bluuebunny/crossref_metadata_2025_split huggingface dataset:
Channel Evolution Model of Semiarid Stream Response to Urban‐Induced Hydromodification1
Authors: Hawley Robert J. , Bledsoe Brian P. , Stein Eric D. , Haines Brian E. 
Published: April 2012

Hawley, Robert J., Brian P. Bledsoe, Eric D. Stein, and Brian E. Haines, 2012. Channel Evolution Model of Semiarid Stream Response to Urban‐Induced Hydromodification. Journal of the American Water Resources Association (JAWRA) 48(4): 722‐744. DOI: 10.1111/j.1752‐1688.2012.00645.xAbstract:  We present a novel channel evolution model (CEM) that qualitatively describes morphologic responses of semiarid channels to altered hydrologic and sediment regimes associated with urbanization (hydromodification). The CEM is based on southern California data from 83 detailed channel surveys, hundreds of synoptic surveys, and historical analyses of aerial photographs along 14 reaches. Channel evolution sometimes follows the well‐known sequence described by Schumm et al. (Incised Channels: Morphology, Dynamics, and Control, Water Resources Publications, Littleton, Colorado, 1984) for incising, single‐thread channels; however, departures from this sequence are common and include transitions of single thread to braided evolutionary endpoints, as opposed to a return to quasi‐equilibrium single‐thread planform. Thresholds and risk factors associated with observed channel response are also presented. In particular, distance to grade control and network position emerged as key controls on channel response trajectory. The CEM and quantitative extensions provide managers with a framework for understanding channel responses and rehabilitation alternatives, and may be transferable to other semiarid settings. It also offers insights regarding channel susceptibility to hydromodification, highlights key boundary conditions for high‐risk channels, and underscores critical knowledge gaps in predicting the complex, discontinuous response trajectories that are highly prevalent in urbanized watersheds.
Calibration Catchment Selection for Flood Regionalization Modeling1
Authors: Wan Jaafar Wan Zurina , Han Dawei 
Published: April 2012

Wan Jaafar, Wan Zurina, and Dawei Han, 2012. Calibration Catchment Selection for Flood Regionalization Modeling. Journal of the American Water Resources Association (JAWRA) 48(4): 698‐706. DOI: 10.1111/j.1752‐1688.2012.00648.xAbstract:  There are two unsolved problems in flood regionalization model development related to the quantity and quality of calibration catchments: (1) how many calibration catchments should be used? and (2) how to select the calibration catchments? This study explores these two questions through a case study on the median annual maximum flood (QMED) model in the United Kingdom. It has been found that the chance of developing a good QMED model decreases significantly when the number of calibration catchments drops below a critical number (e.g., 60 in the case study). However, no significant improvement is achieved if the number of calibration catchments is above it. This number could be used as a benchmark for choosing randomly selected calibration catchments. Across a broad range of calibration catchment numbers, there are good and poor calibrated models regardless of calibration catchment numbers. High quality models could be developed from a small number of calibration catchments and also poor models from a large number of calibration catchments. This indicates that the number of calibration catchments may not be the dominating factor for developing a high quality regionalization model. Instead, the information content could be more important. The study has demonstrated that the standard deviation values between the best and poorest groups are distinctive and could be used in choosing appropriate calibration catchments.
Effects of Essential Oils on Methane Production and Fermentation by, and Abundance and Diversity of, Rumen Microbial Populations
Authors: Patra Amlan K. , Yu Zhongtang 
Published: April 2012

ABSTRACTFive essential oils (EOs), namely, clove oil (CLO), eucalyptus oil (EUO), garlic oil (GAO), origanum oil (ORO), and peppermint oil (PEO), were testedin vitroat 3 different doses (0.25, 0.50, and 1.0 g/liter) for their effect on methane production, fermentation, and select groups of ruminal microbes, including total bacteria, cellulolytic bacteria, archaea, and protozoa. All the EOs significantly reduced methane production with increasing doses, with reductions by 34.4%, 17.6%, 42.3%, 87%, and 25.7% for CLO, EUO, GAO, ORO, and PEO, respectively, at 1.0 g/liter compared with the control. However, apparent degradability of dry matter and neutral detergent fiber also decreased linearly with increasing doses by all EOs except GAO. The concentrations of total volatile fatty acids were not affected by GAO, EUO, or PEO but altered linearly and quadratically by CLO and ORO, respectively. All the EOs also differed in altering the molar proportions of acetate, propionate, and butyrate. As determined by quantitative real-time PCR, all the EOs decreased the abundance of archaea, protozoa, and major cellulolytic bacteria (i.e.,Fibrobacter succinogenes,Ruminococcus flavefaciens, andR. albus) linearly with increasing EO doses. On the basis of denaturing gradient gel electrophoresis analysis, different EOs changed the composition of both archaeal and bacterial communities to different extents. The Shannon-Wiener diversity index (H′) was reduced for archaea by all EOs in a dose-dependent manner but increased for bacteria at low and medium doses (0.25 and 0.50 g/liter) for all EOs except ORO. Due to the adverse effects on feed digestion and fermentation at high doses, a single EO may not effectively and practically mitigate methane emission from ruminants unless used at low doses in combinations with other antimethanogenic compounds.
Shell Biofilm Nitrification and Gut Denitrification Contribute to Emission of Nitrous Oxide by the Invasive Freshwater Mussel Dreissena polymorpha (Zebra Mussel)
Authors: Svenningsen Nanna B. , Heisterkamp Ines M. , Sigby-Clausen Maria , Larsen Lone H. , Nielsen Lars Peter , Stief Peter , Schramm Andreas 
Published: April 2012

ABSTRACTNitrification in shell biofilms and denitrification in the gut of the animal accounted for N2O emission byDreissena polymorpha(Bivalvia), as shown by gas chromatography and gene expression analysis. The mussel's ammonium excretion was sufficient to sustain N2O production and thus potentially uncouples invertebrate N2O production from environmental N concentrations.
Comparative Analysis of Lactobacillus plantarum WCFS1 Transcriptomes by Using DNA Microarray and Next-Generation Sequencing Technologies
Authors: Leimena Milkha M. , Wels Michiel , Bongers Roger S. , Smid Eddy J. , Zoetendal Erwin G. , Kleerebezem Michiel 
Published: April 2012

ABSTRACT

RNA sequencing is starting to compete with the use of DNA microarrays for transcription analysis in eukaryotes as well as in prokaryotes. The application of RNA sequencing in prokaryotes requires additional steps in the RNA preparation procedure to increase the relative abundance of mRNA and cannot employ the poly(T)-primed approach in cDNA synthesis. In this study, we aimed to validate the use of RNA sequencing (direct cDNA sequencing and 3′-untranslated region [UTR] sequencing) using
Lactobacillus plantarum
WCFS1 as a model organism, employing its established microarray platform as a reference. A limited effect of mRNA enrichment on genome-wide transcript quantification was observed, and comparative transcriptome analyses were performed for
L. plantarum
WCFS1 grown in two different laboratory media. Microarray analyses and both RNA sequencing methods resulted in similar depths of analysis and generated similar fold-change ratios of differentially expressed genes. The highest overall correlation was found between microarray and direct cDNA sequencing-derived transcriptomes, while the 3′-UTR sequencing-derived transcriptome appeared to deviate the most. Overall, a high similarity between patterns of transcript abundance and fold-change levels of differentially expressed genes was detected by all three methods, indicating that the biological conclusions drawn from the transcriptome data were consistent among the three technologies.
Quantitative PCR for Tracking the Megaplasmid-Borne Biodegradation Potential of a Model Sphingomonad
Authors: Hartmann Erica M. , Badalamenti Jonathan P. , Krajmalnik-Brown Rosa , Halden Rolf U. 
Published: April 2012

ABSTRACT

We developed a quantitative PCR method for tracking the
dxnA1
gene, the initial, megaplasmid-borne gene in
Sphingomonas wittichii
RW1's dibenzo-
p
-dioxin degradation pathway. We used this method on complex environmental samples and report on growth of
S. wittichii
RW1 in landfill leachate, thus furnishing a novel tool for monitoring megaplasmid-borne, dioxygenase-encoding genes.
Inclusion of Chicory (Cichorium intybus L.) in Pigs' Diets Affects the Intestinal Microenvironment and the Gut Microbiota
Authors: Liu Haoyu , Ivarsson Emma , Dicksved Johan , Lundh Torbjörn , Lindberg Jan Erik 
Published: April 2012

ABSTRACT

The content and composition of prebiotic plant fiber in the diet is important in promoting gut-related health. This study investigated the effects of the dietary inclusion of chicory forage and roots on the intestinal microenvironment of pigs. Thirty-seven-week-old pigs were fed 1 of 5 diets for 18 days, including a cereal-based control diet and 4 diets with the inclusion of 80 and 160 g kg
−1
of body weight chicory forage (CF80 and CF160), 80 g kg
−1
chicory root (CR80), and a mix of 80 g kg
−1
forage and 80 g kg
−1
chicory root (CFR). The animals maintained good performance and health irrespective of diet. Bacterial community structure and diversity in ileal and colonic samples was assessed using terminal restriction fragment length polymorphism (T-RFLP), combined with cloning and sequencing. Samples clustered perfectly according to gut segment with a higher bacterial diversity in colon than ileum. Distal ileum was dominated by lactic acid bacteria (LAB), and the relative amount of this group was increased by the CF160 and CFR diets. The colonic bacterial community was dominated by butyrate-producing bacteria and
Prevotella
. The increased relative abundance of butyrate-producing bacteria in the colon was positively correlated with the molar proportion of acetic acid and furthermore linked to the chicory forage diets (CF80 and CF160). Diets including chicory roots (CR80 and CFR) were correlated with a higher colonic abundance of
Megasphaera elsdenii
. The fermentation products and pH in digesta responded to diet type and were correlated with shifts in the microbiota, showing that chicory influences the intestinal microenvironment of pigs.
Functional Specificity of Extracellular Nucleases of Shewanella oneidensis MR-1
Authors: Heun Magnus , Binnenkade Lucas , Kreienbaum Maximilian , Thormann Kai M. 
Published: April 2012

ABSTRACTBacterial species such asShewanella oneidensisMR-1 require extracellular nucleolytic activity for the utilization of extracellular DNA (eDNA) as a source of nutrients and for the turnover of eDNA as a structural matrix component during biofilm formation. We have previously characterized two extracellular nucleases ofS. oneidensisMR-1, ExeM and ExeS. Although both are involved in biofilm formation, they are not specifically required for the utilization of eDNA as a nutrient. Here we identified and characterized EndA, a third extracellular nuclease ofShewanella. The heterologously overproduced and purified protein was highly active and rapidly degraded linear and supercoiled DNAs of various origins. Divalent metal ions (Mg2+or Mn2+) were required for function.endAis cotranscribed withphoA, an extracellular phosphatase, and is not upregulated upon phosphostarvation. Deletion ofendAabolished both extracellular degradation of DNA byS. oneidensisMR-1 and the ability to use eDNA as a sole source of phosphorus. PhoA is not strictly required for the exploitation of eDNA as a nutrient. The activity of EndA prevents the formation of large cell aggregates during planktonic growth. However, in contrast to the findings for ExeM,endAdeletion had only minor effects on biofilm formation. The findings strongly suggest that the extracellular nucleases ofS. oneidensisexert specific functions required under different conditions.
Oxalyl-Coenzyme A Reduction to Glyoxylate Is the Preferred Route of Oxalate Assimilation in Methylobacterium extorquens AM1
Authors: Schneider Kathrin , Skovran Elizabeth , Vorholt Julia A. 
Published: April 2012

ABSTRACT

Oxalate catabolism is conducted by phylogenetically diverse organisms, including
Methylobacterium extorquens
AM1. Here, we investigate the central metabolism of this alphaproteobacterium during growth on oxalate by using proteomics, mutant characterization, and
13
C-labeling experiments. Our results confirm that energy conservation proceeds as previously described for
M. extorquens
AM1 and other characterized oxalotrophic bacteria via oxalyl-coenzyme A (oxalyl-CoA) decarboxylase and formyl-CoA transferase and subsequent oxidation to carbon dioxide via formate dehydrogenase. However, in contrast to other oxalate-degrading organisms, the assimilation of this carbon compound in
M. extorquens
AM1 occurs via the operation of a variant of the serine cycle as follows: oxalyl-CoA reduction to glyoxylate and conversion to glycine and its condensation with methylene-tetrahydrofolate derived from formate, resulting in the formation of C3 units. The recently discovered ethylmalonyl-CoA pathway operates during growth on oxalate but is nevertheless dispensable, indicating that oxalyl-CoA reductase is sufficient to provide the glyoxylate required for biosynthesis. Analysis of an oxalyl-CoA synthetase- and oxalyl-CoA-reductase-deficient double mutant revealed an alternative, although less efficient, strategy for oxalate assimilation via one-carbon intermediates. The alternative process consists of formate assimilation via the tetrahydrofolate pathway to fuel the serine cycle, and the ethylmalonyl-CoA pathway is used for glyoxylate regeneration. Our results support the notion that
M. extorquens
AM1 has a plastic central metabolism featuring multiple assimilation routes for C1 and C2 substrates, which may contribute to the rapid adaptation of this organism to new substrates and the eventual coconsumption of substrates under environmental conditions.
Vicriviroc Resistance Decay and Relative Replicative Fitness in HIV-1 Clinical Isolates under Sequential Drug Selection Pressures
Authors: Tsibris Athe M. N. , Hu Zixin , Paredes Roger , Leopold Kay E. , Putcharoen Opass , Schure Allison L. , Mazur Natalie , Coakley Eoin , Su Zhaohui , Gulick Roy M. , Kuritzkes Daniel R. 
Published: April 2012

ABSTRACTWe previously described an HIV-1-infected individual who developed resistance to vicriviroc (VCV), an investigational CCR5 antagonist, during 28 weeks of therapy (Tsibris AM et al., J. Virol.82:8210–8214, 2008). To investigate the decay of VCV resistance mutations, a standard clonal analysis of full-lengthenv(gp160) was performed on plasma HIV-1 samples obtained at week 28 (the time of VCV discontinuation) and at three subsequent time points (weeks 30, 42, and 48). During 132 days, VCV-resistant HIV-1 was replaced by VCV-sensitive viruses whose V3 loop sequences differed from the dominant pretreatment forms. A deep-sequencing analysis showed that the week 48 VCV-sensitive V3 loop form emerged from a preexisting viral variant. Enfuvirtide was added to the antiretroviral regimen at week 30; by week 48, enfuvirtide treatment selected for either the G36D or N43D HR-1 mutation. Growth competition experiments demonstrated that viruses incorporating the dominant week 28 VCV-resistantenvwere less fit than week 0 viruses in the absence of VCV but more fit than week 48 viruses. This week 48 fitness deficit persisted when G36D was corrected by either site-directed mutagenesis or week 48 gp41 domain swapping. The correction of N43D, in contrast, restored fitness relative to that of week 28, but not week 0, viruses. Virus entry kinetics correlated with observed fitness differences; the slower entry of enfuvirtide-resistant viruses corrected to wild-type rates in the presence of enfuvirtide. These findings suggest that while VCV and enfuvirtide select for resistance mutations in only oneenvsubunit, gp120 and gp41 coevolve to maximize viral fitness under sequential drug selection pressures.
A Lentiviral Vector-Based, Herpes Simplex Virus 1 (HSV-1) Glycoprotein B Vaccine Affords Cross-Protection against HSV-1 and HSV-2 Genital Infections
Authors: Chiuppesi Flavia , Vannucci Laura , De Luca Anna , Lai Michele , Matteoli Barbara , Freer Giulia , Manservigi Roberto , Ceccherini-Nelli Luca , Maggi Fabrizio , Bendinelli Mauro , Pistello Mauro 
Published: April 2012

ABSTRACT
Genital herpes is caused by herpes simplex virus 1 (HSV-1) and HSV-2, and its incidence is constantly increasing in the human population. Regardless of the clinical manifestation, HSV-1 and HSV-2 infections are highly transmissible to sexual partners and enhance susceptibility to other sexually transmitted infections. An effective vaccine is not yet available. Here, HSV-1 glycoprotein B (gB1) was delivered by a feline immunodeficiency virus (FIV) vector and tested against HSV-1 and HSV-2 vaginal challenges in C57BL/6 mice. The gB1 vaccine elicited cross-neutralizing antibodies and cell-mediated responses that protected 100 and 75% animals from HSV-1- and HSV-2-associated severe disease, respectively. Two of the eight fully protected vaccinees underwent subclinical HSV-2 infection, as demonstrated by deep immunosuppression and other analyses. Finally, vaccination prevented death in 83% of the animals challenged with a HSV-2 dose that killed 78 and 100% naive and mock-vaccinated controls, respectively. Since this FIV vector can accommodate two or more HSV immunogens, this vaccine has ample potential for improvement and may become a candidate for the development of a truly effective vaccine against genital herpes.
Intimate partner violence and prescription of potentially addictive drugs: prospective cohort study of women in the Oslo Health Study
Authors: Stene Lise Eilin , Dyb Grete , Tverdal Aage , Jacobsen Geir Wenberg , Schei Berit 
Published: April 2012

ObjectivesTo investigate the prescription of potentially addictive drugs, including analgesics and central nervous system depressants, to women who had experienced intimate partner violence (IPV).DesignProspective population-based cohort study.SettingInformation about IPV from the Oslo Health Study 2000/2001 was linked with prescription data from the Norwegian Prescription Database from 1 January 2004 through 31 December 2009.ParticipantsThe study included 6081 women aged 30–60 years.Main outcome measuresPrescription rate ratios (RRs) for potentially addictive drugs derived from negative binomial models, adjusted for age, education, paid employment, marital status, chronic musculoskeletal pain, mental distress and sleep problems.ResultsAltogether 819 (13.5%) of 6081 women reported ever experiencing IPV: 454 (7.5%) comprised physical and/or sexual IPV and 365 (6.0%) psychological IPV alone. Prescription rates for potentially addictive drugs were clearly higher among women who had experienced IPV: crude RRs were 3.57 (95% CI 2.89 to 4.40) for physical/sexual IPV and 2.13 (95% CI 1.69 to 2.69) for psychological IPV alone. After full adjustment RRs were 1.83 (1.50 to 2.22) for physical/sexual IPV, and 1.97 (1.59 to 2.45) for psychological IPV alone. Prescription rates were increased both for potentially addictive analgesics and central nervous system depressants. Furthermore, women who reported IPV were more likely to receive potentially addictive drugs from multiple physicians.ConclusionsWomen who had experienced IPV, including psychological violence alone, more often received prescriptions for potentially addictive drugs. Researchers and clinicians should address the possible adverse health and psychosocial impact of such prescription and focus on developing evidence-based healthcare for women who have experienced IPV.
Loss of epithelial membrane protein-2 expression confers an independent prognosticator in nasopharyngeal carcinoma: a cohort study
Authors: Chen Yi-Hsien , Wu Li-Ching , Wu Wen-Ren , Lin Hung-Jung , Lee Sung-Wei , Lin Ching-Yih , Chang Shih-Lun , Chow Nan-Haw , Huang Hsuan-Ying , Li Chien-Feng , Hsu Han-Ping , Shiue Yow-Ling 
Published: April 2012

ObjectiveTo evaluate the expression of epithelial membrane protein-2 (EMP2) protein and its clinicopathological associations in patients with nasopharyngeal carcinoma.DesignRetrospective population-based cohort study.SettingThis study was based on a biobank in Chi-Mei Medical Center (Tainan, Taiwan) from 1993 to 2002.ParticipantsBiopsies of 124 consecutive nasopharyngeal carcinoma patients without initial distant metastasis and treated with consistent guidelines were assessed. Immunoexpressions of EMP2 were analysed and the outcomes were correlated with clinicopathological features and patient survivals.Primary and secondary outcome measuresImmunoexpressions of EMP2 were analyzed and the outcomes were correlated with clinicopathological features and patient survivals.ResultsLoss of EMP2 expression (49.2%) was correlated with advanced primary tumour (p=0.044), nodal status (p=0.045) and the 7th American Joint Committee on Cancer stage (p=0.027). In multivariate analyses, loss of EMP2 expression emerged as an independent prognosticator for worse disease-specific survival (DSS; p=0.015) and local recurrence-free survival (LRFS; p=0.030), along with the American Joint Committee on Cancer stages III–IV (p=0.034, DSS; p=0.023, LRFS).ConclusionsLoss of EMP2 expression is common and associated with adverse prognosticators and might confer tumour aggressiveness through hampering its interaction with specific membrane protein(s) and hence the downstream signal transduction pathway(s).
Risk of invasive pneumococcal disease in people admitted to hospital with selected immune-mediated diseases: record linkage cohort analyses
Authors: Wotton Clare J , Goldacre Michael J 
Published: April 2012

BackgroundInvasive pneumococcal disease is a serious infection, and it is an important cause of morbidity and mortality in certain groups of ‘at-risk’ people. Those considered ‘at-risk’ in the UK include very young children, people aged 65 years and older and people with certain serious chronic diseases, asplenia or immunosuppression. There is little evidence about whether people with immune-mediated diseases are at increased risk of pneumococcal disease and therefore may benefit from pneumococcal vaccination.MethodsRetrospective cohort studies, using linked hospital data, from the longstanding Oxford Record Linkage Study (1963–2008) and from recent English national linked Hospital Episode Statistics (1999–2008); analysis of whether people with immune-mediated diseases are more likely than others to be admitted to hospital for pneumococcal disease; calculation of rate ratio for pneumococcal disease in cohorts with immune-mediated disease compared with control cohorts.ResultsThere were elevated rate ratios for many of the immune-mediated diseases, for example, Addison's disease in England 3.8 (95% CI 3.4 to 4.2), autoimmune haemolytic anaemia 4.9 (4.4 to 5.3), Crohn's disease 2.2 (2.1 to 2.3), diabetes mellitus 3.7 (3.4 to 4.1), multiple sclerosis 3.7 (3.5 to 3.8), myxoedema 1.60 (1.58 to 1.63), pernicious anaemia 1.74 (1.66 to 1.83), primary biliary cirrhosis 3.3 (2.9 to 3.7), polyarteritis nodosa 5.0 (4.0 to 6.0), rheumatoid arthritis 2.47 (2.41 to 2.52), scleroderma 4.2 (3.8 to 4.7), Sjogren's syndrome 3.2 (2.9 to 3.5) and systemic lupus erythematosus 5.0 (4.6 to 5.4). Findings in the Oxford and all England data sets were similar.ConclusionsPeople admitted to hospital with immune-mediated diseases are at higher risk than those with invasive pneumococcal disease. Vaccination should be considered in this group of patients.