bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive Comparison of Various Techniques for the Analysis of Elemental Distributions in Thin Films
Authors: Abou-Ras D. , Caballero R. , Fischer C.-H. , Kaufmann C.A. , Lauermann I. , Mainz R. , Mönig H. , Schöpke A. , Stephan C. , Streeck C. , Schorr S. , Eicke A. , Döbeli M. , Gade B. , Hinrichs J. , Nunney T. , Dijkstra H. , Hoffmann V. , Klemm D. , Efimova V. , Bergmaier A. , Dollinger G. , Wirth T. , Unger W. , Rockett A.A. , Perez-Rodriguez A. , Alvarez-Garcia J. , Izquierdo-Roca V. , Schmid T. , Choi P.-P. , Müller M. , Bertram F. , Christen J. , Khatri H. , Collins R.W. , Marsillac S. , Kötschau I. 
Published: September 2011

AbstractThe present work shows results on elemental distribution analyses in Cu(In,Ga)Se2 thin films for solar cells performed by use of wavelength-dispersive and energy-dispersive X-ray spectrometry (EDX) in a scanning electron microscope, EDX in a transmission electron microscope, X-ray photoelectron, angle-dependent soft X-ray emission, secondary ion-mass (SIMS), time-of-flight SIMS, sputtered neutral mass, glow-discharge optical emission and glow-discharge mass, Auger electron, and Rutherford backscattering spectrometry, by use of scanning Auger electron microscopy, Raman depth profiling, and Raman mapping, as well as by use of elastic recoil detection analysis, grazing-incidence X-ray and electron backscatter diffraction, and grazing-incidence X-ray fluorescence analysis. The Cu(In,Ga)Se2 thin films used for the present comparison were produced during the same identical deposition run and exhibit thicknesses of about 2 μm. The analysis techniques were compared with respect to their spatial and depth resolutions, measuring speeds, availabilities, and detection limits.
Some thoughts about the future of SBML
Authors: Le Novere Nicolas 
Published: September 2011

AbstractSBML was designed in 2000, merely 2 years after the first official specification of XML. 11 years afterward, the current structure of the language is largely unchanged. Since then, its user base evolved much, as did the whole field of modeling in biology.If one wants SBML to evolve in the next decade, it is time to start discussing the basics now. The presentation covers a series of fundamental issues such as SBML coverage, unity of the language, use of elements and attributes etc.
Purification and physicochemical studies of metalloprotease, cotinifolin from Euphorbia cotinifolia
Authors: Kumar Reetesh 
Published: September 2011

AbstractA detailed procedure for the purification of cotinifolin from the latex of Euphorbia cotinifolia using ion exchange chromatography and hydrophobic interaction chromatography is described.Various biochemical characteristics of cotinifolin and other enzymatic properties along with spectroscopic parameters like circular dichorism and fluorescence have been reported. Cotinifolin is stable over a wide range of pH and under extreme conditions of chaotrops and organic solvents where most proteins lost their functions. Further studies on the identification of physiological substrates, biophysical and structural studies will give insight into the utility of the enzyme in the biotechnological industries and protein engineering.
Dynamic behavior of clathrin in Arabidopsis thaliana unveiled by live imaging
Authors: Ito Emi , Fujimoto Masaru , Ebine Kazuo , Uemura Tomohiro , Ueda Takashi , Nakano Akihiko 
Published: September 2011

SummaryClathrin‐coated vesicles (CCV) are necessary for selective transport events, including receptor‐mediated endocytosis on the plasma membrane and cargo molecule sorting in the trans‐Golgi network (TGN). Components involved in CCV formation include clathrin heavy and light chains and several adaptor proteins that are conserved among plants. Clathrin‐dependent endocytosis has been shown to play an integral part in plant endocytosis. However, little information is known about clathrin dynamics in living plant cells. In this study, we have visualized clathrin in Arabidopsis thaliana by tagging clathrin light chain with green fluorescent protein (CLC–GFP). Quantitative evaluations of colocalization demonstrate that the majority of CLC–GFP is localized to the TGN, and a minor population is associated with multivesicular endosomes and the Golgi trans‐cisternae. Live imaging further demonstrated the presence of highly dynamic clathrin‐positive tubules and vesicles, which appeared to mediate interactions between the TGNs. CLC–GFP is also targeted to cell plates and the plasma membrane. Although CLC–GFP colocalizes with a dynamin isoform at the plasma membrane, these proteins exhibit distinct distributions at newly forming cell plates. This finding indicates independent functions of CLC (clathrin light chains) and dynamin during the formation of cell plates. We have also found that brefeldin A and wortmannin treatment causes distinctly different alterations in the dynamics and distribution of clathrin‐coated domains at the plasma membrane. This could account for the different effects of these drugs on plant endocytosis.
Effect of Shading from Jointing to Maturity on High Molecular Weight Glutenin Subunit Accumulation and Glutenin Macropolymer Concentration in Grain of Winter Wheat
Authors: Li X. , Cai J. , Li H. , Bo Y. , Liu F. , Jiang D. , Dai T. , Cao W. 
Published: September 2011

AbstractAccumulations of high molecular weight glutenin subunits (HMW‐GS) and glutenin macropolymer (GMP) in wheat grains are important indicators of grain quality. Two wheat cultivars, Yangmai 158 (shading tolerant) and Yangmai 11 (shading intolerant) which contains the same subunit pairs of 7 + 8 and 2 + 12, were used to evaluate the impacts of shading on HMW‐GS accumulation and GMP concentration in the grain. Three shading levels were implemented from jointing to maturity, i.e. S1, S2 and S3, in which the plants received 8 %, 15 % and 23 % less radiation of the control (S0), respectively. The initial formation of HMW‐GS was pre‐dated by shading. The rapid HMW‐GS accumulation duration was shortened, and the accumulation rate during late grain filling period was lowered in the two relatively severe shaded treatments (S2 & S3). Thus, the total HMW‐GS accumulation in single grain at maturity was lower in S2 and S3 than in the control (S0). However, concentrations of HMW‐GS and GMP at maturity increased because of the reduced single grain weight in S2 and S3, as compared to S0. In contrast, the low density shading (S1) prolonged the rapid accumulation duration of HMW‐GS, hence increased the accumulation and concentration of HMW‐GS in the grains. Consequently, S1 reduced falling number and SDS‐sedimentation volume, while shortened dough development time (DDT) and dough stability time (DST). In contrast, S2 and S3 increased falling number, wet‐gluten concentration and SDS‐sedimentation volume, and lengthened the DDT and DST. In addition, the fluctuations in accumulations of HMW‐GS and GMP and most quality traits because of shading in Yangmai 158 were less than Yangmai 11. The interrelations between HMW‐GS accumulation, GMP concentration and quality of grain and dough were further discussed.
Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome
Authors: Hodkinson Brendan P. , Gottel Neil R. , Schadt Christopher W. , Lutzoni François 
Published: September 2011

SummaryAlthough common knowledge dictates that the lichen thallus is formed solely by a fungus (mycobiont) that develops a symbiotic relationship with an alga and/or cyanobacterium (photobiont), the non‐photoautotrophic bacteria found in lichen microbiomes are increasingly regarded as integral components of lichen thalli. For this study, comparative analyses were conducted on lichen‐associated bacterial communities to test for effects of photobiont‐types (i.e. green algal vs. cyanobacterial), mycobiont‐types and large‐scale spatial distances (from tropical to arctic latitudes). Amplicons of the 16S (SSU) rRNA gene were examined using both Sanger sequencing of cloned fragments and barcoded pyrosequencing. Rhizobiales is typically the most abundant and taxonomically diverse order in lichen microbiomes; however, overall bacterial diversity in lichens is shown to be much higher than previously reported. Members of Acidobacteriaceae, Acetobacteraceae, Brucellaceae and sequence group LAR1 are the most commonly found groups across the phylogenetically and geographically broad array of lichens examined here. Major bacterial community trends are significantly correlated with differences in large‐scale geography, photobiont‐type and mycobiont‐type. The lichen as a microcosm represents a structured, unique microbial habitat with greater ecological complexity and bacterial diversity than previously appreciated and can serve as a model system for studying larger ecological and evolutionary principles.
Outcome predictors in acute surgical admissions for lower gastrointestinal bleeding
Authors: Newman J. , Fitzgerald J. E. F. , Gupta S. , von Roon A. C. , Sigurdsson H. H. , Allen‐Mersh T. G. 
Published: September 2011

AbstractAim  The BLEED criterion is a triaging model for lower gastrointestinal bleeding (LGIB), which was developed and validated in the USA. We assessed the BLEED criteria in a UK population and aimed to elucidate factors that can be implemented for early risk stratification.Method  Patients were identified from a prospectively maintained surgical admission database at a central London teaching hospital. Data were collected on 26 clinical factors available on initial presentation. The primary‐outcome end‐points included severe bleeding (persistent bleeding within the first 24 h, blood transfusion, a decrease in haematocrit of ≥ 20% or recurrent bleeding after ≥ 24 hours of stability) and adverse outcome (emergency surgery to control bleeding, intensive care unit [ITU] admission or death).Results  One hundred and eighty‐four clinical episodes were identified, representing 3% of all surgical referrals. Twelve patients with upper gastrointestinal bleeding were excluded. Severe bleeding occurred in 110 (64%) patients. An adverse outcome was recorded in 20 (11.6%) patients, and 10 (5.4%) patients died during admission. The commonest aetiologies were diverticular disease, haemorrhoids and malignancy. Four prognosticators of adverse outcome were identified, these being: creatinine > 150μm (P = 0.002); age > 60 years (P = 0.001); abnormal haemodynamic parameters on presentation (P = 0.05); persistent bleeding within the first 24 h (P = 0.05); and area under the receiver–operating characteristics curve (AUC) = 0.79. The BLEED criteria were shown to be nonpredictive (AUC = 0.60).Conclusion  The BLEED criterion was not shown to have any predictive value in this patient cohort. Our study has determined an independent set of prognostic factors that could be incorporated into initial triaging of patients presenting with LGIB. This may facilitate the early identification of patients requiring more aggressive resuscitation, admission to a monitored bed and consideration for early radiological or surgical intervention.
Extreme Measures of Agricultural Financial Risk
Authors: Morgan Wyn , Cotter John , Dowd Kevin 
Published: September 2011

AbstractThe agricultural marketing environment is inherently risky. Having accurate measures of risk helps farmers, policy‐makers and financial institutions make better informed decisions about how to deal with this risk. This article examines three tail quantile‐based risk measures applied to the estimation of extreme agricultural financial risk for corn and soybean production in the US: Value at Risk, Expected Shortfall and Spectral Risk Measures. We use Extreme Value Theory to model the tail returns and present results for these three different risk measures using agricultural futures market returns data. We compare estimated risk measures in terms of size and precision, and find that they are all considerably higher than Gaussian estimates. The estimated risk measures are also quite imprecise, and become more so as the risks involved become more extreme.
The natural history of hepatitis C virus infection acquired during childhood
Authors: Robinson Joan L. , Doucette Karen 
Published: September 2011

AbstractBackgroundThe outcome of patients with hepatitis C virus (HCV) infection acquired during childhood in the absence of antiviral therapy is not clear.AimsThe purpose of this study was to review the outcome of untreated HCV acquired in childhood. Only population‐based studies were included, as referred cases would be predicted to have more severe disease.MethodsA systematic review of the literature was completed up to October 2010 to identify studies where a population was screened for HCV infection that was presumably acquired during childhood. Demographical and clinical data were collected on infected patients who had not been treated with an antiviral. Primary outcome was development of a severe adverse outcome (cirrhosis, hepatoma, need for a liver transplant or liver‐related death).ResultsThere were 25 studies reporting a total of 733 infected patients. Liver biopsy results were provided for 180 patients (25%), revealing cirrhosis in eight (1.0% of the total and 4.0% of those who had a biopsy). None of the other patients developed a severe adverse outcome. As a result of the small number of patients with a severe adverse outcome, risk factors for HCV progression could not be identified.ConclusionAlthough HCV can lead to liver transplantation and death during childhood, the vast majority of patients with disease acquired during childhood have slowly progressive disease. There is no clear indication for antiviral therapy in the majority of children with HCV infection.
Deep brain stimulation induces rapidly reversible transcript changes in Parkinson's leucocytes
Authors: Soreq Lilach , Bergman Hagai , Goll Yael , Greenberg David S. , Israel Zvi , Soreq Hermona 
Published: September 2011

AbstractSubthalamic deep brain stimulation (DBS) reversibly modulates Parkinson's disease (PD) motor symptoms, providing an unusual opportunity to compare leucocyte transcripts in the same individuals before and after neurosurgery and 1 hr after stimulus cessation (ON‐ and OFF‐stimulus). Here, we report DBS‐induced reversibility and OFF‐stimulus restoration in 12 of 16 molecular functions and 3 of 4 biological processes shown in exon microarrays to be differentially expressed between PD patients and controls, post‐DBS from pre‐DBS and OFF from ON states. Intriguingly, 6 of 18 inflammation and immune‐related functions exhibited reversibility, and the extent of stimulus‐induced changes correlated with the neurological DBS efficacy, suggesting mechanistic implications. A minimal list of 29 transcripts that changed in all three comparisons between states discriminated pre‐surgery and OFF states from post‐surgery and controls. Six of these transcripts were found to be able to distinguish between PD patients and both healthy controls and patients with other neurological diseases in a previously published whole blood 3’ array data study of early PD patients. Our findings support the future use of this approach for identifying targets for therapeutic intervention and assessing the efficacy of current and new treatments in this and other neurological diseases.
Racial disparities in preterm birth: an overview of the potential role of nutrient deficiencies
Authors: DUNLOP ANNE L. , KRAMER MICHAEL R. , HOGUE CAROL J.R. , MENON RAMKUMAR , RAMAKRISHAN USHA 
Published: September 2011

AbstractObjective. To give an overview of the literature for evidence of nutrient deficiencies as contributors to the disparity in preterm birth (PTB) between African‐American and Caucasian women. Design. Structured literature survey. Methods. We searched MEDLINE to identify observational and experimental studies that evaluated the relation between nutrient intake and/or supplementation and PTB. For nutrients for which studies supported an association, we searched MEDLINE for studies of the prevalence of deficiency in the USA by race. Main Outcome Measures. Summarized findings on nutrients for which there is both evidence of a role in PTB and variability in the prevalence of deficiency by race. Results. Nutrient deficiencies for which there are varying levels of evidence for an association with PTB and a greater burden among African‐American compared with Caucasian women include deficiencies of iron, folic acid, zinc, vitamin D, calcium and magnesium, and imbalance of ω‐3 and ω‐6 polyunsaturated fatty acids. There are inadequate high‐quality studies that investigate the role of nutrient deficiencies in PTB, their potential interaction with other risks, the proportion of excess risk for which they account, and whether supplementation can reduce the risk of, and racial disparities in, PTB in US populations. Conclusion. Deficiencies of several nutrients have varying levels of evidence of association with PTB and are of greater burden among African‐American compared with Caucasian women. Although further research is needed, strategies that improve the nutritional status of African‐American women may be a means of addressing a portion of the racial disparity in PTB.
Association of the FcγRIIB‐nt645+25A/G polymorphism with the expression level of the FcγRIIb receptor, the antibody response to Porphyromonas gingivalis and the severity of periodontitis
Authors: Sugita N. , Iwanaga R. , Kobayashi T. , Yoshie H. 
Published: September 2011

Sugita N, Iwanaga R, Kobayashi T, Yoshie H. Association of the FcγRIIB‐nt645+25A/G polymorphism with the expression level of the FcγRIIb receptor, the antibody response to Porphyromonas gingivalis and the severity of periodontitis. J Periodont Res 2012; 47: 105–113. © 2011 John Wiley & Sons A/SBackground and Objective:  Human FcγRIIb is an immunoglobulin G (IgG) receptor that inhibits the activation of B lymphocytes through cross‐linking with the B‐cell receptor via immune complexes. This function acts as a negative regulator of antibody production. Our previous studies have demonstrated the gene polymorphisms in FcγRIIb to be associated with periodontitis. In this study, we presented a polymorphism –FcγRIIB‐nt645+25A/G (rs2125685) – in intron 4 and analyzed its functional relevance to periodontitis. We examined whether the FcγRIIB‐nt645+25A/G polymorphism is associated with periodontal parameters, the IgG response to the periodontopathic bacterium Porphyromonas gingivalis and/or the expression level of FcγRIIb on peripheral B lymphocytes.Material and Methods:  Thirty‐two patients with chronic periodontitis were genotyped with nested PCR and by direct sequencing of genome DNA. The levels of serum IgG and of specific IgG subclasses for P. gingivalis sonicate and for the recombinant 40‐kDa outer membrane protein (OMP) were determined. The expression levels of FcγRIIb on peripheral B lymphocytes from 19 healthy donors were measured by flow cytometry.Results:  Patients with the FcγRIIB‐nt645+25AA genotype showed significantly higher mean clinical attachment levels compared to patients with the FcγRIIB‐nt645+25GG genotype (p = 0.003) and a significantly lower IgG response to P. gingivalis sonicate and to the 40‐kDa OMP. The expression levels of FcγRIIb protein on the cell surface in peripheral B lymphocytes were higher in healthy donors with the FcγRIIB‐nt645+25AA genotype than in those with the FcγRIIB‐nt645+25GG genotype (p = 0.03).Conclusion:  The higher expression levels of FcγRIIb in subjects with the FcγRIIB‐nt645+25AA genotype may induce a lower level of production of IgG against P. gingivalis and therefore more severe periodontitis.
A compliant tendon increases fatigue resistance and net efficiency during fatiguing cyclic contractions of mouse soleus muscle
Authors: Lichtwark G. A. , Barclay C. J. 
Published: September 2011

Abstract
Aim:  As muscles fatigue, their ability to generate mechanical work decreases as a result of decreased force generation and in cyclic activity, slower the relaxation. The purpose of this study was to determine whether a compliant tendon, connected in series with a muscle, would increase sustained work output during cyclic contractions.
Methods:  Experiments were performed in vitro (37 °C) using fibre bundles from mouse soleus muscles (n = 7). Each muscle performed two series of 40 brief contractions at a contraction frequency of 2 Hz and with a sinusoidal length change. One series was performed using the fibre bundle only and one with the fibre bundle and a compliant strip of latex connected between the muscle and the force recording apparatus.
Results:  When contracting with the latex strip, muscle work output was better maintained during the second half of the protocol than when performed without the latex, overall energy cost was reduced and mechanical efficiency was increased.
Conclusion:  The provision of a compliant tendon analogue increased the level of work output that could be sustained during cyclic contractions and reduced energy expenditure. It is proposed that both metabolic and mechanical consequences of the compliant tendon contribute to the improved performance.
Energy balances and greenhouse gas emissions of palm oil biodiesel in Indonesia
Authors: Harsono Soni Sisbudi , Prochnow Annette , Grundmann Philipp , Hansen Anja , Hallmann Claudia 
Published: September 2011

AbstractThis study presents a cradle‐to‐gate assessment of the energy balances and greenhouse gas (GHG) emissions of Indonesian palm oil biodiesel production, including the stages of land‐use change (LUC), agricultural phase, transportation, milling, biodiesel processing, and comparing the results from different farming systems, including company plantations and smallholder plantations (either out growers or independent growers) in different locations in Kalimantan and Sumatra of Indonesia. The findings demonstrate that there are considerable differences between the farming systems and the locations in net energy yields (43.6–49.2 GJ t−1 biodiesel yr−1) as well as GHG emissions (1969.6–5626.4 kg CO2eq t−1 biodiesel yr−1). The output to input ratios are positive in all cases. The largest GHG emissions result from LUC effects, followed by the transesterification, fertilizer production, agricultural production processes, milling, and transportation. Ecosystem carbon payback times range from 11 to 42 years.
Direct shoot organogenesis from hypocotyl explants of Jatropha curcasL. an important bioenergy feedstock
Authors: Sahoo Nirmala , Thirunavoukkarasu Manikannan , Behera Priya Ranjan , Satpathy Gargi Bala , Panda Prasanna Kumar 
Published: September 2011

AbstractMultiple shoots were induced on hypocotyl segments reared from in vitro germinated seedlings of Jatropha curcas L., using Murashige and Skoog (MS) medium supplemented with N6‐benzyl adenine (BA) and kinetin (kin) either alone or in combination with indole‐3‐acetic acid (IAA). The combined treatment of 7.05 μm kin and 1.425 μm IAA resulted in maximum shoot production with an average shoot bud initiation of 12.1 per explant. The regenerated microshoots were transferred to root induction medium containing half‐strength MS salts supplemented with either indole‐3‐butyric acid (IBA) or IAA. Rooting of microshoots was best achieved on half‐strength MS medium supplemented with IBA (9.8 μm). Rooted plantlets were subsequently acclimatized under green house condition and the plantlets showed 70% survival.