bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sustainable syntrophic growth of Dehalococcoides ethenogenes strain 195 with Desulfovibrio vulgaris Hildenborough and Methanobacterium congolense: global transcriptomic and proteomic analyses
Authors: Men Yujie , Feil Helene , VerBerkmoes Nathan C , Shah Manesh B , Johnson David R , Lee Patrick K H , West Kimberlee A , Zinder Stephen H , Andersen Gary L , Alvarez-Cohen Lisa 
Published: September 2011

Abstract
Dehalococcoides ethenogenes strain 195 (DE195) was grown in a sustainable syntrophic association with Desulfovibrio vulgaris Hildenborough (DVH) as a co-culture, as well as with DVH and the hydrogenotrophic methanogen Methanobacterium congolense (MC) as a tri-culture using lactate as the sole energy and carbon source. In the co- and tri-cultures, maximum dechlorination rates of DE195 were enhanced by approximately three times (11.0±0.01 μmol per day for the co-culture and 10.1±0.3 μmol per day for the tri-culture) compared with DE195 grown alone (3.8±0.1 μmol per day). Cell yield of DE195 was enhanced in the co-culture (9.0±0.5 × 107 cells per μmol Cl− released, compared with 6.8±0.9 × 107 cells per μmol Cl− released for the pure culture), whereas no further enhancement was observed in the tri-culture (7.3±1.8 × 107 cells per μmol Cl− released). The transcriptome of DE195 grown in the co-culture was analyzed using a whole-genome microarray targeting DE195, which detected 102 significantly up- or down-regulated genes compared with DE195 grown in isolation, whereas no significant transcriptomic difference was observed between co- and tri-cultures. Proteomic analysis showed that 120 proteins were differentially expressed in the co-culture compared with DE195 grown in isolation. Physiological, transcriptomic and proteomic results indicate that the robust growth of DE195 in co- and tri-cultures is because of the advantages associated with the capabilities of DVH to ferment lactate to provide H2 and acetate for growth, along with potential benefits from proton translocation, cobalamin-salvaging and amino acid biosynthesis, whereas MC in the tri-culture provided no significant additional benefits beyond those of DVH.
Black reefs: iron-induced phase shifts on coral reefs
Authors: Kelly Linda Wegley , Barott Katie L , Dinsdale Elizabeth , Friedlander Alan M , Nosrat Bahador , Obura David , Sala Enric , Sandin Stuart A , Smith Jennifer E , Vermeij Mark J A , Williams Gareth J , Willner Dana , Rohwer Forest 
Published: September 2011

Abstract
The Line Islands are calcium carbonate coral reef platforms located in iron-poor regions of the central Pacific. Natural terrestrial run-off of iron is non-existent and aerial deposition is extremely low. However, a number of ship groundings have occurred on these atolls. The reefs surrounding the shipwreck debris are characterized by high benthic cover of turf algae, macroalgae, cyanobacterial mats and corallimorphs, as well as particulate-laden, cloudy water. These sites also have very low coral and crustose coralline algal cover and are call black reefs because of the dark-colored benthic community and reduced clarity of the overlying water column. Here we use a combination of benthic surveys, chemistry, metagenomics and microcosms to investigate if and how shipwrecks initiate and maintain black reefs. Comparative surveys show that the live coral cover was reduced from 40 to 60% to &lt;10% on black reefs on Millennium, Tabuaeran and Kingman. These three sites are relatively large (&gt;0.75 km2). The phase shift occurs rapidly; the Kingman black reef formed within 3 years of the ship grounding. Iron concentrations in algae tissue from the Millennium black reef site were six times higher than in algae collected from reference sites. Metagenomic sequencing of the Millennium Atoll black reef-associated microbial community was enriched in iron-associated virulence genes and known pathogens. Microcosm experiments showed that corals were killed by black reef rubble through microbial activity. Together these results demonstrate that shipwrecks and their associated iron pose significant threats to coral reefs in iron-limited regions.
AluHunter: a database of potentially polymorphic Alu insertions for use in primate phylogeny and population genetics
Authors: Bergey Christina M. 
Published: September 2011

Abstract
Summary: AluHunter is a database of taxon-specific primate Alu elements for use in phylogeny and population genetics. The software automatically isolates potentially polymorphic Alu insertions in sequences submitted to GenBank by screening the elements against reference genomes. The resultant database of variable markers is a valuable resource for researchers interested in characterizing Alu elements in their primate taxon of interest.
Availability and Implementation: The AluHunter database can be accessed at http://www.aluhunter.com.
Contact: cmb433@nyu.edu
Analysis of dermatomyositis‐specific autoantibodies and clinical characteristics in Japanese patients
Authors: IKEDA Nobuaki , TAKAHASHI Kazuo , YAMAGUCHI Yukie , INASAKA Mai , KUWANA Masataka , IKEZAWA Zenro 
Published: September 2011

AbstractDermatomyositis (DM) is an idiopathic systemic inflammatory disease that is often accompanied by interstitial lung disease (ILD) or internal malignancy. New autoantibodies, anti‐clinically amyopathic dermatomyositis 140 (anti‐CADM‐140) antibody (Ab) and anti‐155/140 Ab, as well as anti‐aminoacyl‐tRNA synthetase (anti‐ARS) Ab and anti‐Mi‐2 Ab, have been discovered and their utility indicated. However, the association between these autoantibodies and the clinical characteristics of DM is not fully understood, and it is unclear whether anti‐155/140 Ab is “specific” to DM patients with internal malignancy. Therefore, we analyzed 55 DM patients and 18 non‐DM patients with malignancy to evaluate the clinical characteristics, especially skin manifestations, in association with DM‐specific autoantibodies detected by immunoprecipitation. Six patients (11%) had anti‐CADM‐140 Ab, nine (16%) had anti‐155/140 Ab, eight (15%) had anti‐ARS Ab and six (11%) had anti‐Mi‐2 Ab. The frequency of DM patients positive for any type of autoantibody was 53%. Among the 20 DM patients with ILD, three (15%) had both anti‐CADM‐140 Ab and rapidly progressive ILD, and required intensive therapy (P < 0.05). ILD found in anti‐ARS Ab‐positive patients did not progress rapidly. The prevalence of muscle involvement in patients with anti‐CADM‐140 Ab was 83%. Among the 18 DM patients with internal malignancy, four (22%) had anti‐155/140 Ab, and internal malignancy was found in four cases (44%) of nine anti‐155/140 Ab‐positive patients. None of the non‐DM patients with malignancy were positive for anti‐155/140 Ab. In conclusion, the results of the present study indicate that anti‐155/140 Ab is specific to DM patients with internal malignancy and that we may be able to predict prognosis of ILD and the presence of malignancy to some extent, suggesting that examination of autoantibodies in DM patients is clinically very useful. However, further investigation is needed because several findings differ from those of previous reports.
Communications during epidural catheter placement for labour analgesia
Authors: Slater P. , Sellors J. , Cyna A. M. 
Published: September 2011

SummaryEvidence suggests that anaesthetists’ communication can affect patient experience. There is a lack of guidance for anaesthetists as to the optimal verbal communication to use during insertion of epidurals on the labour ward. We recorded the verbal communication used by 14 anaesthetists during the siting of epidural catheters in women on the labour ward; a classification of the language used was subsequently devised. We found that commands and information statements were the most common types of communication used. Individual anaesthetists differed markedly in their use of positive and negative verbal language. This classification of verbal communication that we produced may be of value in future training and research of verbal communication used by anaesthetists on the labour ward.You can respond to this article at http://www.anaesthesiacorrespondence.com
Pharmacokinetic interaction between domperidone and ketoconazole leads to QT prolongation in healthy volunteers: a randomized, placebo‐controlled, double‐blind, crossover study
Authors: Boyce Malcolm J. , Baisley Kathy J. , Warrington Steven J. 
Published: September 2011

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT• Domperidone, a dopamine antagonist metabolized mainly by CYP3A, has been used as an anti‐emetic and prokinetic agent by mouth for over 30 years.• Domperidone has a good safety record. However, early studies of high dose intravenous domperidone were associated with QTc prolongation and arrhythmias, including torsade de pointes.• There have been no thorough QTc studies of domperidone.WHAT THIS STUDY ADDS• We assessed the effect on QTc of oral domperidone and ketoconazole, alone and in combination.• •Ketoconazole, a CYP3A inhibitor, tripled domperidone concentrations, whilst domperidone did not affect ketoconazole concentrations.• •Domperidone and ketoconazole, alone and in combination, increased QTc significantly in men, and there was a positive correlation between increased QTc and concentrations of domperidone and ketoconazole in both sexes.• The effect of domperidone alone on QTc was small and not clinically important, but domperidone should not be co‐administered with ketoconazole.AIMS To assess the steady‐state pharmacokinetic and QTc effects of domperidone and ketoconazole, given alone and together.METHODS A randomized, placebo‐controlled, double‐blind, crossover study was carried out. Healthy subjects (14 men, 10 women; age 18–39 years; mean weight 73.5 kg, range 53.8–98.8 kg; 23 Europid, 1 Afro‐Caribbean) received orally, for 7 days each, placebo, domperidone 10 mg, four doses daily, at 4 h intervals, ketoconazole 200 mg 12‐hourly and domperidone and ketoconazole together. The washout period was 15 days. Pharmacokinetics and serial 12‐lead ECGs were assessed on day 7, and serial ECGs on day −1 and at follow‐up. Two subjects withdrew before the third treatment period, so data were available for 22–24 subjects.RESULTS Ketoconazole tripled domperidone concentrations at steady‐state. Domperidone, ketoconazole and their combination significantly increased QTcF in men. Overall adjusted mean differences from placebo were 4.20 (95% CI 0.77, 7.63), 9.24 (95% CI 5.85, 12.63) and 15.90 (95% CI 12.47, 19.33) ms, respectively. In women, QTcF was not significantly different from placebo on either domperidone or ketoconazole alone, or in combination. However, QTc was positively correlated with plasma drug concentrations, in both men and women. ΔQTcF increased by about 2 ms per 10 ng ml–1 rise in domperidone concentration, and per 1 µg ml–1 rise in ketoconazole concentration.CONCLUSIONS Ketoconazole tripled the plasma concentrations of domperidone. Domperidone and ketoconazole increased QTcF in men, whether given together or separately. The effect of domperidone alone was below the level of clinical importance. The negative result in women is unexplained.
Differential inhibition of trastuzumab- and cetuximab-induced cytotoxicity of cancer cells by immunoglobulin G1 expressing different GM allotypes
Authors: Namboodiri A M , Pandey J P 
Published: September 2011

Summary
Antibody-dependent cell-mediated cytotoxicity (ADCC), which links the innate and the adaptive arms of immunity, is a major host immunosurveillance mechanism against tumours, as well as the leading mechanism underlying the clinical efficacy of therapeutic antibodies such as cetuximab and trastuzumab, which target tumour antigens, human epidermal growth factor receptor (HER)1 and HER2, respectively. Immunoglobulin (Ig)G antibody-mediated ADCC is triggered upon ligation of Fcγ receptor (FcγR) to the Fc region of IgG molecules. It follows that genetic variation in FcγR and Fc could contribute to the differences in the magnitude of ADCC. Genetic variation in FcγR is known to contribute to the differences in the magnitude of ADCC, but the contribution of natural genetic variation in Fc, GM allotypes, in this interaction has hitherto not been investigated. Using an ADCC inhibition assay, we show that IgG1 expressing the GM 3+, 1−, 2− allotypes was equally effective in inhibiting cetuximab- and trastuzumab-mediated ADCC of respective target cells, in the presence of natural killer (NK) cells expressing either valine or phenylalanine allele of FcγRIIIa. In contrast, IgG1 expressing the allelic GM 17+, 1+, 2+ allotypes was significantly more effective in inhibiting the ADCC – mediated by both monoclonal antibodies – when NK cells expressed the valine, rather than the phenylalanine, allele of FcγRIIIa. These findings have important implications for engineering antibodies (with human γ1 constant region) against malignancies characterized by the over-expression of tumour antigens HER1 and HER2 – especially for patients who, because of their FcγRIIIa genotype, are unlikely to benefit from the currently available therapeutics.
Plasma myeloperoxidase level and peripheral arterial disease
Authors: Haslacher Helmuth , Perkmann Thomas , Gruenewald Julia , Exner Markus , Endler Georg , Scheichenberger Vanessa , Wagner Oswald , Schillinger Martin 
Published: September 2011

Eur J Clin Invest 2012; 42 (5): 463–469AbstractBackground  Myeloperoxidase (MPO) is involved in a multitude of inflammatory processes involving oxidative modification of soluble components and cellular surfaces. Thus, MPO plays a key role in promoting atherosclerosis via oxidative stress by modification of both high‐ and low‐density lipoprotein and production of other bioactive molecules. A polymorphism (MPO 463G>A, rs2333227) results in different expression rates of MPO. We aimed to assess whether MPO could be of clinical use as a risk marker for vascular disease in a high‐risk group.Material and methods  Plasma MPO levels of 406 patients suffering from peripheral arterial disease (PAD) were measured on an Abbott Architect i2000sr and grouped into patients with high (>115 ng/mL) and low (< 115 ng/mL) MPO levels. Genotyping of rs2333227 was performed on an ABI TaqMan 7900HT RT‐PCR thermocycler.Results  The relative risk of major adverse cardiovascular events (MACE) for patients with high plasma MPO is 1·2 (95%CI: 1·038–1·377, P < 0·05), initial event‐free periods in male patients are significantly longer in patients with MPO <115 ng/mL (mean = 875 days compared with mean = 734 days, P < 0·05) In smokers, an increased hazard ratio was computed for patients with high MPO levels (HR = 3·127, 95%CI: 1·258–7·772, P < 0·05). Effects of MPO [‐463A] allele on initial MACE‐free intervals did not persist after multivariate analysis.Conclusions  Hence, we suggest consideration of plasma MPO for risk stratification of MACE in patients with PAD. In contrast, MPO‐463G>A is not an independent risk factor for MACE in patients suffering from PAD.
Wind as a main driver of the net ecosystem carbon balance of a semiarid Mediterranean steppe in the South East of Spain
Authors: Rey Ana , Belelli‐Marchesini Luca , Were Ana , Serrano‐ortiz Penelope , Etiope Giuseppe , Papale Dario , Domingo Francisco , Pegoraro Emiliano 
Published: September 2011

AbstractDespite the advance in our understanding of the carbon exchange between terrestrial ecosystems and the atmosphere, semiarid ecosystems have been poorly investigated and little is known about their role in the global carbon balance. We used eddy covariance measurements to determine the exchange of CO2 between a semiarid steppe and the atmosphere over 3 years. The vegetation is a perennial grassland of Stipa tenacissima L. located in the SE of Spain. We examined diurnal, seasonal and interannual variations in the net ecosystem carbon balance (NECB) in relation to biophysical variables. Cumulative NECB was a net source of 65.7, 143.6 and 92.1 g C m−2 yr−1 for the 3 years studied, respectively. We separated the year into two distinctive periods: dry period and growing season. The ecosystem was a net source of CO2 to the atmosphere, particularly during the dry period when large CO2 positive fluxes of up to 15 μmol m−2 s−1 were observed in concomitance with large wind speeds. Over the growing season, the ecosystem was a slight sink or neutral with maximum rates of −2.3 μmol m−2 s−1. Rainfall events caused large fluxes of CO2 to the atmosphere and determined the length of the growing season. In this season, photosynthetic photon flux density controlled day‐time NECB just below 1000 μmol m−2 s−1. The analyses of the diurnal and seasonal data and preliminary geological and gas‐geochemical evaluations, including C isotopic analyses, suggest that the CO2 released was not only biogenic but most likely included a component of geothermal origin, presumably related to deep fluids occurring in the area. These results highlight the importance of considering geological carbon sources, as well as the need to carefully interpret the results of eddy covariance partitioning techniques when applied in geologically active areas potentially affected by CO2‐rich geofluid circulation.
Quantifying the effects of ozone on plant reproductive growth and development
Authors: Leisner Courtney P. , Ainsworth Elizabeth A. 
Published: September 2011

AbstractTropospheric ozone (O3) is a harmful air pollutant that can negatively impact plant growth and development. Current O3 concentrations ([O3]) decrease forest productivity and crop yields and future [O3] will likely increase if current emission rates continue. However, the specific effects of elevated [O3] on reproductive development, a critical stage in the plant's lifecycle, have not been quantitatively reviewed. Data from 128 peer‐reviewed articles published from 1968 to 2010 describing the effects of O3 on reproductive growth and development were analysed using meta‐analytic techniques. Studies were categorized based on experimental conditions, photosynthetic type, lifecycle, growth habit and flowering class. Current ambient [O3] significantly decreased seed number (−16%), fruit number (−9%) and fruit weight (−22%) compared to charcoal‐filtered air. In addition, pollen germination and tube growth were decreased by elevated [O3] compared to charcoal‐filtered air. Relative to ambient air, fumigation with [O3] between 70 and 100 ppb decreased yield by 27% and individual seed weight by 18%. Reproductive development of both C3 and C4 plants was sensitive to elevated [O3], and lifecycle, flowering class and reproductive growth habit did not significantly affect a plant's response to elevated [O3] for many components of reproductive development. However, elevated [O3] decreased fruit weight and fruit number significantly in indeterminate plants, and had no effect on these parameters in determinate plants. While gaps in knowledge remain about the effects of O3 on plants with different growth habits, reproductive strategies and photosynthetic types, the evidence strongly suggests that detrimental effects of O3 on reproductive growth and development are compromising current crop yields and the fitness of native plant species.
Pharmacokinetics of oral meloxicam in ruminant and preruminant calves
Authors: MOSHER R. A. , COETZEE J. F. , CULL C. A. , GEHRING R. , KuKANICH B. 
Published: September 2011

Mosher, R. A., Coetzee, J. F., Cull, C. A., Gehring, R., KuKanich, B. Pharmacokinetics of oral meloxicam in ruminant and preruminant calves. J. vet. Pharmacol. Therap. 35, 373–381.The pharmacokinetics of oral meloxicam has been studied in ruminant, but not preruminant calves. Oral meloxicam was administered at 0.5 mg/kg to six ruminant calves via gavage (RG); to six preruminant calves via gavage (PRG); and to six preruminant calves via suckling in milk replacer (PRF). Plasma drug concentrations, determined over 120‐h postadministration, were analyzed by compartmental and noncompartmental methods. The rate of drug absorption was faster (P < 0.01) in PRF (0.237 ± 0.0478/h) than RG calves (0.0815 ± 0.0188/h), while absorption in PRG calves (0.153 ± 0.128/h) was not different from other groups. Cmax was lower (P = 0.03) in PRF (1.27 ± 0.430 μg/mL) than in PRG calves (2.20 ± 0.467 μg/mL), while Cmax of RG calves (1.95 ± 0.955 μg/mL) was not different from other groups. V/F was higher in PRF calves (365 ± 57 mL/kg) than either PRG (177 ± 63 mL/kg, P < 0.01) or RG (232 ± 83 mL/kg, P = 0.01) calves. These observations were likely due to differences in bioavailability, physiological maturity, and timing of the drug delivery into different compartments of the ruminant gastrointestinal tract. Results suggest that an adjustment in meloxicam dose may be necessary when administered with milk replacer.
Elephant behaviour and conservation: social relationships, the effects of poaching, and genetic tools for management
Authors: ARCHIE ELIZABETH A. , CHIYO PATRICK I. 
Published: September 2011

AbstractGenetic tools are increasingly valuable for understanding the behaviour, evolution, and conservation of social species. In African elephants, for instance, genetic data provide basic information on the population genetic causes and consequences of social behaviour, and how human activities alter elephants’ social and genetic structures. As such, African elephants provide a useful case study to understand the relationships between social behaviour and population genetic structure in a conservation framework. Here, we review three areas where genetic methods have made important contributions to elephant behavioural ecology and conservation: (1) understanding kin‐based relationships in females and the effects of poaching on the adaptive value of elephant relationships, (2) understanding patterns of paternity in elephants and how poaching can alter these patterns, and (3) conservation genetic tools to census elusive populations, track ivory, and understand the behavioural ecology of crop‐raiding. By comparing studies from populations that have experienced a range of poaching intensities, we find that human activities have a large effect on elephant behaviour and genetic structure. Poaching disrupts kin‐based association patterns, decreases the quality of elephant social relationships, and increases male reproductive skew, with important consequences for population health and the maintenance of genetic diversity. In addition, we find that genetic tools to census populations or gather forensic information are almost always more accurate than non‐genetic alternatives. These results contribute to a growing understanding of poaching on animal behaviour, and how genetic tools can be used to understand and conserve social species.
Atypical DNA recognition mechanism used by the EspR virulence regulator of Mycobacterium tuberculosis
Authors: Blasco Benjamin , Stenta Marco , Alonso‐Sarduy Livan , Dietler Giovanni , Peraro Matteo Dal , Cole Stewart T. , Pojer Florence 
Published: September 2011

SummaryThe human pathogen Mycobacterium tuberculosis requires the ESX‐1 secretion system for full virulence. EspR plays a key role in ESX‐1 regulation via direct binding and transcriptional activation of the espACD operon. Here, we describe the crystal structures of EspR, a C‐terminally truncated form, EspRΔ10, as well as an EspR–DNA complex. EspR forms a dimer with each monomer containing an N‐terminal helix–turn–helix DNA binding motif and an atypical C‐terminal dimerization domain. Structural studies combined with footprinting experiments, atomic force microscopy and molecular dynamic simulations allow us to propose a model in which a dimer of EspR dimers is the minimal functional unit with two subunits binding two consecutive major grooves. The other two DNA binding domains are thus free to form higher‐order oligomers and to bridge distant DNA sites in a cooperative way. These features are reminiscent of nucleoid‐associated proteins and suggest a more general regulatory role for EspR than was previously suspected.