bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nitrogen forms affect root growth, photosynthesis, and yield of tomato under alternate partial root‐zone irrigation
Authors: Chen Chu , Xu Fei , Zhu Ji‐Rong , Wang Rong‐Fu , Xu Zhi‐Heng , Shu Liang‐Zuo , Xu Wen‐Wen 
Published: December 2015

AbstractTo increase efficiency of water and nitrogen (N) fertilizer use, this study was conducted with a split‐root pot experiment to investigate the effects of different forms of N fertilizer on root growth, photosynthesis, instantaneous water use efficiency (IWUE), and yield of tomato (Lycopersicon esculentum L.) under alternate partial root‐zone irrigation (APRI). Three irrigation modes comprised conventional irrigation (CI) and two kinds of APRI, i.e., APRI with water content in the drying soil compartment controlled at ≥ 60% or 40% of the water‐holding capacity (APRI‐60, APRI‐40). Two N forms included ammonium‐N and nitrate‐N supplied as calcium nitrate or ammonium sulfate, respectively. The results show that APRI‐60 enhanced root growth and increased leaf IWUE with a slight yield reduction compared with CI regardless of the N form supplied. In contrast, APRI‐40 significantly decreased root growth and inhibited photosynthesis, thereby resulting in a significant yield loss. In addition, at the flowering stage tomato plants grew better with ammonium‐N than nitrate‐N supply; however, at the fruit expansion stage and maturity stage, the tomato plants had a higher biomass accumulation and yield with nitrate‐N than ammonium‐N supply. Therefore, the application of APRI should consider the soil water condition coupled with an appropriate N form. In the present study, APRI controlled at ≥ 60% of the water‐holding capacity (WHC) for the drying soil side with nitrate‐N supply was the best water‐fertilizer supply for tomato cultivation.
Microbial community, and biochemical and physiological properties of Korean traditional black raspberry (Robus coreanus Miquel) vinegar
Authors: Song Nho‐Eul , Cho Sung‐Ho , Baik Sang‐Ho 
Published: December 2015

AbstractBACKGROUNDThe aim of this study was to elucidate the changes in microbial community and biochemical and physiological properties of traditional Muju black raspberry (Robus coreanus Miquel) vinegar (TMBV) during fermentation by culture‐independent methods.RESULTSDuring vinegar fermentation, ethanol produced up to 120 g L−1 until day 35, with continuously increasing yeast concentration to a total of log 7.6 CFU mL−1. After day 35, acetic acid bacteria (AAB) concentrations rose to log 5.8 CFU mL−1 until day 144. Denaturing gradient gel electrophoresis analysis showed that Saccharomyces cerevisiae was detected until day 87 of the fermentation, at which point Acetobacter pasteurianus gradually took over as the dominant species. Total sugar was reduced to 6.6 °Brix and total acidity produced up to 44 g L−1.CONCLUSIONIn this study, we established the physicochemical analysis and growth dynamics of yeast and AAB during alcoholic and acetic acid fermentation of black raspberry by a traditional method. Overall, S. cerevisiae and A. pasteurianus species appeared to dominate the TMBV fermentation. In conclusion, this study demonstrated a suitable fermentation system for TMBV by the static surface method. © 2015 Society of Chemical Industry
Oregano (Lippia graveolens) essential oil added within pectin edible coatings prevents fungal decay and increases the antioxidant capacity of treated tomatoes
Authors: Rodriguez‐Garcia Isela , Cruz‐Valenzuela M Reynaldo , Silva‐Espinoza Brenda A , Gonzalez‐Aguilar Gustavo A , Moctezuma Edgar , Gutierrez‐Pacheco M Melissa , Tapia‐Rodriguez Melvin R , Ortega‐Ramirez Luis A , Ayala‐Zavala J Fernando 
Published: December 2015

AbstractBACKGROUNDTomato is a fruit widely consumed due to its flavor and nutritional value; however, it is susceptible to fungi contamination. Oregano essential oil (OEO) is a fungicide whose constituents are volatile; therefore, their incorporation within edible coatings can protect them and maintain their efficacy. In this context, this study evaluated the effect of OEO applied within pectin coatings on the inhibition of Alternaria alternata growth, antioxidant content and sensorial acceptability of tomatoes.RESULTSThe major volatile compounds of OEO were carvacrol (47.41%), p‐cymene (26.44%) and thymol (3.02%). All the applied OEO concentrations (15.7, 25.9 and 36.1 g L−1) inhibited the in vitro growth of A. alternata, whereas the in vivo effective concentrations were 25.9 and 36.1 g L−1. Additionally, there was an increment of total phenols and antioxidant activity in coated tomatoes compared to controls. Aroma acceptability of tomatoes was not affected by the pectin–OEO coating; additionally, the pectin, pectin–OEO 15.7 g L−1 treatments and control tomatoes showed higher flavor acceptability than those coated with pectin–OEO 25.9 and 36.1 g L−1.CONCLUSIONPectin–OEO coatings showed antifungal effect and increased the antioxidant activity without negative effects on the sensorial acceptability of tomatoes. © 2015 Society of Chemical Industry
Enrichment of two isoflavone aglycones in black soymilk by Rhizopus oligosporus NTU 5 in a plastic composite support bioreactor
Authors: Liu Chi‐Te , Erh Mei‐Hui , Lin Shin‐Pin , Lo Kai‐Yin , Chen Kuan‐I , Cheng Kuan‐Chen 
Published: December 2015

AbstractBACKGROUNDA plastic composite support (PCS) bioreactor was implemented to evaluate the effects on isoflavone deglycosylation in black soymilk fermented by Rhizopus oligosporus NTU 5.RESULTSEvaluation for the optimal PCS for mycelia immobilisation was conducted, which led to the significant results that the most mycelium weight (0.237 g per PCS, P < 0.05) is held by an S‐type PCS; therefore, it was selected for black soymilk fermentation. It was found that the PCS fermentation system without pH control exhibits better efficiency of isoflavone bioconversion (daidzin to daidzein, and genistin to genistein) than the one with pH control at pH 6.5. As for the long‐run fermentation, those without pH control indeed accelerate the isoflavone bioconversion by continuously releasing β‐glucosidase into soymilk. Deglycosylation can be completed in 8 to 24 h and sustained for at least 34 days as 26 batches. The non‐pH‐control fermentation system also exhibits the highest total phenolic content (ranged from 0.147 to 0.340 mg GAE mL−1 sample) when compared to the pH‐controlled and suspended ones. Meanwhile, the black soymilk from the 22nd batch with 8 h fermentation demonstrated the highest DPPH radical scavenging effect (54.7%).CONCLUSIONA repeated‐batch PCS fermentation system was established to accelerate the deglycosylation rate of isoflavone in black soymilk. © 2015 Society of Chemical Industry
Development of an SPME‐GC‐MS method for the specific quantification of dimethylamine and trimethylamine: use of a new ratio for the freshness monitoring of cod fillets
Authors: Dehaut Alexandre , Duthen Simon , Grard Thierry , Krzewinski Frédéric , N'Guessan Assi , Brisabois Anne , Duflos Guillaume 
Published: December 2015

AbstractBACKGROUNDFish is a highly perishable food, so it is important to be able to estimate its freshness to ensure optimum quality for consumers. The present study describes the development of an SPME‐GC‐MS technique capable of quantifying both trimethylamine (TMA) and dimethylamine (DMA), components of what has been defined as partial volatile basic nitrogen (PVB‐N). This method was used, together with other reference methods, to monitor the storage of cod fillets (Gadus morhua) conserved under melting ice.RESULTSCareful optimisation enabled definition of the best parameters for extracting and separating targeted amines and an internal standard. The study of cod spoilage by sensory analysis and TVB‐N assay led to the conclusion that the shelf‐life of cod fillet was between 6 and 7 days. Throughout the study, TMA and DMA were specifically quantified by SPME‐GC‐MS; the first was found to be highly correlated with the values returned by steam distillation assays. Neither TMA‐N nor DMA‐N were able to successfully characterise the decrease in early freshness, unlike dimethylamine/trimethylamine ratio (DTR), whose evolution is closely related to the results of sensory analysis until the stage where fillets need to be rejected.CONCLUSIONDTR was proposed as a reliable indicator for the early decrease of freshness until fish rejection. © 2015 Society of Chemical Industry
Iron(III) Porphyrin‐Based Porous Material as Photocatalyst for Highly Efficient and Selective Degradation of Congo Red
Authors: Xiao Zhenyu , Zhou Yan , Xin Xuelian , Zhang Qinhui , Zhang Liangliang , Wang Rongming , Sun Daofeng 
Published: December 2015

A highly efficient and selective photocatalyst, UPC‐CMP‐1 has been successfully synthesized by a Sonogashira–Hagihara coupling reaction between iron(III) 5,10,15,20‐tetrakis‐(4′‐bromophenyl) porphine and 1,4‐diethynylbenzene. The scanning electron microscopy shows UPC‐CMP‐1 possesses a dendrite‐like nanostructure. Interestingly, within 120 s, UPC‐CMP‐1 can decompose 88.3% of Congo red (CR) molecules under visible light irradiation. Furthermore, UPC‐CMP‐1 exhibits high selectivity to CR over other dyes. These results reveal that conjugated microporous polymer should be an excellent candidate on the application of dye degradation.
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Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach
Authors: Bordron Philippe , Latorre Mauricio , Cortés Maria‐Paz , González Mauricio , Thiele Sven , Siegel Anne , Maass Alejandro , Eveillard Damien 
Published: December 2015

AbstractFollowing the trend of studies that investigate microbial ecosystems using different metagenomic techniques, we propose a new integrative systems ecology approach that aims to decipher functional roles within a consortium through the integration of genomic and metabolic knowledge at genome scale. For the sake of application, using public genomes of five bacterial strains involved in copper bioleaching: Acidiphilium cryptum, Acidithiobacillus ferrooxidans, Acidithiobacillus thiooxidans, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans, we first reconstructed a global metabolic network. Next, using a parsimony assumption, we deciphered sets of genes, called Sets from Genome Segments (SGS), that (1) are close on their respective genomes, (2) take an active part in metabolic pathways and (3) whose associated metabolic reactions are also closely connected within metabolic networks. Overall, this SGS paradigm depicts genomic functional units that emphasize respective roles of bacterial strains to catalyze metabolic pathways and environmental processes. Our analysis suggested that only few functional metabolic genes are horizontally transferred within the consortium and that no single bacterial strain can accomplish by itself the whole copper bioleaching. The use of SGS pinpoints a functional compartmentalization among the investigated species and exhibits putative bacterial interactions necessary for promoting these pathways.
Next generation sequencing‐based copy number analysis reveals low prevalence of deletions and duplications in 46 genes associated with genetic cardiomyopathies
Authors: Ceyhan‐Birsoy Ozge , Pugh Trevor J. , Bowser Mark J. , Hynes Elizabeth , Frisella Ashley L. , Mahanta Lisa M. , Lebo Matt S. , Amr Sami S. , Funke Birgit H. 
Published: December 2015

AbstractBackgroundDiagnostic testing for genetic cardiomyopathies has undergone dramatic changes in the last decade with next generation sequencing (NGS) expanding the number of genes that can be interrogated simultaneously. Exon resolution copy number analysis is increasingly incorporated into routine diagnostic testing via cytogenomic arrays and more recently via NGS. While NGS is an attractive option for laboratories that have no access to array platforms, its higher false positive rate requires weighing the added cost incurred by orthogonal confirmation against the magnitude of the increase in diagnostic yield. Although copy number variants (CNVs) have been reported in various cardiomyopathy genes, their contribution has not been systematically studied.MethodsWe performed single exon resolution NGS‐based deletion/duplication analysis for up to 46 cardiomyopathy genes in >1400 individuals with cardiomyopathies including HCM, DCM, ARVC, RCM, and LVNC.Results and ConclusionClinically significant deletions and duplications were identified in only 9 of 1425 (0.63%) individuals. The majority of those (6/9) represented intragenic events. We conclude that the added benefit of exon level deletion/duplication analysis is low for currently known cardiomyopathy genes and may not outweigh the increased cost and complexity of incorporating it into routine diagnostic testing for these disorders.
Exploring the association of dairy product intake with the fatty acids C15:0 and C17:0 measured from dried blood spots in a multipopulation cohort: Findings from the Food4Me study
Authors: Albani Viviana , Celis‐Morales Carlos , Marsaux Cyril F. M. , Forster Hannah , O'Donovan Clare B. , Woolhead Clara , Macready Anna L. , Fallaize Rosalind , Navas‐Carretero Santiago , San‐Cristobal Rodrigo , Kolossa Silvia , Mavrogianni Christina , Lambrinou Christina P. , Moschonis George , Godlewska Magdalena , Surwiłło Agnieszka , Gundersen Thomas E. , Kaland Siv E. , Manios Yannis , Traczyk Iwona , Drevon Christian A. , Gibney Eileen R. , Walsh Marianne C. , Martinez J. Alfredo , Saris Wim H. M. , Daniel Hannelore , Lovegrove Julie A. , Gibney Michael J. , Adamson Ashley J. , Mathers John C. , Brennan Lorraine ,   on behalf of the Food4Me Study
Published: December 2015

ScopeThe use of biomarkers in the objective assessment of dietary intake is a high priority in nutrition research. The aim of this study was to examine pentadecanoic acid (C15:0) and heptadecanoic acid (C17:0) as biomarkers of dairy foods intake.Methods and resultsThe data used in the present study were obtained as part of the Food4me Study. Estimates of C15:0 and C17:0 from dried blood spots and intakes of dairy from a Food Frequency Questionnaire were obtained from participants (n = 1180) across seven countries. Regression analyses were used to explore associations of biomarkers with dairy intake levels and receiver operating characteristic analyses were used to evaluate the fatty acids. Significant positive associations were found between C15:0 and total intakes of high‐fat dairy products. C15:0 showed good ability to distinguish between low and high consumers of high‐fat dairy products.ConclusionC15:0 can be used as a biomarker of high‐fat dairy intake and of specific high‐fat dairy products. Both C15:0 and C17:0 performed poorly for total dairy intake highlighting the need for caution when using these in epidemiological studies.
Surgical trends in the correction of female stress urinary incontinence in academic centers within the United States
Authors: Cantrell Alexander B. , Rothschild Jennifer , Durbin‐Johnson Blythe , Gonzalez Rafael , Kurzrock Eric A. 
Published: December 2015

AimsThere is a lack of data describing the current state of stress urinary incontinence (SUI) procedures in academic centers. Urologists, gynecologists, and urogynecologists perform these operations, but the relative volume each group accounts for is unknown. The purpose of this study was to evaluate the distribution of cases in academic centers between specialties and associated patient characteristics.MethodsA hospital consortium database was used to identify patients treated surgically for SUI between 2009 and 2014. Patient and surgeon variables were evaluated. Patient variables (age, region, insurance, race) and surgeon volume were analyzed. Sub‐analysis was conducted to determine concomitant prolapse repairs.ResultsOf the 50,315 stress urinary incontinence procedures performed, 22% were performed by urologists. Overall volume dropped 39% and mean surgeon volumes for all three groups decreased with time. Average median volume for urogynecologists (29/year) differed from both urologists (3/year) and non‐urogynecologists (2/year). There was a significant difference in rate of concomitant prolapse repairs performed by urogynecologists (56%), gynecologists (54%), and urologists (26%).ConclusionsThese data portray the changing pattern of SUI procedure practice in academic centers. Academic urologists are performing less than 25% of SUI procedures, with an overall decline in number of procedures across all specialties. Urogynecologists and gynecologists are performing a significantly higher proportion of concomitant prolapse repairs. Neurourol. Urodynam. 36:394–398, 2017. © 2015 Wiley Periodicals, Inc.
Wide‐field Two Photon Microscopy
Authors: Döge Nadine , Thiel Erik , Seewald Gunter , Albrecht Stephanie , Vogt Annika , Liebscher Julia , Schönborn Karl‐Heinz 
Published: December 2015

AbstractTwo Photon Microscopy (2PM) generates microscopic images out of depth of biological samples. Up to now the method is restricted by narrow limitations of the field of view, the imaging depth and the orientation of the image field. A new approach overcomes these boundaries and delivers high resolution images revealing very specific information on clinically and biologically relevant tissue and cell structures. The status of the 2PM technology is critically reviewed and the options are discussed. The advantages of the new approach demonstrated by excellent tissue images.
Broadband Polarization‐maintaining Fiber Optics
Authors: Knigge Anja , Oechnser Ulrich , Brenner Bernhard , Scholz Tim 
Published: December 2015

AbstractModern fluorescence microscopy allows the fundamental building blocks of all life to be studied at a level of detail and accuracy that would have been inconceivable just a few years ago. One example is the movement of intracellular motor proteins responsible for muscle contraction or for the transport of biological cargo along microtubules within the cell. To study these systems using fluorescence microscopy, laser light over a wide range of wavelengths is required that has to be coupled precisely into the microscope. With free‐beam optics, this can only be done to a limited extent and at considerable cost.
The effect of exposure misclassification in spontaneous ADR reports on the time to detection of product‐specific risks for biologicals: a simulation study
Authors: Vermeer Niels S. , Ebbers Hans C. , Straus Sabine M. J. M. , Leufkens Hubert G. M. , Egberts Toine C. G. , De Bruin Marie L. 
Published: December 2015

AbstractBackground and ObjectiveThe availability of accurate product‐specific exposure information is essential in the pharmacovigilance of biologicals, because differences in the safety profile may emerge between products containing the same active substance. In spontaneous adverse drug reaction (ADR) reports, drug exposure may, however, be misclassified, that is, attributed to the incorrect product. The aim of this study was to explore the effect of exposure misclassification on the time to detection of product‐specific risks in spontaneous reporting systems.MethodsWe used data simulations to explore the effect of exposure misclassification. We simulated an active substance‐specific subset of a spontaneous reporting system and used the proportional reporting ratio for signal detection. The effect of exposure misclassification was evaluated in three test cases representing product‐specific ADRs that may occur for biologicals and studied in relative terms by varying the model parameters (market share and relative risk).ResultsWe found that exposure misclassification results in the largest delay in identification of risks that have a weak association (relative risk < 2 or 3) with the product of interest and in situations where the product associated with the unique risk has a large (>50%) market share. The absolute public health impact of exposure misclassification, in terms of cases/time to detection, varied considerably across the test cases.ConclusionExposure misclassification in ADR reports may result in a delayed detection of product‐specific risks, particularly in the detection of weak drug–event associations. Our findings can help inform the future implementation and refinement of product‐specific and batch‐specific signal detection procedures. Copyright © 2015 John Wiley & Sons, Ltd.
Amphiphilic diblock copolymers bearing pendant aromatic acetal groups: Synthesis and tunable pH‐triggered assembly/disassembly transition behavior
Authors: Zhang Wanbin , Fan Xiaodong , Zhang Haitao , Zhu Xiuzhong , Tian Wei 
Published: December 2015

ABSTRACTA novel aromatic acetal‐based acid‐labile monomer 2‐phenyl‐5‐ethyl‐5‐acryloxymethyl‐1,3‐dioxacyclohexane (HEDPA) was synthesized and polymerized by reversible addition fragmentation chain transfer (RAFT) polymerization using alkynyl functional chain transfer agent (CTA‐Alk). Afterward, a series of amphiphilic diblock copolymers composed of fixed hydrophobic poly(2‐phenyl‐5‐ethyl‐5‐acryloxymethyl‐1,3‐dioxacyclohexane) (PDAEP) segments and various lengths of hydrophilic mPEG segments were prepared through click reaction between alkynyl‐terminated PDAEP and azido‐terminated mPEG. The self‐assembly behaviors of the diblock copolymers were investigated by dynamic light scattering (DLS), transmission electron microscopy (TEM), fluorescence spectroscopy, and 1H NMR. These results indicated that the diblock copolymers could self‐assemble into nano‐sized micelles with PDAEP cores and PEG coronas in aqueous solution. DLS, fluorescence spectroscopy and UV–vis spectroscopy were used to monitor the pH‐triggered assembly/disassembly transition of the micelles. These results showed that the assembly/disassembly transition behaviors of the diblock copolymers micelles can be adjusted by changing the lengths of the mPEG segments. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016, 54, 1537–1547
Evaluation of free modeling targets in CASP11 and ROLL
Authors: Kinch Lisa N. , Li Wenlin , Monastyrskyy Bohdan , Kryshtafovych Andriy , Grishin Nick V. 
Published: December 2015

ABSTRACTWe present an assessment of ‘template‐free modeling’ (FM) in CASP11and ROLL. Community‐wide server performance suggested the use of automated scores similar to previous CASPs would provide a good system of evaluating performance, even in the absence of comprehensive manual assessment. The CASP11 FM category included several outstanding examples, including successful prediction by the Baker group of a 256‐residue target (T0806‐D1) that lacked sequence similarity to any existing template. The top server model prediction by Zhang's Quark, which was apparently selected and refined by several manual groups, encompassed the entire fold of target T0837‐D1. Methods from the same two groups tended to dominate overall CASP11 FM and ROLL rankings. Comparison of top FM predictions with those from the previous CASP experiment revealed progress in the category, particularly reflected in high prediction accuracy for larger protein domains. FM prediction models for two cases were sufficient to provide functional insights that were otherwise not obtainable by traditional sequence analysis methods. Importantly, CASP11 abstracts revealed that alignment‐based contact prediction methods brought about much of the CASP11 progress, producing both of the functionally relevant models as well as several of the other outstanding structure predictions. These methodological advances enabled de novo modeling of much larger domain structures than was previously possible and allowed prediction of functional sites. Proteins 2016; 84(Suppl 1):51–66. © 2015 Wiley Periodicals, Inc.