bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA microarray data imputation and significance analysis of differential expression
Authors: Jörnsten Rebecka , Wang Hui-Yu , Welsh William J. , Ouyang Ming 
Published: August 2005

AbstractMotivation: Significance analysis of differential expression in DNA microarray data is an important task. Much of the current research is focused on developing improved tests and software tools. The task is difficult not only owing to the high dimensionality of the data (number of genes), but also because of the often non-negligible presence of missing values. There is thus a great need to reliably impute these missing values prior to the statistical analyses. Many imputation methods have been developed for DNA microarray data, but their impact on statistical analyses has not been well studied. In this work we examine how missing values and their imputation affect significance analysis of differential expression.Results: We develop a new imputation method (LinCmb) that is superior to the widely used methods in terms of normalized root mean squared error. Its estimates are the convex combinations of the estimates of existing methods. We find that LinCmb adapts to the structure of the data: If the data are heterogeneous or if there are few missing values, LinCmb puts more weight on local imputation methods; if the data are homogeneous or if there are many missing values, LinCmb puts more weight on global imputation methods. Thus, LinCmb is a useful tool to understand the merits of different imputation methods. We also demonstrate that missing values affect significance analysis. Two datasets, different amounts of missing values, different imputation methods, the standard t-test and the regularized t-test and ANOVA are employed in the simulations. We conclude that good imputation alleviates the impact of missing values and should be an integral part of microarray data analysis. The most competitive methods are LinCmb, GMC and BPCA. Popular imputation schemes such as SVD, row mean, and KNN all exhibit high variance and poor performance. The regularized t-test is less affected by missing values than the standard t-test.Availability: Matlab code is available on request from the authors.Contact: rebecka@stat.rutgers.edu; ouyangmi@umdnj.edu
INVOLVEMENT OF ENDOTHELIAL CYCLO‐OXYGENASE METABOLITES IN NORADRENALINE‐INDUCED CONTRACTION OF RAT CORONARY ARTERY
Authors: Wang Aimin , Nishihashi Tsuyoshi , Trandafir Cristina C , Murakami Shizuka , Ji Xu , Shimizu Yoshiharu , Kurahashi Kazuyoshi 
Published: August 2005

SUMMARY1. Noradrenaline (NA; 0.3 µmol/L) caused a contraction of the rat coronary artery that markedly increased in the presence of the nitric oxide synthase (NOS) inhibitor NG‐nitro‐l‐arginine methyl ester (l‐NAME; 100 µmol/L) and arachidonic acid (1 µmol/L; P < 0.05).2. The present experiments attempted to elucidate the endothelium dependency of the contraction and to pharmacologically characterize the factors involved in the contraction induced by NA (0.3 µmol/L) in the presence of l‐NAME and arachidonic acid in ring preparations of the rat coronary artery.3. The NA (0.3 µmol/L)‐induced contraction was attenuated by a chemical remover of the endothelium (saponin at concentrations of 0.1 and 0.4 mg/mL) in a concentration‐dependent manner (P < 0.05).4. The cyclo‐oxygenase (COX)‐1 inhibitor flurbiprofen (0.01–1 µmol/L) and the COX‐2 inhibitor nimesulide (0.01–1 µmol/L) attenuated the NA‐induced contraction in a concentration‐dependent manner and the inhibitory effect of flurbiprofen was significantly more potent than that of nimesulide (P < 0.05). The 5‐lipoxigenase inhibitor ZM‐230487 (1 µmol/L) did not affect the NA‐induced contraction.5. The thromboxane A2 (TXA2) synthetase inhibitor OKY‐046 (30 µmol/L) and the TXA2 antagonist S‐1452 (0.1–10 µmol/L) did not attenuate the NA‐induced contraction.6. These results indicate that the contraction induced by NA in the rat coronary artery in the presence of l‐NAME and arachidonic acid is endothelium dependent and is due to endothelial COX metabolites of arachidonic acid.
Alpha‐toxin is produced by skin colonizing Staphylococcus aureus and induces a T helper type 1 response in atopic dermatitis
Authors: Breuer K. , Wittmann M. , Kempe K. , Kapp A. , Mai U. , Dittrich‐Breiholz O. , Kracht M. , Mrabet‐Dahbi S. , Werfel T. 
Published: August 2005

SummaryBackground
Staphylococcus aureus is a well known trigger factor of atopic dermatitis (AD). Besides the superantigens, further exotoxins are produced by S. aureus and may have an influence on the eczema.Objective
To explore the impact of staphylococcal α‐toxin on human T cells, as those represent the majority of skin infiltrating cells in AD.Methods
Adult patients with AD were screened for cutaneous colonization with α‐toxin producing S. aureus. As α‐toxin may induce necrosis, CD4+ T cells were incubated with sublytic α‐toxin concentrations. Proliferation and up‐regulation of IFN‐γ on the mRNA and the protein level were assessed. The induction of t‐bet translocation in CD4+ T cells was detected with the Electrophoretic Mobility Shift Assay.Results
Thirty‐four percent of the patients were colonized with α‐toxin producing S. aureus and α‐toxin was detected in lesional skin of these patients by immunohistochemistry. Sublytic α‐toxin concentrations induced a marked proliferation of isolated CD4+ T cells. Microarray analysis indicated that α‐toxin induced particularly high amounts of IFN‐γ transcripts. Up‐regulation of IFN‐γ was confirmed both on the mRNA and the protein level. Stimulation of CD4+ T cells with α‐toxin resulted in DNA binding of t‐bet, known as a key transcription factor involved into primary T helper type 1 (Th1) commitment.Conclusion
α‐toxin is produced by S. aureus isolated from patients with AD. We show here for the first time that sublytic α‐toxin concentrations activate T cells in the absence of antigen‐presenting cells. Our results indicate that α‐toxin is relevant for the induction of a Th1 like cytokine response. In AD, this facilitates the development of Th1 cell dominated chronic eczema.
Birch pollen‐related food allergy to legumes: identification and characterization of the Bet v 1 homologue in mungbean (Vigna radiata), Vig r 1
Authors: Mittag D. , Vieths S. , Vogel L. , Wagner‐Loew D. , Starke A. , Hunziker P. , Becker W.‐M. , Ballmer‐Weber B. K. 
Published: August 2005

SummaryBackground
Recently allergic reactions to legumes mediated by Bet v 1‐homologous food allergens were described for soy and peanut. In this study we assessed allergic reactions to another legume, to mungbean seedlings, and identified its Bet v 1‐homologous allergen Vig r 1.Methods
Ten patients were selected who had a history of allergic reactions to mungbean seedlings and a respiratory allergy to birch pollen. The Bet v 1 homologue in mungbean seedlings, Vig r 1, was cloned by a PCR strategy, expressed in Escherichia coli, and purified by preparative SDS‐PAGE. In all sera, specific IgE against birch pollen, Bet v 1, Bet v 2, Vig r 1, and the Bet v 1 homologues in soy (Gly m 4) and cherry (Pru av 1) was determined by CAP‐FEIA. Cross‐reactivity of specific IgE with Vig r 1, Bet v 1, Gly m 4, and Pru av 1 was assessed by immunoblot inhibition. Expression of Vig r 1 during development of mungbean seedlings and under wounding stress was analysed by immunoblotting. The Vig r 1 double band was analysed by matrix‐assisted laser desorption/ionization time‐of‐flight and liquid chromatography/tandem mass spectrometry (LC/MS/MS).Results
All patients were sensitized to birch pollen and Bet v 1, 20% to Bet v 2, and 90% to Gly m 4. Seventy percent of the patients showed IgE binding to a double band at 15 kDa in mungbean extract that was inhibited after pre‐incubation of sera with rBet v 1. PCR cloning revealed that the mungbean homologue of Bet v 1 had a molecular weight of 16.2 kDa, a calculated pI of 4.6% and 42.8% amino acid sequence identity with Bet v 1. MS analysis confirmed similarity of the double band with the deduced Vig r 1 sequence, but also indicated the existence of other Vig r 1 isoforms. ImmunoCAP analysis detected IgE against Vig r 1 in 80% of the sera. IgE binding to Vig r 1 was inhibited with Gly m 4 in six of six and with rPru av 1 in four of six patients. Vig r 1 expression occurred during development of seedlings and was increased by wounding stress.Conclusions
Food allergy to mungbean seedlings can be caused by primary sensitization to birch pollen and is mediated by Vig r 1 in the majority of the patients with birch pollen‐related allergy to mungbean seedlings.
Microarray‐based survey of a subset of putative olfactory genes in the mosquito Anopheles gambiae
Authors: Biessmann H. , Nguyen Q. K. , Le D. , Walter M. F. 
Published: August 2005

AbstractFemale Anopheles gambiae mosquitoes respond to odours emitted from humans in order to find a blood meal, while males are nectar feeders. This complex behaviour is controlled at several levels, but is probably initiated by the interaction of various molecules in the antennal sensilla. Important molecules in the early odour recognition events include odourant binding proteins (OBPs), which may be involved in odour molecule transport, odourant receptors (ORs) that are expressed in the chemosensory neurones and odour degrading enzymes (ODEs). To obtain a better understanding of the expression patterns of genes that may be involved in host odour reception in females, we generated a custom microarray to study their steady state mRNA levels in chemosensory tissues, antennae and palps. These results were supported by quantitative RT PCR. Our study detected several OBPs that are expressed at significantly higher levels in antennae and palps of females vs. males, while others showed the opposite expression pattern. Most OBPs are slightly down‐regulated 24 h after blood feeding, but some, especially those with higher expression levels in males, are up‐regulated in blood‐fed females, suggesting a shift in blood‐fed females from human host seeking to nectar feeding.
The glass transition approach to determination of drying protocols for colour stability in dehydrated pear slices
Authors: Ling Hang‐Ing , Birch John , Lim Miang 
Published: August 2005

SummaryColour stability in dehydrated fruit is often attained by use of sulphite treatment to inhibit browning during processing and storage. However, colour stability may be able to be conferred on products by ensuring that the molecular mobility is restricted in dried fruit by drying to sufficiently low moisture to raise the glass transition temperature (under mild conditions). Pear slices were dehydrated at a low temperature (40 °C) to a low final moisture content (below 5%) after it was shown that, for a moisture content of 22% (which is the moisture content of commercial dehydrated pears) pretreatment with sulphite would be necessary to stabilise the colour. The use of longer drying regimes resulted in a moisture content where the food matrix would be closer to the glassy state and conferred colour stability on the dehydrated product compared to a product containing more moisture. For these low‐moisture products, pretreatment with sulphite would not be necessary to preserve colour stability.
The spatial pattern of air seeding thresholds in mature sugar maple trees
Authors: CHOAT BRENDAN , LAHR ELEANOR C. , MELCHER PETER J. , ZWIENIECKI MACIEJ A. , HOLBROOK N MICHELE 
Published: August 2005

ABSTRACTAir seeding threshold (Pa) of xylem vessels from current year growth rings were measured along the vertical axis of mature sugar maple trees (Acer saccharum Marsh.), with sampling points in primary leaf veins, petioles, 1‐, 3‐, and 7‐year‐old branches, large branches, the trunk and roots. The air seeding threshold was taken as the pressure required to force nitrogen gas through intervessel pit membranes. Although all measurements were made on wood produced in the same year, Pa varied between different regions of A. saccharum, with distal organs such as leaves and petioles having lower Pa than basal regions. Mean (SE) Pa ranged from 1.0 (± 0.1) MPa in primary leaf veins to 4.8 (± 0.1) MPa in the main trunk. Roots exhibited a Pa of 2.8 (± 0.2) MPa, lower than all other regions of the tree except leaf veins and petioles. Mean xylem vessel diameter increased basipetally, with the widest vessels occurring in the trunk and roots. Within the shoot, wider vessels had greater air seeding thresholds, contrasting with trends previously reported. However, further experimentation revealed that differences in Pa between regions of the stem were driven by the presence of primary xylem conduits, rather than differences in vessel diameter. In 1‐year‐old branches, Pa was significantly lower in primary xylem vessels than in adjacent secondary xylem vessels. This explained the lower values of Pa measured in petioles and leaf veins, which possessed a greater ratio of primary xylem to secondary xylem than other regions. The difference in Pa between primary and secondary xylem was attributed to the greater area of primary cell wall (pit membrane) exposed in primary xylem conduits with helical or annular thickening.
NO signalling in cytokinin‐induced programmed cell death
Authors: CARIMI FRANCESCO , ZOTTINI MICHELA , COSTA ALEX , CATTELAN IRENE , DE MICHELE ROBERTO , TERZI MARIO , LO SCHIAVO FIORELLA 
Published: August 2005

ABSTRACTCell death can be induced by cytokinin 6‐benzylaminopurine (BA) at high dosage in suspension‐cultured Arabidopsis cells. Herein, we provide evidence that BA induces nitric oxide (NO) synthesis in a dose‐dependent manner. A reduction in cell death can be observed when the cytokinin is supplemented with the NO scavenger 2‐(4‐carboxyphenyl)‐4,4,5,5‐tetramethylimidazoline‐1‐oxyl‐3‐oxide (cPTIO) or the nitric oxide synthase (NOS) inhibitors: 2‐aminoethyl‐isothiourea (AET) and NG.‐monomethyl‐ l‐arginine ( l‐NMMA), which suggests that NO is produced via a NOS and is a signalling component of this form of programmed cell death. In BA‐treated cells, mitochondrial functionality is altered via inhibition of respiration. This inhibition can be prevented by addition of either cPTIO or AET implying that NO acts at the mitochondrial level.
Climatic adaptation in Picea abies progenies is affected by the temperature during zygotic embryogenesis and seed maturation
Authors: JOHNSEN ØYSTEIN , FOSSDAL CARL GUNNAR , NAGY NINA , MØLMANN JØRGEN , DæHLEN OLA GRAM , SKRØPPA TORE 
Published: August 2005

ABSTRACTThe temperature during maternal reproduction affects adaptive traits in progenies of Norway spruce (Picea abies (L) Karst.). Seed production in a cold environment advances bud set and cold acclimation in the autumn and dehardening and flushing in spring, whereas a warm reproductive environment delays timing of these traits. We repeated crosses between the same parents and produced seeds under contrasting temperatures. Elevated temperatures were applied at different time points from female meiosis to embryogenesis, followed by full‐sib progeny tests in common environments. We measured timing of terminal bud formation, cold acclimation in the autumn and transcription levels of conifer phytochromes PhyO, PhyN, PhyP, and the class IV chitinase PaChi4 in these tests. No progeny differences were found that could be related to temperature differences during prezygotic stages and fertilization. In contrast, progeny performance was strongly associated with the degree‐days from proembryo to mature seeds. Progenies with a warm embryonic history formed terminal buds later, were less hardy and expressed lower transcription levels of the Phy and PaChi4 genes. We hypothesize that temperature during zygotic embryogenesis and seed maturation regulates an ‘epigenetic memory’ in the progeny, involving differential expression of genes that may regulate bud phenology, cold acclimation and embryogenesis in Norway spruce.
The impact of overweight on the development of diabetes after heart transplantation
Authors: Kahn J , Rehak P , Schweiger M , Wasler A , Wascher T , Tscheliessnigg KH , Müller H 
Published: August 2005

Abstract: Background: Overweight is defined with a body mass index (BMI) >25. A BMI >25 is known as an independent risk factor for increased morbidity and mortality. The influence of an increased BMI on the development of diabetes and on survival after heart transplantation (HTX) was investigated.Methods: A total of 137 patients (116 men, 21 women), who underwent HTX at our Department from 1986 to 2002, were included in the study. For group stratification, the pre‐operative BMI values were taken (group I: BMI ≤25; group II: BMI > 25). Groups were compared for primary disease, age and sex, development of renal failure, development of diabetes, and survival. The probability of survival and the freedom‐from‐diabetes interval were calculated by the use of Kaplan–Meier method.Results: No significant differences between groups I and II were found concerning primary disease, age and sex, and occurrence of renal failure. There was a tendency towards increased survival (p = 0.18) in group I. Patients of group II developed diabetes after HTX more frequently than those of group I (p < 0.001). Cox regression revealed that pre‐operative BMI >25 is a highly significant independent risk factor for post‐operative development of diabetes mellitus (DM) (p < 0.001).Conclusion: Overweight prior to HTX appears to negatively influence long‐term survival after HTX, although this difference did not reach statistical significance. Pre‐operative overweight is a significant and independent risk factor for the development of post‐transplant diabetes.
A T−786C polymorphism in 5′‐flanking region of the endothelial nitric oxide synthase gene and endothelium‐dependent arterial dilation in Type 2 diabetes
Authors: Guang‐da X. , Qiong‐shu W. , Wen J. 
Published: August 2005

AbstractObjective  Several studies have shown that the T−786C polymorphism in 5′‐flanking region of the endothelial nitric oxide synthase (eNOS) gene is associated with coronary artery disease in non‐diabetic population. In the present study, we attempted to assess whether the T−786C polymorphism of eNOS gene is associated with endothelial dysfunction Type 2 diabetes.Research design and methods  A total of 162 Type 2 diabetic men were studied. PCR/allele‐specific probes were used to analyse the T−786C polymorphism of eNOS gene, and high resolution ultrasound was used to measure brachial artery diameter at rest, after reactive hyperaemia and after sublingual glyceryltrinitrate.Results  The flow‐mediated arterial dilation among subjects with T/C or C/C was 3.73 ± 0.50%, which was significantly lower than that in subjects with T/T (4.15 ± 0.49%) (P = 0.000). On multiple linear regression analysis, the presence of C allele, mean blood pressure, low‐density lipoprotein (LDL) and serum lipoprotein (a) [Lp(a)] were independent determinants for reduced endothelium‐dependent arterial dilation (R2 = 0.175, P = 0.0021). The flow‐mediated arterial dilation in smokers with T/C or C/C was significantly lower than that in smokers with T/T (P < 0.001), but not in non‐smokers. In addition, the presence of C allele, LDL and Lp(a) were independent determinants for reduced endothelium‐dependent arterial dilation (R2 = 0.258, P = 0.0017) in smokers, but not in non‐smokers.Conclusion  The C allele of T−786C polymorphism of eNOS gene is a genetic risk factor for endothelial dysfunction in Type 2 diabetic patients, especially among smokers.
Nocturnal neuropathic pain in diabetic patients may be caused by spinal stenosis
Authors: Goldman S. M. 
Published: August 2005

AbstractBackground  Nocturnal exacerbation of neuropathic symptoms (NENS) is a recognized symptom of diabetic peripheral neuropathy (DPN). Symptoms are often worse in bed, may not be controlled with medication and disrupt sleep patterns. NENS can also be present in patients with spinal stenosis (SS), with or without concomitant peripheral neuropathy and may be related to sleep position. Extension position of the spine decreases the diameter of both the central canal and lateral recesses, which may compress or otherwise affect nerves controlling sensation from the feet and legs. Altering sleep position can reduce or eliminate symptoms. Modifications include sleeping in a recliner, with a pillow underneath the thighs if sleeping on the back, between the thighs if sleeping on the side, or under the stomach transversely if sleeping on the stomach. In addition, reducing nerve compression during the day by full‐time use of a wheeled walker set to induce lumbosacral flexion may reduce NENS.Methods and results  Retrospective patient review identified patients presenting with DPN including NENS, who noted alteration of NENS by changing body position, who also had walking and standing limitations consistent with SS. They underwent ‘positional testing’, involving modification of sleep position, and full‐time 3‐day use of a rollator walker, which may reduce symptoms of SS. Most reported good or excellent improvement of NENS.Conclusions  NENS, especially if affected by body position, or if accompanying a pattern of walking limitation improved with wheeled support, should lead to suspicion of SS. Positional testing should be considered in possible cases. Clinical use and further investigation are indicated.
The Corporate Management of Human Resources Under Conditions of Decentralization
Authors: Hendry Chris 
Published: August 2005

SUMMARYThis paper relates an aspect of recent corporate change – namely, decentralization – to the strategic management of human resources. Corporate attention to human resources in the decentralized organization is of particular interest because it represents a significant departure from decentralized norms, and signals a major revision of thinking about the role, status, and activities of the personnel function. At the centre of the argument is the notion of the internal labour market, a hitherto neglected theme in treatments of decentralization. The paper begins by outlining the circumstances that encouraged decentralization in the 1980s. It then sets out the influences on the operation of a corporate internal labour market, before identifying initiatives taken by some firms to offset the shortcomings of decentralization without overturning it. In the process, the shift in the centre of gravity of the corporate personnel function, away from industrial relations management and towards human resource development, has been reinforced.
Programmed Strategic Decision Making: The View From Mintzberg's Window1
Authors: Cray David , Haines George H. , Mallory Geoffrey R. 
Published: August 2005

SUMMARYA class of decisions, asset mix decisions made by pension fund managers, which exhibit characteristics of both programmed and strategic choices is examined in this paper. The decisions are classified using the scheme developed by Mintzberg et al., (1976) to highlight the circumstances under which strategic decisions may be programmed. The types of strategic decisions which lend themselves to programming are considered. The advantages and disadvantages of programming strategic decisions are also discussed.