bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of a novel acetate-utilizing bacterium belonging to Synergistes group 4 in anaerobic digester sludge
Authors: Ito Tsukasa , Yoshiguchi Kazumi , Ariesyady Herto Dwi , Okabe Satoshi 
Published: May 2011

Abstract
Major acetate-utilizing bacterial and archaeal populations in methanogenic anaerobic digester sludge were identified and quantified by radioisotope- and stable-isotope-based functional analyses, microautoradiography-fluorescence in situ hybridization (MAR-FISH) and stable-isotope probing of 16S rRNA (RNA-SIP) that can directly link 16S rRNA phylogeny with in situ metabolic function. First, MAR-FISH with 14C-acetate indicated the significant utilization of acetate by only two major groups, unidentified bacterial cells and Methanosaeta-like filamentous archaeal cells, in the digester sludge. To identify the acetate-utilizing unidentified bacteria, RNA-SIP was conducted with 13C6-glucose and 13C3-propionate as sole carbon source, which were followed by phylogenetic analysis of 16S rRNA. We found that bacteria belonging to Synergistes group 4 were commonly detected in both 16S rRNA clone libraries derived from the sludge incubated with 13C-glucose and 13C-propionate. To confirm that this bacterial group can utilize acetate, specific FISH probe targeting for Synergistes group 4 was newly designed and applied to the sludge incubated with 14C-acetate for MAR-FISH. The MAR-FISH result showed that bacteria belonging to Synergistes group 4 significantly took up acetate and their active population size was comparable to that of Methanosaeta in this sludge. In addition, as bacteria belonging to Synergistes group 4 had high K m for acetate and maximum utilization rate, they are more competitive for acetate over Methanosaeta at high acetate concentrations (2.5–10 mm). To our knowledge, it is the first time to report the acetate-utilizing activity of uncultured bacteria belonging to Synergistes group 4 and its competitive significance to acetoclastic methanogen, Methanosaeta.
Breaking the regioselectivity rule for acrylate insertion in the Mizoroki–Heck reaction
Authors: Wucher Philipp , Caporaso Lucia , Roesle Philipp , Ragone Francesco , Cavallo Luigi , Mecking Stefan , Göttker-Schnetmann Inigo 
Published: May 2011

In modern methods for the preparation of small molecules and polymers, the insertion of substrate carbon–carbon double bonds into metal–carbon bonds is a fundamental step of paramount importance. This issue is illustrated by Mizoroki–Heck coupling as the most prominent example in organic synthesis and also by catalytic insertion polymerization. For unsymmetric substrates H
2
C = CHX the regioselectivity of insertion is decisive for the nature of the product formed. Electron-deficient olefins insert selectively in a 2,1-fashion for electronic reasons. A means for controlling this regioselectivity is lacking to date. In a combined experimental and theoretical study, we now report that, by destabilizing the transition state of 2,1-insertion via steric interactions, the regioselectivity of methyl acrylate insertion into palladium–methyl and phenyl bonds can be inverted entirely to yield the opposite “regioirregular” products in stoichiometric reactions. Insights from these experiments will aid the rational design of complexes which enable a catalytic and regioirregular Mizoroki–Heck reaction of electron-deficient olefins.
Origins of saccharide-dependent hydration at aluminate, silicate, and aluminosilicate surfaces
Authors: Smith Benjamin J. , Rawal Aditya , Funkhouser Gary P. , Roberts Lawrence R. , Gupta Vijay , Israelachvili Jacob N. , Chmelka Bradley F. 
Published: May 2011

Sugar molecules adsorbed at hydrated inorganic oxide surfaces occur ubiquitously in nature and in technologically important materials and processes, including marine biomineralization, cement hydration, corrosion inhibition, bioadhesion, and bone resorption. Among these examples, surprisingly diverse hydration behaviors are observed for oxides in the presence of saccharides with closely related compositions and structures. Glucose, sucrose, and maltodextrin, for example, exhibit significant differences in their adsorption selectivities and alkaline reaction properties on hydrating aluminate, silicate, and aluminosilicate surfaces that are shown to be due to the molecular architectures of the saccharides. Solid-state
1
H,
13
C,
29
Si, and
27
Al nuclear magnetic resonance (NMR) spectroscopy measurements, including at very high magnetic fields (19 T), distinguish and quantify the different molecular species, their chemical transformations, and their site-specific adsorption on different aluminate and silicate moieties. Two-dimensional NMR results establish nonselective adsorption of glucose degradation products containing carboxylic acids on both hydrated silicates and aluminates. In contrast, sucrose adsorbs intact at hydrated silicate sites and selectively at anhydrous, but not hydrated, aluminate moieties. Quantitative surface force measurements establish that sucrose adsorbs strongly as multilayers on hydrated aluminosilicate surfaces. The molecular structures and physicochemical properties of the saccharides and their degradation species correlate well with their adsorption behaviors. The results explain the dramatically different effects that small amounts of different types of sugars have on the rates at which aluminate, silicate, and aluminosilicate species hydrate, with important implications for diverse materials and applications.
Model-based gene set analysis for Bioconductor
Authors: Bauer Sebastian , Robinson Peter N. , Gagneur Julien 
Published: May 2011

Abstract
Summary: Gene Ontology and other forms of gene-category analysis play a major role in the evaluation of high-throughput experiments in molecular biology. Single-category enrichment analysis procedures such as Fisher's exact test tend to flag large numbers of redundant categories as significant, which can complicate interpretation. We have recently developed an approach called model-based gene set analysis (MGSA), that substantially reduces the number of redundant categories returned by the gene-category analysis. In this work, we present the Bioconductor package mgsa, which makes the MGSA algorithm available to users of the R language. Our package provides a simple and flexible application programming interface for applying the approach.
Availability: The mgsa package has been made available as part of Bioconductor 2.8. It is released under the conditions of the Artistic license 2.0.
Contact: peter.robinson@charite.de; julien.gagneur@embl.de
Apocalypse in world fisheries? The reports of their death are greatly exaggerated
Authors: Daan Niels , Gislason Henrik , Pope John G. , Rice Jake C. 
Published: May 2011

Abstract
Daan, N., Gislason, H., Pope, J. G., and Rice, J. C. 2011. Apocalypse in world fisheries? The reports of their death are greatly exaggerated. – ICES Journal of Marine Science, 68: 1375–1378. The catch-based methods underlying the forecast that by 2048 all commercially exploited stocks will have collapsed have been severely criticized, and a recent and more-elaborate analysis by a group of scientists that included the lead author of the original article has led to a quite different interpretation. Nonetheless, the 2006 forecast of a forthcoming apocalypse in the oceans is still uncritically referred to by critics of current management and fisheries science. In the title, the quote by Mark Twain is paraphrased to underline the fact that this prediction is both technically and conceptually flawed: (i) any series of random numbers subjected to the algorithm underlying the prediction will show a pattern similar to that observed in catch statistics; (ii) this pattern should be accounted for in making predictions; and (iii) interpreting the period of maximum harvest in a time-series as generally reflecting a period during which a stock was fully exploited is incorrect, because history often has shown that these maximum yields were taken during a period of overexploitation and could not have been sustainable.
Involvement of Tuberomamillary Histaminergic Neurons in Isoflurane Anesthesia
Authors: Luo Tao , Leung L. Stan 
Published: May 2011

Background
The brain histaminergic system plays a critical role in maintenance of arousal. Previous studies suggest that histaminergic neurotransmission might be a potential mediator of general anesthetic actions. However, it is not clear whether histaminergic tuberomamillary nucleus (TMN) is necessarily involved in the sedative/hypnotic effects of general anesthetics.

Methods
Male Long Evans rats underwent either TMN orexin-saporin/sham lesion or implantation of intracerebroventricular cannula 2 weeks before the experiment. The behavioral endpoint of loss of righting reflex was used to assess the hypnotic property of isoflurane, propofol, pentobarbital, and ketamine in animals. Histaminergic cell loss was assessed by adenosine deaminase expression in the TMN using immunohistochemistry.

Results
Rats with bilateral TMN orexin-saporin lesion induced an average 72% loss of histaminergic cells compared with sham-lesion rats. TMN orexin-saporin lesion or intracerebroventricular administration of triprolidine (an H1 receptor antagonist) decreased the 50% effective concentration for loss of righting reflex value and prolonged emergence time to isoflurane anesthesia. However, TMN orexin-saporin lesion had no significant effect on the anesthetic sensitivity to propofol, pentobarbital, and ketamine.

Conclusions
These findings suggest a role of the TMN histaminergic neurons in modulating isoflurane anesthesia and that the neural circuits for isoflurane-induced hypnosis may differ from those of γ-aminobutyric acid-mediated anesthetics and ketamine.
Resistance to activated protein C is a risk factor for pregnancy‐related venous thrombosis in the absence of the F5 rs6025 (factor V Leiden) polymorphism
Authors: Bergrem Astrid , Dahm Anders Erik Astrup , Jacobsen Anne Flem , Mowinckel Marie‐Christine , Sandvik Leiv , Sandset Per Morten 
Published: May 2011

SummaryResistance to activated protein C (aPC) is most commonly due to the F5 rs6025 (factor V Leiden) polymorphism, which increases the risk of venous thrombosis. In the present population‐based study of 313 cases and 353 controls, we investigated whether reduced sensitivity to aPC was associated with a history of pregnancy‐related venous thrombosis. Calibrated automated thrombography was used to determine the sensitivity to aPC, and normalized aPC sensitivity ratio (n‐aPC‐sr) was calculated. Pregnant women and women using oral contraceptives and/or anticoagulants were excluded due to the effect on the n‐aPC‐sr. In women without the F5 rs6025 polymorphism, free tissue factor pathway inhibitor (TFPI), free protein S and protein C activity were associated with n‐aPC‐sr. Unadjusted odds ratio for venous thrombosis for women with n‐aPC‐sr in the 4th quartile as compared with n‐aPC‐sr below the 4th quartile was 2·4 (95% confidence interval 1·7–3·6). Adjusting for free protein S, free TFPI and age did not influence the odds ratios. Also in carriers of the F5 rs6025 polymorphism the risk for venous thrombosis was increased for women with higher n‐aPC‐sr. Our findings substantiate the importance of the aPC resistant phenotype as a risk factor for pregnancy‐related venous thrombosis.
Attainment of complete/very good partial response following rituximab‐based therapy is an important determinant to progression‐free survival, and is impacted by polymorphisms in FCGR3A in Waldenstrom macroglobulinaemia
Authors: Treon Steven P. , Yang Guang , Hanzis Christine , Ioakimidis Leukothea , Verselis Sigitas J. , Fox Edward A. , Xu Lian , Hunter Zachary R. , Tseng Hsiuyi , Manning Robert J. , Patterson Christopher J. , Sheehy Patricia , Turnbull Barry 
Published: May 2011

SummaryThe incorporation of rituximab into various regimens has improved depth of response in Waldenstrom macroglobulinaemia (WM), though the impact of achieving better responses remains to be determined. We examined response depth on progression‐free survival (PFS) in 159 rituximab‐naïve WM patients who received rituximab‐based therapy. The median follow‐up was 33·5 months, and categorical responses were as follows: complete response (CR, 8·8%); very good partial response (VGPR, 13·2%); partial response (50%); minor response (18·9%); Non‐Responders (8·8%). Sequencing for polymorphic variants of FCGR2A, FCGR2B, and FCGR3A was performed, and impact on response depth determined. Achievement of better categorical responses was incrementally associated with improved PFS (P < 0·0001). No separation was observed between CR and VGPR, and attainment of at least a VGPR was associated with improved time‐to‐progression. Neither age, serum IgM, haematocrit, platelet count, serum β2microglobulin, WM International Prognostic Scoring System score, and treatment group predicted for CR/VGPR. Polymorphisms at FCGR3A‐48 and ‐158 were associated with improved categorical responses, particularly attainment of CR/VGPR (P ≤ 0·03). The attainment of CR/VGPR was associated with significantly longer PFS in rituximab‐naïve WM patients undergoing rituximab‐based therapy, and was predicted by polymorphisms in FCGR3A.
Carbon sequestration potential of tropical pasture compared with afforestation in Panama
Authors: WOLF SEBASTIAN , EUGSTER WERNER , POTVIN CATHERINE , TURNER BENJAMIN L. , BUCHMANN NINA 
Published: May 2011

AbstractTropical forest ecosystems play an important role in regulating the global climate, yet deforestation and land‐use change mean that the tropical carbon sink is increasingly influenced by agroecosystems and pastures. Despite this, it is not yet fully understood how carbon cycling in the tropics responds to land‐use change, particularly for pasture and afforestation. Thus, the objectives of our study were: (1) to elucidate the environmental controls and the impact of management on gross primary production (GPP), total ecosystem respiration (TER) and net ecosystem CO2 exchange (NEE); (2) to estimate the carbon sequestration potential of tropical pasture compared with afforestation; and (3) to compare eddy covariance‐derived carbon budgets with biomass and soil inventory data. We performed comparative measurements of NEE in a tropical C4 pasture and an adjacent afforestation with native tree species in Sardinilla (Panama) from 2007 to 2009. Pronounced seasonal variation in GPP, TER and NEE were closely related to radiation, soil moisture, and C3 vs. C4 plant physiology. The shallow rooting depth of grasses compared with trees resulted in a higher sensitivity of the pasture ecosystem to water limitation and seasonal drought. During 2008, substantial amounts of carbon were sequestered by the afforestation (–442 g C m–2, negative values denote ecosystem carbon uptake), which was in agreement with biometric observations (–450 g C m–2). In contrast, the pasture ecosystem was a strong carbon source in 2008 and 2009 (261 g C m–2), associated with seasonal drought and overgrazing. In addition, soil carbon isotope data indicated rapid carbon turnover after conversion from C4 pasture to C3 afforestation. Our results clearly show the potential for considerable carbon sequestration of tropical afforestation and highlight the risk of carbon losses from pasture ecosystems in a seasonal tropical climate.
The role of BLIMP1 and its putative downstream target TFAP2C in germ cell development and germ cell tumours
Authors: Schäfer S. , Anschlag J. , Nettersheim D. , Haas N. , Pawig L. , Schorle H. 
Published: May 2011

SummaryDuring the past years, much information has been gathered regarding the genetic and epigenetic programmes leading to the specification and maintenance of primordial germ cells. Expression of the transcriptional regulator BLIMP1 (PRDM1) is regarded as the main event in germ cell specification. BLIMP1 induces a set of target genes, one of them being transcription factor TFAP2C (AP‐2γ, Tcfap2c). In murine loss of function models Blimp1 and Tcfap2c share an identical phenotype, strengthening the assumption that they act in the same pathway. One major role of this pathway is the inhibition of somatic differentiation in germ cells. BLIMP1 and TFAP2C are also expressed in carcinoma in situ (CIS, IGCNU, TIN) and in seminoma. As pointed out herein, the presence of both proteins helps to explain the undifferentiated nature of these germ cell tumours. In addition, we performed a meta‐analysis of high‐throughput datasets searching for TFAP2C/Tcfap2c target genes. This analysis leads us to suggest Nanos3, Dmrt1 and Dnmt3b as potential TFAP2C/Tcfap2c target genes with relevance to germ cell development and germ cell tumours.
The effects of leadership and ward factors on job satisfaction in nursing homes: a multilevel approach
Authors: Havig Anders K , Skogstad Anders , Veenstra Marijke , Romøren Tor I 
Published: May 2011

Aims and objectives.  To examine (1) the relationships between job satisfaction and task‐ and relationship‐oriented leadership and (2) the direct and moderating effects on job satisfaction of three ward‐level factors: workload, use of teams and staff stability.Background.  Job satisfaction in nursing homes is vital to meeting the challenges related to recruitment and turnover.Design.  Cross‐sectional design.Method.  A multilevel analysis approach was used to recognise a hierarchal structure of determined factors and to capture variation in job satisfaction at the individual and ward level. A questionnaire was sent to 444 registered nurses, auxiliary nurses and unskilled nursing assistants. Structured interviews were administered to 40 ward managers and 13 directors, and 900 hours of field observations was conducted in 40 nursing home wards throughout Norway.Results.  We found a significant relationship between job satisfaction and task‐oriented and relationship‐oriented leadership styles, with a stronger effect for task orientation. The effect of the two leadership styles varied significantly across wards. Furthermore, staff stability had both a significant positive direct effect and a moderating effect on job satisfaction, whereas the two other ward‐level predictors yielded no significant contributions.Conclusion.  The relatively stronger effect of task‐oriented leadership on job satisfaction, particularly in wards with low staff stability, is in contrast to most previous studies and suggests that there may be specific conditions in nursing homes that favour the use of this leadership style. The varying effect of both leadership styles indicates that staff in different nursing home wards could benefit from the use of different leadership styles.Relevance to clinical practice.  The study highlights the importance of using different leadership behaviour and the importance of high staff stability to ensure job satisfaction among nursing home personnel.
Attitudes to organ donation among Swedish ICU nurses
Authors: Flodén Anne , Persson Lars‐Olof , Rizell Magnus , Sanner Margareta , Forsberg Anna 
Published: May 2011

Aims and objectives.  To present data on Swedish ICU nurses’ attitudes to brain death and organ donation and to test a questionnaire designed to explore these issues in terms of validity and reliability.Background.  Previous studies have identified various barriers to organ donation. The single most important factor was the attitude of ICU staff.Design.  A 34‐item instrument was developed to explore attitudes and experiences of organ donation.Method.  The questionnaire was sent to 50% of ICU nurses in Sweden (n = 1013) and the response rate was 69% (n = 702). The expected scale dimensionality was examined both by explorative principal component analysis and confirmatory multi‐trait analysis. Scale reliability was further estimated using Cronbach’s alpha. Chi‐squared test was used to compare proportions between ICU specialities and Pearson correlations were calculated to investigate relationships between each of the factors verified and the single items.Results.  The main findings were that less than half of the ICU nurses trusted clinical diagnosis of brain death without a confirmatory cerebral angiography. Twenty‐five percent of the respondents indicated that mechanical ventilation was withdrawn to reduce the possible suffering of a person assumed to be clinically dead, without the issue of organ donation being raised. A total of 39% had experienced occasions when the question about organ donation was never raised with the relatives. Four factors were verified and labelled: personal attitudes to organ donation as a situation; Organisational attitudes to organ donation as a phenomenon; Environmental resources; and Personal wish to donate, which accounted for 70% of the variance.Conclusions.  Swedish ICU nurses reported several barriers to organ donation. An action plan including education in brain death diagnostics, interpersonal relationships and interaction with relatives as well as regular follow‐up regarding donation issues in various ICU settings would be useful.Relevance to clinical practice.  All nurses working in ICUs are obliged to participate in organ donation and are therefore included in these results.
Mutations in the nucleotide binding pocket of MreB can alter cell curvature and polar morphology in Caulobacter
Authors: Dye Natalie A. , Pincus Zachary , Fisher Isabelle C. , Shapiro Lucy , Theriot Julie A. 
Published: May 2011

SummaryThe maintenance of cell shape in Caulobacter crescentus requires the essential gene mreB, which encodes a member of the actin superfamily and the target of the antibiotic, A22. We isolated 35 unique A22‐resistant Caulobacter strains with single amino acid substitutions near the nucleotide binding site of MreB. Mutations that alter cell curvature and mislocalize the intermediate filament crescentin cluster on the back surface of MreB's structure. Another subset have variable cell widths, with wide cell bodies and actively growing thin extensions of the cell poles that concentrate fluorescent MreB. We found that the extent to which MreB localization is perturbed is linearly correlated with the development of pointed cell poles and variable cell widths. Further, we find that a mutation to glycine of two conserved aspartic acid residues that are important for nucleotide hydrolysis in other members of the actin superfamily abolishes robust midcell recruitment of MreB but supports a normal rate of growth. These mutant strains provide novel insight into how MreB's protein structure, subcellular localization, and activity contribute to its function in bacterial cell shape.
The combined actions of the copper‐responsive repressor CsoR and copper‐metallochaperone CopZ modulate CopA‐mediated copper efflux in the intracellular pathogen Listeria monocytogenes
Authors: Corbett David , Schuler Stephanie , Glenn Sarah , Andrew Peter W. , Cavet Jennifer S. , Roberts Ian S. 
Published: May 2011

SummaryWe have characterized the csoR‐copA‐copZ copper resistance operon of the important human intracellular pathogen Listeria monocytogenes. Transcription of the operon is specifically induced by copper, and mutants lacking the P1‐type ATPase CopA have reduced copper tolerance and over‐accumulate copper relative to wild type. The copper‐responsive repressor CsoR autoregulates transcription by binding to a single 32 bp site spanning the −10 and −35 elements of the promoter. Copper co‐ordination by CsoR derepresses transcription of the operon and alters CsoR:DNA complex assembly as determined by DNase I footprinting and electrophoretic mobility shift assays, with some DNA‐binding capacity being retained in the presence of 2 mole equivalents of copper. Analysis of the CsoR copper sensory site demonstrated that substitution of Cys42 with Ala generated a CsoR variant that was unresponsive to copper. Importantly, in the absence of CopZ, copper responsiveness of csoR‐copA‐copZ expression is substantially increased, implying that CopZ reduces the access of CsoR to copper. Furthermore, CopZ is shown to confer copper resistance in mutants lacking copper‐inducible csoR‐copA‐copZ expression, thus providing protection from the deleterious effects of copper within the cytoplasm.