bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial community transcription patterns during a marine phytoplankton bloom
Authors: Rinta‐Kanto Johanna M. , Sun Shulei , Sharma Shalabh , Kiene Ronald P. , Moran Mary Ann 
Published: October 2011

SummaryBacterioplankton consume a large proportion of photosynthetically fixed carbon in the ocean and control its biogeochemical fate. We used an experimental metatranscriptomics approach to compare bacterial activities that route energy and nutrients during a phytoplankton bloom compared with non‐bloom conditions. mRNAs were sequenced from duplicate bloom and control microcosms 1 day after a phytoplankton biomass peak, and transcript copies per litre of seawater were calculated using an internal mRNA standard. Transcriptome analysis revealed a potential novel mechanism for enhanced efficiency during carbon‐limited growth, mediated through membrane‐bound pyrophosphatases [V‐type H(+)‐translocating; hppA]; bloom bacterioplankton participated less in this metabolic energy scavenging than non‐bloom bacterioplankton, with possible implications for differences in growth yields on organic substrates. Bloom bacterioplankton transcribed more copies of genes predicted to increase cell surface adhesiveness, mediated by changes in bacterial signalling molecules related to biofilm formation and motility; these may be important in microbial aggregate formation. Bloom bacterioplankton also transcribed more copies of genes for organic acid utilization, suggesting an increased importance of this compound class in the bioreactive organic matter released during phytoplankton blooms. Transcription patterns were surprisingly faithful within a taxon regardless of treatment, suggesting that phylogeny broadly predicts the ecological roles of bacterial groups across ‘boom’ and ‘bust’ environmental backgrounds.
Which fast track elements predict early recovery after colon cancer surgery?
Authors: Vlug M. S. , Bartels S. A. L. , Wind J. , Ubbink D. T. , Hollmann M. W. , Bemelman W. A. ,   on behalf of the collaborative LAFA study group
Published: October 2011

AbstractAim  It is questioned whether all separate fast track elements are essential for enhanced postoperative recovery. We aimed to determine which baseline characteristics and which fast track elements are independent predictors of faster postoperative recovery in patients undergoing resection for colon cancer.Method  Data from the LAFA trial database were used. In this trial, fast track care was compared with standard perioperative care in 400 patients undergoing laparoscopic or open surgery for colonic cancer. During admission 19 fast track elements per patient were prospectively evaluated and scored whether or not they were successfully applied. To identify predictive factors six baseline characteristics and those fast track items that were successfully achieved were entered in a univariate and multivariate linear regression analysis with total postoperative hospital stay (THS) as the primary outcome.Results  In 400 patients, two baseline characteristics and two fast track elements were found to be significant independent predictors of THS: female sex [B = 0.85; 95% CI 0.75–0.96; reduction of 15% (CI 14–25%) in THS], laparoscopic resection [B = 0.85; 95% CI 0.75–0.96; reduction of 15% (CI 14–25%) in THS], ‘normal diet at postoperative days 1, 2 and 3’ [B = 0.70; 95% CI 0.61–0.81; reduction of 30% (CI 19–39%) in THS] and ‘enforced mobilization at postoperative days 1, 2 and 3’ [B = 0.68; 95% CI 0.59–0.80; reduction of 32% (CI 20–41%) in THS].Conclusion  Evaluating only those fast track elements that were successfully achieved, enforced advancement of oral intake, early mobilization, laparoscopic surgery and female sex were independent determinants of early recovery.
Biomarkers for diabetes prediction, pathogenesis or pharmacotherapy guidance? Past, present and future possibilities
Authors: Sattar N. 
Published: October 2011

Diabet. Med. 29, 5–13 (2012)AbstractAn ideal biomarker should refine identification of those at risk of disease occurrence or progression, improve prediction of complications of disease, and/or guide and help tailor responses to different therapies. Biomarkers that give insights into disease pathogenesis are also of interest. With this in mind, this review describes biomarker studies relevant to diabetes, focusing on those conducted by the author, his colleagues and collaborators. The review highlights several points. (1) Novel biomarkers may not improve prediction of new‐onset diabetes in a meaningful way beyond what can be achieved with simple measures combined with HbA1c, and a sensible way ahead may be to combine diabetes and cardiovascular disease prediction using HbA1c and such measures. (2) In terms of disease pathogenesis, associations do not necessarily infer causality; potential for residual confounding and reverse causality should always be borne in mind. The potential relevance of such issues to understanding the relationship of some topical variables/pathways, namely adiponectin, inflammation and vitamin D, with diabetes will be highlighted. (3) How baseline and serial data on biomarkers arising from the liver have improved our understanding of the role of hepatic fat in diabetes pathogenesis will be explored. (4) Future goals for diabetes biomarker research should focus on predicting complications and determining subgroups who may respond better to particular therapies. (5) All novel biomarker research (regardless of analytical platforms used) needs to be tested against information available from commonly measured variables in clinical practice. Otherwise, many claims of clinical utility can be exaggerated. In summary, biomarker research in diabetes is continuing apace in a number of areas, but it remains to be seen whether the promise of biomarker research to improve the care of our patients becomes a reality.
Clones, hermaphrodites and pregnancies: nature's oddities offer evolutionary lessons on reproduction
Authors: Avise J.C. 
Published: October 2011

AbstractI love the term ‘natural history’ because it encapsulates the sentiment that nature's operations have evolutionary etiologies.CharlesDarwin was a natural historianpar excellenceand his elucidation of natural selection, artificial selection, and sexual selection fundamentally changed how scientists interpret the origins of biological features previously ascribed to sentient craftsmanship by supernatural agents.Darwin's insights on evolutionary forces grew from his exceptional knowledge of natural history, yet two key topics steeped in natural history – sex and reproductive genetics – remained poorly understood (and probably even shunned) inDarwin'sVictorian era. That situation changed dramatically in the latter half of the 20th century with societal awakenings about sexuality that also happened to coincide with the introduction of molecular parentage analyses that unveiled a plethora of formerly hidden ‘sexcapades’ throughout the biological world. Here I summarize some of the evolutionary revelations that have emerged from selection theory as applied to genetic and phylogenetic information on clonality, hermaphroditism, and pregnancy, three procreative phenomena that are relatively rare in vertebrate animals and thus offer alternative evolutionary perspectives on standard reproductive modes. Collectively, these three peculiarities of nature illustrate how the abnormal in biology can enlighten evolutionary thought about the norm.
Regional and local patterns of ectomycorrhizal fungal diversity and community structure along an altitudinal gradient in the Hyrcanian forests of northern Iran
Authors: Bahram Mohammad , Põlme Sergei , Kõljalg Urmas , Zarre Shahin , Tedersoo Leho 
Published: October 2011

Summary
Altitudinal gradients strongly affect the diversity of plants and animals, yet little is known about the altitudinal effects on the distribution of microorganisms, including ectomycorrhizal fungi.
By combining morphological and molecular identification methods, we addressed the relative effects of altitude, temperature, precipitation, host community and soil nutrient concentrations on species richness and community composition of ectomycorrhizal fungi in one of the last remaining temperate old‐growth forests in Eurasia.
Molecular analyses revealed 367 species of ectomycorrhizal fungi along three altitudinal transects. Species richness declined monotonically with increasing altitude. Host species and altitude were the main drivers of the ectomycorrhizal fungal community composition at both the local and regional scales. The mean annual temperature and precipitation were strongly correlated with altitude and accounted for the observed patterns of richness and community.
The decline of ectomycorrhizal fungal richness with increasing altitude is consistent with the general altitudinal richness patterns of macroorganisms. Low environmental energy reduces the competitive ability of rare species and thus has a negative effect on the richness of ectomycorrhizal fungi. Because of multicollinearity with altitude, the direct effects of climatic variables and their seasonality warrant further investigation at the regional and continental scales.
Inherited thrombophilias and adverse pregnancy outcomes: a case–control study in an Australian population
Authors: SAID JOANNE M. , HIGGINS JOHN R. , MOSES ERIC K. , WALKER SUSAN P. , MONAGLE PAUL T. , BRENNECKE SHAUN P. 
Published: October 2011

AbstractObjective. The primary aim of this study was to examine the association between inherited thrombophilias and adverse pregnancy outcomes in an Australian population. Design. Case–control study. Setting. Two Australian tertiary level maternity hospitals. Population. One hundred and fifteen cases with adverse pregnancy outcomes, comprising severe pre‐eclampsia (n=45), fetal growth restriction (n=44), placental abruption (n=16) or stillbirth (n=10), and 115 controls matched for ethnicity, parity and maternal age. Methods. Genotyping for factor V Leiden, prothrombin gene mutation, methylenetetrahydrofolate reductase 677 and 1298 and thrombomodulin polymorphism was performed using Taqman assays in an ABI prism 7700 Sequencer. Pregnancy outcome data were extracted from the medical record at the time of recruitment. Main Outcome Measures. Prevalence of inherited thrombophilias in women with adverse pregnancy outcomes and matched control women. Results. There were no differences in baseline characteristics between cases and control women, apart from duration of gestation and neonatal birthweight. Overall, there was no significant difference in the prevalence of these inherited thrombophilia polymorphisms between cases and control women. Heterozygosity for the factor V Leiden mutation, however, was significantly associated with an increased risk of both stillbirth (odds ratio 9.33, 95% confidence interval 1.36–64.15, p=0.02) and placental abruption (odds ratio 8.62, 95% confidence interval 1.57–47.17, p=0.01). Conclusions. Overall, this study does not support a significant association between inherited thrombophilia polymorphisms and adverse pregnancy outcomes. Our two statistically significant findings should be interpreted with caution given the small number of patients in these subgroups (10 stillbirths and 16 placental abruption cases) and the wide confidence intervals.
Interleukin‐6 in oral diseases: a review
Authors: Nibali L , Fedele S , D’Aiuto F , Donos N 
Published: October 2011

Oral Diseases (2012) 18, 236–243Interleukin‐6 (IL‐6) is a pleomorphic cytokine involved in a number of physiologic and pathologic processes including response to trauma and infection and development and progression of inflammation and malignancy. IL‐6 is emerging as an important mediator and novel therapeutic target for chronic inflammatory diseases and cancer. The present study reviews the available evidence regarding the association between IL‐6 and a range of oral diseases including infections (periodontal disease and endodontic infections), immunologically mediated disorders (oral lichen planus and Sjögren’s syndrome) and malignancy (oral cancer and precancer). The role of common genetic variants of IL‐6 in determining individual susceptibility to certain oral diseases, as well as novel therapeutic strategies based on IL‐6 inhibition are also discussed.
Nightguard Vital Bleaching: Side Effects and Patient Satisfaction 10 to 17 Years Post‐Treatment
Authors: BOUSHELL LEE W. , RITTER ANDRÉ V. , GARLAND GLENN E. , TIWANA KAREN K. , SMITH LYNN R. , BROOME ANGELA , LEONARD RALPH H. 
Published: October 2011

ABSTRACTStatement of the Problem:  The long‐term patient satisfaction and safety of nightguard vital bleaching (NGVB) requires further evaluation.Purpose of the Study:  The purpose of this study was to evaluate patients' satisfaction and identify side effects of NGVB up to 17 years post‐treatment.Materials and Methods:  Thirty‐one participants who had completed previous NGVB studies using 10% carbamide peroxide were contacted at least 10 years post‐treatment (range 10–17 years, average 12.3 years). Participants reported shade satisfaction (very satisfied [VS], partially satisfied [PS], or not satisfied [NS]) as well as potential complications. Participants had teeth # 6 to 11 examined for tooth vitality, gingival inflammation (Löe's Gingival Index [GI]), and radiographically for external cervical resorption (ECR).Results:  All of the participants had successful lightening of their teeth. Sixty‐one percent (19) had not retreated their teeth. Of those who had not retreated their teeth and who responded to the question of whitening satisfaction, 31% (4/13) were VS, 54% (7/13) were PS, and 15% (2/13) were NS with their current shade. Of those who had retreated their teeth, all were VS or PS. Ninety‐one percent of the examined teeth had GI = 0 (normal), 7% had GI = 1 (mild inflammation), and 2% had GI = 2 (moderate inflammation). Sixty‐nine percent of teeth tested responded to a cold stimulus. Radiographs did not detect ECR or apical lesions. No participant reported having a gingival biopsy post‐treatment, and 87% would whiten again.Conclusions:  Patient satisfaction with NGVB may last as long as 12.3 years in average (range 10–17 years) post‐treatment. GI and ECR findings were considered within the normal expectations for the sample studied, suggesting minimal clinical post‐NGVB side effects up to 17 years.CLINICAL SIGNIFICANCENightguard vital bleaching provides patient satisfaction with minimal side effects up to 17 years post‐treatment.(J Esthet Restor Dent ••:••–••, 2011)
The Proteome of the Locus Ceruleus in Parkinson's Disease: Relevance to Pathogenesis
Authors: van Dijk Karin D. , Berendse Henk W. , Drukarch Benjamin , Fratantoni Silvina A. , Pham Thang V. , Piersma Sander R. , Huisman Evelien , Brevé John J.P. , Groenewegen Henk J. , Jimenez Connie R. , van de Berg Wilma D.J. 
Published: October 2011

AbstractThe locus ceruleus is among the earliest affected brain regions in Parkinson's disease (PD) showing Lewy body pathology and neuronal loss. To improve our understanding of the pathogenesis of PD, we performed the first proteomic analysis ever of post‐mortem locus ceruleus tissue of six pathologically confirmed PD patients, and six age‐ and gender‐matched non‐neurological controls. In total 2495 proteins were identified, of which 87 proteins were differentially expressed in the locus ceruleus of PD patients compared with controls. The majority of these differentially expressed proteins are known to be involved in processes that have been implicated in the pathogenesis of PD previously, including mitochondrial dysfunction, oxidative stress, protein misfolding, cytoskeleton dysregulation and inflammation. Several individual proteins were identified that have hitherto not been associated with PD, such as regucalcin, which plays a role in maintaining intracellular calcium homeostasis, and isoform 1 of kinectin, which is involved in transport of cellular components along microtubules. In addition, pathway analysis suggests a pathogenetic role for aminoacyl‐tRNA‐biosynthesis. These findings indicate that the proteome of the locus ceruleus of PD patients and non‐neurological controls provides data that are relevant to the pathogenesis of PD, reflecting both known and potentially novel pathogenetic pathways.
Afterglow Thermoluminescence Measured in Isolated Chloroplasts
Authors: Belatik Ahmed , Essemine Jemaa , Hotchandani Surat , Carpentier Robert 
Published: October 2011

AbstractThe thermoluminescence afterglow (AG) measured in plant leaves originates from the S2/S3QB− charge pair recombination in photosystem II (PSII) initiated by reverse electron flow from stromal reductants to PQ and then to the QB site in PSII centers that are in the S2/S3QB state. In this study, we show that this luminescence, absent in isolated thylakoid membranes, can be measured in intact chloroplasts that retain their stromal content including the electron acceptor pool (oxidized ferredoxin/NADP+) of photosystem I. The properties of the chloroplasts AG emission is similar to the AG in leaves in terms of temperature maximum, period‐four modulation, far‐red light stimulation, and antimycin A inhibition.
High mobility reduces beta‐diversity among orthopteran communities – implications for conservation
Authors: MARINI LORENZO , ÖCKINGER ERIK , BATTISTI ANDREA , BOMMARCO RICCARDO 
Published: October 2011

Abstract. 1. The analysis ofβ‐diversity, i.e. species turnover, across space is central to a wide array of ecological and evolutionary topics, also providing critical information to conservation planning. Although dispersal limitation has been demonstrated to play an important role in determining insect community structure, very little research has been done to test whether mobility might affect the diversity distribution of species across multiple spatial scales.2. We considered orthopterans (EnsiferaandCaelifera) inhabiting hay meadows to test whether species mobility modifiesβ‐diversity patterns across three nested spatial scales (1‐m2plots within meadow, 1000‐m2meadows within landscape, and 19.6‐km2landscapes within a region) and along a gradient of management intensity.3. Orthopteran community composition varied most significantly over broader spatial scales. Larger proportion of regionalγ‐diversity was mainly composed ofβ‐diversity at the landscape scale, whereas this proportion was smaller at the plot and meadow scale.4. Mobility, but not management, strongly modifiedβ‐diversity patterns. Sedentary species contributed to a greater proportion ofβ‐diversity across all the investigated scales compared with mobile species.5. Measures currently included in most agri‐environment schemes have only focused on the extensive management at the field scale. Our results imply that orthopteran diversity would benefit from maintaining extensively managed meadows scattered throughout the whole region, as the loss of species‐rich isolated grassland patches due to abandonment or eutrophication might cause severe reductions of the regional species pool. Increasing connectivity might be also considered as a complementary measure to increase species occupancy and population persistence, particularly for sedentary species.
Collaborative research to support transition towards integrating flood risk management in urban development
Authors: van Herk S. , Zevenbergen C. , Rijke J. , Ashley R. 
Published: October 2011

AbstractUrban development and regeneration present windows of opportunity to help reduce flood vulnerability. Much recent research stresses the need for better integration of flood risk into planning processes. However, there is limited experience in incorporating flood risk management in urban planning. Demonstration projects can help in overcoming this lack of experience and facilitate a transition towards integrated flood risk management and spatial planning; taking longer term flexible and adaptive approaches. This paper demonstrates that the process of research, if collaborative, can contribute to the better integration of flood risk in urban planning. Collaborative research can support demonstration projects and their wider uptake, as well as policy development and subsequently a transition to integrated flood risk management. It also provides greater freedom to use different approaches, consider a broader range of problems and solutions, bring stakeholders together and facilitate capacity building. This paper calls for collaborative research that facilitates social learning and is impact focussed, preferably supporting innovative demonstration projects.
Movement Choremes: Bridging Cognitive Understanding and Formal Characterizations of Movement Patterns1
Authors: Klippel Alexander 
Published: October 2011

AbstractThis article discusses an approach to characterizing movement patterns (paths/trajectories) of individual agents that allows for relating aspects of cognitive conceptualization of movement patterns with formal spatial characterizations. To this end, we adopt a perspective of characterizing movement patterns on the basis of perceptual and conceptual invariants that we termmovement choremes(MCs). MCs are formally grounded by behaviorally validating qualitative spatio‐temporal calculi. Relating perceptual and cognitive aspects of space and formal theories of spatial information has shown promise to foster understanding of the semantics of movement patterns. Specifically, we discuss our approach in relation to existing qualitative formalisms such as the region connection calculus and the Egenhofer’s intersection formalisms. We show that the MC approach is compatible with these approaches but offers additional opportunities to improve the cognitive adequacy of these formalisms. We summarize this paper using a movement taxonomy that also provides guidance for future research.
Characterization of a DHA-1-Producing Klebsiella pneumoniae Strain Involved in an Outbreak and Role of the AmpR Regulator in Virulence
Authors: Hennequin Claire , Robin Frédéric , Cabrolier Nadège , Bonnet Richard , Forestier Christiane 
Published: October 2011

ABSTRACT

A clonal strain of
Klebsiella pneumoniae
producing the plasmid-encoded cephalosporinase DHA-1 was isolated from four patients admitted to the teaching hospital of Clermont-Ferrand, France, in 2006. It was responsible for severe infections in three of the patients; the fourth was colonized only in the gastrointestinal tract. The strain had at least two plasmids encoding resistance to antibiotics (quinolones, aminoglycosides, chloramphenicol, sulfonamides, and trimethoprim), as shown by disk diffusion assay, and harbored only a few genes for virulence factors (
wabG
and
mrkD
), as shown by PCRs. DHA-1 synthesis is regulated by an upstream, divergently transcribed gene,
ampR
, which is also involved in the expression of virulence factors in
Pseudomonas aeruginosa
. To investigate the role of AmpR in
K. pneumoniae
, we cloned the wild-type
ampR
gene from the DHA-1 clonal isolate into a previously characterized
K. pneumoniae
background plasmid-cured strain, CH608.
ampR
was also introduced into a CH608 isogenic mutant deleted of
ampD
, in which AmpR is present only in its activator form, resulting in constitutive hyperproduction of the β-lactamase. We showed that
ampR
was involved in the upregulation of capsule synthesis and therefore in resistance to killing by serum. AmpR also modulated biofilm formation and type 3 fimbrial gene expression, as well as colonization of the murine gastrointestinal tract and adhesion to HT-29 intestinal epithelial cells. These results show the pleiotropic role of
ampR
in the pathogenesis process of
K. pneumoniae
.