bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discriminative detection and enumeration of microbial life in marine subsurface sediments
Authors: Morono Yuki , Terada Takeshi , Masui Noriaki , Inagaki Fumio 
Published: February 2009

Abstract
Detection and enumeration of microbial life in natural environments provide fundamental information about the extent of the biosphere on Earth. However, it has long been difficult to evaluate the abundance of microbial cells in sedimentary habitats because non-specific binding of fluorescent dye and/or auto-fluorescence from sediment particles strongly hampers the recognition of cell-derived signals. Here, we show a highly efficient and discriminative detection and enumeration technique for microbial cells in sediments using hydrofluoric acid (HF) treatment and automated fluorescent image analysis. Washing of sediment slurries with HF significantly reduced non-biological fluorescent signals such as amorphous silica and enhanced the efficiency of cell detachment from the particles. We found that cell-derived SYBR Green I signals can be distinguished from non-biological backgrounds by dividing green fluorescence (band-pass filter: 528/38 nm (center-wavelength/bandwidth)) by red (617/73 nm) per image. A newly developed automated microscope system could take a wide range of high-resolution image in a short time, and subsequently enumerate the accurate number of cell-derived signals by the calculation of green to red fluorescence signals per image. Using our technique, we evaluated the microbial population in deep marine sediments offshore Peru and Japan down to 365 m below the seafloor, which provided objective digital images as evidence for the quantification of the prevailing microbial life. Our method is hence useful to explore the extent of sub-seafloor life in the future scientific drilling, and moreover widely applicable in the study of microbial ecology.
The alkaline phosphatase PhoX is more widely distributed in marine bacteria than the classical PhoA
Authors: Sebastian Marta , Ammerman James W 
Published: February 2009

Abstract
Phosphorus (P) is a vital nutrient for all living organisms and may control the growth of bacteria in the ocean. Bacteria induce alkaline phosphatases when inorganic phosphate (Pi) is insufficient to meet their P-requirements, and therefore bulk alkaline phosphatase activity measurements have been used to assess the P-status of microbial assemblages. In this study, the molecular basis of marine bacterial phosphatases and their potential role in the environment were investigated. We found that only a limited number of homologs to the classical Escherichia coli alkaline phosphatase (PhoA) were present in marine isolates in the Bacteroidetes and γ-proteobacteria lineages. In contrast, PhoX, a recently described phosphatase, was widely distributed among diverse bacterial taxa, including Cyanobacteria, and frequently found in the marine metagenomic Global Ocean Survey database. These taxa included ecologically important groups such as Roseobacter and Trichodesmium. PhoX was induced solely upon P-starvation and accounted for approximately 90% of the phosphatase activity in the model marine bacterium Silicibacter pomeroyi. Analysis of the available transcriptomic datasets and their corresponding metagenomes indicated that PhoX is more abundant than PhoA in oligotrophic marine environments such as the North Pacific Subtropical Gyre. Those analyses also revealed that PhoA may be important when Bacteroidetes are abundant, such as in algal bloom episodes. However, PhoX appears to be much more widespread. Its identification as a gene that mediates organic P acquisition in ecologically important groups, and as a marker of Pi-stress, constitutes an important step toward a better understanding of the marine P cycle.
Quantitative detection of culturable methanogenic archaea abundance in anaerobic treatment systems using the sequence-specific rRNA cleavage method
Authors: Narihiro Takashi , Terada Takeshi , Ohashi Akiko , Wu Jer-Horng , Liu Wen-Tso , Araki Nobuo , Kamagata Yoichi , Nakamura Kazunori , Sekiguchi Yuji 
Published: February 2009

Abstract
A method based on sequence-specific cleavage of rRNA with ribonuclease H was used to detect almost all known cultivable methanogens in anaerobic biological treatment systems. To do so, a total of 40 scissor probes in different phylogeny specificities were designed or modified from previous studies, optimized for their specificities under digestion conditions with 32 methanogenic reference strains, and then applied to detect methanogens in sludge samples taken from 6 different anaerobic treatment processes. Among these processes, known aceticlastic and hydrogenotrophic groups of methanogens from the families Methanosarcinaceae, Methanosaetaceae, Methanobacteriaceae, Methanothermaceae and Methanocaldococcaceae could be successfully detected and identified down to the genus level. Within the aceticlastic methanogens, the abundances of mesophilic Methanosaeta accounted for 5.7–48.5% of the total archaeal populations in mesophilic anaerobic processes, and those of Methanosarcina represented 41.7% of the total archaeal populations in thermophilic processes. For hydrogenotrophic methanogens, members of the Methanomicrobiales, Methanobrevibacter and Methanobacterium were detected in mesophilic processes (1.2–17.2%), whereas those of Methanothermobacter, Methanothermaceae and Methanocaldococcaceae were detected in thermophilic process (2.0–4.8%). Overall results suggested that those hierarchical scissor probes developed could be effective for rapid and possibly on-site monitoring of targeted methanogens in different microbial environments.
A MULTIWAVELENGTH VIEW OF STAR FORMATION IN INTERACTING GALAXIES IN THE PAVO GROUP
Authors: Machacek M. , Ashby M. L. N. , Jones C. , Forman W. R. , Bastian N. 
Published: February 2009

ABSTRACT
We combine Spitzer Infrared Array Camera mid-infrared and Chandra X-ray observations of the dominant galaxies NGC 6872 and NGC 6876 in the Pavo group with archival optical and H i data to study interaction-induced star formation. In the spiral galaxy NGC 6872, 8.0 μm and 5.8 μm nonstellar emission having colors consistent with polycyclic aromatic hydrocarbons (PAHs) is concentrated primarily in clumps in three regions: in a 5 kpc radius outer ring about the center of the spiral galaxy, in a bridge of emission connecting NGC 6872's northern spiral arm to IC 4970, and along the full extent of both NGC 6872's tidal arms. PAH emission is correlated with young star clusters and dense H i regions. We find no strong differences in the mid-infrared colors of the star-forming regions in the spiral galaxy NGC 6872 as a function of position relative to the tidally interacting companion galaxy IC 4970. We find 11 very luminous X-ray sources (≳ (0.5–5) ×1039 erg s−1 ) clustered to the southwest in NGC 6872, near bright star-forming regions. In NGC 6872's tidal features, young star clusters form at the boundaries of diffuse X-ray gas, suggesting that stars form as gas stripped by the interactions cools. The nucleus of NGC 6872 is a weak X-ray point source with 0.5–8 keV luminosity of 8.5 × 1039 erg s−1 , but there is little evidence in the inner 1 kpc of NGC 6872 for PAH emission from recent star formation or nuclear activity. However, a 4 kpc “stream,” leading from the outer ring of NGC 6872 to the nucleus, may signal the transport of interstellar matter into NGC 6872's nuclear region. Nonstellar emission, consistent with PAH emission, is also found in the central region of elliptical galaxy NGC 6877, companion to the dominant Pavo group elliptical galaxy NGC 6876. However, in the central region of NGC 6876, the dust emission is more likely due to silicate emission from old asymptotic giant branch stars.
A flexible two-stage procedure for identifying gene sets that are differentially expressed
Authors: Heller Ruth , Manduchi Elisabetta , Grant Gregory R. , Ewens Warren J. 
Published: February 2009

AbstractMotivation: Microarray data analysis has expanded from testing individual genes for differential expression to testing gene sets for differential expression. The tests at the gene set level may focus on multivariate expression changes or on the differential expression of at least one gene in the gene set. These tests may be powerful at detecting subtle changes in expression, but findings at the gene set level need to be examined further to understand whether they are informative and if so how.Results: We propose to first test for differential expression at the gene set level but then proceed to test for differential expression of individual genes within discovered gene sets. We introduce the overall false discovery rate (OFDR) as an appropriate error rate to control when testing multiple gene sets and genes. We illustrate the advantage of this procedure over procedures that only test gene sets or individual genes.Availability: R code (www.r-project.org) for implementing our approach is included as supplementary material.Contact: ruheller@whatron.upenn.edu
Enumeration of condition-dependent dense modules in protein interaction networks
Authors: Georgii Elisabeth , Dietmann Sabine , Uno Takeaki , Pagel Philipp , Tsuda Koji 
Published: February 2009

Abstract
Motivation: Modern systems biology aims at understanding how the different molecular components of a biological cell interact. Often, cellular functions are performed by complexes consisting of many different proteins. The composition of these complexes may change according to the cellular environment, and one protein may be involved in several different processes. The automatic discovery of functional complexes from protein interaction data is challenging. While previous approaches use approximations to extract dense modules, our approach exactly solves the problem of dense module enumeration. Furthermore, constraints from additional information sources such as gene expression and phenotype data can be integrated, so we can systematically mine for dense modules with interesting profiles.
Results: Given a weighted protein interaction network, our method discovers all protein sets that satisfy a user-defined minimum density threshold. We employ a reverse search strategy, which allows us to exploit the density criterion in an efficient way. Our experiments show that the novel approach is feasible and produces biologically meaningful results. In comparative validation studies using yeast data, the method achieved the best overall prediction performance with respect to confirmed complexes. Moreover, by enhancing the yeast network with phenotypic and phylogenetic profiles and the human network with tissue-specific expression data, we identified condition-dependent complex variants.
Availability: A C++ implementation of the algorithm is available at http://www.kyb.tuebingen.mpg.de/~georgii/dme.html.
Contact: koji.tsuda@tuebingen.mpg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Acupuncture at “Zusanli" (St.36) and “Sanyinjiao" (SP.6) Points on the Gastrointestinal Tract: A Study of the Bioavailability of  99mTc‐Sodium Pertechnetate in Rats
Authors: Senna-Fernandes Vasco , França Daisy L. M. , de Souza Deise , Santos Kelly C. M. , Sousa Rafael S. , Manoel Cristiano V. , Santos-Filho Sebastião D. , Cortez Célia M. , Bernardo-Filho Mario , Guimarães Marco Antonio M. 
Published: February 2009

The objective of this study is to investigate the differences of acupuncture effect between the Zusanli (St.36) and Sanyinjiao (SP.6) points on the gastrointestinal‐tract (GIT) segment performed by the bioavailability of
99mTc‐sodium‐pertechnetate (Na99mTcO4) in rats. Male Wistar rats (n = 21) were allocated into three groups of seven each. Group 1 was treated by acupuncture bilaterally at St.36; Group 2 at SP.6; and Group 3 was untreated (control). After 10 min of needle insertion in anesthetized rats, 0.3 mL of Na99mTcO4 (7.4 MBq) was injected via ocular‐plexus. After 20 min, the exitus of animals was induced by cervical‐dislocation and GIT organs isolated. However, immediately before the exitus procedure, blood was collected by cardiac‐puncture for blood radio‐labeling (BRL). The radioactivity uptake of the blood constituents was calculated together with the GIT organs by a well gamma counter. The percentage of injected dose per gram of tissue (%ID/g) of Na99mTcO4 was calculated for each GIT organs, while BRL was calculated in %ID. According to the one‐way ANOVA, the stomach, jejunum, ileum from the treated groups (Group 1 and Group 2) had significant differences compared to the controls (Group 3). However, between the treated groups (Group 1 and Group 2), there were significant differences (P < .05) in the stomach, jejunum, ileum, cecum, transverse and rectum. In BRL analysis, Group 2 showed significant increase and decrease of the insoluble and soluble fractions of the blood cells, respectively (P < .0001). The authors suggest that St.36 may have a tendency of up‐regulation effect on GIT, whereas SP.6, down‐regulation effect. However, further rigorous experimental studies to examine the effectiveness of acupuncture in either acupuncture points need to be carried out.
Anti‐inflammatory effects of eplerenone on viral myocarditis
Authors: Xiao Jie , Shimada Miho , Liu Wenling , Hu Dayi , Matsumori Akira 
Published: February 2009

AimsInflammation contributes to increased cardiovascular morbidity and mortality associated with activation of the renin–angiotensin–aldosterone system. The aim of this study was to investigate whether eplerenone, a selective aldosterone receptor antagonist, has anti‐inflammatory effects on viral myocarditis.Methods and resultsFour‐week‐old inbred male DBA/2 mice were inoculated intraperitoneally with 10 plaque‐forming units (pfu) of the encephalomyocarditis (EMC) virus. Mice were fed with standard chow (control) or with chow containing 2.5 mg/kg of eplerenone, starting either on day 0 (inoculation) or day 7. Survival at 28 days was significantly higher in the mice which started eplerenone treatment on day 0 (35 vs. 15% in controls, each n = 40, P < 0.05). The area of myocardial fibrosis on day 28 was significantly smaller in the eplerenone‐treated mice than in controls (19.8 ± 2.6%, n = 14, vs. 33.4 ± 5.4%, n = 6, mean ± SEM, P < 0.05). Gene expression of mouse mast cell proteases‐4 and ‐5, matrix metalloproteinase‐9, and type I procollagen on day 6 after EMC virus inoculation was significantly decreased in the hearts of eplerenone‐treated mice.ConclusionThese results suggest that eplerenone has anti‐inflammatory effects, and exerts its beneficial effects on viral myocarditis by suppression of genes related to mast cells and cardiac remodelling in the hearts of mice.
In vivo animal studies with sugammadex
Authors: Booij L. H. D. J. , Van Egmond J. , Driessen J. J. , De Boer H. D. 
Published: February 2009

SummaryA review is presented of animal studies of the selective steroidal neuromuscular blocking drug binding agent sugammadex. These studies demonstrate that sugammadex is faster in onset than the currently used acetylcholinesterase inhibitors, has no muscarinic effects, and is characterised by lack of adverse effects on other organs. These results offer support for the further development of sugammadex for clinical use in humans.
Sugammadex in clinical practice
Authors: Mirakhur R. K. 
Published: February 2009

SummaryThe availability of sugammadex allows greater flexibility in the use of rocuronium and vecuronium during anaesthesia and surgery. The neuromuscular block induced by both drugs can be reversed from both superficial and deep levels of block by adjusting the dose of sugammadex. The dose of sugammadex for reversal of shallow block produced by these neuromuscular blocking drugs is approximately 2 mg.kg−1 and for deep block the dose is 4 mg.kg−1. A larger dose of sugammadex (16 mg.kg−1) administered 3 min after the neuromuscular blocking drug allows rapid reversal of a neuromuscular block induced by 1–1.2 mg.kg−1 of rocuronium, thereby raising the possibility of using rocuronium as a replacement for suxamethonium. The use of sugammadex has not been reported to be associated with recurrence of block provided a dose that is adequate for reversal has been used. Sugammadex appears to have an acceptable safety profile. There are no requirements for dose adjustment for age or the use of potent volatile anaesthetic agents.
Neuromuscular blocking drugs and their antagonists in patients with organ disease
Authors: Craig R. G. , Hunter J. M. 
Published: February 2009

SummaryThe pharmacodynamics and pharmacokinetics of the currently available neuromuscular blocking and reversal drugs may be altered by organ disease. Adverse effects such as prolonged neuromuscular block, postoperative residual curarisation, recurarisation, the muscarinic effects of the anticholinesterases, and the side‐effects of the antimuscarinics are encountered more frequently. This review will consider these potential problems and assess the role of sugammadex in enabling the anaesthetist to avoid them. It will also present the latest knowledge regarding the safety and efficacy of sugammadex in patients with renal, hepatic, cardiovascular and pulmonary disease.
Clinical implications of sugammadex
Authors: Caldwell J. E. , Miller R. D. 
Published: February 2009

SummarySugammadex is a cyclodextrin molecule that encapsulates and inactivates rocuronium and vecuronium. As a result, any degree of neuromuscular block produced by rocuronium or vecuronium can be rapidly and completely reversed without autonomic effects. Because sugammadex is optimised for reversing rocuronium it is most likely to be used in conjunction with this drug. Sugammadex will allow deep levels of block to be maintained until the very end of surgery, and will allow block to be reversed at any time after rocuronium administration, even just a few minutes. The recommended dose‐range is 2–16 mg.kg‐1 (ascender), depending on the level of block. The availability of sugammadex reversal may increase the use of rocuronium, and decrease the use of suxamethonium and benzylisoquinoline neuromuscular blocking drugs. In addition, it will certainly increase pharmacy costs, which may be offset by faster recovery and discharge from the post‐anesthesia recovery unit. Sugammadex may also change monitoring practices in that post‐tetanic count will be required to quantify deep block, and quantitative monitoring of recovery may be driven by cost concerns in order to allow the use of the smallest dose of sugammadex that gives a satisfactory train‐of‐four ratio. Alternatively, monitoring may essentially be abandoned since a large dose of sugammadex will reliably reverse any degree of rocuronium‐induced block. The ultimate clinical utility of sugammadex will be clear only after large‐scale clinical use.
Monitoring neuromuscular block: an update
Authors: Fuchs‐Buder T. , Schreiber J.‐U. , Meistelman C. 
Published: February 2009

SummaryThe first part of this article presents an update of the basic considerations of neuromuscular monitoring. It emphasises the need to assure supramaximal stimulation, to place the stimulating electrodes correctly and to use appropriate sites for nerve stimulation as well as appropriate stimulation patterns. The second part focuses on current developments and ongoing discussion. The authors describe the performance of acceleromyography and the need for initial calibration when using these quantitative devices.
Population pharmacokinetics of sirolimus inde novoChinese adult renal transplant patients
Authors: Jiao Zheng , Shi Xiao‐jin , Li Zhong‐dong , Zhong Ming‐kang 
Published: February 2009

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT?• Sirolimus is an immunosuppressive agent used for the prophylaxis of renal allograft rejection.• Several conventional pharmacokinetic and population pharmacokinetic studies have been conducted to assess the pharmacokinetic characteristics of sirolimus in White or African‐American recipients.WHAT THIS STUDY ADDS?• The population pharmacokinetics of sirolimus in Chinese adult renal transplant recipients was characterized for the first time.• New drug–drug interactions between herbal medicines and sirolimus were identified as the covariates on sirolimus clearance.AIMSThis study was aimed at determining the population pharmacokinetics of sirolimus and identifying factors that explain pharmacokinetic variability inde novoChinese adult renal transplant patients.METHODSData were retrospectively extracted from a formal multicentre clinical trial, which was originally designed to evaluate the safety and efficacy of ciclosporin dose reduction and ciclosporin elimination in patients receiving sirolimus. All patients received 12‐month treatment, i.e. induction therapy with ciclosporin, sirolimus and corticosteroids during the first 3 months followed by either ciclosporin dose reduction or ciclosporin discontinuation thereafter. Eight‐hundred and four sirolimus trough blood concentrations (C0) from 112 patients were used to develop a population pharmacokinetic model using thenonmemprogram. A one‐compartment model with first‐order absorption and elimination was selected as the base model. The influence of demographic characteristics, biochemical and haematological indices, ciclosporin daily dose, ciclosporinC0as well as other commonly used co‐medications were explored.RESULTSThe typical values with interindividual variability for apparent clearance (CL/F) and apparent volume of distribution (V/F) were 10.1 l h−1(23.8%) and 3670 l (56.7%), respectively. The residual variability was 29.9%. CL/Fdecreased significantly with silymarin or glycyrrhizin co‐therapy in hepatically impaired patients, and with increasing total cholesterol levels or ciclosporinC0. Moreover, CL/Fincreased nonlinearly with increasing sirolimus daily dose. The median parameter estimates from a nonparametric bootstrap procedure were comparable and within 5% of the estimates fromnonmem.CONCLUSIONSThese results provide important information for clinicians to optimize sirolimus regimens in Chinese renal transplant patients.
A laboratory assessment of coronal bacterial leakage in root canals filled with new and conventional sealers
Authors: Eldeniz A. U. , Ørstavik D. 
Published: February 2009

AbstractAim  To evaluate the resistance to ex vivo bacterial leakage over a 40‐day period of root canal fillings with five new root canal sealers: RC Sealer, Epiphany, EndoREZ, GuttaFlow and Acroseal, compared with Apexit, AH Plus and RoekoSeal.Methodology  One hundred and forty‐four single rooted human teeth were divided randomly into eight test (n = 15) and two control groups (n = 12). The root canals were filled using a single cone technique with gutta‐percha except in the Epiphany and EndoREZ groups. These were filled with Resilon and resin‐coated gutta‐percha, respectively. The gutta‐percha surface of the GuttaFlow group was coated with an experimental primer prior to filling. Positive controls were filled with gutta‐percha without sealer and tested with bacteria, whereas negative controls were sealed with wax to test the seal between the chambers. Filled roots were incorporated in a split chamber model system using Streptococcus mutans as a microbial marker. Leakage was assessed for turbidity of the broth in the lower chamber every day for 40 days. Survival analysis was performed using the Kaplan–Meier product limit method and event times were compared using the Log‐rank test (α = 0.05).Results  Epiphany, GuttaFlow with test primer and Apexit prevented leakage significantly better than AH Plus, RC Sealer, RoekoSeal, EndoREZ and Acroseal (P < 0.05). None of the specimens in the AH Plus, RC Sealer, RoekoSeal and EndoREZ groups resisted bacterial penetration for 40 days.Conclusion  The new sealers, Epiphany and GuttaFlow with primer, along with Apexit, showed better resistance to bacterial penetration than the other new or traditional sealers tested.