal‐induced transcription factors. TFII‐I consists of six GTF2I repeat domains, called I‐repeats R1–R6. The structure and function of the GTF2I domain are not clearly understood, even though it contains a helix‐loop‐helix motif, which is considered to be the protein–protein interaction area, based on biochemical analyses. Here, we report the solution structure of the fifth repeat of the six GTF2I repeat domains from murine TFII‐I, which was determined by heteronuclear multidimensional NMR spectroscopy (PDB code 1Q60). The three‐dimensional structure of the GTF2I domain is classified as a new fold, consisting of four helices (residues 8–24, 34–39, 63–71, and 83–91), two antiparallel beta strands (residues 44–47 and 77–80), and a well‐defined loop containing two β‐turns between sheet 1 and helix 3. All of the repeats probably have similar folds to that of repeat 5, because the conserved residues in the GTF2I repeat domains are assembled on the hydrophobic core, turns, and secondary structure elements, as revealed by a comparison of the sequences of the first through the sixth GTF2I repeats in TFII‐I.
The administration of desmopressin by nasal spray: a dose‐determination study in patients with mild haemophilia A or von Willebrand's disease
Authors: LETHAGEN S. , EGERVALL K. , BERNTORP E. , BENGTSSON B. 
Published: June 2007

SummaryDesmopressin is an important haemostatic agent in many types of bleeding disorders. The intranasal route for administration of desmopressin has attracted much interest because it is convenient and makes self‐treatment possible. In the present study the effects of three doses (300, 450 and 600 μg) of desmopressin delivered by nasal spray and those of 0.3 μg/kg injected intravenously were compared in five patients with haemophilia A and 11 with von Willebrand's disease. There was no statistically significant difference in peak VIII:C concentration in the haemophilia patients and no difference in peak vWF concentration in von Willebrand patients between the four desmopressin dosages. Bleeding time response was comparable after all four dosages. We recommend a spray dosage of 300 μg for home treatment. As cover for major surgery or in connection with severe bleedings, however, intravenous administration is to be recommended.
Implementation of a nurse practitioner policy for the requisition and administration of drugs in a haemophilia comprehensive care centre
Authors: CAHILL M. R. , WOOSEY C. P. , HAYDEN S. M. , Mac Clean M. , Colvin B. T. 
Published: June 2007

Summary The evolution of comprehensive care centres for haemophilia has altered the work of those involved in the care of haemophilia patients. The role of the haemophilia sister has expanded and the concept of the haemophilia nurse specialist has emerged.We describe the implementation of a local policy which has enabled haemophilia nurse specialists to requisition and administer clotting factor concentrates, DDAVP, tranexamic acid and hepatitis vaccines independently, in hospital and community settings. Since the introduction of this policy on 2 August 1994, prescribing practice has not changed in the haemophilia centre, nor has the involvement of medical staff in the care of haemophilia patients. This approach is widely applicable in other centres and should be a logical progression of the haemophilia nurse specialist's role.
Low‐dose activated factor IX complex concentrates (FEIBAR) for post‐operative haemostasis in a patient with high responding factor VIII inhibitors
Authors: BHAVE A. , SRIVASTAVA A. , LEE V. , DANIEL A. J. , DENNISON D. , SUNDERAJ G. D. , SUDARSANAM A. 
Published: June 2007

Replacement therapy in patients with severe haemophilia A is associated with the development of inhibitory antibodies in about 15% [1,2]. The presence of inhibitors of factor VIII greatly complicates and compromises the treatment of these patients because of the lack of any completely satisfactory product to treat them. Haemostatic management for surgery in patients with inhibitors is very difficult. A product frequently used to treat bleeding episodes in such patients is prothrombin complex concentrate (PCC) [3] or its activated derivative (APCC) [4]. Activated recombinant human factor VII is another option [5]. For both these modalities of treatment, there are no laboratory tests that can be used to monitor clinical efficacy [5, 6]. Porcine factor VII is therefore the preferred product for surgery in patients with high‐responding factor VIII inhibitors [7]. Unfortunately, none of these products are readily available in most developing countries, including India.We report the management of a patient with high‐responding factor VIII inhibitor using low doses of FEIBAR (Immuno, Austria) in the post‐operative period.
Current strategy for genetic analysis of haemophilia A families
Authors: DARDIK RIMA , PERETZ HAVA , USHER SALI , SELIGSOHN URI , MARTINOWITZ URI 
Published: June 2007

Summary. Carrier detection and prenatal diagnosis of haemophilia A, which was based in the last decade mainly on linkage polymorphism analysis, has been greatly facilitated by the recent discovery that two types of inversion disrupting the factor VIII gene are common mutations observed in 42–48% of severe haemophilia A cases. In this study DNA analysis was performed in 64 unrelated severe haemophilia A patients and 173 women belonging to their families, and in four women from a family with a deceased haemophilic relative whose DNA was unavailable (a total of 177 females from 65 unrelated families). Factor VIII gene inversions were found in 32 out of the 65 families (49%), 29 involving recombination with the distal A gene and three with the proximal A gene. Definitive information regarding carriership of haemophilia was provided to all 81 women belonging to the 32 inversion‐positive families, among them one woman previously uninformative for any of the polymorphisms examined, five women who were informative only for extragenic polymorphisms, and four suspected carriers who were relatives of the deceased haemophiliac. In 33 inversion‐negative families, 96 females were examined by analysis of the BclI restriction fragment length polymorphism (RFLP) in intron 18 and of the multiallelic dinucleotide repeats in introns 13 and 22, followed by analysis of other intragenic polymorphisms. This procedure yielded an informativity rate of almost 100%. Of the 96 females examined by linkage polymorphism analysis, 78 belonged to 25 families with more than one haemophiliac and 29 of them were obligate carriers. In 47 of the 49 suspected carriers linkage polymorphism analysis enabled definition of carriership based on intragenic polymorphisms. 18 of the 96 females belonged to eight families with sporadic haemophilia cases and only eight of the 18 suspected carriers could be diagnosed by exclusion.In nine pregnant women carrying factor VIII gene inversions, mRNA extracted from chorionic villus samples (CVS) was analysed for factor VIII gene inversion by reverse transcription/polymerase chain reaction (RT/PCR). This procedure enabled rapid prenatal diagnoses in six male fetuses. Taken together, our data indicate that a high rate of informativity and carrier definition is possible by the strategy of first screening for factor VIII gene inversions, and, if none are found, sequential use of highly informative intragenic polymorphisms, followed by less informative intragenic and extragenic polymorphisms.
Topoedaphic and morphological complexity of foliar damage and mortality within western juniper (Juniperus occidentalis var. occidentalis) woodlands following an extreme meteorological event
Authors: Soulé Peter T. , Knapp Paul A. 
Published: June 2007

AbstractAim  An extreme early season freeze event in October 2002 resulted in significant foliar damage and/or mortality within western juniper woodlands. We identify the geographical patterns of tree damage based on morphological, topographical and edaphic parameters, and discuss the ecological implications of this event.Location  Oregon, USA (44.0–44.2° N, 120.3–120.9° W).Methods  We sampled trees on four matched pairs of disturbed and minimally disturbed study sites within the core area of tree damage. We collected information about age, morphology (height, basal area, level of foliar damage), and topographic position (elevation, slope, aspect) for each tree sampled using dendroecological and GPS/GIS procedures. We collected plot‐level data on tree density and degree of cover for shrubs and grasses. We used a series of Mann–Whitney, Kruskal–Wallis and Wilcoxon tests and graphical analyses to determine if significant differences exist in our collected variables both between matched pairs and within our disturbed sites.Results  Topographically, we found that aspect was a critical element regulating damage, with trees in colder microenvironments (north‐westerly slopes) experiencing less damage because they were further along in the annual process of cold‐hardening. The majority of damaged trees were found in areas of higher density and more even age structure that are typical of recent juniper afforestation. Morphologically, we show that trees with greater basal areas and/or less stature were less likely to have foliar damage, consistent with winter cavitation.Main conclusions  Our results show that the spatial pattern of damage was closely related to topography and tree morphology, parameters that, in turn, correspond closely to differences between the historical locales of western juniper and juniper woodlands that have emerged in a 100+ year period of rapid afforestation. This freeze event fits the criteria for a large, infrequent disturbance in that it was spatially complex and may act as an endogenous factor that can contribute to stand maintenance.
Omega‐3 fatty acid regulates inflammatory cytokine/mediator messenger RNA expression in Porphyromonas gingivalis‐induced experimental periodontal disease
Authors: Kesavalu L. , Bakthavatchalu V. , Rahman M. M. , Su J. , Raghu B. , Dawson D. , Fernandes G. , Ebersole J. L. 
Published: June 2007

Introduction:  Porphyromonas gingivalis is strongly implicated in the etiology of adult periodontitis by inducing inflammatory cytokines, resulting in gingival and periodontal tissue inflammation and alveolar bone resorption. This study tested the hypothesis that supplementing the diet with omega‐3 fatty acid (ω‐3 FA; i.e. fish oil) would exert anti‐inflammatory effects in the gingival tissues of P. gingivalis‐infected rats.Methods:  Rats were fed either fish oil or corn oil diets ad libitum for 22 weeks and infected with P. gingivalis strain 381 or strain A7A1‐28. After sacrifice, rat gingival tissues were excised and the RNA was isolated and analyzed for proinflammatory mediators [interleukin‐1β (IL‐1β), tumor necrosis factor‐α (TNF‐α), IL‐6], T helper type 1 and type 2 cytokines [interferon‐γ (IFN‐γ), IL‐4, IL‐10), antioxidant enzymes [catalase (CAT), superoxide dismutase (SOD)], and genes critical for eicosanoid mediator production [cyclo‐oxygenase‐2 (COX‐2), 5‐lipoxygenase (5‐LO)] by reverse transcription‐polymerase chain reaction using rat‐specific primers.Results:  Rats on the ω‐3 FA diet exhibited decreased proinflammatory cytokine gene expression (IL‐1β, TNF‐α) and enhanced IFN‐γ, CAT and SOD messenger RNA expression compared to rats fed a corn oil diet, supporting a diet‐induced modulation of host inflammatory reactions. Analyses of alveolar bone resorption in the rats related to gene expression profiles demonstrated significant positive correlations with IL‐1β, IL‐6 and COX‐2 and negative correlations with CAT and SOD.Conclusion:  These findings suggest that diets enriched for ω‐3 FA modulate the local gingival inflammatory milieu of the host following oral P. gingivalis infection, which impacts on alveolar bone resorption in rats.
Adrenal Cortex of the Dog (Canis familiaris): I. Histomorphologic Changes during Growth, Maturity, and Aging1
Authors: Hullinger Ronald L. 
Published: June 2007

AbstractThe adrenal glands of 56 dogs ranging in age from birth to 13.6 years were examined for a determination of normal zonal and cellular morphology patterns throughout development, maturity and aging. Routine light microscopic techniques as well as lipid and cholesterol staining were used. The zona arcuata is described as developing between the fibrous and cellular layers of the capsule forming the cortical blastema layer, a zona biproliferativa. It is proposed that both centrifugal and centripetal migration of cortical parenchyma can result. The formation of accessory nodules is described as compensatory hyperplasia. Histomorphometric analysis revealed growth in the zona fasciculata to be by hyperplasia and the zonal volume percentages to be arcuata, 27%; fasciculata, 50%; reticularis, 23%.
Prenatal Dental Development in the Dog, Canis familiaris: Chronology of Tooth Germ Formation and Calcification of Deciduous Teeth
Authors: Williams R. C. , Evans H. E. 
Published: June 2007

AbstractObservations on a sizeable collection of purebred canine fetuses of known age has afforded the opportunity to report baseline data on the timing of tooth germ development in the dog. The chronology of development of the deciduous dentition has been studied in a collection of 172 embryos and fetuses from purebred Beagles of known gestation. Microscopic examination of serial sections, enlarged reconstructions from serial sections and alizarin‐stained clearings were used to visualize stages of development. These observations establish that the dental lamina is initiated at 25 days gestation and that calcification begins at 42 days in the deciduous teeth.
Ultrastructural Observations on the Tapetum lucidum fibrosum
Authors: Bortolami R. , Callegari E. , Lucchi M. L. 
Published: June 2007

AbstractThe ultrastructural comparison made between the tapetum cellulosum of the cat and the tapetum fibrosum of the sheep has shown that the rods and the collagen fibrils have the same diameters and the same spatial arrangement.
Blastocystenimplantation bei der Hauskatze Lidit‐ und elektronenmikroskopisdie Untersuchung*
Authors: Leiser R. 
Published: June 2007

SummaryBlastocyst implantation in the domestic cat A light and electronmicroscopic investigationImplantation in the cat begins 121/2 days post coitum and lasts to the 14th day. Several hours before implantation begins the extraembryonic trophoblast, in what could be considered a precontact or sensitization phase, shows fine structural evidence of secretory activity. The uterine epithelium at the same times gives evidence of being at first resorptive and, after a differentiation, of being secretory. Secretion also in the gland epithelium can be observed.The attachment of the embryo to the endometrium begins with an appositional phase. The trophoblast is now distinctly resorptive and forms with the uterine epithelium microvilli‐free areas of contact lying between the openings of the uterine glands. Then follows an adhesion phase during which additional junctional complexes are formed between an actively proliferating trophoblast and the uterine epithelium which shows now symplasmic differentiation. Finally, in the intrusion phase the uterine epithelium completely disintegrates. In this manner the syncytiotrophoblast which differentiates from the cytotrophoblast invades the maternal tissues until it reaches the endothelium of the uterine blood vessels.
Die Entwicklung des Plazentastieles beim Meerschweinchen
Authors: Uhlendorf Brigitte , Kaufmann Peter 
Published: June 2007

AbstractAs basis for detailed studies into the significance of the guinea pig subplacenta the formal development of the placental stalk which contains the subplacenta in its center was investigated in this species. Fifty conventional, domesticated, genetically undefined guinea pigs pregnant 8–63 days were used. The placentas were studied on semi‐thin and paraffin sections on some of which morphometric observations were made. The findings provide the first three‐dimensional picture of the subplacenta and give information of its development. The studies show that this region has neither a growth function nor a maternofetal transport function.
Studies on the Development of the Fetal and Neonatal Bovine Stomach
Authors: Kano Yutaka , Fukaya Kosaku , Asari Masao , Eguchi Yasunobu 
Published: June 2007

Abstract37 Holstein fetuses and 5 newborn holstein calves were used in a study of the development and neonatal anatomy of the bovine stomach. Care was taken to prevent alterations in pulmonary volume and modification of topographic relationships between stomach compartments. Polymerized synthetic polyester resin was used to form anatomic casts of stomach compartments. This technique provided the basis for a description of relative sizes and relationships of stomach compartments and the nature of the mucosal surfaces.
Consideraciones sobre el sistema urinario del Gallus gallus– Indian River; I. Formación y tributaris del uréter
Authors: Dias Por S. Mello , Silva P. Pinto , Campos V. J. M. , Orsi A. M. , Dayoub M. C. Oliveira , Define R. M. 
Published: June 2007

AbstractIn the literature reviewed, there are certain differences of opinion with regard to the formation and tributareis to the ureter. Therefore, dissection of 40 fowls injected with neoprene latex, k neoprene latex and celobar (radiopaque mass) and vinyl acetate casts through the ureter and blood vessels revealed the formation and disposition of the tributaries to the ureter, and its origin and number of collectors. The results were described in relation to the renal lobes.