bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mixtures of common t-factor analyzers for clustering high-dimensional microarray data
Authors: Baek Jangsun , McLachlan Geoffrey J. 
Published: March 2011

Abstract
Motivation: Mixtures of factor analyzers enable model-based clustering to be undertaken for high-dimensional microarray data, where the number of observations n is small relative to the number of genes p. Moreover, when the number of clusters is not small, for example, where there are several different types of cancer, there may be the need to reduce further the number of parameters in the specification of the component-covariance matrices. A further reduction can be achieved by using mixtures of factor analyzers with common component-factor loadings (MCFA), which is a more parsimonious model. However, this approach is sensitive to both non-normality and outliers, which are commonly observed in microarray experiments. This sensitivity of the MCFA approach is due to its being based on a mixture model in which the multivariate normal family of distributions is assumed for the component-error and factor distributions.
Results: An extension to mixtures of t-factor analyzers with common component-factor loadings is considered, whereby the multivariate t-family is adopted for the component-error and factor distributions. An EM algorithm is developed for the fitting of mixtures of common t-factor analyzers. The model can handle data with tails longer than that of the normal distribution, is robust against outliers and allows the data to be displayed in low-dimensional plots. It is applied here to both synthetic data and some microarray gene expression data for clustering and shows its better performance over several existing methods.
Availability: The algorithms were implemented in Matlab. The Matlab code is available at http://blog.naver.com/aggie100.
Contact: jbaek@jnu.ac.kr
Supplementary information: Supplementary data are available at Bioinformatics online.
Preparation of Meiotic Chromosomes from Adult Drosophila Testes
Authors: Bonaccorsi Silvia , Giansanti Maria G. , Cenci Giovanni , Gatti Maurizio 
Published: March 2011

INTRODUCTIONSeveral techniques have been developed for the preparation of Drosophila male meiotic chromosomes. All of these techniques allow a clear visualization of chromosomes, but not of other cellular structures such as the cytoskeleton and the spindle. The protocol described here is particularly useful for the analysis of adult testes.
Sonoporation for Gene Transfer into Embryos
Authors: Ohta Sho , Yukiko Ogino , Suzuki Kentro , Kamimura Mika , Tachibana Katsuro , Yamada Gen 
Published: March 2011

INTRODUCTIONSonoporation is a method for the introduction of genes into tissues such as those of chick embryos. It enables gene incorporation into target tissue by the combination of ultrasound exposure and subsequent rupture of microbubbles. Sonoporation has several advantages: (1) It is simple, involving two main steps—preparation of a microbubble–DNA mixture, followed by injection and ultrasound treatment of the target tissue; (2) it allows highly efficient gene incorporation into mesenchymal tissues; (3) it does not induce significant tissue damage—most of the sonoporated chick embryos survived without showing significant embryonic abnormalities or cell death; and (4) it can be used to introduce genes into several chick embryonic tissues (e.g., branchial arch and lateral plate mesoderm). To demonstrate the utility of sonoporation, an expression vector containing the Sonic hedgehog (Shh) gene was incorporated into the developing chick limb bud, leading to additional digit formation in the Shh-expressing embryos. Sonoporation may not be appropriate for the introduction of genes into tissues with cavitated or open structures. Sonoporation into the neural tube and limb ectoderm often resulted in dispersed gene expression due to diffusion of the injected microbubbles before ultrasound treatment. Despite these problems, sonoporation is a useful method for the analysis of gene function(s) in vivo and brings a new area of gene transfer to medical, molecular, and developmental biology. This protocol describes the use of sonoporation to introduce vectors into embryonic chick limb bud.
Liposome-Mediated Transfection
Authors: Dean David A. , Gasiorowski Joshua Z. 
Published: March 2011

INTRODUCTIONThe efficient delivery of exogenous DNA to cells for expression and function studies is an essential technique of modern cell biology. Cationic liposomes are the most widely used class of carrier for transfection and a number of products are available commercially: Lipofectin (a 1:1 mixture of DOTMA [N-[1(2,3-dioleoyloxy)propyl]-N,N,N-trimethylammonium chloride] and DOPE [dioleoyl phosphatidylethanolamine]), Transfectam, and DOTAP [1,2-dioleoyloxy-3-trimethylammonium propane]:DOPE. However, all these reagents are costly; it can be less expensive to purchase purified lipids and formulate homemade transfection reagents by adding equimolar amounts of each lipid suspended in chloroform, mixing, and drying under inert gas. The reagents can be stored until they are reconstituted in an appropriate buffer. Although each manufacturer provides detailed instructions for the use of its reagent, the following general steps are used for essentially all formulations; times, concentrations, and volumes might differ slightly. The following volumes are sufficient for transfecting a 35-mm dish or one well of a six-well dish.
Clinicopathological features of 171 cases of primary thyroid lymphoma: a long‐term study involving 24 553 patients with Hashimoto’s disease
Authors: Watanabe Natsuko , Noh Jaeduk Y. , Narimatsu Hiroto , Takeuchi Kengo , Yamaguchi Takuhiro , Kameyama Kaori , Kobayashi Kazuhiko , Kami Masahiro , Kubo Atsushi , Kunii Yo , Shimizu Taeko , Mukasa Koji , Otsuka Fumiko , Miyara Ayako , Minagawa Akinobu , Ito Koichi , Ito Kunihiko 
Published: March 2011

SummaryThere are few large‐scale reports of primary thyroid lymphoma (PTL). This study clinically and pathologically reviewed 171 patients with PTL and 24 553 patients with Hashimoto’s disease at Ito Hospital between January 1990 and December 2004, to investigate the clinical features and the treatment outcomes of PTL. The median age of the patients with PTL was 67 years (range, 27–90 years). The pathological diagnosis of PTL patients included diffuse large B‐cell lymphoma (DLBCL) (n = 74), DLBCL with mucosa‐associated lymphoid tissue (MALT) lymphoma (n = 13), MALT lymphoma (n = 80) and others (n = 4). Of the 167 patients with B‐cell lymphoma, treatment included combined modality therapy (CMT) (n = 95), radiation therapy (RT) alone (n = 60) and chemotherapy alone (n = 6). Information on treatment was not available in six patients. Information on treatment response was available in 154 patients; 149 patients (97%) responded to treatment. According to the institutional treatment strategy of Ito Hospital, 45 of 54 patients with stage IE disease received RT alone, and 87 of 113 stage IIE patients received CMT. The 5‐year overall survival rate was 85% (95% confidence interval, 79–91%). This study demonstrated that PTL showed good response to radiotherapy and chemotherapy and had a favourable prognosis.
Social rehabilitation in long‐term conditions: learning about the process
Authors: Portillo Mari Carmen , Cowley Sarah 
Published: March 2011

portillo m.c. & cowley s. (2011) Social rehabilitation in long‐term conditions: learning about the process. Journal of Advanced Nursing67(6), 1329–1340.AbstractAim.  This paper is a report of a study of the process of social rehabilitation, and the analysis of the main elements and influencing factors which are important in the process.Background.  The process of social rehabilitation lacks conceptual and empirical understanding in Neurology because most rehabilitation programmes have focused on cognitive and physical recovery.Methods.  An action research project was undertaken in two neurological wards of a highly specialized hospital in Spain, and was completed in 2006. A social rehabilitation programme based on the assessment of social needs and individualized social education was planned with health professionals, and implemented and evaluated with patients and carers. Several instruments were used to explore how patients and carers perceived the process of social rehabilitation before and after the programme: semi‐structured interviews, socio‐demographic forms, field notes, participant observations, and scales of activities of daily living, social impairment and adjustment. Comparative content and statistical analyses were undertaken.Findings.  Social rehabilitation was identified as a dynamic process in which the environment, activities, social interaction, self‐recognition and awareness of social problems, coping and satisfaction played an essential role. Some defining criteria for social rehabilitation related to patients’ and carers’ attitudes, behaviour and the external implications that the socialization process had for them.Conclusion.  This study shows the advantages of multidisciplinary work, and user and family involvement in social rehabilitation and provides in‐depth knowledge about how patients and carers experience and could face barriers to develop a role in their family environment, social groups and society.
Making DNA without iron – induction of a manganese‐dependent ribonucleotide reductase in response to iron starvation
Authors: Andrews Simon C. 
Published: March 2011

SummaryRibonucleotide reductases supply cells with their deoxyribonucleotides. Three enzyme types are known, classes I, II and III. Class II enzymes are anaerobic whereas class I enzymes are aerobic, and so class I and II enzymes are often produced by the same organism under opposing oxygen regimes. Escherichia coli contains two types of class I enzyme (Ia and Ib) with the Fe‐dependent Ia enzyme (NrdAB) performing the major role aerobically, leaving the purpose of the Ib enzyme (NrdEF) unclear. Several papers have recently focused on the class Ib enzymes showing that they are Mn (rather than Fe) dependent and suggesting that the E. coli NrdEF may function under redox‐stress conditions. A paper published in this issue of Molecular Microbiology from James Imlay's group confirms that this unexplained NrdEF Ib enzyme is Mn‐dependent, but shows that it does not substitute for NrdAB during redox stress. Instead, a role during iron restriction is demonstrated. Thus, the purpose of NrdEF (and possibly other class Ib enzymes) is to enhance growth under aerobic, low‐iron conditions, and to functionally replace the Fe‐dependent NrdAB when iron is unavailable. This finding reveals a new mechanism by which bacteria adjust to life under iron deprivation.
The protective shell: sclereids and their mechanical function in corollas of some species of Camellia (Theaceae)
Authors: Zhang W. , Wang X.‐Q. , Li Z.‐Y. 
Published: March 2011

AbstractStudies of rain‐wash effects on pollen have shown that flower structures can protect susceptible pollen from rain. It remains unclear, however, how a thin corolla can withstand external force and perform its protective function. The sclereids in petals of several species of Camellia (Theaceae) were anatomically investigated to determine their mechanical properties. To examine the effects of changing physical environment on the occurrence of sclereids in petals, sclereid density in petals of six species, including wild samples from different rainfall zones and samples from a greenhouse under mild conditions without wind and rain, were examined and statistically analysed. The results showed that the occurrence of sclereids in petals varied with physical environment. The number of sclereids in the same species increased with the increasing rainfall. There were abundant sclereids in petals of the wild species, but few or no sclereids in species cultivated in the greenhouse. Moreover, the anatomical features of sclereids, especially the unique distribution pattern that has not hitherto been described, were correlated with external environmental pressures. Our observations reveal a novel mechanical system in the corolla and provide further evidence for the hypothesis that flower structures may protect rain‐susceptible pollen.
Decreased structural defence of an invasive thistle under warming
Authors: Zhang R. , Leshak A. , Shea K. 
Published: March 2011

AbstractPlant structural defences play a key role in preventing fitness loss due to herbivory. However, how structural defences are affected by potential climate change is rarely examined. We examined how leaf morphological traits that relate to the structural defence of an invasive thistle, Carduus nutans, change in a warmer climate. We manipulated warming using open‐top chambers (OTCs) and examined the morphology of leaves at three different positions (the 5th, 10th and 15th leaves, counted from the top of the plant) in two destructive summer censuses. We found that structural defence traits were different under ambient versus warmed conditions. Prickle densities (both the number of prickles per leaf area and the number of prickles per leaf mass) were significantly lower in plants grown in a warmer climate. Our results suggest that plant structural defences may be reduced under warming, and therefore should be considered when examining species’ responses to climate change.
Development of a genetic system for the moderately halophilic bacterium Halobacillus halophilus: generation and characterization of mutants defect in the production of the compatible solute proline
Authors: Köcher Saskia , Averhoff Beate , Müller Volker 
Published: March 2011

SummaryA procedure for markerless mutagenesis gene deletions was developed for the moderately halophilic model strain Halobacillus halophilus. Gene transfer was achieved by protoplast fusion and allelic replacement by a two‐step procedure. In the first step the non‐replicating plasmid integrated over the upstream or the downstream region of the target gene or operon into the chromosome to obtain single‐crossover mutants. When cells were grown under non‐selective conditions a second homologous recombination happened (segregation). This resulted in either the wild‐type or the mutated allele. The method was used to delete the proHJA operon from H. halophilus. The mutant still produced proline and thus was not proline auxotroph but it completely lost the ability to produce proline as a compatible solute. However, growth was not impaired and the loss of the solute proline was compensated for by an increase in glutamate, glutamine and ectoine concentration. Expressions of the genes encoding the biosynthesis enzymes of theses solutes were upregulated and the activity of the key enzyme in glutamine biosynthesis, the glutamine synthetase, was increased. A model for the proline biosynthesis in the ΔproHJA mutant is discussed.
The burden of cardiovascular disease associated with high body mass index in the Asia–Pacific region
Authors: Lee C. M. Y. , Colagiuri S. , Ezzati M. , Woodward M. 
Published: March 2011

SummaryStudying obesity in the Asia–Pacific region is difficult because of the diverse ethnic background and different stages of economic and nutrition transition. The burden of cardiovascular disease associated with overweight (defined as body mass index ≥25 kg m−2) was previously estimated for countries within the region. However, using the conventional cut‐point of 25 kg m−2 ignores the continuous association between body mass index and cardiovascular disease from approximately 20 kg m−2. By estimating the proportion of cardiovascular disease that would be prevented if the theoretical mean body mass index in the population was shifted to 21 kg m−2, nationally representative data from 15 countries suggested the population attributable fractions for cardiovascular disease were approximately three times higher than the previous estimates. Coronary heart disease attributable to body mass index other than 21 kg m−2 ranged from 2% in India to 58% in American Samoa. Similarly, the population attributable fraction for ischaemic stroke ranged from 3% in India to 64% in American Samoa. If cardiovascular risk increases from 21 kg m−2 applies to all populations, most countries in the region will need to aim towards substantially reducing their current population mean body mass index in order to lower the burden of cardiovascular disease associated with excess weight.
Preventing chronic diseases by promoting healthy diet and lifestyle: public policy implications for China
Authors: Hu F. B. , Liu Y. , Willett W. C. 
Published: March 2011

SummaryFuelled by rapid urbanization and changes in dietary and lifestyle choices, chronic diseases have emerged as a critical public health issue in China. The Healthy China 2020 programme recently announced by the Chinese government has set an overarching goal of promoting public health and making health care accessible and affordable for all Chinese citizens by year 2020. One of important components of the programme is to reduce chronic diseases by promoting healthy eating and active lifestyles. Chronic diseases not only affect health and quality of life, but also have economical and social consequences. With a limited infrastructure for chronic disease care, China is ill‐equipped to deal with the escalating chronic disease epidemic, which threatens to reverse the gains of economic development in recent decades. Population‐based intervention studies conducted in China and elsewhere have demonstrated the efficacy and effectiveness of several preventive strategies to reduce risk of chronic diseases in high‐risk individuals and the general population. However, translating these findings into practice requires changes in health systems and public policies. To achieve the goals set by the Healthy China 2020 programme, prevention of chronic diseases should be elevated to a national public policy priority.
College students' intentions to use e‐portfolios: From the perspectives of career‐commitment status and weblog‐publication behaviours
Authors: Tzeng Jeng‐Yi , Chen Ssu‐Han 
Published: March 2011

AbstractThe growing popularity of a school‐wide e‐portfolio system in colleges and universities has raised concerns regarding whether students will use it or consider it important to have an e‐portfolio system, especially when its use is not required by their curriculum. This study investigated college students' intentions to use and the students' attitudes towards using an e‐portfolio system, and did so from the perspectives of career‐commitment status and weblog‐publication behaviours. The results indicate that career‐commitment status substantially influences college students' intentions and attitudes relative to using an e‐portfolio system. Also, overlap in the functions of weblogs and e‐portfolios (which allow people to use them interchangeably) does not directly result in higher or lower levels of intention to use an e‐portfolio system. A composite system providing career services, goal‐oriented self‐presentation and personality‐driven self‐expression is recommended.
Chronic treatment with angiotensin‐(1‐7) improves renal endothelial dysfunction in apolipoproteinE‐deficient mice
Authors: Stegbauer J , Potthoff SA , Quack I , Mergia E , Clasen T , Friedrich S , Vonend O , Woznowski M , Königshausen E , Sellin L , Rump LC 
Published: March 2011

BACKGROUND AND PURPOSE ApolipoproteinE‐deficient [apoE (−/−)] mice, a model of human atherosclerosis, develop endothelial dysfunction caused by decreased levels of nitric oxide (NO). The endogenous peptide, angiotensin‐(1‐7) [Ang‐(1‐7)], acting through its specific GPCR, the Mas receptor, has endothelium‐dependent vasodilator properties. Here we have investigated if chronic treatment with Ang‐(1‐7) improved endothelial dysfunction in apoE (−/−) mice.EXPERIMENTAL APPROACH ApoE (−/−) mice fed on a lipid‐rich Western diet were divided into three groups and treated via osmotic minipumps with either saline, Ang‐(1‐7) (82 µg·kg−1·h−1) or the same dose of Ang‐(1‐7) together with D‐Ala‐Ang‐(1‐7) (125 µg·kg−1·h−1) for 6 weeks. Renal vascular function was assessed in isolated perfused kidneys.KEY RESULTS Ang‐(1‐7)‐treated apoE (−/−) mice showed improved renal endothelium‐dependent vasorelaxation induced by carbachol and increased renal basal cGMP production, compared with untreated apoE (−/−) mice. Tempol, a reactive oxygen species (ROS) scavenger, improved endothelium‐dependent vasorelaxation in kidneys of saline‐treated apoE (−/−) mice whereas no effect was observed in Ang‐(1‐7)‐treated mice. Chronic treatment with D‐Ala‐Ang‐(1‐7), a specific Mas receptor antagonist, abolished the beneficial effects of Ang‐(1‐7) on endothelium‐dependent vasorelaxation. Renal endothelium‐independent vasorelaxation showed no differences between treated and untreated mice. ROS production and expression levels of the NAD(P)H oxidase subunits gp91phox and p47phox were reduced in isolated preglomerular arterioles of Ang‐(1‐7)‐treated mice, compared with untreated mice, whereas eNOS expression was increased.CONCLUSION AND IMPLICATIONS Chronic infusion of Ang‐(1‐7) improved renal endothelial function via Mas receptors, in an experimental model of human cardiovascular disease, by increasing levels of endogenous NO.
Evidence for a differential opioidergic involvement in the analgesic effect of antidepressants: prediction for efficacy in animal models of neuropathic pain?
Authors: Wattiez A‐S , Libert F , Privat A‐M , Loiodice S , Fialip J , Eschalier A , Courteix C 
Published: March 2011

BACKGROUND AND PURPOSEAntidepressants are one of the recommended treatments for neuropathic pain. However, their analgesic action remains unpredictable, and there are no selection criteria for clinical use. Better knowledge of their mechanism of action could help highlight differences underlying their unequal efficacy.EXPERIMENTAL APPROACHWe compared the activity of a tricyclic antidepressant (clomipramine) with selective 5‐HT and noradrenaline reuptake inhibitors (milnacipran and duloxetine) in streptozocin‐induced diabetic and chronic constriction nerve injury‐induced neuropathic rats, after repeated injections. We looked for an opioidergic mechanism in their action.KEY RESULTSAbolition of mechanical hyperalgesia was observed in mononeuropathic rats after five injections of clomipramine (5 mg·kg−1, s.c.) and milnacipran (10 or 20 mg·kg−1, i.p.) and in diabetic rats after clomipramine. An additional antinociceptive effect was obtained with five injections of duloxetine (3 mg·kg−1, i.p.) in both models and milnacipran (10 mg·kg−1, i.p.) in diabetic rats. These effects were observed with plasma antidepressant concentrations similar to those found in patients treated for neuropathic pain. Naloxone (1 mg·kg−1, i.v.) only suppressed the anti‐hyperalgesic effects of clomipramine in both models of pain and of milnacipran in the traumatic model.CONCLUSIONS AND IMPLICATIONSThe opioid system appears to be involved in the mechanism of action of antidepressants that only have an anti‐hyperalgesic effect but not in those that have a stronger (i.e. antinociceptive) effect. These differences between the antidepressants occurred whatever the aetiology of the neuropathy and, if confirmed in clinical trials, could be used to decide which antidepressant is administered to a patient with neuropathic pain.