bluuebunny/crossref_metadata_2025 huggingface dataset:
The Microbiome and Musculoskeletal Conditions of Aging: A Review of Evidence for Impact and Potential Therapeutics
Authors: Steves Claire J , Bird Sarah , Williams Frances MK , Spector Tim D
Published: December 2015

Recently, we have begun to realize that the billions of microorganisms living in symbiosis with us have an influence on disease. Evidence is mounting that the alimentary tract microbiome, in particular, influences both host metabolic potential and its innate and adaptive immune system. Inflammatory states characterize many bone and joint diseases of aging. This prompts the hypothesis that the gut microbiome could alter the inflammatory state of the individual and directly influence the development of these common and burdensome clinical problems. Because the microbiome is easily modifiable, this could have major therapeutic impact. This perspective discusses evidence to date on the role of the microbiome and the highly prevalent age-related disorders of osteoporosis, osteoarthritis, gout, rheumatoid arthritis, sarcopenia, and frailty. It also reviews data on the effects of probiotics and prebiotic interventions in animal and human models. Despite suggestive findings, research to date is not conclusive, and we identify priorities for research to substantiate and translate findings. © 2015 American Society for Bone and Mineral Research.
Trade‐off Between Risk and Incentives: Evidence from New‐ and Old‐Economy Firms
Authors: Tebourbi Imen
Published: December 2015

The sensitivity of managerial compensation to the firm's risk is a controversial issue. While some articles find evidence supporting the agency theory that predicts a negative relationship between pay‐performance sensitivity and risk, others support the managerial ownership that predicts a positive relationship between these factors. This article reconciles these theories and provides evidence that these two theories are not conflicting, when tested properly, using industries risk characteristics. In this articled, we distinguish between new‐ and old‐economy industries, and demonstrate that managerial ownership theory applies to new‐economy firms, which are high‐tech firms that operate in more uncertain environments, whereas the agency theory applies to old‐economy firms that operate in more traditional industries. We further control for the size effect and find a positive relationship between pay‐performance sensitivity and risk for medium and large size new‐economy firms. Furthermore, we find that high‐tech companies increased their CEOs noncash compensation dramatically during the high‐tech market crash between 2000 and 2002 to cushion the fall in their CEOs wealth in the company. This caused CEOs pay‐performance sensitivity to risk to become negatively related to their firms' risk during that period. © 2016 Wiley Periodicals, Inc.
Reversed shunting in CREST syndrome
Authors: Kafes Habibe , Sen Fatih , Unal Sefa , Acar Burak , Ozeke Ozcan
Published: December 2015

The patent foramen ovale (PFO) is one of the most common congenital defects and may as well stand for “potential for opening” in addition to patent foramen ovale. Although patients are usually asymptomatic because the defect is flap‐like and does not permit significant left‐to‐right shunting, the pathological conditions that result in cardiac rotation or higher than normal right atrial pressures can reverse the normal left atrial to right atrial pressure gradient and cause a right‐to‐left shunt through a PFO. Pulmonary complications of systemic sclerosis (SSc) are common, and are the leading cause of SSc‐related death. The most common pulmonary manifestations of SSc are pulmonary hypertension (PAH), interstitial lung disease, and any combination thereof. Compared with the idiopathic form of PAH (IPAH), patients with SSc‐associated PAH have a threefold increased risk of death and may receive a diagnosis late in the course of disease because of insidious onset and the high prevalence of cardiac, musculoskeletal, and pulmonary parenchymal comorbidities. © 2015 Wiley Periodicals, Inc. J Clin Ultrasound 44:390–391, 2016
Arc‐Disjoint Directed and Undirected Cycles in Digraphs
Authors: Bang‐Jensen Jørgen , Kriesell Matthias , Maddaloni Alessandro , Simonsen Sven
Published: December 2015

The dicycle transversal number of a digraph D is the minimum size of a dicycle transversal of D, that is a set of vertices of D, whose removal from D makes it acyclic.

An arc a of a digraph D with at least one cycle is a transversal arc if a is in every directed cycle of D (making acyclic). In [3] and [4], we completely characterized the complexity of following problem: Given a digraph D, decide if there is a dicycle B in D and a cycle C in its underlying undirected graph such that . It turns out that the problem is polynomially solvable for digraphs with a constantly bounded number of transversal vertices (including cases where ). In the remaining case (allowing arbitrarily many transversal vertices) the problem is NP‐complete. In this article, we classify the complexity of the arc‐analog of this problem, where we ask for a dicycle B and a cycle C that are arc‐disjoint, but not necessarily vertex‐disjoint. We prove that the problem is polynomially solvable for strong digraphs and for digraphs with a constantly bounded number of transversal arcs (but possibly an unbounded number of transversal vertices). In the remaining case (allowing arbitrarily many transversal arcs) the problem is NP‐complete.
Testing Serial Crime Events for Randomness in Day‐of‐Week Patterns with Small Samples
Authors: Wheeler Andrew P.
Published: December 2015

This paper discusses exact tests for evaluating whether a series of offences are randomly distributed across days of the week for small sample sizes. The context is if an analyst has identified a series of related events, can the analyst determine if those events are randomly distributed with respect to the day‐of‐week given only a few offences? This paper develops exact reference distributions because the number of potential permutations is small, and this research finds that the likelihood ratioG‐test under realistic circumstances is quite powerful. Only three crimes need to occur on the same day of the week to reject the null. Several examples of using the test under realistic circumstances are illustrated; a series of thefts of catalytic converters where the exact dates are unknown, gang shootings, and arsons over a year. Copyright © 2015 John Wiley & Sons, Ltd.
Critical limits of the degree of compactness and soil penetration resistance for the soybean crop in N Brazil
Authors: Oliveira Pedro Daniel De , Sato Michel Keisuke , Lima Herdjania Veras de , Rodrigues Sueli , Silva Alvaro Pires da
Published: December 2015

In agricultural fields soil compaction is a major cause of physical degradation. Degree of compactness (DC) is a useful parameter for characterizing compaction and the response of crops for different soils. The objectives of this study were: (1) to identify the critical DC and PR values for soybean [Glycine max (L.) Merrill] using plant growth variables and (2) to verify the relationship between DC and PR, and assess which parameter is recommended for the evaluation of soil compaction. The study was conducted in a greenhouse in a completely randomized factorial design of 4 textures × 5 compaction levels for sandy loam and sandy clay loam soils, and 3 compaction levels for the clayey and very clayey soils. Soil samples were collected from the surface of a Xantic Kandiudox from the NE region of the State of Pará, Brazil. The DC was calculated from the maximum bulk density obtained by the Proctor test, and the PR curve was determined in undisturbed samples equilibrated in different matric potentials. The growth and development of the soybean was favored in the DC range of 80 to 85%, regardless of soil texture. The critical degree of compactness for the growth of soybean was around 98% regardless of soil texture, while the critical values for penetration resistance at field capacity varied according to soil texture and bulk density and were 28.2, 5.6, 3.5, and 5.2 MPa for the sandy loam, sand clay loam, clayey and very clayey soils, respectively. The root length was the plant growth variable most susceptible to soil compaction. Change in soil penetration resistance was poorly related with change in degree of compactness showing that one parameter cannot be replaced by the other. Because PR is quickly determined in field and have a direct relationship with plant growth, for the soils evaluated in this study we recommend the use of soil PR to assess the state of soil compaction.
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

To 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.
Achieving optimal SERS through enhanced experimental design
Authors: Fisk Heidi , Westley Chloe , Turner Nicholas J. , Goodacre Royston
Published: December 2015

One of the current limitations surrounding surface‐enhanced Raman scattering (SERS) is the perceived lack of reproducibility. SERS is indeed challenging, and for analyte detection, it is vital that the analyte interacts with the metal surface. However, as this is analyte dependent, there is not a single set of SERS conditions that are universal. This means that experimental optimisation for optimum SERS response is vital. Most researchers optimise one factor at a time, where a single parameter is altered first before going onto optimise the next. This is a very inefficient way of searching the experimental landscape. In this review, we explore the use of more powerful multivariate approaches to SERS experimental optimisation based on design of experiments and evolutionary computational methods. We particularly focus on colloidal‐based SERS rather than thin film preparations as a result of their popularity. © 2015 The Authors. Journal of Raman Spectroscopy published by John Wiley & Sons, Ltd.
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

BACKGROUND

The 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.

RESULTS

During 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.

CONCLUSION

In 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

BACKGROUND

Tomato 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.

RESULTS

The 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.

CONCLUSION

Pectin–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

BACKGROUND

A plastic composite support (PCS) bioreactor was implemented to evaluate the effects on isoflavone deglycosylation in black soymilk fermented by Rhizopus oligosporus NTU 5.

RESULTS

Evaluation 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%).

CONCLUSION

A 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

BACKGROUND

Fish 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.

RESULTS

Careful 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.

CONCLUSION

DTR was proposed as a reliable indicator for the early decrease of freshness until fish rejection. © 2015 Society of Chemical Industry
Gold‐functionalized stainless‐steel wire and tube for fiber‐in‐tube solid‐phase microextraction coupled to high‐performance liquid chromatography for the determination of polycyclic aromatic hydrocarbons
Authors: Bu Yanan , Feng Juanjuan , Sun Min , Zhou Changli , Luo Chuannan
Published: December 2015

A fiber‐in‐tube solid‐phase microextraction device based on a gold‐functionalized stainless‐steel wire and tube was developed and characterized by scanning electron microscopy and energy dispersive X‐ray spectroscopy. In combination with high‐performance liquid chromatography, it was evaluated using six polycyclic aromatic hydrocarbons as model analytes. Important parameters including sampling rate, sample volume, organic solvent content and desorption time were investigated. Under optimized conditions, an online analysis method was established. The linearity was in the range of 0.15–50 μg/L with correlation coefficients ranging from 0.9989 to 0.9999, and limits of detection ranged from 0.05 to 0.1 μg/L. The method was applied to determine model analytes in mosquito‐repellent incense ash and river water samples, with recoveries in the range of 85–120%.
BOOK REVIEW
Authors: Emlet Richard B.
Published: December 2015

BRUSCA, RICHARD C. and GARY J. BRUSCA. 2003. Invertebrates, 2nd edition. Sinauer Associates, Inc., Publishers. ISBN 0‐87893‐097‐3 (hardbound). xix + 936 p. US $109.95.
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

Following 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.
Damage‐inducible intragenic demethylation of the human TP53 tumor suppressor gene is associated with transcription from an alternative intronic promoter
Authors: Blackburn James , Roden Daniel L. , Ng Robert , Wu Jianmin , Bosman Alexis , Epstein Richard J.
Published: December 2015

Wild‐type TP53 exons 5–8 contain CpG dinucleotides that are prone to methylation‐dependent mutation during carcinogenesis, but the regulatory effects of methylation affecting these CpG sites are unclear. To clarify this, we first assessed site‐specific TP53 CpG methylation in normal and transformed cells. Both DNA damage and cell ageing were associated with site‐specific CpG demethylation in exon 5 accompanied by induction of a truncated TP53 isoform regulated by an adjacent intronic promoter (P2). We then synthesized novel synonymous TP53 alleles with divergent CpG content but stable encodement of the wild‐type polypeptide. Expression of CpG‐enriched TP53 constructs selectively reduced production of the full‐length transcript (P1), consistent with a causal relationship between intragenic demethylation and transcription. 450K methylation comparison of normal (TP53‐wildtype) and cancerous (TP53‐mutant) human cells and tissues revealed focal cancer‐associated declines in CpG methylation near the P1 transcription start site, accompanied by rises near the alternate exon 5 start site. These data confirm that site‐specific changes of intragenic TP53 CpG methylation are extrinsically inducible, and suggest that human cancer progression is mediated in part by dysregulation of damage‐inducible intragenic CpG demethylation that alters TP53 P1/P2 isoform expression. © 2015 The Authors. Molecular Carcinogenesis Published by Wiley Periodicals, Inc.
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

Background

Diagnostic 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.

Methods

We 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 Conclusion

Clinically 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

Scope

The 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 results

The 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.

Conclusion

C15:0 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

Aims

There 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.

Methods

A 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.

Results

Of 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%).

Conclusions

These 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

Two 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

Modern 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

Background and Objective

The 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.

Methods

We 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).

Results

We 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.

Conclusion

Exposure 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

A 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
Employing proteomics to unravel the molecular effects of antipsychotics and their role in schizophrenia
Authors: Cassoli Juliana S. , Guest Paul C. , Santana Aline G. , Martins‐de‐Souza Daniel
Published: December 2015

Schizophrenia is an incurable neuropsychiatric disorder managed mostly by treatment of the patients with antipsychotics. However, the efficacy of these drugs has remained only low to moderate despite intensive research efforts since the early 1950s when chlorpromazine, the first antipsychotic, was synthesized. In addition, antipsychotic treatment can produce often undesired severe side effects in the patients and addressing these remains a large unmet clinical need. One of the reasons for the low effectiveness of these drugs is the limited knowledge about the molecular mechanisms of schizophrenia, which impairs the development of new and more effective treatments. Recently, proteomic studies of clinical and preclinical samples have identified changes in the levels of specific proteins in response to antipsychotic treatment, which have converged on molecular pathways such as cell communication and signaling, inflammation and cellular growth, and maintenance. The findings of these studies are summarized and discussed in this review and we suggest that this provides validation of proteomics as a useful tool for mining drug mechanisms of action and potentially for pinpointing novel molecular targets that may enable development of more effective medications.
Complexity reduction of clinical samples for routine mass spectrometric analysis
Authors: Mesmin Cédric , van Oostrum Jan , Domon Bruno
Published: December 2015

The precise measurement of protein abundance levels in highly complex biological samples such as plasma remains challenging. The wide range of protein concentrations impairs the detection of low‐abundant species and the high number of peptide components to analyze results in interferences leading to erroneous quantitative results. The advances in MS instrumentation, with improved selectivity and sensitivity, partially address these issues, but sample preparation techniques remain the pivotal element to obtain robust routine mass spectrometric assays with a low LOD. A number of methodologies have been proposed and refined over the past two decades to reduce the range of protein concentrations and the number of peptide components. Whereas most of the methods have proven their utility for discovery studies, only a few are actually applicable to routine quantitative studies. In this account, common protein‐ and peptide‐based fractionation methods are discussed, and illustrated with practical examples, with a focus on methods suited for clinical samples scheduled for biomarker validation assays and subsequent routine clinical mass spectrometric analyses.
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

We 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.
Contact‐assisted protein structure modeling by global optimization in CASP11
Authors: Joo Keehyoung , Joung InSuk , Cheng Qianyi , Lee Sung Jong , Lee Jooyoung
Published: December 2015

We have applied the conformational space annealing method to the contact‐assisted protein structure modeling in CASP11. For Tp targets, where predicted residue–residue contact information was provided, the contact energy term in the form of the Lorentzian function was implemented together with the physical energy terms used in our template‐free modeling of proteins. Although we observed some structural improvement of Tp models over the models predicted without the Tp information, the improvement was not substantial on average. This is partly due to the inaccuracy of the provided contact information, where only about 18% of it was correct. For Ts targets, where the information of ambiguous NOE (Nuclear Overhauser Effect) restraints was provided, we formulated the modeling in terms of the two‐tier optimization problem, which covers: (1) the assignment of NOE peaks and (2) the three‐dimensional (3D) model generation based on the assigned NOEs. Although solving the problem in a direct manner appears to be intractable at first glance, we demonstrate through CASP11 that remarkably accurate protein 3D modeling is possible by brute force optimization of a relevant energy function. For 19 Ts targets of the average size of 224 residues, generated protein models were of about 3.6 Å
atom accuracy. Even greater structural improvement was observed when additional Tc contact information was provided. For 20 out of the total 24 Tc targets, we were able to generate protein structures which were better than the best model from the rest of the CASP11 groups in terms of GDT‐TS. Proteins 2016; 84(Suppl 1):189–199. © 2015 Wiley Periodicals, Inc.
A novel lipid transfer protein from the dill Anethum graveolens L.: isolation, structure, heterologous expression, and functional characteristics
Authors: Melnikova Daria N. , Mineev Konstantin S. , Finkina Ekaterina I. , Arseniev Alexander S. , Ovchinnikova Tatiana V.
Published: December 2015

A novel lipid transfer protein, designated as Ag‐LTP, was isolated from aerial parts of the dill Anethum graveolens L. Structural, antimicrobial, and lipid binding properties of the protein were studied. Complete amino acid sequence of Ag‐LTP was determined. The protein has molecular mass of 9524.4 Da, consists of 93 amino acid residues including eight cysteines forming four disulfide bonds. The recombinant Ag‐LTP was overexpressed in Escherichia coli and purified. NMR investigation shows that the Ag‐LTP spatial structure contains four α‐helices, forming the internal hydrophobic cavity, and a long C‐terminal tail. The measured volume of the Ag‐LTP hydrophobic cavity is equal to ~800 A3, which is much larger than those of other plant LTP1s. Ag‐LTP has weak antifungal activity and unpronounced lipid binding specificity but effectively binds plant hormone jasmonic acid. Our results afford further molecular insight into biological functions of LTP in plants. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.
Resveratrol Pretreatment Affects CYP2E1 Activity of Chlorzoxazone in Healthy Human Volunteers
Authors: Bedada Satish Kumar , Neerati Prasad
Published: December 2015

The purpose of the present study was to investigate the effect of resveratrol (RSV) pretreatment on CYP2E1 enzyme activity and pharmacokinetics of chlorzoxazone (CHZ) in healthy human volunteers. The open‐label, two period, sequential study was conducted in 12 healthy human volunteers. A single dose of RSV 500 mg was administered once daily for 10 days during treatment phase. A single dose of CHZ 250 mg was administered during control and after treatment phases under fasting conditions. The blood samples were collected after CHZ dosing at predetermined time intervals and analyzed by HPLC. RSV pretreatment significantly enhanced the maximum plasma concentration (Cmax), area under the curve (AUC) and half life (T1/2) and significantly decreased elimination rate constant (Kel), apparent oral clearance (CL/F) and apparent volume of distribution (Vd/F) of CHZ as compared to that of control. In addition, RSV pretreatment significantly decreased the metabolite to parent (6‐OHCHZ/CHZ) ratios of Cmax, AUC and T1/2 and significantly increased the Kel ratio of 6‐OHCHZ/CHZ, which indicated the reduced formation of CHZ to 6‐OHCHZ. The results suggest that the altered CYP2E1 enzyme activity and pharmacokinetics of CHZ might be attributed to RSV mediated inhibition of CYP2E1 enzyme. Thus, there is a potential pharmacokinetic interaction between RSV and CHZ. The inhibition of CYP2E1 by RSV may provide a novel approach for minimizing the hepatotoxicity of ethanol. Copyright © 2015 John Wiley & Sons, Ltd.
Investigations in the infra‐red. I: The absorption and reflection spectra of KHF2, KDF2 and RbHF2 in relation to the constitution of the bifluoride ion
Authors: Ketelaar J. A. A.
Published: December 2015

An arrangement is described for the analysis of the infra‐red spectrum using a prism spectrometer and thermo‐electric radiation receivers. Experimental details are given especially of a self‐constructed telluriumconstantan thermo‐element. With this arrangement the absorption and reflection spectra were investigated of crystals of KHF2, KDF2 and of RbHF2 in the quartz and in the rock‐salt region from 1‐17 μ. The spectrum of RbHF2 is similar to that of the isomorphous potassium compound except for a small shift of a few cm−1 toward lower frequencies. Two fundamental frequencies are observed for KHF2 at 1222 cm−1 (8.18 μ) and at 1450 cm−1 (6.90 μ) in absorption, and at 1238 cm−1 (8.08 μ) and at 1490 cm−1 (7.08 μ) in reflection. For KDF2 the corresponding frequencies are 891 cm−1 and 1046 cm−1 in reflection.

It is shown, that both frequencies belong to the fundamental asymmetric valence frequency ν3 (the “hydrogen” frequency) of the bifluoride ion. It is further shown, that this doubling of the hydrogen frequency is due to the presence of a double minimum in the potential curve for the hydrogen atom, analogous to the doubling observed in the parallel bands of the NH3‐molecule. The phenomenon of protonic resonance is discussed. The distance between the two levels of the zero pair for KHF2 is estimated to be 25 cm−1, that for the first pair is equal to 185 cm−1. A potential curve is drawn, and the height of the potential hump separating the two minima is estimated as 2570 cm−1 or 7.3 kcal/mol. The analysis of the large number of bands observed shows that all are due to the double “hydrogen” frequency ν3 and higher harmonics in combination with the inactive symmetrical frequency ν1 at 580‐550 cm−1.

The stationary state of the HF2−group is a resonance hybride between the two equivalent asymmetric structures. The resonance consists in the migration of the hydrogen ion between the two minima of potential energy, one near each of the two fluorine atoms. However the resonance energy is negligible compared with the total bond energy of the HF2‐group.
Recherches sur L'extinction des Flammes Etude Spéciale du Point de vue de L'effet Antioxygène
Authors: le Bras Jean
Published: December 2015

En utilisant un appareil basé sur le principe du courant gazeux, on a étudié l'extinction de flammes de combustibles divers à l'aide de trois sortes d'extincteurs: l'azote, le bromure d'éthyle et le térachlorure de carbone. Les combustibles sur lesquels ont porté les essais ont été: l'hydrogène, le méthane, l'oxyde de carbone, le gaz d'éclairage, le benzène, le toluène, le xylène, les alcools méthylique, éthylique, propylique et butylique, enfin le sulfure de carbone. Dans des expériences spéciales, on a cherché à élucider les mécanismes extincteurs; on a pu montrer ainsi que le bromure d'éthyle agit comme étouffeur, c'est‐à‐dire d'une façon tout à fait analogue à celle d'une vapeur combustible. Mais le tétrachlorure de carbone se comporte de manières très différentes selon la nature de la flamme sur laquelle il agit et son effet antioxygène est toujours plus ou moins masqué.

En outre, l'appareillage permet de déterminer aisément les limites supérieure et inférieure d'inflammabilité des combustibles; certains des chiffres indiqués constituent des résultats nouveaux.

On a constaté enfin qu'il était possible d'appliquer une loi, analogue à celle de Le Châtelier, pour calculer les taux extincteurs envers des mélanges de combustibles.
Neighbouring group participation in the photolysis of aryl esters of unsaturated 1,4‐dicarboxylic acids
Authors: Alvaro M. , Garcia H. , Primo J. , Miranda M. A.
Published: December 2015

Photolysis of the aryl maleates la,b produces homolysis of the carbonyl‐aryloxy bond, followed by internal addition of the acyl radical to the neighbouring carbonyl group, giving the unexpected products 3 or 4; by contrast the aryl fumarates 2a,b follow the “normal” photo‐Fries pathway.
Synthesis of racemic myo‐inositol 1,3,4‐trisphosphate via a phosphite‐triester approach
Authors: Dreef C. E. , van der Marel G. A. , van Boom J. H.
Published: December 2015

Phosphitylation of (±)‐2,4,5‐tri‐0‐benzyl‐myo‐Inositol with bis(2‐cyanoethyl) chlorophosphine gave, after oxidation followed by basic hydrolysis and subsequently hydrogenolysis, (±)‐myo‐Inositol 1,3,4‐trisphosphate.