bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sulfoquinovose synthase – an important enzyme in the N‐glycosylation pathway of Sulfolobus acidocaldarius
Authors: Meyer Benjamin H. , Zolghadr Behnam , Peyfoon Elham , Pabst Martin , Panico Maria , Morris Howard R. , Haslam Stuart M. , Messner Paul , Schäffer Christina , Dell Anne , Albers Sonja‐Verena 
Published: November 2011

SummaryRecently, the Surface (S)‐layer glycoprotein of the thermoacidophilic crenarchaeote Sulfolobus acidocaldarius was found to be N‐glycosylated with a heterogeneous family of glycans, with the largest having a composition Glc1Man2GlcNAc2 plus 6‐sulfoquinovose. However, genetic analyses of genes involved in the N‐glycosylation process in Crenarchaeota were missing so far. In this study we identify a gene cluster involved in the biosynthesis of sulfoquinovose and important for the assembly of the S‐layer N‐glycans. A successful markerless in‐frame deletion of agl3 resulted in a decreased molecular mass of the S‐layer glycoprotein SlaA and the flagellin FlaB, indicating a change in the N‐glycan composition. Analyses with nanoLC ES‐MS/MS confirmed the presence of only a reduced trisaccharide structure composed of Man1GlcNAc2, missing the sulfoquinovose, a mannose and glucose. Biochemical studies of the recombinant Agl3 confirmed the proposed function as a UDP‐sulfoquinovose synthase. Furthermore, S. acidocaldarius cells lacking agl3 had a significantly lower growth rate at elevated salt concentrations compared with the background strain, underlining the importance of the N‐glycosylation to maintain an intact and stable cell envelope, to enable the survival of S. acidocaldarius in its extreme environment.
CDKB2 is involved in mitosis and DNA damage response in rice
Authors: Endo Masaki , Nakayama Shigeki , Umeda‐Hara Chikage , Ohtsuki Namie , Saika Hiroaki , Umeda Masaaki , Toki Seiichi 
Published: November 2011

SummaryDNA damage checkpoints delay mitotic cell‐cycle progression in response to DNA stress, stalling the cell cycle to allow time for repair. CDKB is a plant‐specific cyclin‐dependent kinase (CDK) that is required for the G2/M transition of the cell cycle. In Arabidopsis, DNA damage leads the degradation of CDKB2, and the subsequent G2 arrest gives cells time to repair damaged DNA. G2 arrest also triggers transition from the mitotic cycle to endoreduplication, leading to the presence of polyploid cells in many tissues. In contrast, in rice (Oryza sativa), polyploid cells are found only in the endosperm. It was unclear whether endoreduplication contributes to alleviating DNA damage in rice (Oryza sativa). Here, we show that DNA damage neither down‐regulates Orysa;CDKB2;1 nor induces endoreduplication in rice. Furthermore, we found increased levels of Orysa;CDKB2;1 protein upon DNA damage. These results suggest that CDKB2 functions differently in Arabidopsis and rice in response to DNA damage. Arabidopsis may adopt endoreduplication as a survival strategy under genotoxic stress conditions, but rice may enhance DNA repair capacity upon genotoxic stress. In addition, polyploid cells due to endomitosis were present in CDKB2;1 knockdown rice, suggesting an important role for Orysa;CDKB2;1 during mitosis.
Using the genomic relationship matrix to predict the accuracy of genomic selection
Authors: Goddard M.E. , Hayes B.J. , Meuwissen T.H.E. 
Published: November 2011

SummaryEstimated breeding values (EBVs) using data from genetic markers can be predicted using a genomic relationship matrix, derived from animal’s genotypes, and best linear unbiased prediction. However, if the accuracy of the EBVs is calculated in the usual manner (from the inverse element of the coefficient matrix), it is likely to be overestimated owing to sampling errors in elements of the genomic relationship matrix. We show here that the correct accuracy can be obtained by regressing the relationship matrix towards the pedigree relationship matrix so that it is an unbiased estimate of the relationships at the QTL controlling the trait. This method shows how the accuracy increases as the number of markers used increases because the regression coefficient (of genomic relationship towards pedigree relationship) increases. We also present a deterministic method for predicting the accuracy of such genomic EBVs before data on individual animals are collected. This method estimates the proportion of genetic variance explained by the markers, which is equal to the regression coefficient described above, and the accuracy with which marker effects are estimated. The latter depends on the variance in relationship between pairs of animals, which equals the mean linkage disequilibrium over all pairs of loci. The theory was validated using simulated data and data on fat concentration in the milk of Holstein cattle.
Analysis of two marine metagenomes reveals the diversity of plasmids in oceanic environments
Authors: Ma Yingfei , Paulsen Ian T. , Palenik Brian 
Published: November 2011

SummaryPlasmid diversity is still poorly understood in pelagic marine environments. Metagenomic approaches have the potential to reveal the genetic diversity of microbes actually present in an environment and the contribution of mobile genetic elements such as plasmids. By searching metagenomic datasets from flow cytometry‐sorted coastal California seawater samples dominated by cyanobacteria (SynMeta) and from the Global Ocean Survey (GOS) putative marine plasmid sequences were identified as well as their possible hosts in the same samples. Based on conserved plasmid replication protein sequences predicted from the SynMeta metagenomes, PCR primers were designed for amplification of one plasmid family and used to confirm that metagenomic contigs of this family were derived from plasmids. These results suggest that the majority of plasmids in SynMeta metagenomes were small and cryptic, encoding mostly their own replication proteins. In contrast, probable plasmid sequences identified in the GOS dataset showed more complexity, consistent with a much more diverse microbial population, and included genes involved in plasmid transfer, mobilization, stability and partitioning. Phylogenetic trees were constructed based on common replication protein functional domains and, even within one replication domain family, substantial diversity was found within and between different samples. However, some replication protein domain families appear to be rare in the marine environment.
Oncological outcome after laparoscopic abdominoperineal excision of the rectum
Authors: Jefferies M. T. , Evans M. D. , Hilton J. , Chandrasekaran T. V. , Beynon J. , Khot U. 
Published: November 2011

AbstractAim  Abdominoperineal excision of the rectum (APER) for cancer has been associated with higher circumferential resection margin (CRM) involvement and failure of local disease control. The aim of this study was to investigate whether the introduction of laparoscopic APER altered the incidence of CRM involvement.Method  Consecutive patients undergoing open or laparoscopic APER for adenocarcinomas of the rectum were studied. Patient demographics, preoperative staging, neoadjuvant treatment, operative findings, length of stay and pathological details were collected from operative and radiology databases and compared.Results  There were 16 laparoscopic and 25 open APER performed over a 3‐year period. Neoadjuvant therapy was given to 43.8% (7/16) of the laparoscopic group and 56.0% (14/25) of the open group. Complete laparoscopic resection was possible in 14 (87.5%) of 16 patients. The median harvested number of nodes was 14 (4–33) in both groups. The median length of stay was 7 (3–13) and 15 (9–40) days in the laparoscopic and open groups (P < 0.001). The CRM was clear in all cases. There was no local recurrence in either group at a median follow‐up of 23 months. There were no in‐hospital deaths and no significant differences in overall survival. There were no significant differences in preoperative or postoperative histopathological T stage between the two groups (P = 0.057 and P = 0.121).Conclusion  Laparoscopic APER for selected rectal cancers can achieve comparable oncological outcome to open surgery but is associated with a much shorter length of stay. Patient and tumour characteristics must be taken into consideration when deciding on a laparoscopic approach for low rectal cancer.
Environmental condition related reproductive strategies and sex ratio in hydras
Authors: Kaliszewicz Anita , Lipińska Agnieszka 
Published: November 2011

AbstractKaliszewicz, A. and Lipińska, A. 2011. Environmental condition related reproductive strategies and sex ratio in hydras. —Acta Zoologica (Stockholm) 00:1–7.Temperature and food supply appeared to affect sex ratio, sex composition and percentage of sexual individuals in three Hydra species: Hydra vulgaris, Hydra circumcincta and Hydra viridissima. We found three sexes present: females, males and hermaphrodites depending on environmental conditions. Hydra vulgaris appeared to be a species with a temperature‐dependent sex determination (TSD). The males and hermaphrodites were present only under rising temperatures, whereas females were observed exclusively at lowering temperatures. Hydras reproduced asexually at constant room temperature. Unlimited food affected sex ratios and induced the presence of males in H. circumcincta at lowering temperatures. Thus, H. circumcincta may be recognised as another Hydra species in which sex is determined by environmental factors (ESD). Under rising temperatures, the number of hermaphroditic individuals was higher when food supply was unlimited in all three species, indicating that hermaphrodites may need more energy to produce both male and female gonads. Both temperature changes and food supply positively affected asexual reproductive strategies in hydras, especially budding rates. Hydra circumcincta appeared to be less agile than other hydras and able to self‐fertilise. It is likely that self‐fertilisation is an adaptation to the low probability of meeting a mate belonging to the other clone.
Sustainable consumption – UK Government activity
Authors: Kerr J. , Foster L. 
Published: November 2011

SummarySustainable consumption is a complex, multifaceted area requiring a partnership approach across the food chain to reduce the environmental impacts of the food we choose to consume. Communicating the environmental benefits of products and the importance of wasting less food, supporting honest environmental labelling and defining methodologies for sustainable food will help inform these choices. Government initiatives to support sustainable fish species consumption, reconnect people with food and work towards a zero‐waste economy will help to tackle environmental and climate change impacts. The Government is committed to addressing global challenges identified by Foresight to meet increasing food demand with less environmental impact. Evidence to underpin sustainable food policy requires a joined‐up approach across funders, industry and the third sector to strengthen research activity and maximise impact. The Department for Environment Food and Rural Affairs' research and development targets the whole food chain from production to consumption. Activity addresses sustainability and resource efficiency; environmental impacts; supply chain and consumer drivers, behaviours and practice; explores synergies, trade‐offs and tensions; and ways to promote availability and take up of sustainable healthy food.
The European Union and International Criminal Justice: Living Up to Its Normative Preferences?
Authors: AOUN ELENA 
Published: November 2011

AbstractEuropean Union Member States have committed themselves, individually and collectively, to the fight against impunity for serious international crimes. The record is, however, ambiguous: support for the current investigations of the International Criminal Court is uneven and Member States are reluctant to exercise universal jurisdiction and develop binding common policies under the ‘third pillar’. This article assesses the extent of the discrepancy between stated normative preferences and flexible practices. It argues that this discrepancy results from the clash of accountability with other prevailing norms and interests, on the one hand, and from the lack of effective drivers pushing Member States towards increased commitment to combat impunity through a set of social mechanisms such as rhetorical action and socialization, on the other.
Competitive Liberalization and the ‘Global Europe’ Services and Investment Agenda: Locating the Commercial Drivers of the EU–ACP Economic Partnership Agreements*
Authors: HERON TONY , SILES‐BRÜGGE GABRIEL 
Published: November 2011

AbstractIn the last decade the European Union (EU) has been negotiating with the African, Caribbean and Pacific (ACP) group of countries to establish Economic Partnership Agreements (EPAs). In this article, EPAs are located within the context of the wider shift in EU trade policy towards bilateralism. This is done with reference to recent work in International Political Economy (IPE) emphasizing the ‘domestic‐societal’ and ‘systemic’ drivers of preferential liberalization. Although these pressures are not necessarily sufficient to explain the EPAs, they do account for why they have gone beyond the original remit of ‘World Trade Organization (WTO) compatibility’ and why aspects of the agreements bear close similarity to the EU's supposedly more commercially oriented bilateral agreements.
How Effective Are Short Message Service Reminders at Increasing Clinic Attendance? A Meta‐Analysis and Systematic Review
Authors: Guy Rebecca , Hocking Jane , Wand Handan , Stott Sam , Ali Hammad , Kaldor John 
Published: November 2011

Background and ObjectivesIn the last few years there has been a steady uptake of mobile phone short message service (SMS) reminders to increase medical attendance rates. We undertook a review of studies that assessed the effectiveness of SMS reminders at increasing the uptake of appointments in health care settings.MethodsWe reviewed studies which involved a comparison of appointment attendance rates between patients who did and did not receive SMS reminders published prior to June 2010. We used meta‐analysis methods to calculate the overall effect on attendance rates, stratified by study design and clinic type.ResultsThe review criteria were met by 18 reports, made up of eight randomized controlled trials (RCTs) and 10 controlled observational studies. Across all studies, there was significant heterogeneity in the estimated effect measure of the relationship between use of SMS reminders and clinic attendance (I2 = 90 percent; p < .01), so a summary effect estimate was not calculated. Stratification by study design showed that the heterogeneity was due to the observational studies. The summary effect from the RCTs was 1.48 (95% CI: 1.23–1.72) with no significant subgroup differences by clinic type (primary care clinics, hospital outpatient clinics), message timing (24, 48, and 72+ hours before the scheduled appointment), and target age group (pediatric, older).ConclusionsShort message service reminders in health care settings substantially increase the likelihood of attending clinic appointments. SMS reminders appear to be a simple and efficient option for health services to use to improve service delivery, as well as resulting in health benefits for the patients who receive the reminders.
Methodological Reporting in Qualitative, Quantitative, and Mixed Methods Health Services Research Articles
Authors: Wisdom Jennifer P. , Cavaleri Mary A. , Onwuegbuzie Anthony J. , Green Carla A. 
Published: November 2011

ObjectivesMethodologically sound mixed methods research can improve our understanding of health services by providing a more comprehensive picture of health services than either method can alone. This study describes the frequency of mixed methods in published health services research and compares the presence of methodological components indicative of rigorous approaches across mixed methods, qualitative, and quantitative articles.Data SourcesAll empirical articles (n = 1,651) published between 2003 and 2007 from four top‐ranked health services journals.Study DesignAll mixed methods articles (n = 47) and random samples of qualitative and quantitative articles were evaluated to identify reporting of key components indicating rigor for each method, based on accepted standards for evaluating the quality of research reports (e.g., use of p‐values in quantitative reports, description of context in qualitative reports, and integration in mixed method reports). We used chi‐square tests to evaluate differences between article types for each component.Principal FindingsMixed methods articles comprised 2.85 percent (n = 47) of empirical articles, quantitative articles 90.98 percent (n = 1,502), and qualitative articles 6.18 percent (n = 102). There was a statistically significant difference (χ2(1) = 12.20, p = .0005, Cramer's V = 0.09, odds ratio = 1.49 [95% confidence interval = 1,27, 1.74]) in the proportion of quantitative methodological components present in mixed methods compared to quantitative papers (21.94 versus 47.07 percent, respectively) but no statistically significant difference (χ2(1) = 0.02, p = .89, Cramer's V = 0.01) in the proportion of qualitative methodological components in mixed methods compared to qualitative papers (21.34 versus 25.47 percent, respectively).ConclusionFew published health services research articles use mixed methods. The frequency of key methodological components is variable. Suggestions are provided to increase the transparency of mixed methods studies and the presence of key methodological components in published reports.
Determinants of Death in the Hospital Among Older Adults
Authors: Kelley Amy S. , Ettner Susan L. , Wenger Neil S. , Sarkisian Catherine A. 
Published: November 2011

ObjectivesTo investigate patient‐level determinants of in‐hospital death, adjusting for patient and regional characteristics.DesignUsing multivariable regression, the relationship between in‐hospital death and participants’ social, functional, and health characteristics was investigated, controlling for regional Hospital Care Intensity Index (HCI) from the Dartmouth Atlas of Health Care.SettingThe Health and Retirement Study, a longitudinal nationally representative cohort of older adults.ParticipantsPeople aged 67 and older who died between 2,000 and 2,006 (N = 3,539) were sampled.MeasurementsIn‐hospital death.ResultsThirty‐nine percent (n = 1,380) of participants died in the hospital (range 34% in Midwest to 45% in Northeast). Nursing home residence, functional dependence, and cancer or dementia diagnosis, among other characteristics, were associated with lower adjusted odds of in‐hospital death. Being black or Hispanic, living alone, and having more medical comorbidities were associated with greater adjusted odds, as was higher HCI. Sex, education, net worth, and completion of an advance directive did not correlate with in‐hospital death.ConclusionBlack race, Hispanic ethnicity, and other functional and social characteristics are correlates of in‐hospital death, even after controlling for the role of HCI. Further work must be done to determine whether preferences, provider characteristics and practice patterns, or differential access to medical and community services drive this difference.
Aspiration Thrombectomy During Primary Percutaneous Coronary Intervention as Adjunctive Therapy to Early (in‐ambulance) Abciximab Administration in Patients with Acute ST Elevation Myocardial Infarction: An Analysis from Leiden MISSION! Acute Myocardial Infarction Treatment Optimization Program
Authors: AHMED TAREK A. N. , ATARY JAEL Z. , WOLTERBEEK RON , HASAN‐ALI HOSAM , ABDEL‐KADER SAMIR S. , SCHALIJ MARTIN J. , JUKEMA J. WOUTER 
Published: November 2011

Background:
The benefits of early abciximab administration and thrombus aspiration in ST elevation myocardial infarction (STEMI) patients undergoing primary percutaneous coronary intervention (PPCI) have previously been elaborated. However, whether there is an adjunctive effect of thrombus aspiration among STEMI patients, with angiographic evidence of thrombus, receiving early prehospital abciximab remains unclear.
Methods:
In the context of a fixed protocol for PPCI, 158 consecutive patients with STEMI were enrolled, in whom abciximab was started early before hospital arrival (in‐ambulance); 79 patients who had PPCI with thrombus aspiration (thrombectomy‐facilitated PCI group), were compared to 79 who had PPCI without thrombus aspiration (conventional PCI group) in a prospective nonrandomized study. The primary end‐point was complete ST‐segment resolution within 90 minutes. Secondary end points included distal embolization, enzymatic infarct size as well as left ventricular ejection fraction (LVEF) assessed by gated single‐photon emission computed tomography. Major adverse cardiac events (MACEs) were evaluated up to 12 months.
Results:
Both groups were comparable for baseline characteristics. ST‐segment resolution was significantly higher in the thrombectomy‐facilitated group (P = 0.002), and multivariate analysis identified thrombectomy as an independent predictor of ST‐segment resolution (OR = 9.4, 95% CI = 2.6–33.5, P = 0.001). Distal embolization was higher in the conventional PCI group among patients with higher thrombus grades. No difference was observed between both groups in infarct size assessed by peak creatine kinase (p = 0.689) and peak Tn‐T levels (P = 0.435). Also, the LVEF at 3 months was similar (P = 0.957). At 12 month clinical follow‐up, thrombus aspiration was, however, associated with reduced all‐cause mortality (log‐rank p = 0.032).
Conclusion:
Among STEMI patients treated with PPCI and in‐ambulance abciximab, it appears that a selective strategy of thrombus aspiration still has additive benefit. (J Interven Cardiol 2012;25:1–9)
PlasmaBNP, a useful marker of fluid overload in hospitalized hemodialysis patients
Authors: Çelik Gülperi , Silinou Emilie , Vo‐Van Cyril , Jean Guillaume , Chazot Charles 
Published: November 2011

AbstractHospitalization for intercurrent illness frequently disrupts the nutritional status of hemodialysis (HD) patients and jeopardizes the dry weight prescription. We report in this study the evolution of brain natriuretic peptide (BNP), blood pressure and body weight in hospitalized patients and the relationship between BNP plasma level and nutritional and inflammation parameters. We have studied 42 patients requiring hospitalization (F/M: 18/24; 72.5 ± 12.5 years old; 19/42 with diabetes). The plasma BNP levels at baseline, during hospitalization (BNP‐Hosp), and in the recovery phase were compared. Predialysis and postdialysis blood pressure and postdialysis body weight were recorded and compared. BNP‐Hosp increased significantly when compared with BNP levels at baseline, from 421 ± 647.2 pg/mL to 1584 ± 1584.4 pg/mL (P < 0.0001). Brain natriuretic peptide decreased from 1223 ± 1342.1 pg/mL during hospitalization to 616 ± 892.1 pg/mL after discharge (P = 0.005). The BNP‐Hosp was positively correlated with C‐reactive protein (P = 0.003) and negatively correlated with serum prealbumin (P = 0.0001) and albumin (P = 0.0001). The postdialysis body weight prescription decreased from 71.0 ± 15.7 kg at baseline to 70.5 ± 15.4 kg during hospitalization and to 67.8 ± 14.4 kg 4 months after discharge (P = 0.0032). Our study displays clearly the significant changes of plasma BNP levels occurring during intercurrent events. Fluid overload triggered by inflammation‐associated catabolism and the lag time for dry weight adjustment is the cause of this finding. Hence, plasma BNP level may be used as a marker of fluid overload in patients with intercurrent events and may allow efficient dry weight adjustment. We cannot rule out an effect of inflammation on BNP synthesis.