bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbial Community Response during the Iron Fertilization Experiment LOHAFEX
Authors: Thiele Stefan , Fuchs Bernhard M. , Ramaiah Nagappa , Amann Rudolf 
Published: October 2012

ABSTRACT

Iron fertilization experiments in high-nutrient, low-chlorophyll areas are known to induce phytoplankton blooms. However, little is known about the response of the microbial community upon iron fertilization. As part of the LOHAFEX experiment in the southern Atlantic Ocean,
Bacteria
and
Archaea
were monitored within and outside an induced bloom, dominated by
Phaeocystis
-like nanoplankton, during the 38 days of the experiment. The microbial production increased 1.6-fold (thymidine uptake) and 2.1-fold (leucine uptake), while total cell numbers increased only slightly over the course of the experiment. 454 tag pyrosequencing of partial 16S rRNA genes and catalyzed reporter deposition fluorescence
in situ
hybridization (CARD FISH) showed that the composition and abundance of the bacterial and archaeal community in the iron-fertilized water body were remarkably constant without development of typical bloom-related succession patterns. Members of groups usually found in phytoplankton blooms, such as
Roseobacter
and
Gammaproteobacteria
, showed no response or only a minor response to the bloom. However, sequence numbers and total cell numbers of the SAR11 and SAR86 clades increased slightly but significantly toward the end of the experiment. It seems that although microbial productivity was enhanced within the fertilized area, a succession-like response of the microbial community upon the algal bloom was averted by highly effective grazing. Only small-celled members like the SAR11 and SAR86 clades could possibly escape the grazing pressure, explaining a net increase of those clades in numbers.
Genomic and Physiological Characterization of the Chromate-Reducing, Aquifer-Derived Firmicute Pelosinus sp. Strain HCF1
Authors: Beller Harry R. , Han Ruyang , Karaoz Ulas , Lim HsiaoChien , Brodie Eoin L. 
Published: October 2012

ABSTRACT

Pelosinus
spp. are fermentative firmicutes that were recently reported to be prominent members of microbial communities at contaminated subsurface sites in multiple locations. Here we report metabolic characteristics and their putative genetic basis in
Pelosinus
sp. strain HCF1, an isolate that predominated anaerobic, Cr(VI)-reducing columns constructed with aquifer sediment. Strain HCF1 ferments lactate to propionate and acetate (the methylmalonyl-coenzyme A [CoA] pathway was identified in the genome), and its genome encodes two [NiFe]- and four [FeFe]-hydrogenases for H
2
cycling. The reduction of Cr(VI) and Fe(III) may be catalyzed by a flavoprotein with 42 to 51% sequence identity to both ChrR and FerB. This bacterium has unexpected capabilities and gene content associated with reduction of nitrogen oxides, including dissimilatory reduction of nitrate to ammonium (two copies of NrfH and NrfA were identified along with NarGHI) and a nitric oxide reductase (NorCB). In this strain, either H
2
or lactate can act as a sole electron donor for nitrate, Cr(VI), and Fe(III) reduction. Transcriptional studies demonstrated differential expression of hydrogenases and nitrate and nitrite reductases. Overall, the unexpected metabolic capabilities and gene content reported here broaden our perspective on what biogeochemical and ecological roles this species might play as a prominent member of microbial communities in subsurface environments.
Enzymatic Characterization of AMP Phosphorylase and Ribose-1,5-Bisphosphate Isomerase Functioning in an Archaeal AMP Metabolic Pathway
Authors: Aono Riku , Sato Takaaki , Yano Ayumu , Yoshida Shosuke , Nishitani Yuichi , Miki Kunio , Imanaka Tadayuki , Atomi Haruyuki 
Published: October 2012

ABSTRACT

AMP phosphorylase (AMPpase), ribose-1,5-bisphosphate (R15P) isomerase, and type III ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) have been proposed to constitute a novel pathway involved in AMP metabolism in the
Archaea
. Here we performed a biochemical examination of AMPpase and R15P isomerase from
Thermococcus kodakarensis
. R15P isomerase was specific for the α-anomer of R15P and did not recognize other sugar compounds. We observed that activity was extremely low with the substrate R15P alone but was dramatically activated in the presence of AMP. Using AMP-activated R15P isomerase, we reevaluated the substrate specificity of AMPpase. AMPpase exhibited phosphorylase activity toward CMP and UMP in addition to AMP. The [S]-
v
plot (plot of velocity versus substrate concentration) of the enzyme toward AMP was sigmoidal, with an increase in activity observed at concentrations higher than approximately 3 mM. The behavior of the two enzymes toward AMP indicates that the pathway is intrinsically designed to prevent excess degradation of intracellular AMP. We further examined the formation of 3-phosphoglycerate from AMP, CMP, and UMP in
T. kodakarensis
cell extracts. 3-Phosphoglycerate generation was observed from AMP alone, and from CMP or UMP in the presence of dAMP, which also activates R15P isomerase. 3-Phosphoglycerate was not formed when 2-carboxyarabinitol 1,5-bisphosphate, a Rubisco inhibitor, was added. The results strongly suggest that these enzymes are actually involved in the conversion of nucleoside monophosphates to 3-phosphoglycerate in
T. kodakarensis
.
Jumper's knee paradox—jumping ability is a risk factor for developing jumper's knee: a 5-year prospective study
Authors: Visnes Håvard , Aandahl Hans Åge , Bahr Roald 
Published: October 2012

BackgroundThe ‘jumper's knee paradox’, where symptomatic athletes appear to perform better in a counter movement jump (CMJ) compared to asymptomatic controls in previous case–control studies is not fully understood.AimThe aim was to examine the relationship between jumping ability and change of jumping ability as potential risk factors for developing jumper's knee.MethodsA 5-year prospective cohort study among elite volleyball players, aged 16–18. Jump tests were done on a portable force plate at the time of inclusion and semiannually. Jumper's knee was diagnosed based on a standardised clinical examination.ResultsAll 150 students (68 males and 82 females) were included and 28 developed jumper's knee (22 males and 6 females). At the time of inclusion, male athletes who went on to develop jumper's knee had significantly better results in CMJ (38.0±5.8 cm) compared to asymptomatic males (34.6±5.5 cm, p=0.03), while no difference was detected in standing jump (SJ: jumper's knee: 30.3±7.4 cm, asymptomatic: 28.1±6.1 cm, p=0.23). In a multivariate logistic regression analysis corrected for gender and previous volleyball training, the OR was 2.09 (1.03–4.25) per cm difference in CMJ at the time of inclusion. Our results did not reveal any significant differences in the change in jumping ability between the groups, although both groups improved their jump performance.ConclusionsVolleyball players with a natural ability for jumping high are at an increased risk for developing jumper's knee.
Comparative outcomes of manual small incision cataract surgery and phacoemulsification performed by ophthalmology trainees in a tertiary eye care hospital in India: a retrospective cohort design
Authors: Khanna Rohit C , Kaza Srivalli , Palamaner Subash Shantha Ghanshyam , Sangwan Virender S 
Published: October 2012

ObjectiveTo compare the outcomes of manual small incision cataract surgery (MSICS) and phacoemulsification performed by ophthalmology trainees.DesignRetrospective cohort design.SettingTertiary eye care centre.ParticipantsA total of 1029 subjects underwent cataract surgeries with MSICS technique or phacoemulsification by trainees during one quarter (July–September 2007). Only 484 (47%) subjects were males. Surgeries which were primarily large incision extracapsular or intracapsular cataract extraction and performed on patients less than 20 years of age were excluded.Outcome measuresThe postoperative best corrected visual acuity (BCVA) along with the rates and types of complications were compared between both the groups.ResultsA total of 1029 surgeries were performed by 22 resident surgeons. In all, 522 (50.7%) were done using MSICS technique and 507 (49.2%) were done by phacoemulsification. Those in the MSICS group were significantly older (age >70 years; 5.7% vs 3.4%; p<0.001) and had worse preoperative visual acuity (visual acuity <6/60; 69.3% vs 40.4%; p<0.001). Postoperatively, the number of patients having BCVA≥6/12 was similar in both the groups (84.3% vs 88%; p=0.09). The complication rates were higher in MSICS group (15.1% vs 7.1%, p<0.001). Most common risk factor for poor outcome (postoperative BCVA<6/60) in both the groups was presence of associated ocular pathologies (OR 7.4 95% CI 3.4 to 16.4) and having a complications (OR 5.7 95% CI 3.0 to 10.8).ConclusionsAlthough the complication rate was higher in the MSICS group, there was no difference in BCVA in both the groups.
Observational study on Takotsubo-like cardiomyopathy: clinical features, diagnosis, prognosis and follow-up
Authors: Cacciotti Luca , Passaseo Ilaria , Marazzi Giuseppe , Camastra Giovanni , Campolongo Giuseppe , Beni Sergio , Lupparelli Fabrizio , Ansalone Gerardo 
Published: October 2012

ObjectivesThe present study attempts to identify appropriate elements that may contribute to clarify the broad clinical features (diagnosis, care, complication and prognosis) of Takotsubo-like cardiomyopathy for improving its management.Design studyObservational study.SettingPrimary level of care referred to the emergency department of Vannini Hospital, Rome, Italy.ParticipantsThe study population consisted of 75 patients, 72 of the them were women and 3 were men with a mean age of 71.9±9.6 years.MethodsFrom February 2004 to November 2010, prospectively included 84 consecutive patients diagnosed for suspected Takotsubo-like cardiomyopathy. To be eligible, patients had to meet all the Mayo clinic criteria in the absence of neurological trauma or intracranial haemorrhage. Moreover, those patients that at follow-up still presented alteration of acute phase at ECG and echocardiogram were excluded. Thus, 75 patients comprised the study population. To follow-up 19 patients were lost.ResultsNone of 75 patients died in acute phase. All patients were promptly discharged (8.4±4.4 days), since they recovered their normal functional status without symptoms. Follow-up information was available for 56 patients. At a mean follow-up time of 2.2±2 years (range, 0.1–6.8 years) two octogenarian patients (2.6%) died because of sudden cardiac death and pulmonary embolism, respectively. The Takotsubo-like cardiomyopathy recurred in one patient.ConclusionsThe results of this study support the previous reports about the good prognosis, also in critically ill patients, of Takotsubo-like cardiomyopathy. Further assessment will be needed to determine a careful and sustained follow-up for choosing the best care and foreseeing the recurrences of this emerging condition.
Urban city transportation mode and respiratory health effect of air pollution: a cross-sectional study among transit and non-transit workers in Nigeria
Authors: Ekpenyong Chris E , Ettebong E O , Akpan E E , Samson T K , Daniel Nyebuk E 
Published: October 2012

ObjectivesTo assess the respiratory health effect of city ambient air pollutants on transit and non-transit workers and compare such effects by transportation mode, occupational exposure and sociodemographic characteristics of participants.DesignCross-sectional, randomised survey.SettingA two primary healthcare centre survey in 2009/2010 in Uyo metropolis, South-South Nigeria.ParticipantsOf the 245 male participants recruited, 168 (50 taxi drivers, 60 motorcyclists and 58 civil servants) met the inclusion criteria. These include age 18–35 years, a male transit worker or civil servant who had worked within Uyo metropolis for at least a year prior to the study, and had no history of respiratory disorders/impairment or any other debilitating illness.Main outcome measureThe adjusted ORs for respiratory function impairment (force vital capacity (FVC) and/or FEV1<80% predicted or FEV1/FVC<70% predicted) using Global Initiative for Chronic Obstructive Lung Diseases (GOLD) and National Institute for Health and Clinical Excellence (NICE) criteria were calculated. In order to investigate specific occupation-dependent respiratory function impairment, a comparison was made between the ORs for respiratory impairment in the three occupations. Adjustments were made for some demographic variables such as age, BMI, area of residence, etc.ResultsExposure to ambient air pollution by occupation and transportation mode was independently associated with respiratory functions impairment and incident respiratory symptoms among participants. Motorcyclists had the highest effect, with adjusted OR 3.10, 95% CI 0.402 to 16.207 for FVC<80% predicted and OR 1.71, 95% CI 0.61 to 4.76 for FEV1/FVC<70% predicted using GOLD and NICE criteria. In addition, uneducated, currently smoking transit workers who had worked for more than 1 year, with three trips per day and more than 1 h transit time per trip were significantly associated with higher odds for respiratory function impairment at p<0.001, respectively.ConclusionsFindings of this study lend weights to the existing literature on the adverse respiratory health effect of ambient air pollution on city transit workers globally. The role of other confounders acting synergistically to cause a more deleterious effect is obvious. In all, the effect depends on the mode and duration of exposure.
A multimethod research investigation of consumer involvement in Australian health service accreditation programmes: the ACCREDIT-SCI study protocol
Authors: Greenfield David , Hinchcliff Reece , Moldovan Max , Mumford Virginia , Pawsey Marjorie , Irene Westbrook Johanna , Braithwaite Jeffrey 
Published: October 2012

IntroductionHealth service accreditation programmes are a regulatory mechanism adopted to drive improvements inpatient safety and quality. Research investigating the benefits or limitations, of consumer involvement in accreditation programmes is negligible. To develop our knowledge in this area the ACCREDIT collaboration (Accreditation Collaborative for the Conduct of Research, Evaluation and Designated Investigations through Teamwork) has developed a research plan, known as the ACCREDIT-SCI (Standards of Consumer Involvement) study protocol. Two complementary studies have been designed: one, to examine the effectiveness of a standard for consumer participation and two, to explore how patient experiences vary across a range of settings with differing accreditation results.Methods and designThe research setting is the Australian healthcare system, and the two studies focus on three accreditation programmes in the primary, acute and aged care domains. The studies will use multimethods: document analysis; interviews and surveys. Participants will be stakeholders across the three domains including: policy officers; frontline healthcare professionals; accreditation agency personnel, including surveyors and healthcare consumers. Drawing on previous experience, the research team has developed purpose-designed tools. Data will be analysed using thematic, narrative and statistical (descriptive and inferential) procedures.Ethics and disseminationThe University of New South Wales Human Research Ethics Committee has approved the two studies (HREC 10274). Findings will be disseminated through seminars, conference presentations, academic publications and research partner websites. The findings will be formulated to facilitate uptake by policy and accreditation agency professionals, researchers and academics, and consumers, nationally and internationally.
It matters what you measure: a systematic literature review examining whether young people in poorer socioeconomic circumstances are more at risk of chlamydia
Authors: Sheringham Jessica , Mann Sue , Simms Ian , Stafford Mai , Hart Graham J , Raine Rosalind 
Published: October 2012

BackgroundEngland has invested in chlamydia screening interventions for young people. It is not known whether young people in poorer socioeconomic circumstances (SEC) are at greater risk of chlamydia and therefore in greater need of screening.ObjectiveTo conduct a systematic review examining socioeconomic variations in chlamydia prevalence or positivity in young people.Data sourcesEight bibliographic databases using terms related to chlamydia and SEC, supplemented by website and reference searches.EligibilityStudies published 1999–2011 in North America, Western Europe, Australia or New Zealand, including populations aged 15–24 years, with chlamydia prevalence or positivity diagnosed by nucleic acid amplification testing.Appraisal and synthesisTwo reviewers independently screened references, extracted data, appraised studies meeting inclusion criteria and rated studies as high, medium or low according to their quality and relevance. Socioeconomic variations in chlamydia were synthesised for medium/high-rated studies only.ResultsNo high-rated studies were identified. Eight medium-rated studies reported variations in chlamydia prevalence by SEC. In 6/8 studies, prevalence was higher in people of poorer SEC. Associations were more often significant when measured by education than when using other indicators. All studies measuring positivity were rated low. Across all studies, methodological limitations in SEC measurement were identified.ConclusionsThe current literature is limited in its capacity to describe associations between SEC and chlamydia risk. The choice of SEC measure may explain why some studies find higher chlamydia prevalence in young people in disadvantaged circumstances while others do not. Studies using appropriate SEC indicators (eg, education) are needed to inform decisions about targeting chlamydia screening.
Human shoreline development and the nutrient stoichiometry of aquatic plant communities in Canadian Shield lakes
Authors: Frost Paul C. , Hicks Andrea L. 
Published: October 2012

Human activities associated with residential development potentially alter ecological processes in lake littoral zones. We determined how the nutrient stoichiometry of aquatic plant communities relates to residential density around lakes of south-central Ontario. We calculated the elemental composition of entire plant communities from multiple sites in 12 lakes using measurements of individual plant C:N:P ratios and their areal biomass. We found considerable variability in the C:N:P ratios of whole aquatic plant communities among sites and lakes, which was not accounted for by intraspecific variability in the elemental composition of aquatic plants. Instead, differences in community-level C:N:P ratios primarily resulted from high interspecific variability in the elemental composition among dominant plant taxa and variable taxonomic composition of sampled plant communities. Plant community composition differed among lakes with and without shoreline residences, and we found lower C:N and C:P ratios in communities from littoral zones in human-developed lakes. Our results thus demonstrate a link between the elemental and taxonomic composition of aquatic plant communities, which may mediate biogeochemical responses of littoral zones to development of lake shorelines.
Predicting the risk of proliferation of the benthic cyanobacteriumLyngbya wolleiin the St. Lawrence River
Authors: Lévesque David , Cattaneo Antonella , Hudon Christiane , Gagnon Pierre 
Published: October 2012

Lyngbya wollei is a toxin-producing cyanobacterium, forming mats of filaments that proliferate in rivers, lakes, and springs in North America. We determined its distribution over a 250 km stretch of the St. Lawrence River (SLR; Quebec, Canada) to elaborate predictive models of its presence and biomass based on chemical and physical characteristics. A 2008 survey revealed L. wollei was generally found downstream of the inflow of small tributaries draining farmlands. As enriched waters flowed slowly through dense submerged vegetation, dissolved inorganic nitrogen (DIN) concentration dropped but dissolved organic carbon (DOC) and total dissolved phosphorus (TDP) remained high, leading to a low DIN:TDP ratio. Models identified DOC (positive effect), TP (negative effect), and DIN:TDP (negative effect) as the most important variables explaining L. wollei distribution. The risk of L. wollei occurrence in the SLR was correctly forecasted in 72%–92% of all cases with an independent data set. Proliferation of L. wollei, a potentially heterotrophic, diazotrophic cyanobacterium, is favoured by organic enrichment and imbalance of DIN:TDP ratio. Its dominance coincided with low macrophyte biomass, yielding a simplified, less productive ecosystem.
Temporal genetic variation as revealed by a microsatellite analysis of European sardine (Sardina pilchardus) archived samples
Authors: Ruggeri Paolo , Splendiani Andrea , Bonanomi Sara , Arneri Enrico , Cingolani Nando , Santojanni Alberto , Belardinelli Andrea , Giovannotti Massimo , Caputo Vincenzo 
Published: October 2012

The Adriatic stock of European sardine ( Sardina pilchardus ) has experienced large interannual demographic fluctuations over the last 30 years, with a severe decline beginning in 1991 and continuing until 1997. In the present study, six microsatellite loci were used on a time series collection of otoliths and scales from sampling locations of northern (Chioggia) and southern (Vieste) Adriatic Sea, with the aim to investigate the genetic effects of these stock biomass fluctuations. The northern samples showed significant reduction in observed heterozygosity (HO) and mean number of alleles (Na) that explain the genetic diversity variation, while the same parameters turned out to be more stable in the southern samples. In addition, we detected the presence of a genetic bottleneck and low effective population size (Ne) values in several northern samples. Even if the northern and southern Adriatic sardine samples belong to the same genetic stock, the more pronounced decrease in genetic variability recorded in the northern sample led us to speculate that a more intensive fishing pressure and a more pronounced oceanographic isolation of this area could have accentuated the effects of the genetic bottleneck.
In-situ Evaluation of Air/Oxygen Percentage Variation by Introducing 1,1,1,3,3-Pentafluoropropane in Ultraviolet Nanoimprint Lithography
Authors: Wang Qing , Hiroshima Hiroshi , Suzuki Kenta , Youn Sung-Won 
Published: October 2012

In UV nanoimprinting, the air percentage is critical to the generation of bubble defects in nanoimprinted samples. In this work, it is found that as the pentafluoropropane gas (CHF2CH2CF3; 1,1,1,3,3-pentafluoropropane, HFC-245fa, CAS No. 460-3-1) is introduced, the air percentage rapidly decreases from 100% to a stable low level of 8%. By comparison with the bubble shrinking results of real nanoimprinting experiments, it is found that the critical value for obtaining a bubble-free UV nanoimprinting was 3.3% in the oxygen concentration or 15.8% in air percentage.
OpenRoads
Authors: Yap Kok-Kiong , Kobayashi Masayoshi , Sherwood Rob , Huang Te-Yuan , Chan Michael , Handigol Nikhil , McKeown Nick 
Published: October 2012

We present OpenRoads, an open-source platform for innovation in mobile networks. OpenRoads enable researchers to innovate using their own production networks, through providing an wireless extension OpenFlow. Therefore, you can think of OpenRoads as "OpenFlow Wireless".
The OpenRoads' architecture consists of three layers: flow, slicing and controller. These layers provide flexible control, virtualization and high-level abstraction. This allows researchers to implement wildly different algorithms and run them concurrently in one network. OpenRoads also incorporates multiple wireless technologies, specifically WiFi and WiMAX. We have deployed OpenRoads, and used it as our production network. Our goal here is for those to deploy OpenRoads and build their own experiments on it.