bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbial diversity and impact on carbonate geochemistry across a changing geochemical gradient in a karst aquifer
Authors: Gray Cassie J , Engel Annette S 
Published: November 2012

Abstract
Although microbes are known to influence karst (carbonate) aquifer ecosystem-level processes, comparatively little information is available regarding the diversity of microbial activities that could influence water quality and geological modification. To assess microbial diversity in the context of aquifer geochemistry, we coupled 16S rRNA Sanger sequencing and 454 tag pyrosequencing to in situ microcosm experiments from wells that cross the transition from fresh to saline and sulfidic water in the Edwards Aquifer of central Texas, one of the largest karst aquifers in the United States. The distribution of microbial groups across the transition zone correlated with dissolved oxygen and sulfide concentration, and significant variations in community composition were explained by local carbonate geochemistry, specifically calcium concentration and alkalinity. The waters were supersaturated with respect to prevalent aquifer minerals, calcite and dolomite, but in situ microcosm experiments containing these minerals revealed significant mass loss from dissolution when colonized by microbes. Despite differences in cell density on the experimental surfaces, carbonate loss was greater from freshwater wells than saline, sulfidic wells. However, as cell density increased, which was correlated to and controlled by local geochemistry, dissolution rates decreased. Surface colonization by metabolically active cells promotes dissolution by creating local disequilibria between bulk aquifer fluids and mineral surfaces, but this also controls rates of karst aquifer modification. These results expand our understanding of microbial diversity in karst aquifers and emphasize the importance of evaluating active microbial processes that could affect carbonate weathering in the subsurface.
Are we missing half of the viruses in the ocean?
Authors: Steward Grieg F , Culley Alexander I , Mueller Jaclyn A , Wood-Charlson Elisha M , Belcaid Mahdi , Poisson Guylaine 
Published: November 2012

Abstract
Viruses are abundant in the ocean and a major driving force in plankton ecology and evolution. It has been assumed that most of the viruses in seawater contain DNA and infect bacteria, but RNA-containing viruses in the ocean, which almost exclusively infect eukaryotes, have never been quantified. We compared the total mass of RNA and DNA in the viral fraction harvested from seawater and using data on the mass of nucleic acid per RNA- or DNA-containing virion, estimated the abundances of each. Our data suggest that the abundance of RNA viruses rivaled or exceeded that of DNA viruses in samples of coastal seawater. The dominant RNA viruses in the samples were marine picorna-like viruses, which have small genomes and are at or below the detection limit of common fluorescence-based counting methods. If our results are typical, this means that counts of viruses and the rate measurements that depend on them, such as viral production, are significantly underestimated by current practices. As these RNA viruses infect eukaryotes, our data imply that protists contribute more to marine viral dynamics than one might expect based on their relatively low abundance. This conclusion is a departure from the prevailing view of viruses in the ocean, but is consistent with earlier theoretical predictions.
Environmental distribution of coral-associated relatives of apicomplexan parasites
Authors: Janouškovec Jan , Horák Aleš , Barott Katie L , Rohwer Forest L , Keeling Patrick J 
Published: November 2012

Abstract
A lineage of plastid-bearing eukaryotic microbes that is closely related to apicomplexan parasites was recently found in a specific association with coral reefs (apicomplexan-related lineage-V, or ARL-V). Here, we address the possible nature of this association using plastid ‘contamination’ in fine-scale bacterial sequence surveys. In a transect between corals and associated macroalgae, ARL-V is specifically associated with the coral, in contrast to all microalgal types (including diatoms, haptophytes, pelagophytes and photosynthetic apicomplexan relatives, Chromera and Vitrella), which are associated with macroalgae. ARL-V is associated with at least 20 species of symbiotic corals through extended time periods and large geographic distances. It is significantly enriched in healthy coral tissue and shallow reef depths. Altogether, the evidence points to a specific relationship between ARL-V and corals, and is suggestive of symbiosis, perhaps based on photosynthesis.
Leucocytosis and thrombosis at diagnosis are associated with poor survival in polycythaemia vera: a population‐based study of 327 patients
Authors: Bonicelli Gilles , Abdulkarim Khadija , Mounier Morgane , Johansson Peter , Rossi Cédric , Jooste Valérie , Andreasson Björn , Maynadié Marc , Girodon François 
Published: November 2012

SummaryThree hundred and twenty‐seven patients from two population‐based cohorts with an established diagnosis of polycythaemia vera were studied for prognostic risk factors for survival and leukaemia in a long‐term survey. The relative survival (RS) was 72% and 46% at 10 and 20 years respectively, from the time of diagnosis. Multivariate analysis identified age >70 years, white blood cell count >13 × 109/l and thrombo‐embolism at diagnosis as independent risk factors. Patients with two or three of these factors had a 10 year RS of 26%, compared with 59% and 84% in patients with one and no risk factors, respectively. Age and leucocyte count are the main predicting factors for survival in polycythaemia vera.
Late relapses following reduced intensity allogeneic transplantation in patients with multiple myeloma: a long‐term follow‐up study
Authors: Sahebi Firoozeh , Shen Yan , Thomas Sandra H. , Rincon Amalia , Murata‐Collins Joyce , Palmer Joycelynne , Krishnan Amrita Y. , Karanes Chatchada , Htut Myo , Somlo George , Forman Stephen J. 
Published: November 2012

SummaryWe analysed the long‐term outcomes of 60 multiple myeloma patients who underwent reduced intensity allogeneic stem cell transplantation between August 2000 and March 2008. Regimens included fludarabine and melphalan conditioning (flu‐mel regimen) for allogeneic haematopoietic cell transplant (HCT) or a planned tandem regimen consisting of high‐dose melphalan conditioning for autograft followed by low‐dose total body irradiation conditioning for allogeneic HCT (auto‐allo regimen). Donors included human‐leucocyte‐antigen‐matched siblings (n = 55) or matched unrelated donors (n = 5). With a median follow‐up of 9·8 years, 7‐year overall survival (OS) and progression‐free survival (PFS) were 60% and 31%, respectively. By multivariate Cox regression analysis, disease status of complete response (CR) or partial response (PR) at transplant and the presence of chronic graft‐versus‐host disease were significantly associated with improved OS. Only disease status was significantly associated with improved PFS. We noted a surprising number of very late relapses, with six patients (10%) relapsing between 6 and 12 years post‐transplant. Among the six late relapse patients, all were transplanted within 14 months of diagnosis, five had normal karyotypes, and five were in CR/PR. Our data provide additional evidence that, while survival may be extended by reduced intensity allogeneic transplant, ultimately, it may not offer a cure.
Hypersensitivity reactions to the Sabin vaccine in children with cow's milk allergy
Authors: Parisi C. A. S. , Smaldini P. L. , Gervasoni M. E. , Maspero J. F. , Docena G. H. 
Published: November 2012

SummaryBackgroundThe Sabin vaccine is used world‐wide, and most children with food allergies receive it without incident. However, in the 2009 vaccination campaign conducted in Argentina, four children experienced immediate‐type hypersensitivity reactions following vaccination.ObjectiveWe aimed to review the medical history of the affected children, study their allergic condition after the episodes and analyse the presence of allergenic vaccine components.MethodsPatients were selected based on their immediate allergic reactions following vaccination. They were assessed for allergies to cow's milk and hen's egg. The presence of cow's milk proteins in the vaccine was tested by various immunoassays involving cow's milk‐ or α‐lactalbumin‐specific polyclonal rabbit antiserum and patient sera.ResultsAll of the patients had a history of milk allergy, and no history or current evidence of egg hypersensitivity was found. Levels of cow's milk‐ and Sabin vaccine‐specific IgE were increased, and the result of a skin prick test with cow's milk proteins or the Sabin vaccine was positive in each patient. In addition, an ELISA using specific rabbit antiserum detected α‐lactalbumin in the Sabin vaccine. When α‐lactalbumin was employed as a soluble inhibitor in a competitive ELISA, binding to vaccine‐coated plates by cow's milk‐ or α‐lactalbumin‐specific rabbit antiserum or by patient serum containing IgE was inhibited.ConclusionsWe have demonstrated that these patients were allergic to cow's milk, and had circulating and mast cell‐bound IgE antibodies specific to cow's milk proteins. We found that the Sabin vaccine contained α‐lactalbumin, which may have been responsible for the reactions elicited following vaccination with the Sabin and dual viral vaccines in combination.
Copy number variation prevalence in known asthma genes and their impact on asthma susceptibility
Authors: Rogers A. J. , Chu J.‐H. , Darvishi K. , Ionita‐Laza I. , Lehmann H. , Mills R. , Lee C. , Raby B. A. 
Published: November 2012

SummaryBackgroundGenetic studies have identified numerous genes reproducibly associated with asthma, yet these studies have focussed almost entirely on single nucleotide polymorphisms (SNPs), and virtually ignored another highly prevalent form of genetic variation: Copy Number Variants (CNVs).ObjectiveTo survey the prevalence of CNVs in genes previously associated with asthma, and to assess whether CNVs represent the functional asthma‐susceptibility variants at these loci.MethodsWe genotyped 383 asthmatic trios participating in the Childhood Asthma Management Program (CAMP) using a competitive genomic hybridization (CGH) array designed to interrogate 20 092 CNVs. To ensure comprehensive assessment of all potential asthma candidate genes, we purposely used liberal asthma gene inclusion criteria, resulting in consideration of 270 candidate genes previously implicated in asthma. We performed statistical testing using FBAT‐CNV.ResultsCopy number variation in asthma candidate genes was prevalent, with 21% of tested genes residing near or within one of 69 CNVs. In six instances, the complete candidate gene sequence resides within the CNV boundaries. On average, asthmatic probands carried six asthma‐candidate CNVs (range 1–29). However, the vast majority of identified CNVs were of rare frequency (< 5%) and were not statistically associated with asthma. Modest evidence for association with asthma was observed for 2 CNVs near NOS1 and SERPINA3. Linkage disequilibrium analysis suggests that CNV effects are unlikely to explain previously detected SNP associations with asthma.Conclusions and Clinical RelevanceAlthough a substantial proportion of asthma‐susceptibility genes harbour polymorphic CNVs, the majority of these variants do not confer increased asthma risk. The lack of linkage disequilibrium (LD) between CNVs and asthma‐associated SNPs suggests that these CNVs are unlikely to represent the functional variant responsible for most known asthma associations.
Land use causes genetic differentiation of life‐history traits in Bromus hordeaceus
Authors: Völler Eva , Auge Harald , Bossdorf Oliver , Prati Daniel 
Published: November 2012

AbstractThere is increasing evidence that species can evolve rapidly in response to environmental change. However, although land use is one of the key drivers of current environmental change, studies of its evolutionary consequences are still fairly scarce, in particular studies that examine land‐use effects across large numbers of populations, and discriminate between different aspects of land use. Here, we investigated genetic differentiation in relation to land use in the annual grass Bromus hordeaceus. A common garden study with offspring from 51 populations from three regions and a broad range of land‐use types and intensities showed that there was indeed systematic population differentiation of ecologically important plant traits in relation to land use, in particular due to increasing mowing and grazing intensities. We also found strong land‐use‐related genetic differentiation in plant phenology, where the onset of flowering consistently shifted away from the typical time of management. In addition, increased grazing intensity significantly increased the genetic variability within populations. Our study suggests that land use can cause considerable genetic differentiation among plant populations, and that the timing of land use may select for phenological escape strategies, particularly in monocarpic plant species.
Hydrogen Ion Balance in Dialysis Therapy
Authors: Gotch Frank A. , Sargent John A. , Keen Marcia L. 
Published: November 2012

ABSTRACTA model to describe hydrogen ion balance (H+B) in acetate and bicarbonate dialysis therapy was developed based on measurement of metabolic addition of hydrogen ion (H+) to the body between and during dialyses and measurement of net buffer repletion during dialysis. Metabolic H+ generation was shown to be equal to 0.77 times the protein catabolic rate plus the total net removal of lactate and β‐hydroxybutyrate ions during dialysis. Buffer repletion was calculated from total net flux of acetate and bicarbonate during dialysis. The model was used for eight paired studies of H+B on one week each of acetate and bicarbonate dialysis and showed that cumulative H+B with acetate was ‐7 ± 28 (M ± SEM) mmol/ week compared to ‐175 ± 45 mmol/week with bicarbonate (P < 0.001). It is concluded that there is an initial, strongly negative H+B when patients on acetate dialysis are converted to bicarbonate. The possible physiologic significance of this is discussed.
Pathogenesis of Dialysis‐Induced Hypoxemia
Authors: Davidson Warren D. , Dolan Martin J. , Whipp Brian J. , Weitzman Richard E. , Wasserman Karlmann 
Published: November 2012

ABSTRACTPatients undergoing hemodialysis with acetate‐containing dialysis solutions develop hypoxemia. To determine the cause of the hypoxemia, we studied and compared the ventilatory, gas‐exchange and blood‐gas responses in chronic renal failure patients undergoing hemodialysis with acetate and bicarbonate dialysis solutions. Seven stable chronic dialysis patients were dialyzed against acetate and bicarbonate solutions in a random order. Dialysis was carried out using a 1.5 m2 hollow fiber dialyzer at a blood flow rate of 200 ml/min and a dialysate flow rate of 500 ml/min. During acetate dialysis, Pao2 fell within 15 minutes from a mean control predialysis concentration of 84 = 6 (SEM) mmHg to a mean of 70 ± 7.5 mmHg (P < 0.05), and remained low throughout the study. Pao2 did not change significantly during bicarbonate dialysis. Total ventilation fell from a predialysis level of 7.2 ± 0.7 L/ min to 5.7 ± 0.6 L/min within 15 minutes (P < 0.05). Paco2 was not significantly changed from predialysis levels with either acetate or bicarbonate dialysis. Measurement of blood concentration of CO2 and bicarbonate across the dialyzer indicated that the total CO2 loss (as CO2 and bicarbonate) through the dialyzer was 3 millimoles per minute or the equivalent of approximately 60 ml of CO2 per minute, i.e., about one third of the patient's metabolic production of CO2.
The Effects of Heterologous Liver Cross‐Hemodialysis on Adenylate Energy Charge of the Remnant Liver after Major Hepatic Resection
Authors: Ozawa Kazue , Kamiyama Yasuo , Kimura Kenichi , Ukikusa Minoru , Kono Yukihiro , Yamato Toshio , Shimahara Yasuyuki , Nakatani Toshio , Asano Motokazu , Irie Ryuichi , Kawashima Sadao , Uchida Kenichi , Ohtoshi Masahiro , Aoyama Hidehisa , Hirai Fumihiko , Yasuda Kazuhiro , Tobe Takayoshi 
Published: November 2012

ABSTRACTThe effect of liver support on the adenylate energy charge (ATP + 0.5ADP)/(ATP + ADP + AMP) of the remnant liver after major hepatic resection was studied in rabbits. The present study emphasized the principle of restoring the decreased energy charge level of the remnant liver after major hepatic resection by use of an ex vivo heterologous liver cross‐he‐modialysis with an interposed Cuprophan membrane. The energy charge level provides the cell with a very sensitive intracellular control mechanism. Regulatory enzymes from biosynthetic sequences exhibit very little activity at low levels of energy charge, and their activities increase sharply at high‐energy charge levels. The energy charge level of the remnant liver maximally decreased from the control level of 0.860 to 0.767 at 24 hours after 70% hepatectomy. The energy charge level increased from 0.767 to 0.857 after two hours of cross‐hemodialysis with an interposed Cuprophan membrane between the 24‐hour, 70% hepatectomized rabbit and an ex vivo pig liver with high energy charge. The above results suggest that this ex vivo pig cross‐hemodialysis may be effective for biosynthesis in the regenerative processes of the remnant liver.
Self‐Injury Among Early Adolescents: Identifying Segments Protected and at Risk*
Authors: Alfonso Moya L. , Kaur Ravneet 
Published: November 2012

BACKGROUND: Self‐injury has been described as a “silent school crisis,” reflecting insufficient knowledge, confusion, lack of effective interventions, and the tendency for adults and youth to shy away from dealing directly with the issue. This purpose of this study was to identify distinct subgroups of youth who may be at increased risk of or reduced risk of nonsuicidal self‐injury (NSSI).METHODS: The middle‐school Youth Risk Behavior Survey was administered in 8 district public middle schools in a large, southeastern county in Florida. A final sample size of 1748, representing approximately 92% of participants who self‐reported attendance at 1 of the 8 middle schools (N = 1907) and 74% of the 2350 surveys originally distributed, was used in this study. Chi‐squared automatic interaction detection (CHAID) was used to identify distinct segments at risk for or protected from NSSI.RESULTS: CHAID analyses suggested large groups of youth at risk for (and not at risk) having ever tried self‐injury including suicidal tendencies, substance use, low belief in life possibilities, and exposure to peer self‐injury. Protective factors identified included having low to zero levels of suicidal tendencies, high belief in life possibilities, lack of substance use, and not being a victim of bullying.CONCLUSION: Engaging adolescents in prevention programs at early stage can reduce the chances of suicidal behavior as well as physical injury. Schools should take the lead in advocating for the development of evidence‐based interventions that are capable of addressing factors that contribute to self‐injury at multiple levels of youth's environments.
Physical Activity and BMI: Evidence From the Panel Study of Income Dynamics Child Development Supplement
Authors: Hohensee Caroline W. , Nies Mary A. 
Published: November 2012

BACKGROUND: This study assessed the association between amount of physical activity and body mass index (BMI) percentile among middle and high school children. Total daily physical activity needs to include both in and out of school physical activity.METHODS: A secondary data analysis was performed on 1306 children drawn from the Panel Study of Income Dynamics Child Development Supplement (CDS III, 2007). The dependent variable in this study was BMI percentile, while the independent variable was physical activity. The multinomial logistic regression model was used to assess the associations between physical activity and BMI percentile controlling for age, gender, race/ethnicity, parental income, and neighborhood safety.RESULTS: Children who engaged in low daily physical activity levels had 1.8 times the odds of being obese versus normal weight than those who engaged in moderate levels [odds ratio (OR) = 1.80, confidence interval (CI) = 1.31, 2.48]. African‐American children had 1.6 times the odds of being obese than normal weight (OR = 1.55, CI = 0.99, 2.43) and Hispanic children had approximately 1.8 times the odds of being obese than normal weight in comparison to non‐Hispanic white children (OR = 1.79, CI = 1.00, 3.21). Females had about 1.5 times the odds of being overweight than normal weight than males (OR = 1.49, CI = 1.04, 2.13).CONCLUSIONS: This study suggests that the accumulation of 30 minutes or more of daily physical activity may be effective in decreasing obesity prevalence among middle and high school‐aged children.
Dynamics of hepatitis B virus quasispecies heterogeneity and virologic response in patients receiving low‐to‐moderate genetic barrier nucleoside analogs
Authors: Peveling‐Oberhag J. , Herrmann E. , Kronenberger B. , Farnik H. , Susser S. , Sarrazin C. , Zeuzem S. , Hofmann W.‐P. 
Published: November 2012

SummaryWe characterized the early dynamics of hepatitis B virus (HBV) quasispecies evolution during the first weeks of antiviral therapy with low‐to‐moderate genetic barrier antiviral drugs and associated these data with antiviral response patterns. Fifteen chronic hepatitis B patients (men, 10; mean age, 34; HBeAg positive, 6) who received lamivudine or telbivudine for at least 52 weeks were included. HBV DNA was extracted from serum, and a 910‐bp fragment covering domains A–F of the reverse transcriptase region was amplified, cloned and sequenced. Parameters of quasispecies heterogeneity, genetic diversity and complexity were calculated and were correlated with complete virologic response, defined as undetectable HBV DNA at week 52. Nine patients achieved complete virologic response during the observational period. While baseline HBV DNA levels and HBeAg status were associated with virologic response, baseline quasispecies complexity and diversity of responders showed no significant difference to those of nonresponders (P > 0.05). However, at week 4, quasispecies complexity of nonresponders was significantly higher compared with that of responders on the nucleotide level (P = 0.01) and the aa level (P = 0.04). The number of synonymous substitutions per synonymous site dropped significantly in responders at week 4 (P = 0.04), while there was no difference in nonresponders. The HBV quasispecies complexity at the early stage of antiviral therapy (week 4) with the low‐to‐moderate genetic barrier nucleoside analogs lamivudine or telbivudine was associated with subsequent virologic response. Further studies are needed to confirm HBV quasispecies evolution as additional predictive marker for beneficial treatment outcome.
Footwall mineralization during Late Miocene extension along the West Cycladic Detachment System, Lavrion, Greece
Authors: Berger Alexandra , Schneider David A. , Grasemann Bernhard , Stockli Daniel 
Published: November 2012

AbstractThe West Cycladic Detachment System (WCDS) has been mapped from the western Cycladic islands to Lavrion (mainland Greece), where several top‐to‐SSW low‐angle normal faults at different structural levels are observed. Near the detachment horizon, hydrothermal fluid flow originating from Miocene intrusions lead to high‐temperature carbonate strata‐bound Pb–Ag–Zn ore deposits. Zircon (U–Th)/He cooling ages from the mineralized footwall are 7.1 ± 0.6 to 7.9 ± 0.6 Ma. Carbon‐ and O‐isotope analyses of the carbonate host indicate high water‐to‐rock ratios during brittle deformation‐induced metasomatism, and that this interaction, unrelated to proximity of the intrusions, plays the dominant role in the mineralization. The Late Miocene geology of Lavrion is strikingly similar to Serifos island on the SE termination of the WCDS, both characterized by strong localization of detachment faulting and the interaction of brittle deformation with the injection of fluids related to granitoid intrusions.