bluuebunny/crossref_metadata_2025_split huggingface dataset:
LNA‐substituted degenerate primers improve detection of nitrogenase gene transcription in environmental samples
Authors: Burbano Claudia Sofía , Reinhold‐Hurek Barbara , Hurek Thomas 
Published: December 2009

SummaryIn order to study the active diazotrophic bacterial community and to capture the majority of its individuals in environmental samples, strategies improving gene detection by increasing sensitivity and efficiency of PCR reactions are highly desirable. Since LNA (locked nucleic acids) modifications might alleviate a low sensitivity and specificity often limiting PCR reactions utilizing degenerate primers, the effect of LNA substituted primers on the detection of nifH transcripts in roots of rice and sugar cane by direct reverse transcription polymerase chain reaction (RT‐PCR) was studied. The LNA substitution of the RT primer increased the sensitivity of the RT‐PCR up to 26‐fold, whereas LNA substitution of the PCR primers decreased specificity. Terminal restriction fragment length polymorphism (T‐RFLP) analysis of RT‐PCR products showed that LNA substitutions in the RT‐primer did not change the pattern of nifH cDNA phylotypes. The use of the LNA‐substituted RT‐primer allowed the detection of nifH transcripts in sugar cane, where DNA primers alone failed to produce RT‐PCR products. These results suggest that similar improvements to PCR detection of nucleic acids can be expected for other environmental samples and genes likewise, when LNA‐substituted primers are used.
Molecular evaluation of the human gut methanogenic archaeal microbiota reveals an age‐associated increase of the diversity
Authors: Mihajlovski Agnès , Doré Joël , Levenez Florence , Alric Monique , Brugère Jean‐François 
Published: December 2009

SummaryThe methanogenic diversity of the human intestinal microbiota has long been viewed as composed of two Methanobacteriales: Methanobrevibacter smithii and Methanosphaera stadtmanae. Recently, Mx‐01, a new phylotype hypothesized to belong to a putative sixth methanogenic order, was recovered from human faeces. Here we examined the diversity and the distribution of methanogens among healthy people of three age groups by analysing mcrA and 16S rDNA clones. The mcrA analysis of ∼1200 clones revealed that the usual Methanobacteriales were present without any significant difference among adults and elderly (respectively 60% and 80% of carriers, n = 40, P = 0.3). In addition, four new phylotypes that grouped with Mx‐01 in the same monophyletic clade were recovered. These phylotypes were significantly more frequently detected in elderly people (40%, n = 20) than in adults (10%, n = 20, P = 0.065). In parallel, new 16S rDNA phylotypes affiliated near or within Thermoplasmatales were recovered. Altogether, these results indicate an age‐related apparition of Mx‐phylotypes, putatively methanogenic, which are formed of several species carrying a mcrA gene and that are not related to any of the five methanogenic orders. These species may be related to Thermoplasmatales or may cohabit with archaeal species related to Thermoplasmatales.
Role of insulin-like growth factor 1 receptor and c-Src in endothelin-1- and angiotensin II-induced PKB phosphorylation, and hypertrophic and proliferative responses in vascular smooth muscle cellsThis article is one of a selection of papers published in a special issue on Advances in Cardiovascular Research.
Authors: Bouallegue Ali , Vardatsikos George , Srivastava Ashok K. 
Published: December 2009

Endothelin-1 (ET-1) and angiotensin II (Ang II) are vasoactive peptides believed to contribute to the pathogenesis of vascular abnormalities such as hypertension, atherosclerosis, hypertrophy, and restenosis. The concept of transactivation of growth factor receptors, such as epidermal growth factor receptor (EGFR), in triggering vasoactive peptide-induced signaling events has gained much recognition during the past several years. We have demonstrated that insulin-like growth factor type 1 receptor (IGF-1R) plays a role in transducing the effect of H2O2, leading to protein kinase B (PKB) phosphorylation. Since vasoactive peptides elicit their responses through generation of reactive oxygen species, including H2O2, we investigated whether IGF-1R transactivation plays a similar role in ET-1- and Ang II-induced PKB phosphorylation and hypertrophic responses in vascular smooth muscle cells (VSMC). AG1024, a specific inhibitor of IGF-1R protein tyrosine kinase (PTK), attenuated both ET-1- and Ang II-induced PKB phosphorylation in a dose-dependent manner. ET-1 and Ang II treatment also induced the phosphorylation of tyrosine residues in the autophosphorylation sites of IGF-1R, which were blocked by AG1024. In addition, both ET-1 and Ang II evoked tyrosine phosphorylation of c-Src, a nonreceptor PTK, whereas pharmacological inhibition of c-Src PTK activity by PP2, a specific inhibitor of Src-family tyrosine kinase, significantly reduced PKB phosphorylation as well as tyrosine phosphorylation of IGF-1R induced by the 2 vasoactive peptides. Furthermore, protein and DNA synthesis enhanced by ET-1 and Ang II were attenuated by AG1024 and PP2. In conclusion, these data suggest that IGF-1R PTK and c-Src PTK play a critical role in mediating PKB phosphorylation as well as hypertrophic and proliferative responses induced by ET-1 and Ang II in A10 VSMC.
Brain renin–angiotensin–aldosterone system and ventricular remodeling after myocardial infarct: a reviewThis article is one of a selection of papers published in a special issue on Advances in Cardiovascular Research.
Authors: Westcott Katherine V. , Huang Bing S. , Leenen Frans H.H. 
Published: December 2009

After a myocardial infarct (MI), a variety of mechanisms contribute to progressive cardiac remodeling and dysfunction. Progressive activation of central sympathoexcitatory pathways appears to depend on a neuromodulatory pathway, involving local production of aldosterone and release of endogenous ouabain-like compounds (‘ouabain’) possibly from magnocellular neurons in the supraoptic and paraventricular nuclei. ‘Ouabain’ may lower the membrane potential of neurons and thereby enhance activity of angiotensinergic pathways. These central pathways appear to coordinate progressive activation of several peripheral mechanisms such as sympathetic tone and circulating and cardiac renin–angiotensin–aldosterone system (RAAS). Central blockade of aldosterone production, mineralocorticoid receptors, ‘ouabain’ activity, or AT1 receptors similarly prevents activation of these peripheral mechanisms. Cardiac remodeling after MI involves progressive left ventricular dilation, fibrosis, and decrease in contractile performance. Central blockade of this neuromodulatory pathway causes a marked attenuation of the remodeling and dysfunction, presumably by inhibiting increases in (cardiac) sympathetic activity and RAAS. At the cellular level, these systems may contribute to the cardiac remodeling by activating proinflammatory cytokines and cardiac myocyte apoptosis. New therapeutic approaches, specifically preventing activation of this brain neuromodulatory pathway, may lead to more optimal and specific approaches to the prevention of heart failure after MI.
Dual effect of polyphenolic compounds on cardiac Na+/K+-ATPase during development and persistence of hypertension in ratsThis article is one of a selection of papers published in a special issue on Advances in Cardiovascular Research.
Authors: Vlkovičová Jana , Javorková Veronika , Mézešová Lucia , Pecháňová Olga , Andriantsitohaina Ramaroson , Vrbjar Norbert 
Published: December 2009

The enzyme kinetics of cardiac Na+/K+-ATPase were used for characterizing the ATP- and Na+-binding sites after administration of red wine polyphenolic compounds (Provinol) during developing and sustained hypertension. Hypertension was induced in rats (LN group) by the nitric oxide synthase inhibitor NG-nitro-l-arginine methyl ester (l-NAME, 40 mg·kg–1·day–1). Provinol (40 mg·kg–1·day–1) was applied during developing hypertension (LNPF4 group) and sustained hypertension (LNPF7/3 group). Provinol reduced the number of active Na+/K+-ATPase molecules in cardiac tissue, as indicated by decreased Vmaxvalues (by 33% in LNPF4 and 26% in LNPF7/3 compared with LN). Concerning qualitative properties of the enzyme, Provinol induced different effects on the ATP- and Na+-binding sites of Na+/K+-ATPase. The ATP-binding site was impaired by Provinol, as indicated by increased Kmvalue (by 52% in LNPF4 vs. LN), suggesting worsened utilization of substrate by the enzyme. In sustained hypertension, however, Provinol had no effect on the ATP-binding site, as indicated by unchanged Kmvalue (LNPF7/3 vs. LN). On the other hand, the Na+-binding site was protected by Provinol, as suggested by decreased KNavalue (by 72% in LNPF4 and 69% in LNPF7/3 vs. LN), indicating an increased affinity of the enzyme for sodium. Thus, Provinol appeared to stimulate the extrusion of Na+from cardiac cells, especially in the physiologically important range of sodium concentrations (2–10 mmol·L–1), during both developing and sustained hypertension.
TOWARDS A MORE FUNDAMENTAL THEORY BEYOND QUANTUM MECHANICS, AVOIDING THE SCHRÖDINGER PARADOX
Authors: CARAVAGLIOS FRANCESCO 
Published: December 2009

The main distinction between classical mechanics and quantum mechanics is the lack in the latter of a full mechanical determinism: different final states can arise from the same physical state, after the measurement. No hidden variable is supposed to exist, nothing can discriminate two apparently identical states even if they give a different result. In this paper we try to put the basis for a more fundamental theory that (approximately) coincides with quantum mechanics when comparing statistics, but it is more fundamental, since it mathematically describes measurement processes giving an explicit time evolution of the wave function during the collapse. The theory is deterministic even if the Heisenberg uncertainty principle is still valid. The theory distinguishes physical states that collapse and physical states that do not collapse. The theory can be made compatible with all experiments done in the past, but new phenomena such as violations of the Born law or the superposition principle could transpire. However, even if we have probably shown that it is possible to build ad hoc a theory that can describe both the wave function collapse and the Schrödinger linear evolution, a simple and unified construction is still missing.
On Two Iterative Methods for Mixed Monotone Variational Inequalities
Authors: Lu Xiwen , Xu Hong-Kun , Yin Ximing 
Published: December 2009

AbstractA mixed monotone variational inequality (MMVI) problem in a Hilbert space "Equation missing" is formulated to find a point "Equation missing" such that "Equation missing" for all "Equation missing", where "Equation missing" is a monotone operator and "Equation missing" is a proper, convex, and lower semicontinuous function on "Equation missing". Iterative algorithms are usually applied to find a solution of an MMVI problem. We show that the iterative algorithm introduced in the work of Wang et al., (2001) has in general weak convergence in an infinite-dimensional space, and the algorithm introduced in the paper of Noor (2001) fails in general to converge to a solution.
Approximating Fixed Points of Nonexpansive Nonself Mappings in CAT(0) Spaces
Authors: Laowang W , Panyanak B 
Published: December 2009

AbstractSuppose that "Equation missing" is a nonempty closed convex subset of a complete CAT(0) space "Equation missing" with the nearest point projection "Equation missing" from "Equation missing" onto "Equation missing". Let "Equation missing" be a nonexpansive nonself mapping with "Equation missing". Suppose that "Equation missing" is generated iteratively by "Equation missing", "Equation missing", "Equation missing", where "Equation missing" and "Equation missing" are real sequences in "Equation missing" for some "Equation missing". Then "Equation missing""Equation missing"-converges to some point "Equation missing" in "Equation missing". This is an analog of a result in Banach spaces of Shahzad (2005) and extends a result of Dhompongsa and Panyanak (2008) to the case of nonself mappings.
Emission Scenario Dependency of Precipitation on Global Warming in the MIROC3.2 Model
Authors: Shiogama Hideo , Emori Seita , Takahashi Kiyoshi , Nagashima Tatsuya , Ogura Tomoo , Nozawa Toru , Takemura Toshihiko 
Published: December 2009

Abstract
The precipitation sensitivity per 1 K of global warming in twenty-first-century climate projections is smaller in an emission scenario with larger greenhouse gas concentrations and aerosol emissions, according to the Model for Interdisciplinary Research on Climate 3.2 (MIROC3.2) coupled atmosphere–ocean general circulation model. The authors examined the reasons for the precipitation sensitivity to emission scenarios by performing separated individual forcing runs under high and low emission scenarios. It was found that the dependency on emission scenario is mainly caused by differences in black and organic carbon aerosol forcing (the sum of which is cooling forcing) between the emission scenarios and that the precipitation is more sensitive to carbon aerosols than well-mixed greenhouse gases. They also investigated the reason for the larger precipitation sensitivity (larger magnitude of precipitation decrease per 1 K cooling of temperature) in the carbon aerosol runs. Surface dimming due to the direct and indirect effects of carbon aerosols effectively decreases evaporation and precipitation, which enhances the precipitation sensitivity in the carbon aerosol runs. In terms of the atmospheric moisture cycle, although changes of vertical circulation offset the effects of changes in the atmospheric moisture in both the carbon aerosol and greenhouse gas runs, the amplitude of vertical circulation change per 1 K temperature change is less in the carbon aerosol runs. Furthermore, the second indirect effect of organic carbon aerosol counteracts the influence of the vertical circulation change. These factors lead to suppression of changes in the moisture’s atmospheric residence time and increase of the precipitation sensitivity in the carbon aerosol runs.
PreDisorder: ab initio sequence-based prediction of protein disordered regions
Authors: Deng Xin , Eickholt Jesse , Cheng Jianlin 
Published: December 2009

Abstract

Background
Disordered regions are segments of the protein chain which do not adopt stable structures. Such segments are often of interest because they have a close relationship with protein expression and functionality. As such, protein disorder prediction is important for protein structure prediction, structure determination and function annotation.

Results
This paper presents our protein disorder prediction server, PreDisorder. It is based on our ab initio prediction method (MULTICOM-CMFR) which, along with our meta (or consensus) prediction method (MULTICOM), was recently ranked among the top disorder predictors in the eighth edition of the Critical Assessment of Techniques for Protein Structure Prediction (CASP8). We systematically benchmarked PreDisorder along with 26 other protein disorder predictors on the CASP8 data set and assessed its accuracy using a number of measures. The results show that it compared favourably with other ab initio methods and its performance is comparable to that of the best meta and clustering methods.

Conclusion
PreDisorder is a fast and reliable server which can be used to predict protein disordered regions on genomic scale. It is available at http://casp.rnet.missouri.edu/predisorder.html.
The role of virulence factors in the outcome of staphylococcal peritonitis in CAPD patients
Authors: Barretti Pasqual , Montelli Augusto C , Batalha Jackson EN , Caramori Jacqueline CT , Cunha Maria de Lourdes RS 
Published: December 2009

Abstract

Background
Peritonitis continues to be the most frequent cause of peritoneal dialysis (PD) failure, with an important impact on patient mortality. Gram-positive cocci such as Staphylococcus epidermidis, other coagulase-negative staphylococci (CoNS), and Staphylococcus aureus are the most frequent etiological agents of PD-associated peritonitis worldwide. The objective of the present study was to compare peritonitis caused by S. aureus and CoNS and to evaluate the factors influencing outcome.

Methods
Records of 86 new episodes of staphylococcal peritonitis that occurred between 1996 and 2000 in the Dialysis unit of a single university hospital were studied (35 due to S. aureus, 24 to S. epidermidis and 27 to other CoNS). The production of slime, lipase, lecithinase, nuclease (DNAse), thermonuclease (TNAse), α- and β-hemolysin, enterotoxins (SEA, SEB, SEC, SED) and toxic shock syndrome toxin-1 (TSST-1) was studied in S. aureus and CoNS. Antimicrobial susceptibility was evaluated based on the minimal inhibitory concentration determined by the E-test. Outcome predictors were evaluated by two logistic regression models.

Results
The oxacillin susceptibility rate was 85.7% for S. aureus, 41.6% for S. epidermidis, and 51.8% for other CoNS (p = 0.001). Production of toxins and enzymes, except for enterotoxin A and α-hemolysin, was associated with S. aureus episodes (p < 0.001), whereas slime production was positive in 23.5% of CoNS and 8.6% of S. aureus strains (p = 0.0047). The first model did not include enzymes and toxins due to their association with S. aureus. The odds of resolution were 9.5 times higher for S. epidermidis than for S. aureus (p = 0.02) episodes, and were similar for S. epidermidis and other CoNS (p = 0.8). The resolution odds were 68 times higher for non-slime producers (p = 0.001) and were not influenced by oxacillin resistance among vancomycin-treated cases (p = 0.89). In the second model, the resolution rate was similar for S. aureus and S. epidermidis (p = 0.70), and slime (p = 0.001) and α-hemolysin (p = 0.04) production were independent predictors of non-resolution.

Conclusion
Bacterial species and virulence factors rather than antibiotic resistance influence the outcome of staphylococcal peritonitis.
Quality assessment of DNA derived from up to 30 years old formalin fixed paraffin embedded (FFPE) tissue for PCR-based methylation analysis using SMART-MSP and MS-HRM
Authors: Kristensen Lasse S , Wojdacz Tomasz K , Thestrup Britta B , Wiuf Carsten , Hager Henrik , Hansen Lise Lotte 
Published: December 2009

Abstract

Background
The High Resolution Melting (HRM) technology has recently been introduced as a rapid and robust analysis tool for the detection of DNA methylation. The methylation status of multiple tumor suppressor genes may serve as biomarkers for early cancer diagnostics, for prediction of prognosis and for prediction of response to treatment. Therefore, it is important that methodologies for detection of DNA methylation continue to evolve. Sensitive Melting Analysis after Real Time - Methylation Specific PCR (SMART-MSP) and Methylation Sensitive - High Resolution Melting (MS-HRM) are two methods for single locus DNA methylation detection based on HRM.

Methods
Here, we have assessed the quality of DNA extracted from up to 30 years old Formalin Fixed Paraffin Embedded (FFPE) tissue for DNA methylation analysis using SMART-MSP and MS-HRM. The quality assessment was performed on DNA extracted from 54 Non-Small Cell Lung Cancer (NSCLC) samples derived from FFPE tissue, collected over 30 years and grouped into five years intervals. For each sample, the methylation levels of the CDKN2A (p16) and RARB promoters were estimated using SMART-MSP and MS-HRM assays designed to assess the methylation status of the same CpG positions. This allowed for a direct comparison of the methylation levels estimated by the two methods for each sample.

Results

CDKN2A promoter methylation levels were successfully determined by SMART-MSP and MS-HRM in all 54 samples. Identical methylation estimates were obtained by the two methods in 46 of the samples. The methylation levels of the RARB promoter were successfully determined by SMART-MSP in all samples. When using MS-HRM to assess RARB methylation five samples failed to amplify and 15 samples showed a melting profile characteristic for heterogeneous methylation. Twenty-seven of the remaining 34 samples, for which the methylation level could be estimated, gave the same result as observed when using SMART-MSP.

Conclusion
MS-HRM and SMART-MSP can be successfully used for single locus methylation studies using DNA derived from up to 30 years old FFPE tissue. Furthermore, it can be expected that MS-HRM and SMART-MSP will provide similar methylation estimates when assays are designed to analyze the same CpG positions.
Mutation analysis of the AATF gene in breast cancer families
Authors: Haanpää Maria , Reiman Mervi , Nikkilä Jenni , Erkko Hannele , Pylkäs Katri , Winqvist Robert 
Published: December 2009

Abstract

Background
About 5-10% of breast cancer is due to inherited disease predisposition. Many previously identified susceptibility factors are involved in the maintenance of genomic integrity. AATF plays an important role in the regulation of gene transcription and cell proliferation. It induces apoptosis by associating with p53. The checkpoint kinases ATM/ATR and CHEK2 interact with and phosphorylate AATF, enhancing its accumulation and stability. Based on its biological function, and direct interaction with several known breast cancer risk factors, AATF is a good candidate gene for being involved in heritable cancer susceptibility.

Methods
Here we have screened the entire coding region of AATF in affected index cases from 121 Finnish cancer families for germline defects, using conformation sensitive gel electrophoresis and direct sequencing.

Results
Altogether seven different sequence changes were observed, one missense variant and six intronic ones. Based on the in silico analyses of these sequence alterations, as well as their occurrence in cases and controls, none of them, however, were predicted to be pathogenic.

Conclusions
To our knowledge, this is the first study reporting the mutation screening of the AATF gene in familial breast cancer cases. No evidence for the association with breast cancer was observed.
Prognostic impact of H3K27me3 expression on locoregional progression after chemoradiotherapy in esophageal squamous cell carcinoma
Authors: He Li-Ru , Liu Meng-Zhong , Li Bin-Kui , Rao Hui-Lan , Liao Yi-Ji , Guan Xin-Yuan , Zeng Yi-Xin , Xie Dan 
Published: December 2009

Abstract

Background
Trimethylation of lysine 27 on histone H3 (H3K27me3) by enhancer of zeste homolog 2 (EZH2) is an epigenetic mark that mediates gene silencing. EZH2 is overexpressed and correlates with poor prognosis in many cancers. However, the clinical implication of H3K27me3 in human malignancies has not been well established. We wished to ascertain whether a correlation exists between the expression of H3K27me3 and clinical outcome in a group of patients with esophageal squamous cell carcinoma (ESCC) treated with definitive chemoradiotherapy (CRT).

Methods
The method of immunohistochemistry (IHC) was utilized to examine the protein expression of H3K27me3 in 98 pretreatment biopsy specimens of ESCC and in 30 samples of normal esophageal mucosa. The clinical/prognostic significance of H3K27me3 expression was statistically analyzed.

Results
The expression frequency and expression levels of H3K27me3 were significantly higher in ESCCs than in normal tissues. There was a positive correlation between H3K27me3 expression and WHO grade (P = 0.016), tumor size (P = 0.019), T status (P = 0.024), locoregional progression (P = 0.009) and EZH2 expression (P = 0.036). High H3K27me3 expression was associated with poor locoregional progression-free survival (LPFS) (P = 0.010) in ESCC. Further analysis demonstrated that H3K27me3 could stratify patient outcome in T2-3 (P = 0.048), N0 (P = 0.005) and M0 (P = 0.018) stages as well as in CRT effective group (P = 0.022).

Conclusions
Our data suggests that H3K27me3 expression examined by IHC might be useful for stratifying LPFS for different subsets of ESCC patients treated with definitive CRT.