bluuebunny/crossref_metadata_2025_split huggingface dataset:
Drei‐Front‐Konfigurationen mit Energiezufuhr
Authors: Rues D. 
Published: June 2007

AbstractEs werden die verschiedenen Möglichkeiten der Energiezufuhr auf Diskontinuitätsflächen in einer Überschallparallelströmung betrachtet. Dabei zeigt sich, daß die Energiezufuhr auf einer Front unter gleichzeitiger Ausbildung nur einer Stoßwelle nicht möglich ist, sondern daß sich zusätzlich zu der Energiefront noch mindestens zwei Stoßfronten ausbilden müssen. Für eine Anströmmachzahl M∞ = 10 und eine Energiezufuhr qi/W = 0,1 werden die verschiedenen möglichen Frontwinkel sowie die Drücke und die Stromlinienwinkel hinter den Fronten berechnet. Für einige Bereiche ergeben sich dabei mehrere Lösungen, während für andere, wozu natürlich auch der Choking‐Bereich gehört, keine stationären Lösungen existieren.
Ein einfaches Modell zur Berechnung von Vertikalschwingungen im inhomogenen linear elastischen Halbraum
Authors: Schimmerl J. 
Published: June 2007

AbstractEin elastisch isotroper inhomogener Halbraum soll durch ein einachsig zylindersymmetrisches Modell so ersetzt werden, daß er bei Schwingungen ein möglichst analoges Verhalten zeigt. Dies wird so erreicht, daß für den gegebenen veränderlichen Elastizitätsmodul E(z) die zugehörige Querschnittsfläche F(z) gesucht wird, die das dispersionsfreie Modell charakterisiert. Neben der Berechnung der Spannung σ, der Verschiebung w und der Amplitude W bei Schwingungen eines Fundaments auf dem inhomogenen Halbraum wird die Möglichkeit der Bestimmung von Bodenkennziffern aus charakteristischen Meßkurven angedeutet.
Selective COX‐2 Inhibitors, Eicosanoid Synthesis and Clinical Outcomes: A Case Study of System Failure
Authors: James M. J. , Cook‐Johnson R. J. , Cleland L. G. 
Published: June 2007

AbstractElucidation of differences between the active sites of COX‐1 and COX‐2 allowed the targeted design of the selective COX‐2 inhibitors known as coxibs. They were marketed as non‐steroidal anti‐inflammatory drugs (NSAIDs) that had improved upper gastrointestinal (GI) safety compared with older non‐selective NSAIDs such as diclofenac and naproxen. Two GI safety studies conducted with arthritis patients demonstrated that in terms of upper GI safety, celecoxib was not superior to diclofenac (CLASS study) but rofecoxib was superior to naproxen (VIGOR study). However, the VIGOR study revealed also that rofecoxib had increased cardiovascular (CV) risk compared with naproxen. This clinical outcome was supported by the existence of plausible eicosanoid‐based biological mechanisms whereby selective COX‐2 inhibition could increase CV risk. Nevertheless, the existence of CV risk with rofecoxib was successfully discounted by its pharmaceutical company owner, Merck & Co, with the assistance of specialist opinion leaders and rofecoxib achieved widespread clinical use for 4–5 years. Rofecoxib was withdrawn from the market when several clinical trials in colorectal cancer and post‐operative pain revealed increased CV risk with not only rofecoxib, but also coxibs. The commercial success of rofecoxib provides a case‐study of failure of the medical journal literature to guide drug usage. Attention to ethical issues may have provided a more useful guide for prescribers.
Production of 14‐Oxo‐cis‐11‐eicosenoic Acid from Lesquerolic Acid by Sphingobacterium multivorum NRRL B‐23212
Authors: Kuo Tsung Min , Isbell Terry A. , Rooney Alejandro , Levinson William E. , Frykman Hans 
Published: June 2007

AbstractThe objective of this study was to explore the extent of microbial conversion of lesquerolic acid (14‐hydroxy‐cis‐11‐eicosenoic acid; LQA) by whole cell catalysis and to identify the newly converted products. Among compost isolates including NRRL strains B‐23212 (Sphingobacterium multivorum), B‐23213 (Acinetobacter sp.), B‐23257 (Enterobacter cloacae B), B‐23259 (Escherichia sp.) and B‐23260 (Pseudomonas aeruginosa) the S.multivorum strain was the only microorganism that converted LQA to produce a new product identified as 14‐oxo‐cis‐11‐eicosenoic acid by GC‐MS and NMR analyses. The conversion yield was 47.4% in 48 h at 200 rpm and 28°C in small shake flask experiments. In comparison, both Acinetobacter and Pseudomonas strains failed to convert LQA to major new products but used LQA apparently as an energy source during fermentation. For structural analysis, 6.88 g of 14‐oxo‐cis‐11‐eicosenoic acid was produced from converting 11 g LQA (a 62% yield) in 72 h at 200 rpm and 28 °C in Fernbach flasks using 18‐h‐old NRRL B‐23212 cultures and an improved medium that also contained EDTA and glycerol in lieu of glucose as carbon source. NRRL B‐23212 was further identified by 16S rRNA gene sequence analysis as a unique strain of S. multivorum. Therefore, S. multivorum NRRL B‐23212 possesses an enzymatic activity presumably a secondary alcohol dehydrogenase for converting LQA to produce 14‐oxo‐cis‐11‐eicosenoic acid, a first report that demonstrates the functional modification of LQA by whole cell catalysis.
Excision of the tricuspid valve in a baby with Candida endocarditis
Authors: du Plessis Frederik A. , Helbing Willem A. , Bogers Ad J.J.C. 
Published: June 2007

AbstractWe report on the management of Candida endocarditis in a 5-month old infant. The orifice of the tricuspid valve was totally obstructed, and the tension apparatus of the valve destroyed. Excision of the valve led to severe failure of the right heart. The combined use of anti-failure treatment, and reduction of right ventricular afterload with oxygen, nitric oxide and sildenafil, proved successful.
Parenteral long-acting amoxicillin reduces intestinal bacterial community diversity in piglets even 5 weeks after the administration
Authors: Janczyk Pawel , Pieper Robert , Souffrant Wolfgang Bernhard , Bimczok Diane , Rothkötter Hermann-Josef , Smidt Hauke 
Published: June 2007

AbstractWe investigated the long-term effects of a single intramuscular administration of amoxicillin (15 mg kg−1) 1 day after birth, on piglet intestinal microbiota. Animals received no creep feed before weaning on day 28 of age. For the next 11 days, the piglets received a wheat–barley-based diet. Colon digesta samples were collected on day 39 and subjected to denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene fragments. DGGE fingerprint diversity indices differed between the group treated with amoxicillin and the untreated group (0.8±0.19 and 1.03±0.17, respectively, P=0.012). Reamplification and sequencing of two bands present in all samples revealed that a Roseburia faecalis-related population was strongly reduced in relative abundance (98% identity) in the treated group, while an enterobacterial population with 100% identity to Shigella spp., Escherichia coli and Salmonella enterica serovar Typhi was enriched. A band corresponding to Lactobacillus sobrius was present only in the control group. The protective effect of prophylactic antibiotic administration may be outweighed by the long-lasting disturbance of the gut ecosystem.
Bayesian modelling of shared gene function
Authors: Sykacek P. , Clarkson R. , Print C. , Furlong R. , Micklem G. 
Published: June 2007

AbstractMotivation: Biological assays are often carried out on tissues that contain many cell lineages and active pathways. Microarray data produced using such material therefore reflect superimpositions of biological processes. Analysing such data for shared gene function by means of well-matched assays may help to provide a better focus on specific cell types and processes. The identification of genes that behave similarly in different biological systems also has the potential to reveal new insights into preserved biological mechanisms.Results: In this article, we propose a hierarchical Bayesian model allowing integrated analysis of several microarray data sets for shared gene function. Each gene is associated with an indicator variable that selects whether binary class labels are predicted from expression values or by a classifier which is common to all genes. Each indicator selects the component models for all involved data sets simultaneously. A quantitative measure of shared gene function is obtained by inferring a probability measure over these indicators.Through experiments on synthetic data, we illustrate potential advantages of this Bayesian approach over a standard method. A shared analysis of matched microarray experiments covering (a) a cycle of mouse mammary gland development and (b) the process of in vitro endothelial cell apoptosis is proposed as a biological gold standard. Several useful sanity checks are introduced during data analysis, and we confirm the prior biological belief that shared apoptosis events occur in both systems. We conclude that a Bayesian analysis for shared gene function has the potential to reveal new biological insights, unobtainable by other means.Availability: An online supplement and MatLab code are available at http://www.sykacek.net/research.html#mcabfContact: peter@sykacek.netSupplementary information: Supplementary data are available at Bioinformatics online.
Statistical assessment of functional categories of genes deregulated in pathological conditions by using microarray data
Authors: Maglietta R. , Piepoli A. , Catalano D. , Licciulli F. , Carella M. , Liuni S. , Pesole G. , Perri F. , Ancona N. 
Published: June 2007

Abstract
Motivation: A major challenge in current biomedical research is the identification of cellular processes deregulated in a given pathology through the analysis of gene expression profiles. To this end, predefined lists of genes, coding specific functions, are compared with a list of genes ordered according to their values of differential expression measured by suitable univariate statistics.
Results: We propose a statistically well-founded method for measuring the relevance of predefined lists of genes and for assessing their statistical significance starting from their raw expression levels as recorded on the microarray. We use prediction accuracy as a measure of relevance of the list. The rationale is that a functional category, coded through a list of genes, is perturbed in a given pathology if it is possible to correctly predict the occurrence of the disease in new subjects on the basis of the expression levels of the genes belonging to the list only. The accuracy is estimated with multiple random validation strategy and its statistical significance is assessed against a couple of null hypothesis, by using two independent permutation tests. The utility of the proposed methodology is illustrated by analyzing the relevance of Gene Ontology terms belonging to biological process category in colon and prostate cancer, by using three different microarray data sets and by comparing it with current approaches.
Availability: Source code for the algorithms is available from author upon request.
Contact: ancona@ba.issia.cnr.it
Supplementary information: Colon cancer data set and a complete description of experimental results are available at: ftp://bioftp:76bioftpxxx@marx.ba.issia.cnr.it/supp-info.htm
Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications
Authors: Yu Haiyuan , Jansen Ronald , Stolovitzky Gustavo , Gerstein Mark 
Published: June 2007

Abstract
Motivation: Many classifications of protein function such as Gene Ontology (GO) are organized in directed acyclic graph (DAG) structures. In these classifications, the proteins are terminal leaf nodes; the categories ‘above’ them are functional annotations at various levels of specialization and the computation of a numerical measure of relatedness between two arbitrary proteins is an important proteomics problem. Moreover, analogous problems are important in other contexts in large-scale information organization—e.g. the Wikipedia online encyclopedia and the Yahoo and DMOZ web page classification schemes.
Results: Here we develop a simple probabilistic approach for computing this relatedness quantity, which we call the total ancestry method. Our measure is based on counting the number of leaf nodes that share exactly the same set of ‘higher up’ category nodes in comparison to the total number of classified pairs (i.e. the chance for the same total ancestry). We show such a measure is associated with a power-law distribution, allowing for the quick assessment of the statistical significance of shared functional annotations. We formally compare it with other quantitative functional similarity measures (such as, shortest path within a DAG, lowest common ancestor shared and Azuaje's information-theoretic similarity) and provide concrete metrics to assess differences. Finally, we provide a practical implementation for our total ancestry measure for GO and the MIPS functional catalog and give two applications of it in specific functional genomics contexts.
Availability: The implementations and results are available through our supplementary website at: http://gersteinlab.org/proj/funcsim
Contact: mark.gerstein@yale.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
FLOWERING LOCUS T Protein May Act as the Long-Distance Florigenic Signal in the Cucurbits
Authors: Lin Ming-Kuem , Belanger Helene , Lee Young-Jin , Varkonyi-Gasic Erika , Taoka Ken-Ichiro , Miura Eriko , Xoconostle-Cázares Beatriz , Gendler Karla , Jorgensen Richard A. , Phinney Brett , Lough Tony J. , Lucas William J. 
Published: June 2007

AbstractCucurbita moschata, a cucurbit species responsive to inductive short-day (SD) photoperiods, and Zucchini yellow mosaic virus (ZYMV) were used to test whether long-distance movement of FLOWERING LOCUS T (FT) mRNA or FT is required for floral induction. Ectopic expression of FT by ZYMV was highly effective in mediating floral induction of long-day (LD)–treated plants. Moreover, the infection zone of ZYMV was far removed from floral meristems, suggesting that FT transcripts do not function as the florigenic signal in this system. Heterografting demonstrated efficient transmission of a florigenic signal from flowering Cucurbita maxima stocks to LD-grown C. moschata scions. Real-time RT-PCR performed on phloem sap collected from C. maxima stocks detected no FT transcripts, whereas mass spectrometry of phloem sap proteins revealed the presence of Cm-FTL1 and Cm-FTL2. Importantly, studies on LD- and SD-treated C. moschata plants established that Cmo-FTL1 and Cmo-FTL2 are regulated by photoperiod at the level of movement into the phloem and not by transcription. Finally, mass spectrometry of florally induced heterografted C. moschata scions revealed that C. maxima FT, but not FT mRNA, crossed the graft union in the phloem translocation stream. Collectively, these studies are consistent with FT functioning as a component of the florigenic signaling system in the cucurbits.
Neuronal features of oligodendrogliomas—an ultrastructural and immunohistochemical study
Authors: Vyberg M , Ulhøi B P , Teglbjærg P S 
Published: June 2007

Aims:  To assess neuronal differentiation in oligodendrogliomas (ODGs).Methods and results:  An electron microscopic and immunohistochemical study of 41 consecutive cases was performed. In all cases, tumour cells with neuritic structures were identified ultrastructurally, including synapses and neurosecretory granules. For the immunohistochemical identification of synaptophysin, monoclonal antibody clones 27G12, Snp88 and SY38 and a polyclonal antibody were compared in optimized protocols on slides from a spectrum of tissues and 16 ODGs. 27G12 gave the best signal‐to‐noise ratio, while SY38 gave the poorest. When 27G12 was applied on all 41 ODGs, widespread immunoreactivity was obtained in 100%. Among three antibodies to chromogranin compared similarly, clone LK2H10 and a polyclonal antibody gave identical patterns of immunoreactivity, whereas clone DAK‐A3 gave weaker reactions. When LK2H10 was applied on all tumours, staining was found in 12 (29%). All tumours but one stained strongly for glial fibrillary acidic protein and all for synapsin I. Fluorescence in situ hybridization analysis showed a concomitant 1p/19q deletion in 12/16 ODGs.Conclusions:  Our study provides evidence for widespread neuronal differentiation in ODGs, suggesting that these tumours may be derived from progenitor cells with limited commitment. Antibody selection and protocol optimization are mandatory for reliable immunohistochemistry results.
Nuclear survivin is associated with disease recurrence and poor survival in patients with cutaneous malignant melanoma
Authors: Piras F , Murtas D , Minerba L , Ugalde J , Floris C , Maxia C , Colombari R , Perra M T , Sirigu P 
Published: June 2007

Aims:  Survivin is expressed in neoplastic cells and appears to be associated with resistance to therapy and shorter survival in various types of tumours. The aim of the present study was to determine whether nuclear or cytoplasmic expression of survivin is related to disease recurrence and overall survival of patients with Stage I and II melanoma according to the American Joint Committee on Cancer (AJCC) staging system.Methods and results:  Immunohistochemistry was performed on formalin‐fixed paraffin‐embedded sections of primary cutaneous melanoma from 50 patients. Survival rates were estimated using the Kaplan–Meier method and compared using the log rank test. Association of clinical variables (gender, age, tumour location, thickness, Clark level and AJCC stage) with survivin expression was analysed by Fisher's exact test. Patients with nuclear immunoreactivity for survivin had an increased risk of disease recurrence during the first three postoperative years (P < 0.05) and of death (P < 0.05). Cytoplasmic immunoreactivity was not correlated with either survival or clinical variables.Conclusions:  Nuclear presence of survivin may be an independent biomarker for disease recurrence and overall survival in patients with Stage I and II melanoma.
Expression of Bax, Bcl‐xL and Bcl‐2 proteins in relation to grade of inflammation and stage of fibrosis in chronic hepatitis C
Authors: Piekarska A , Kubiak R , Szymczak W , Piekarski J 
Published: June 2007

Aims:  To determine the expression of regulators of apoptosis in chronic hepatitis C.Methods and results:  Expression of Bax, Bcl‐xL and Bcl‐2 proteins was assessed immunohistochemically in liver biopsy specimens obtained from 89 adults with chronic hepatitis C. Expression of Bax in hepatocytes correlated inversely with grade of inflammation (P < 0.001) and stage of fibrosis (P = 0.011), classified according to the Scheuer score; expression of Bcl‐xL in hepatocytes did not correlate with grade of inflammation (P = 0.106) or stage of fibrosis (P = 0.078); maximum Bcl‐xL expression was observed in grade 3 inflammation and stage 4 fibrosis. Expression of Bcl‐2 protein in hepatocytes was present in only two cases (both with advanced disease); the expression of Bcl‐2 protein in interlobular bile duct epithelial cells correlated with the grade of inflammation (P = 0.018), but not with stage of fibrosis (P = 0.154). The expression of Bcl‐2 protein in lymphoid cells infiltrating portal zones and lobules did not correlate with grade of inflammation (P = 0.113) or stage of fibrosis (P = 0.815).Conclusion:  Major differences in expression of studied proteins were observed in relation to grade of inflammation and stage of fibrosis in chronic hepatitis C.
Gastric mucin is expressed in a subset of endocervical tunnel clusters: type A tunnel clusters of gastric phenotype
Authors: Kondo T , Hashi A , Murata S‐I , Fischer S E , Nara M , Nakazawa T , Yuminamochi T , Hoshi K , Katoh R 
Published: June 2007

Aims:  Gastric mucin expression has been demonstrated in a group of endocervical glandular lesions. The aim of this study was to gain further insight into endocervical lesions with a gastric phenotype.Methods and results:  Various types of tunnel clusters (TC) were examined for gastric mucin by alcian blue/periodic acid–Schiff staining and immunohistochemistry for HIK1083. Five of 34 cases of TC expressed gastric mucin defined by PAS dominant neutral mucin and immunopositivity for pyloric gland mucin. Histologically, TC expressing gastric mucin showed lobular arrangements of small to medium‐sized glands composed of mucin‐rich columnar cells and were classified as Flumann's type A TC. Neither type B TC nor normal endocervical glands expressed PAS dominant neutral mucin and none of them was immunopositive for pyloric gland mucin. Five patients with type A TC of gastric phenotype ranged in age from 33 to 79 years (mean 58 years) and were multiparous. Type A TC of gastric phenotype, ranging from 2 to 4 mm in maximum diameter, were incidental findings in hysterectomy specimens.Conclusion:  Type A TC of gastric phenotype could be related to lobular endocervical glandular hyperplasia of gastric phenotype. The pathogenesis of gastric metaplasia in TC remains unclear.
Grading of dysplasia in Barrett's oesophagus: substantial interobserver variation between general and gastrointestinal pathologists
Authors: Kerkhof M , Van Dekken H , Steyerberg E W , Meijer G A , Mulder A H , De Bruïne A , Driessen A , Ten Kate F J , Kusters J G , Kuipers E J , Siersema P D ,   for the CYBAR study group
Published: June 2007

Aims:  To determine interobserver variation in grading of dysplasia in Barrett's oesophagus (BO) between non‐expert general pathologists and expert gastrointestinal pathologists on the one hand and between expert pathologists on the other hand.Methods and results:  In this prospective multicentre study, non‐expert and expert pathologists graded biopsy specimens of 920 patients with endoscopic BO, which were blindly reviewed by one member of a panel of expert pathologists (panel experts) and by a second panel expert in case of disagreement on dysplasia grade. Agreement between two of three pathologists was established as the final diagnosis. Analysis was performed by κ statistics. Due to absence of intestinal metaplasia, 127/920 (14%) patients were excluded. The interobserver agreement for dysplasia [no dysplasia (ND) versus indefinite for dysplasia/low‐grade dysplasia (IND/LGD) versus high‐grade dysplasia (HGD)/adenocarcinoma (AC)] between non‐experts and first panel experts and between initial experts and first panel experts was fair (κ = 0.24 and κ = 0.27, respectively), and substantial for differentiation of HGD/AC from ND/IND/LGD (κ = 0.62 and κ = 0.58, respectively).Conclusions:  There was considerable interobserver variability in the interpretation of ND or IND/LGD in BO between non‐experts and experts, but also between expert pathologists. This suggests that less subjective markers are needed to determine the risk of developing AC in BO.
Prospective comparison of subjective arousal during the pre‐sleep period in primary sleep‐onset insomnia and normal sleepers
Authors: ROBERTSON JENNIFER A. , BROOMFIELD NIALL M. , ESPIE COLIN A. 
Published: June 2007

SummaryPsychophysiological insomnia (PI) is the most common insomnia subtype, representing 12–15% of all sleep centre referrals. Diagnostic guidelines describe PI as an intrinsic sleep disorder involving both hyperarousal and learned sleep‐preventing associations. Whilst evidence for the first component is reasonably compelling, evidence for learned (conditioned) sleep effects is markedly lacking. Indeed, to date no study has attempted to capture directly the conditioned arousal effect assumed to characterize the disorder. Accordingly, the present study explored variations in subjective arousal over time in 15 PI participants (sleep onset type) and 15 normal sleepers (NS). Self‐report measures of cognitive arousal, somatic arousal and sleepiness were taken at three time points: 3 h before bedtime (early to mid‐evening); 1 h before bedtime (late evening); and in the bedroom at lights out (bedtime) across four, 24‐h cycles. Fluctuations in mean arousal and sleepiness values, and in day‐to‐day variation were examined using analyses of variance. Participants with PI were significantly more cognitive aroused and significantly less sleepy relative to NS, within the bedroom environment. These results support the tenet of conditioned mental arousal to the bedroom, although competing explanations cannot be ruled out. Results are discussed with reference to extant insomnia models.