bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a liquid chromatography/tandem mass spectrometry method to investigate the presence of biomarkers of DNA damage in urine related to red meat consumption and risk of colorectal cancer
Authors: Da Pieve Chiara , Sahgal Natasha , Moore Sharon A. , Velasco‐Garcia Maria N. 
Published: October 2013

RATIONALEThe consumption of red meat is known to enhance the endogenous formation of N‐nitroso compounds (NOCs), which are potent carcinogens. DNA damage related to NOCs, and hence red meat, has been detected in colorectal cells and in blood. We proposed to extend previous studies to a non‐invasive approach for the detection of O6‐carboxymethylguanine (O6CMG) and O6‐carboxymethyl‐2'‐deoxyguanosine (O6CMdG) in urine in relation to red meat intake using liquid chromatography/tandem mass spectrometry (LC/MS/MS). The presence of the adduct in urine samples either as the free base or as 2'‐deoxynucleoside could help in determining the repair mechanism involved when such lesions are produced. A non‐invasive assessment of DNA adducts could also allow for large‐scale analyses in the population and cancer prevention dietary strategies.METHODSAn LC/MS/MS method for the quantitation of O6CMG and O6CMdG was developed. Urine samples collected from healthy volunteers on red meat and vegetarian diets were analysed either by direct injection or after purification by solid‐phase extraction (SPE). A separate LC/MS/MS method for O6‐methylguanine (O6MeG) and O6‐methyl‐2'‐deoxyguanosine (O6MedG), which are possible hydrolysis products forming during the sample pre‐treatment, was also developed.RESULTSThe developed LC/MS/MS method allowed the simultaneous measurement of O6CMG and O6CMdG. The limits of detection (LODs) were 0.38 ng/mL for O6CMG and 0.18 ng/mL for O6CMdG. The direct injection analysis of the clinical samples showed low sensitivity due to high background signal that was improved by SPE purification. However, the concentrations of the adducts in clinical samples were still found to be below the LOD.CONCLUSIONSNovel, reproducible, and accurate LC/MS/MS methods were developed for the determination of the urinary content of O6CMG and O6CMdG, and of the possible formation of O6MeG and O6MedG by decarboxylation. Clinical samples from volunteers on different diets were analysed. Further studies are required to discover a link between the presence of these biomarkers in urine and red meat consumption. Copyright © 2013 John Wiley & Sons, Ltd.
What's Love Got to Do with It: Relationship Functioning and Mental and Physical Quality of Life Among Pregnant Adolescent Couples
Authors: Kershaw Trace , Murphy Alexandrea , Divney Anna , Magriples Urania , Niccolai Linda , Gordon Derrick 
Published: October 2013

AbstractThe study objective was to describe relationship adjustment and its association with mental and physical quality of life for young couples expecting a baby. 296 young pregnant couples recruited from urban obstetric clinics reported on relationship strengths (e.g., equity, romantic love, and attractiveness), relationship risks (e.g., attachment, intimate partner violence), external family support, relationship adjustment, and mental and physical quality of life. Using the Actor Partner Interdependence Model we assessed both actor and partner effects of relationship variables on relationship adjustment and quality of life. Sixty‐one percent of couples had at least one member with moderate or severe relationship distress. Lower attachment avoidance, lower attachment anxiety, higher relationship equity, lack of intimate partner violence, feelings of love, perceived partner attractiveness, and family support of the relationship related to better relationship adjustment. Associations were fairly consistent across gender. Better relationship adjustment related to more positive mental and physical quality of life for both young women and men. Our results highlight the potential importance of strong relationships on the well‐being of expecting parents. Our results suggest that secure attachments, equitable relationships, feelings of love, and a lack of violence may be particularly important in having strong relationships and improved mental and physical health during pregnancy.
The social structure of microbial community involved in colonization resistance
Authors: He Xuesong , McLean Jeffrey S , Guo Lihong , Lux Renate , Shi Wenyuan 
Published: October 2013

Abstract
It is well established that host-associated microbial communities can interfere with the colonization and establishment of microbes of foreign origins, a phenomenon often referred to as bacterial interference or colonization resistance. However, due to the complexity of the indigenous microbiota, it has been extremely difficult to elucidate the community colonization resistance mechanisms and identify the bacterial species involved. In a recent study, we have established an in vitro mice oral microbial community (O-mix) and demonstrated its colonization resistance against an Escherichia coli strain of mice gut origin. In this study, we further analyzed the community structure of the O-mix by using a dilution/regrowth approach and identified the bacterial species involved in colonization resistance against E. coli. Our results revealed that, within the O-mix there were three different types of bacterial species forming unique social structure. They act as ‘Sensor’, ‘Mediator’ and ‘Killer’, respectively, and have coordinated roles in initiating the antagonistic action and preventing the integration of E. coli. The functional role of each identified bacterial species was further confirmed by E. coli-specific responsiveness of the synthetic communities composed of different combination of the identified players. The study reveals for the first time the sophisticated structural and functional organization of a colonization resistance pathway within a microbial community. Furthermore, our results emphasize the importance of ‘Facilitation’ or positive interactions in the development of community-level functions, such as colonization resistance.
The paradox of enrichment in phytoplankton by induced competitive interactions
Authors: Tubay Jerrold M. , Ito Hiromu , Uehara Takashi , Kakishima Satoshi , Morita Satoru , Togashi Tatsuya , Tainaka Kei-ichi , Niraula Mohan P. , Casareto Beatriz E. , Suzuki Yoshimi , Yoshimura Jin 
Published: October 2013

AbstractThe biodiversity loss of phytoplankton with eutrophication has been reported in many aquatic ecosystems, e.g., water pollution and red tides. This phenomenon seems similar, but different from the paradox of enrichment via trophic interactions, e.g., predator-prey systems. We here propose the paradox of enrichment by induced competitive interactions using multiple contact process (a lattice Lotka-Volterra competition model). Simulation results demonstrate how eutrophication invokes more competitions in a competitive ecosystem resulting in the loss of phytoplankton diversity in ecological time. The paradox is enhanced under local interactions, indicating that the limited dispersal of phytoplankton reduces interspecific competition greatly. Thus, the paradox of enrichment appears when eutrophication destroys an ecosystem either by elevated interspecific competition within a trophic level and/or destabilization by trophic interactions. Unless eutrophication due to human activities is ceased, the world's aquatic ecosystems will be at risk.
Three-dimensional Imaging of Crystalline Inclusions Embedded in Intact Maize Stalks
Authors: Badger John , Lal Jyotsana , Harder Ross , Inouye Hideyo , Gleber S. Charlotte , Vogt Stefan , Robinson Ian , Makowski Lee 
Published: October 2013

AbstractMineral inclusions in biomass are attracting increased scrutiny due to their potential impact on processing methods designed to provide renewable feedstocks for the production of chemicals and fuels. These inclusions are often sculpted by the plant into shapes required to support functional roles that include the storage of specific elements, strengthening of the plant structure and providing a defense against pathogens and herbivores.In situcharacterization of these inclusions faces substantial challenges since they are embedded in an opaque, complex polymeric matrix. Here we describe the use of Bragg coherent diffraction imaging (BCDI) to study mineral inclusions within intact maize stalks. Three-dimensional BCDI data sets were collected and used to reconstruct images of mineral inclusions at 50–100 nm resolution. Asymmetries in the intensity distributions around the Bragg peaks provided detailed information about the deformation fields within these crystal particles revealing lattice defects that result in distinct internal crystal domains.
Kindlin-3 regulates integrin activation and adhesion reinforcement of effector T cells
Authors: Moretti Federico A. , Moser Markus , Lyck Ruth , Abadier Michael , Ruppert Raphael , Engelhardt Britta , Fässler Reinhard 
Published: October 2013

Significance
T cells use integrins for adhesion to endothelial cells and extravasation. Thus, their blocking with Abs prevents T cell extravasation and ameliorates autoimmune diseases, such as multiple sclerosis (MS). Given the side effects of these Abs, we explored the integrin activator Kindlin-3 as potential therapeutic target. Mice lacking Kindlin-3 in T cells were immunized with an autoantigen to induce experimental autoimmune encephalitis (EAE), a model of MS. Although these mice developed EAE, adoptively transferred autoreactive T cells from Kindlin-3–deficient mice to healthy recipients failed to induce EAE. We found that autoreactive Kindlin-3–null T cells extravasate only when the brain microvasculature expresses high integrin ligand levels. Thus, blockage of Kindlin-3 is not a viable alternative approach to treating MS.
Domain‐specific physical activity and health‐related quality of life in university students
Authors: Pedišić Željko , Rakovac Marija , Titze Sylvia , Jurakić Danijel , Oja Pekka 
Published: October 2013

AbstractInformation on the relationship between domain‐specific physical activity (PA) and health‐related quality of life (HRQoL) in the general population and specific groups is still scarce. The aim of this study was to determine the relationship between PA in work, transport, domestic and leisure‐time domains and HRQoL among university students. PA and HRQoL were assessed in a random stratified sample of 1750 university students using the International Physical Activity Questionnaire – long form and 12‐item Short Form Health Survey, respectively. The Spearman's rank correlations, adjusted for age, community size, personal monthly budget, body mass index, smoking habits and alcohol intake ranged from −0.11 to 0.18 in female students and −0.29 to 0.19 in male students. Leisure‐time, domestic, transport‐related PA and total PA were positively related to HRQoL. Inverse correlations with HRQoL were only found for work‐related PA in male students. Multiple linear regression analysis showed that only leisure‐time PA was related to the Physical Summary Component score (β = 0.08 for females and β = 0.10 for males, P < 0.05). Domain‐specific PA levels were not significantly related to the Mental Component Summary score. To get a more comprehensive insight in the relationship between PA and HRQoL, future studies should not only analyse total PA levels but also domain‐specific PA levels. The evidence on the positive relationship of leisure‐time, transport and domestic PA with HRQoL can potentially be used to support evidence‐based promotion of PA in a university setting, and as a hypothesis for future longitudinal studies on such potential causal relationships.
The Gene sml0013 of Synechocystis Species Strain PCC 6803 Encodes for a Novel Subunit of the NAD(P)H Oxidoreductase or Complex I That Is Ubiquitously Distributed among Cyanobacteria
Authors: Schwarz Doreen , Schubert Hendrik , Georg Jens , Hess Wolfgang R. , Hagemann Martin 
Published: October 2013

Abstract
The NAD(P)H oxidoreductase or complex I (NDH1) complex participates in many processes such as respiration, cyclic electron flow, and inorganic carbon concentration in the cyanobacterial cell. Despite immense progress in our understanding of the structure-function relation of the cyanobacterial NDH1 complex, the subunits catalyzing NAD(P)H docking and oxidation are still missing. The gene sml0013 of Synechocystis 6803 encodes for a small protein of unknown function for which homologs exist in all completely known cyanobacterial genomes. The protein exhibits weak similarities to the NDH-dependent flow6 (NDF6) protein, which was reported from Arabidopsis (Arabidopsis thaliana) chloroplasts as a NDH subunit. An sml0013 inactivation mutant of Synechocystis 6803 was generated and characterized. It showed only weak differences regarding growth and pigmentation in various culture conditions; most remarkably, it exhibited a glucose-sensitive phenotype in the light. The genome-wide expression pattern of the Ɗsml0013::Km mutant was almost identical to the wild type when grown under high CO2 conditions as well as after shifts to low CO2 conditions. However, measurements of the photosystem I redox kinetic in cells of the Ɗsml0013::Km mutant revealed differences, such as a decreased capability of cyclic electron flow as well as electron flow into respiration in comparison with the wild type. These results suggest that the Sml0013 protein (named NdhP) represents a novel subunit of the cyanobacterial NDH1 complex, mediating its coupling either to the respiratory or the photosynthetic electron flow.
Volumetric quantification of lung nodules in CT with iterative reconstruction (ASiR and MBIR)
Authors: Chen Baiyu , Barnhart Huiman , Richard Samuel , Robins Marthony , Colsher James , Samei Ehsan 
Published: October 2013

Purpose:Volume quantifications of lung nodules with multidetector computed tomography (CT) images provide useful information for monitoring nodule developments. The accuracy and precision of the volume quantification, however, can be impacted by imaging and reconstruction parameters. This study aimed to investigate the impact of iterative reconstruction algorithms on the accuracy and precision of volume quantification with dose and slice thickness as additional variables.Methods:Repeated CT images were acquired from an anthropomorphic chest phantom with synthetic nodules (9.5 and 4.8 mm) at six dose levels, and reconstructed with three reconstruction algorithms [filtered backprojection (FBP), adaptive statistical iterative reconstruction (ASiR), and model based iterative reconstruction (MBIR)] into three slice thicknesses. The nodule volumes were measured with two clinical software (A: Lung VCAR, B: iNtuition), and analyzed for accuracy and precision.Results:Precision was found to be generally comparable between FBP and iterative reconstruction with no statistically significant difference noted for different dose levels, slice thickness, and segmentation software. Accuracy was found to be more variable. For large nodules, the accuracy was significantly different between ASiR and FBP for all slice thicknesses with both software, and significantly different between MBIR and FBP for 0.625 mm slice thickness with Software A and for all slice thicknesses with Software B. For small nodules, the accuracy was more similar between FBP and iterative reconstruction, with the exception of ASIR vs FBP at 1.25 mm with Software A and MBIR vs FBP at 0.625 mm with Software A.Conclusions:The systematic difference between the accuracy of FBP and iterative reconstructions highlights the importance of extending current segmentation software to accommodate the image characteristics of iterative reconstructions. In addition, a calibration process may help reduce the dependency of accuracy on reconstruction algorithms, such that volumes quantified from scans of different reconstruction algorithms can be compared. The little difference found between the precision of FBP and iterative reconstructions could be a result of both iterative reconstructionˈs diminished noise reduction at the edge of the nodules as well as the loss of resolution at high noise levels with iterative reconstruction. The findings do not rule out potential advantage of IR that might be evident in a study that uses a larger number of nodules or repeated scans.
Quantifying Long-Term Scientific Impact
Authors: Wang Dashun , Song Chaoming , Barabási Albert-László 
Published: October 2013

Citation GrabbersIs there quantifiable regularity and predictability in citation patterns? It is clear that papers that have been cited frequently tend to accumulate more citations. It is also clear that, with time, even the most novel paper loses its currency. Some papers, however, seem to have an inherent “fitness” that can be interpreted as a community's response to the research.Wanget al.(p.127; see the Perspective byEvans) developed a mechanistic model to predict citation history. The model links a paper's ultimate impact, represented by the total number of citations the paper will ever receive, to a single measurable parameter inferred from its early citation history. The model was used to identify factors that influence a journal's impact factor.
Clinical Utility of Viral Load in Management of Cytomegalovirus Infection after Solid Organ Transplantation
Authors: Razonable Raymund R. , Hayden Randall T. 
Published: October 2013

SUMMARY
The negative impact of cytomegalovirus (CMV) infection on transplant outcomes warrants efforts toward improving its prevention, diagnosis, and treatment. During the last 2 decades, significant breakthroughs in diagnostic virology have facilitated remarkable improvements in CMV disease management. During this period, CMV nucleic acid amplification testing (NAT) evolved to become one of the most commonly performed tests in clinical virology laboratories. NAT provides a means for rapid and sensitive diagnosis of CMV infection in transplant recipients. Viral quantification also introduced several principles of CMV disease management. Specifically, viral load has been utilized (i) for prognostication of CMV disease, (ii) to guide preemptive therapy, (iii) to assess the efficacy of antiviral treatment, (iv) to guide the duration of treatment, and (v) to indicate the risk of clinical relapse or antiviral drug resistance. However, there remain important limitations that require further optimization, including the interassay variability in viral load reporting, which has limited the generation of standardized viral load thresholds for various clinical indications. The recent introduction of an international reference standard should advance the major goal of uniform viral load reporting and interpretation. However, it has also become apparent that other aspects of NAT should be standardized, including sample selection, nucleic acid extraction, amplification, detection, and calibration, among others. This review article synthesizes the vast amount of information on CMV NAT and provides a timely review of the clinical utility of viral load testing in the management of CMV in solid organ transplant recipients. Current limitations are highlighted, and avenues for further research are suggested to optimize the clinical application of NAT in the management of CMV after transplantation.
Investigational Antimicrobial Agents of 2013
Authors: Pucci Michael J. , Bush Karen 
Published: October 2013

SUMMARY
New antimicrobial agents are always needed to counteract the resistant pathogens that continue to be selected by current therapeutic regimens. This review provides a survey of known antimicrobial agents that were currently in clinical development in the fall of 2012 and spring of 2013. Data were collected from published literature primarily from 2010 to 2012, meeting abstracts (2011 to 2012), government websites, and company websites when appropriate. Compared to what was reported in previous surveys, a surprising number of new agents are currently in company pipelines, particularly in phase 3 clinical development. Familiar antibacterial classes of the quinolones, tetracyclines, oxazolidinones, glycopeptides, and cephalosporins are represented by entities with enhanced antimicrobial or pharmacological properties. More importantly, compounds of novel chemical structures targeting bacterial pathways not previously exploited are under development. Some of the most promising compounds include novel β-lactamase inhibitor combinations that target many multidrug-resistant Gram-negative bacteria, a critical medical need. Although new antimicrobial agents will continue to be needed to address increasing antibiotic resistance, there are novel agents in development to tackle at least some of the more worrisome pathogens in the current nosocomial setting.
Clinical Outcomes with Rapid Detection of Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus Isolates from Routine Blood Cultures
Authors: Nicolsen Nicole C. , LeCroy Nicholas , Alby Kevin , Laux Jeffrey , Lin Feng-Chang , Daniels Lindsay , Weber David J. , Miller Melissa B. 
Published: October 2013

ABSTRACT

Staphylococcus aureus
is a common cause of bacteremia, with a substantial impact on morbidity and mortality. Because of increasing rates of methicillin-resistant
Staphylococcus aureus
, vancomycin has become the standard empirical therapy. However, beta-lactam antibiotics remain the best treatment choice for methicillin-susceptible strains. Placing patients quickly on the optimal therapy is one goal of antimicrobial stewardship. This retrospective, observational, single-center study compared 33 control patients utilizing only traditional full-susceptibility methodology to 22 case patients utilizing rapid methodology with CHROMagar medium to detect and differentiate methicillin-resistant and methicillin-susceptible
Staphylococcus aureus
strains hours before full susceptibilities were reported. The time to targeted therapy was statistically significantly different between control patients (mean, 56.5 ± 13.6 h) and case patients (44.3 ± 17.9 h) (
P
= 0.006). Intensive care unit status, time of day results emerged, and patient age did not make a difference in time to targeted therapy, either singly or in combination. Neither length of stay (
P
= 0.61) nor survival (
P
= 1.0) was statistically significantly different. Rapid testing yielded a significant result, with a difference of 12.2 h to targeted therapy. However, there is still room for improvement, as the difference in time to susceptibility test result between the full traditional methodology and CHROMagar was even larger (26.5 h). This study supports the hypothesis that rapid testing plays a role in antimicrobial stewardship by getting patients on targeted therapy faster.