bluuebunny/crossref_metadata_2025 huggingface dataset:
Field degradation of aminopyralid and clopyralid and microbial community response to application in Alaskan soils
Authors: Tomco Patrick L. , Duddleston Khrystyne N. , Schultz Emily Jo , Hagedorn Birgit , Stevenson Timothy J. , Seefeldt Steven S.
Published: August 2015

High-latitude regions experience unique conditions that affect the degradation rate of agrochemicals in the environment. In the present study, data collected from 2 field sites in Alaska, USA (Palmer and Delta) were used to generate a kinetic model for aminopyralid and clopyralid degradation and to describe the microbial community response to herbicide exposure. Field plots were sprayed with herbicides and sampled over the summer of 2013. Quantification was performed via liquid chromatrography/tandem mass spectrometry, and microbial diversity was assessed via next-generation sequencing of bacterial 16S ribosomal ribonucleic acid (rRNA) genes. Both compounds degraded rapidly via pseudo-first–order degradation kinetics between 0 d and 28 d (t1/2 = 9.1–23.0 d), and then degradation slowed thereafter through 90 d. Aminopyralid concentration was 0.048 μg/g to 0.120 μg/g at 90 d post application, whereas clopyralid degraded rapidly at the Palmer site but was recovered in Delta soil at a concentraction of 0.046 μg/g. Microbial community diversity was moderately impacted by herbicide treatment, with the effect more pronounced at Delta. These data predict reductions in crop yield when sensitive plants (potatoes, tomatoes, marigolds, etc.) are rotated onto treated fields. Agricultural operations in high-latitude regions, both commercial and residential, rely heavily on cultivation of such crops and care must be taken when rotating. Environ Toxicol Chem 2016;35:485–493. © 2015 SETAC
Monetary Aggregates to Improve Early Output Gap Estimates in the Euro Area: An Empirical Assessment
Authors: Boysen‐Hogrefe Jens
Published: August 2015

Output gap estimates at the current edge are subject to severe revisions. This study analyzes whether monetary aggregates can be used to improve the reliability of early output gap estimates as proposed by several theoretical models. A real‐time experiment shows that real M1 can improve output gap estimates for euro area data. For many periods the cyclical component of real M1 shows good results, while a forecasting strategy based on projecting GDP series seems to be more robust and provides superior results during the Great Recession. Broader monetary aggregates provide no superior information for output gap estimates. Copyright © 2015 John Wiley & Sons, Ltd.
Expression profile of COL2A1 and the pseudogene SLC6A10P predicts tumor recurrence in high‐grade serous ovarian cancer
Authors: Ganapathi Mahrukh K. , Jones Wendell D. , Sehouli Jalid , Michener Chad M. , Braicu Ioana E. , Norris Eric J. , Biscotti Charles V. , Vaziri Susan A.J. , Ganapathi Ram N.
Published: August 2015

Tumor recurrence, following initial response to adjuvant chemotherapy, is a major problem in women with high‐grade serous ovarian cancer (HGSOC). Microarray analysis of primary tumors has identified genes that may be useful in risk stratification/overall survival, but are of limited value in predicting the >70% rate for tumor recurrence. In this study, we performed RNA‐Seq analysis of primary and recurrent HGSOC to first identify unique differentially expressed genes. From this dataset, we selected 21 archetypical coding genes and one noncoding RNA, based on statistically significant differences in their expression profile between tumors, for validation by qPCR in a larger cohort of 110 ovarian tumors (71 primary and 39 recurrent) and for testing association of specific genes with time‐to‐recurrence (TTR). Kaplan–Meier tests revealed that high expression of collagen type II, alpha 1 (COL2A1) was associated with delayed TTR (HR = 0.47, 95% CI: 0.27–0.82, p = 0.008), whereas low expression of the pseudogene, solute carrier family 6 member 10 (SLC6A10P), was associated with longer TTR (HR = 0.53, 95% CI: 0.30–0.93, p = 0.027). Notably, TTR was significantly delayed for tumors that simultaneously highly expressed COL2A1 and lowly expressed SLC6A10P (HR = 0.21, 95% CI: 0.082–0.54, p = 0.0011), an estimated median of 95 months as compared to an estimated median of 16 months for subjects expressing other levels of COL2A1 and SLC6A10P. Thus, evaluating expression levels of COL2A1 and SLC6A10P at primary surgery could be beneficial for clinically managing recurrence of HGSOC.
Is cell culture a risky business? Risk analysis based on scientist survey data
Authors: Shannon Mark , Capes‐Davis Amanda , Eggington Elaine , Georghiou Ronnie , Huschtscha Lily I. , Moy Elsa , Power Melinda , Reddel Roger R. , Arthur Jonathan W.
Published: August 2015

Cell culture is a technique that requires vigilance from the researcher. Common cell culture problems, including contamination with microorganisms or cells from other cultures, can place the reliability and reproducibility of cell culture work at risk. Here we use survey data, contributed by research scientists based in Australia and New Zealand, to assess common cell culture risks and how these risks are managed in practice. Respondents show that sharing of cell lines between laboratories continues to be widespread. Arrangements for mycoplasma and authentication testing are increasingly in place, although scientists are often uncertain how to perform authentication testing. Additional risks are identified for preparation of frozen stocks, storage and shipping.
In vitro M‐like cells genesis through a tissue‐engineered triple‐culture intestinal model
Authors: Araújo Francisca , Pereira Carla , Costa Joana , Barrias Cristina , Granja Pedro L. , Sarmento Bruno
Published: August 2015

Although fewer in number, M‐cells are considered antigen sampling cells, acting as a gateway for antigens from the gut lumen and presenting an impressive aptitude for particle transcytosis. These features make M‐cells attractive targets for oral drug delivery studies, but this has been poorly explored. New and reproducible tissue‐like in vitro models for studying intestinal sampling and permeability mechanisms are needed. The combination of different cell players in such models offers improved microenvironments with higher physiologic relevance. Here, a tissue‐engineered model was established, by co‐culturing Caco‐2 absorptive cells, HT29‐MTX mucus‐producing cells and Raji B lymphocytes. After 3 weeks of cell co‐culture, the presence of M‐like cells was evidenced by the loss of brush‐border organization, detected by the lack of microvilli. The triple‐culture model showed to be efficient for insulin transport, a process that was influenced by the tightness of junctions between epithelial cells and the presence of mucus and M‐like cells. Ultimately, the proposed tissue‐engineered model provides a more complete and reliable tool to perform drug permeability tests, as compared to traditional models, and may also find applicability as an in vitro system to study transdifferentiation mechanisms of M cells. © 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater 104B:782–788, 2016.
A New Practical Route to ZSM‐5 Nanoparticles and Optimization of Synthetic Parameters through D‐optimal Design of Experiments
Authors: Soltanali Saeed , Halladj Rouein , Rashidi Alimorad , Bazmi Mansour , Khodabakhshi Saeed
Published: August 2015

A D‐optimal experimental design with three levels of SiO2/Al2O3, template/SiO2, H2O/SiO2, Na2O/SiO2 and TPABr/TPAOH ratio parameters has been used to optimize the experimental parameters by an analysis of variances (ANOVA). The effects of these ratios in the initial synthetic mixture on the size of the ZSM‐5 zeolite nanoparticles have been studied. XRD and FE‐SEM analyses were used to characterize synthetic samples. Fischer test results showed that H2O/SiO2 and TPABr/TPAOH ratios are the most and least effective parameters, respectively, in the range studied. The most important two‐way interaction variables were the interaction of template/SiO2 and TPABr/TPAOH molar ratios. The average particle size was in the 34–79 nm range. Furthermore, a mathematical model for the synthesis of ZSM‐5 zeolite nanoparticles was derived using experimental results. The optimized gel composition is as follows: SiO2/Al2O3=91.20, template/SiO2=0.16, H2O/SiO2=40.42, Na2O/SiO2=0.0147 and TPABr/TPAOH=0.
Diorganotin(IV) Complexes with Monohydrate Disodium Salt of Iminodiacetic Acid: Synthesis, Characterization, Crystal Structure and Biological Activities
Authors: Hussain Shabbir , Ali Saqib , Shahzadi Saira , Rizzoli Corrado , Shahid Muhammad
Published: August 2015

Diorganotin(IV) derivatives have been synthesized by the reaction of R2SnL2 (R=n‐Bu 1, Ph 2) with monohydrate disodium salt of iminodiacetic acid (Na2L) in 1 : 1 M/L ratio under reflux conditions. The compounds have been characterized by FT‐IR, NMR (1H and 13C) spectoscopy, electron ionization mass spectrometry (EIMS), thermogravimetric analyses (TGA) and single crystal XRD. FTIR data indicates a mono‐dentate binding mode of the carboxylic acid group as well as participation of the amino nitrogen and aqua oxygen in coordination with organotin(IV) moieties. NMR data demonstrates a tetra‐coordinated environment around tin(IV) in solution. Mass spectrometric and thermogravimetric analyses verify the close similarities between the molecular structures of both complexes. The thermal stability of diphenyltin(IV) derivative (2) was found slightly higher than that of the free ligand (Na2L). Single crystal X‐ray analysis of the complex 1 have shown a hexa‐coordinated geometry around Sn(IV) with trans configuration. There are evidences for the existence of intermolecular hydrogen bonding in the structure of the complexes. The products displayed significant antibacterial and antifungal activities in contrast to the biologically inactive ligand precursor. However, the hemolytic cytoxicity of the complexes was comparatively high than the free ligand.
Downregulation of Long Noncoding RNA Meg3 Affects Insulin Synthesis and Secretion in Mouse Pancreatic Beta Cells
Authors: You LiangHui , Wang Ning , Yin DanDan , Wang LinTao , Jin FeiYan , Zhu YaNan , Yuan QingXin , De Wei
Published: August 2015

Increasing evidence indicates that long noncoding RNAs (lncRNAs) are involved in diverse biological process. Mouse maternal expressed gene 3 (Meg3) is an imprinted gene and essential for development. Here, we explored the relationship between Meg3 and the function of mouse beta cells in vitro and in vivo. Real‐time PCR analyses revealed that Meg3 was more abundantly expressed in Balb/c mouse islets than exocrine glands. Moreover, the expression of Meg3 in islets was decreased in T1DM (NOD female mice) and T2DM (db/db mice) models. Meg3 expression was modulated dynamically by glucose in Min6 cells and isolated mouse islets. The function role of Meg3 was investigated in Min6 cells and normal mouse by knockdown of Meg3 using small interfering RNA. After suppression of Meg3 expression in vitro, insulin synthesis and secretion were impaired and the rate of beta cells apoptosis was increased. Moreover, knockdown of Meg3 in vivo led to the impaired glucose tolerance and decreased insulin secretion, consisted with the reduction of insulin positive cells areas by immunochemistry assays. Notably, islets from Meg3 interference groups showed significant decrease of Pdx‐1 and MafA expression in mRNA and protein levels. These results indicate that Meg3 may function as a new regulator of maintaining beta cells identity via affecting insulin production and cell apoptosis. J. Cell. Physiol. 231: 852–862, 2016. © 2015 Wiley Periodicals, Inc.
Identification of artistic materials in paintings and drawings by Raman spectroscopy: some challenges and future outlook
Authors: Centeno Silvia A.
Published: August 2015

The aim of the present article is to highlight publications that illustrate some advances in the application of Raman spectroscopy to investigate materials typically observed in manuscripts, drawings, prints, and paintings in museums' and cultural institutions' collections, and to discuss some of the challenges and future prospects. Copyright © 2015 John Wiley & Sons, Ltd.
A reversed‐phase compatible thin‐layer chromatography autography for the detection of acetylcholinesterase inhibitors
Authors: Ramallo I. Ayelen , García Paula , Furlan Ricardo L. E.
Published: August 2015

A dual readout autographic assay to detect acetylcholinesterase inhibitors present in complex matrices adsorbed on reversed‐phase or normal‐phase thin‐layer chromatography plates is described. Enzyme gel entrapment with an amphiphilic copolymer was used for assay development. The effects of substrate and enzyme concentrations, pH, incubation time, and incubation temperature on the sensitivity and the detection limit of the assay were evaluated. Experimental design and response surface methodology were used to optimize conditions with a minimum number of experiments. The assay allowed the detection of 0.01% w/w of physostigmine in both a spiked Sonchus oleraceus L. extract chromatographed on normal phase and a spiked Pimenta racemosa (Mill.) J.W. Moore leaf essential oil chromatographed on reversed phase. Finally, the reversed‐phase thin‐layer chromatography assay was applied to reveal the presence of an inhibitor in the Cymbopogon citratus (DC.) Stapf essential oil. The developed assay is able to detect acetylcholinesterase inhibitors present in complex matrixes that were chromatographed in normal phase or reversed‐phase thin‐layer chromatography. The detection limit for physostigmine on both normal and reversed phase was of 1×10−4 μg. The results can be read by a change in color and/or a change in fluorescence.
One‐Step In Situ Synthesis of Polyamide Microcapsules With Inorganic Payload and Their Transformation into Responsive Thermoplastic Composite Materials
Authors: Dencheva Nadya , Denchev Zlatan , Lanceros‐Méndez Senentxu , Ezquerra Sanz Tiberio
Published: August 2015

Well‐dispersed loads of powdered metals, metal oxides, several carbon allotropes, or nanoclays are incorporated into polyamide 6 microcapsules (PAMC) via a one‐step in situ fabrication technique. It is based on activated anionic polymerization (AAP) of ϵ‐caprolactam in a hydrocarbon solvent performed in the presence of the respective micro‐ or nanosized loads. The forming PAMC are with controllable shape, size and load content. The results obtained show that the melt processing of PAMC is a facile method to fabricate thermoplastic hybrids with high mechanical resistance and tailored electro‐magnetic characteristics. This novel concept requires low polymerization temperatures, no functionalization or compatibilization of the loads and is scalable for industrial production levels.
Comparison of Loading Efficiency between Hyperbranched Polymers and Cross‐Linked Nanogels at Various Branching Densities
Authors: Graff Robert W. , Shi Yi , Wang Xiaofeng , Gao Haifeng
Published: August 2015

The effect of branching point structures and densities is studied between azido‐containing hyperbranched polymers and cross‐linked nanogels on their loading efficiency of alkynyl‐containing dendron molecules. Hyperbranched polymers that contained “T”‐shaped branching linkage from which three chains radiated out and cross‐linked nanogels that contained “X”‐shaped branching linkage with four radiating chains are synthesized in microemulsion using either atom transfer radical polymerization (ATRP) or conventional radical polymerization (RP) technique. Both polymers have similar density of azido groups in the structure and exhibit similar hydrodynamic diameter in latexes before purification. Subsequent copper‐catalyzed azide–alkyne cycloaddition reactions between these polymers and alkynyl‐containing dendrons in various sizes (G1–G3) demonstrate an order of dendron loading efficiencies (i.e., final conversion of alkynyl‐containing dendron) as hyperbranched polymers > nanogels synthesized by ATRP > nanogels synthesized by RP. Decreasing the branching density or using smaller dendron molecules increases the click efficiency of both polymers. When G2 dendrons with a molecular weight of 627 Da are used to click with the hyperbranched polymers composed of 100% inimer, a maximum loading efficiency of G2 in the loaded hyperbranched polymer is 58% of G2 by weight. These results represent the first comparison between hyperbranched polymers and cross‐linked nanogels to explore the effect of branching structures on their loading efficiencies.

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The Significance and Therapeutic Potential of GATA3 Expression and Mutation in Breast Cancer: A Systematic Review
Authors: Du Feng , Yuan Peng , Wang Teng , Zhao Jiuda , Zhao Zitong , Luo Yang , Xu Binghe
Published: August 2015

GATA3 is a critical transcription factor in the development of various human systems. The notion that GATA3 expression is required for the differentiation and maintenance of normal breast tissue has been well established. Recently, GATA3 is found to actively participate in the multistep process leading breast cancer pathogenesis, including tumorigenesis, tumor differentiation, epithelial mesenchymal transition, and metastasis through regulation of various target genes. On the other hand, several studies have raised questions and highlighted the role of GATA3‐low or GATA3‐negative cells during the malignant development of breast cancer. In addition to gene expression, GATA3 mutations provide another dimension of complexity. As one of the most frequently mutated genes in breast cancer, GATA3 mutations may have an effect on DNA‐binding ability, protein production, and transactivation activity. Recognition of the multiple function of GATA3 in breast cancer will serve to deepen our understanding of the nature of this disease and develop novel therapeutic approaches.
Modeling diseases with latency and nonlinear incidence rates: global dynamics of a multi‐group model
Authors: Wang Jinliang , Liu Xianning
Published: August 2015

In this paper, we perform global stability analysis of a multi‐group SEIR epidemic model in which we can consider the heterogeneity of host population and the effects of latency and nonlinear incidence rates. For a simpler version that assumes an identical natural death rate for all groups, and with a gamma distribution for the latency, the basic reproduction number is defined by the theory of the next generation operator and proved to be a sharp threshold determining whether or not disease spread. Under certain assumptions, the disease‐free equilibrium is globally asymptotically stable if R0≤1 and there exists a unique endemic equilibrium which is globally asymptotically stable if R0>1. The proofs of global stability of equilibria exploit a matrix‐theoretic method using Perron eigenvetor, a graph‐theoretic method based on Kirchhoff's matrix tree theorem and Lyapunov functionals. Copyright © 2015 John Wiley & Sons, Ltd.
Global existence and blowup of solutions for nonlinear coupled wave equations with viscoelastic terms
Authors: Hao Jianghao , Cai Li
Published: August 2015

In this paper, we study a system of nonlinear coupled wave equations with damping, source, and nonlinear strain terms. We obtain several results concerning local existence, global existence, and finite time blow‐up property with positive initial energy by using Galerkin method and energy method, respectively. Copyright © 2015 John Wiley & Sons, Ltd.
Resveratrol selectively induces apoptosis in malignant cells with the JAK2V617F mutation by inhibiting the JAK2 pathway
Authors: Trung Ly Quoc , Espinoza J. Luis , An Dao T. , Viet Nguyen Hoang , Shimoda Kazuya , Nakao Shinji
Published: August 2015

Scope

Resveratrol is a natural occurring polyphenol with several health promoting activities, including anticancer potential. Here, we analyzed the cytotoxic effects of resveratrol against malignant cells characterized by aberrant activation of the Janus kinase 2 (JAK2).

Methods and results

Cell‐cycle analysis, proliferation, apoptosis, and Western blotting assays were performed to study the effect of resveratrol on malignant cells exhibiting an excessive activation of the JAK2 pathway secondary to the JAK2V617F mutation. Resveratrol inhibited proliferation and induced apoptosis in JAK2V617F mutant tumor cells and its selectivity was 1.5–6.9 times greater than that observed in other tumor cells without the JAK2V617F mutation. In addition, resveratrol inhibited the phosphorylation of JAK1, JAK2, and Tyk2 and their downstream mediators, including STAT3 and STAT5. In primary cultures, resveratrol treatment inhibited erythroid progenitor colony formation in blood samples obtained from JAK2V617F polycythemia vera patients. Moreover, resveratrol synergized with the selective JAK2 inhibitor ruxolitinib, eliminating tumor cells with the JAK2 mutation.

Conclusion

Resveratrol may have therapeutic potential against myeloproliferative neoplasms associated with the aberrant activation of the JAK2 pathway.
Changes in the human plasma and urinary metabolome associated with acute dietary exposure to sucrose and the identification of potential biomarkers of sucrose intake
Authors: Beckmann Manfred , Joosen Annemiek M. , Clarke Michelle M. , Mugridge Owen , Frost Gary , Engel Barbara , Taillart Kathleen , Lloyd Amanda J. , Draper John , Lodge John K.
Published: August 2015

Scope

The intake of sucrose is of public health concern but limited information is available on the metabolic effects of short‐term exposure. Our aim was to use metabolomics to investigate the metabolic impact of acute sucrose exposure.

Methods and results

We performed a randomized, parallel, single‐dose feeding study on healthy females (n = 90, aged 29.9 ± 4.7 years, BMI 23.3 ± 2.5 kg/m2) consuming either 0, 50, or 100 g sucrose in 500 mL water. Blood and urine samples were taken before and 24 h post sucrose intake. Urine and plasma samples underwent detailed metabolite profiling analysis using established protocols. Flow‐injection electrospray MS fingerprinting analysis showed that 3 h after intake was the most informative time point in urine and plasma and out of 120 explanatory signals, highlighted 16 major metabolite signals in urine and 25 metabolite signals in plasma that were discriminatory and correlated with sucrose intake over time. The main confirmed metabolites positively correlated with intake were sucrose, fructose, and erythronic acid, while those negatively correlating with intake included fatty acids and derivatives, acyl‐carnitines, and ketone bodies. GC‐TOF‐MS profiling analysis confirmed the fingerprinting data.

Conclusion

Acute exposure to sucrose identified a number of metabolites correlated with sucrose intake and several compounds attributed to metabolic fasting.
Which Factors Influence Self‐Efficacy in Patients with Chronic Inflammatory Polyarthritis?
Authors: Grønning Kjersti , Bratås Ola , Steinsbekk Aslak
Published: August 2015

Objectives

Patients with rheumatoid arthritis (RA), psoriatic arthritis (PsA) or unspecified polyarthritis (UA) deal with several symptoms such as joint stiffness, pain, physical limitations and fatigue. Self‐efficacy is about patients’ beliefs and abilities to handle the symptoms and implications of having arthritis. Patients’ self‐efficacy is also a phenomenon that nurses may affect through patient education. Therefore, the aim of the present study was to investigate the factors that predict self‐efficacy in patients with chronic inflammatory polyarthritis.

Methods

The participants (n = 132) were recruited from St Olavs University Hospital in central Norway from 2008 to 2010, and consisted of adult patients with RA, PsA or UA. We performed secondary analyses on data collected in a randomized controlled trial studying the long‐term effects of nurse‐led patient education. We carried out bivariate and multivariate linear regression analyses. The predictor variables consisted of baseline data on demographics, disease characteristics (diagnosis, disease duration, disease activity, use of disease‐modifying anti‐rheumatic drugs, pain and tiredness) and psychological variables (well‐being, psychological distress and patient activation). The dependent variables were self‐efficacy over other symptoms and self‐efficacy over for pain after one year.

Results

The analyses showed that female gender and patient activation predicted higher self‐efficacy over other symptoms, whereas female gender and better well‐being predicted higher self‐efficacy over pain.

Conclusion

To strengthen arthritis patients’ self‐efficacy, nurses need to focus on patients’ well‐being and activation. Nurses also need to be aware of possible gender differences regarding patients’ self‐efficacy. Copyright © 2015 John Wiley & Sons, Ltd.
Optimizing testing methods and collection of reference data for differentiating critical illness polyneuropathy from critical illness MYOPATHIES
Authors: Marrero Humberto Gonzalez , Stålberg Erik V.
Published: August 2015

Introduction: In severe acute quadriplegic myopathy in intensive care unit (ICU) patients, muscle fibers are electrically inexcitable; in critical illness polyneuropathy, the excitability remains normal. Conventional electrodiagnostic methods do not provide the means to adequately differentiate between them. In this study we aimed to further optimize the methodology for the study of critically ill ICU patients and to create a reference database in healthy controls. Methods: Different electrophysiologic protocols were tested to find sufficiently robust and reproducible techniques for clinical diagnostic applications. Results: Many parameters show large test–retest variability within the same healthy subject. Reference values have been collected and described as a basis for studies of weakness in critical illness. Conclusions: Using the ratio of neCMAP/dmCMAP (response from nerve and direct muscle stimulation), refractory period, and stimulus–response curves may optimize the electrodiagnostic differentiation of patients with critical illness myopathy from those with critical illness polyneuropathy. Muscle Nerve 53: 555–563, 2016
Single and competitive protein adsorption on polymeric surfaces
Authors: Vijaya Bhaskar Thanga Bhuvanesh , Roch Toralf , Romero Oscar , Ma Nan , Kratz Karl , Lendlein Andreas
Published: August 2015

The biological response to material surfaces is often influenced by protein layers formed at the bio‐interface. Understanding this protein layer is of paramount importance for biomedical materials and cell culture devices, which often require protein coating for optimal cell growth. An insert system fitting exactly into standard tissue culture plates was developed and can be used for biological investigations without the influence of the cell culture material. Inserts prepared from polystyrene (PS), polycarbonate (PC), poly(styrene‐co‐acrylonitrile) (PSAN) and poly(ether imide) (PEI) exhibit a similar surface roughness and wettability so that only the chemistry is varied. Previously, stem cell adhesion responses were found to be different for these inserts, possibly because of their different protein adsorption profiles. This work investigated if the surface functional groups of these inserts influence their protein binding ability. Single and competitive adsorption of two most abundant blood proteins, human serum albumin (HSA) and immunoglobulin G (IgG) on these polymers was investigated by labeling both proteins with different near‐infrared (IR) dyes. PEI showed the highest protein adsorption propensity in single and competitive adsorption of IgG and HSA while PS exhibited the least adsorption capability, whereas PSAN and PC showed an intermediate protein adsorption profile. Chemical inertness of PS could be the reason for this low protein binding ability and limited cell growth. Conclusively, a novel method to efficiently detect protein adsorption on polymer surfaces was established, and using this method the high relevance of the chemical composition of polymeric substrates on their protein adsorption profile could be proven. Copyright © 2015 John Wiley & Sons, Ltd.
Effects of the interaction between siloxane hydrolysate and PANI on the properties of PANI/SiO2 hybrid materials
Authors: Han Yuanyuan , Yu Qingjie , Xu Jianming , Liu Jie , Yin Yongqiang , Li Baoxia
Published: August 2015

PANI/SiO2 Hybrids were synthesized via a sol‐gel process using tetramethoxysilane (TMOS), γ‐glycidoxypropyltrimethoxysilane (GPTMS), and 3‐(trimethoxysily1)propyl methacrylate (MSMA) as precursors, respectively. The effect of the interaction between siloxane hydrolysate and PANI on the microstructure and properties of the PANI/SiO2 Hybrid Materials was studied using scanning electron microscopy, Fourier‐transform infrared, UV–vis, 1H NMR, thermo gravimetric analysis, and potentiodynamic polarization analysis. Experiment results demonstrated that, an appropriate interaction between siloxane hydrolysate and PANI is useful to achieve a homogeneous and stable hybrid. The weak interaction between silanols and PANI will cause the phase separation between siloxane hydrolysate and PANI, whereas the strong interaction may lead to the formation of bulk materials and precipitation. In comparison with TMOS and MSMA, more hydrogen bonds are formed in the PANI/SiO2 hybrid materials using GPTMS as precursor, which make it have a homogeneous and smooth surface without detectable cracks and present excellent corrosion protection properties. POLYM. COMPOS., 38:657–662, 2017. © 2015 Society of Plastics Engineers
Graphene‐containing ordered mesoporous carbons synthesized by one‐pot aqueous route and its electrochemical performance
Authors: Qiu Jielong , Wang Yi , Wu Fangjun , Liu Wei , Zhang Shuting
Published: August 2015

Graphene‐containing ordered mesoporous carbons (GOMCs) with low inner resistance, well‐defined mesoporous, and high specific surface area was prepared via a one‐pot aqueous route, followed by carbonization in nitrogen atmosphere. A sandwich‐like microstructure was built by a cooperative self‐assembly reaction among graphene oxide (GO) sheets, resorcinol–hexamethylenetetramine (HMTA) aqueous solution and amphiphilic triblock copolymer. By adjusting the ratio of GO and the soft template F127 in the precursor mixture, carbons with a controllable pore structure and a maximum surface area of 1,195 m2/g has been prepared. The supercapacitor based on GOMC‐2.0‐F1.5 shows a high electric conductivity (no obvious IR drop was found during charge/discharge process), high specific capacitance (209 F/g), and excellent cycling stability (no capacitance loss was found after 5,000 cycles). POLYM. COMPOS., 38:1438–1446, 2017. © 2015 Society of Plastics Engineers
Weak conservation of structural features in the interfaces of homologous transient protein–protein complexes
Authors: Sudha Govindarajan , Singh Prashant , Swapna Lakshmipuram S. , Srinivasan Narayanaswamy
Published: August 2015

Residue types at the interface of protein–protein complexes (PPCs) are known to be reasonably well conserved. However, we show, using a dataset of known 3‐D structures of homologous transient PPCs, that the 3‐D location of interfacial residues and their interaction patterns are only moderately and poorly conserved, respectively. Another surprising observation is that a residue at the interface that is conserved is not necessarily in the interface in the homolog. Such differences in homologous complexes are manifested by substitution of the residues that are spatially proximal to the conserved residue and structural differences at the interfaces as well as differences in spatial orientations of the interacting proteins. Conservation of interface location and the interaction pattern at the core of the interfaces is higher than at the periphery of the interface patch. Extents of variability of various structural features reported here for homologous transient PPCs are higher than the variation in homologous permanent homomers. Our findings suggest that straightforward extrapolation of interfacial nature and inter‐residue interaction patterns from template to target could lead to serious errors in the modeled complex structure. Understanding the evolution of interfaces provides insights to improve comparative modeling of PPC structures.
The value of protein structure classification information—Surveying the scientific literature
Authors: Fox Naomi K. , Brenner Steven E. , Chandonia John‐Marc
Published: August 2015

The Structural Classification of Proteins (SCOP) and Class, Architecture, Topology, Homology (CATH) databases have been valuable resources for protein structure classification for over 20 years. Development of SCOP (version 1) concluded in June 2009 with SCOP 1.75. The SCOPe (SCOP–extended) database offers continued development of the classic SCOP hierarchy, adding over 33,000 structures. We have attempted to assess the impact of these two decade old resources and guide future development. To this end, we surveyed recent articles to learn how structure classification data are used. Of 571 articles published in 2012–2013 that cite SCOP, 439 actually use data from the resource. We found that the type of use was fairly evenly distributed among four top categories: A) study protein structure or evolution (27% of articles), B) train and/or benchmark algorithms (28% of articles), C) augment non‐SCOP datasets with SCOP classification (21% of articles), and D) examine the classification of one protein/a small set of proteins (22% of articles). Most articles described computational research, although 11% described purely experimental research, and a further 9% included both. We examined how CATH and SCOP were used in 158 articles that cited both databases: while some studies used only one dataset, the majority used data from both resources. Protein structure classification remains highly relevant for a diverse range of problems and settings. Proteins 2015; 83:2025–2038. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.
Educational Expansion and Intergenerational Proximity in Sweden
Authors: Chudnovskaya Margarita , Kolk Martin
Published: August 2015

Education is one of the most important drivers of regional migration in European countries, and educational expansion has been a major social phenomenon in the last decades. We use decomposition analysis to examine how the expansion of tertiary education has affected intergenerational distance between adult children and their parents in Sweden. We use administrative register data for the complete population of Sweden and examine changes in intergenerational proximity between 1980 and 2010, using couples at the birth of their first child as the study population. An explicit policy goal of tertiary expansion was to widen the geographical access to tertiary education and the enrolment grew at newer regional institutions during this period. We additionally explore if this policy of regional expansion influenced average distance to parents. We find that intergenerational distances increased over the study period and that this was mainly attributed to the increased enrolment at traditional, older, universities. Copyright © 2015 John Wiley & Sons, Ltd.
Experimental Research Methods in Migration: From Natural to True Experiments
Authors: Baláž Vladimír , Williams Allan M
Published: August 2015

Migration researchers have demonstrated relatively limited engagement with experimental research. The strongest engagement has been with natural experiments, which observe actual migrant behaviour, typically analysing migration behaviour before and after particular events, but have limitations in terms of control over the ‘experiment’. In contrast, researchers have relatively neglected the contribution of true experiments involving the manipulation or simulation of changes in the environment or institutions that shape migration. The paper compares the relative strengths of two types of true experiments – field and laboratory – in terms of their validity and reliability, reviews their current application in migration studies, and sets out opportunities to develop future research around these methodologies. Copyright © 2015 John Wiley & Sons, Ltd.
Have Destination Choices of Foreign Residents Contributed to Reducing Regional Population Disparity in Japan? Analysis Based on the 2010 Population Census Microdata
Authors: Hanaoka Kazumasa , Ishikawa Yoshitaka , Takeshita Shuko
Published: August 2015

In relation to the beginning of Japan's total population decline, the problem of regional disparity has been attracting a great deal of attention in the country. Have the destination choices of foreign residents in recent years contributed to reducing such disparity? The purpose of this study is to analyse the destination choices of new immigrants and foreign residents moving within Japan in the period 2005–2010, using microdata from the 2010 Population Census. The results are compared with those obtained from the period 1995–2000. Three major findings are obtained: First, the empirical validities of three theoretical perspectives (effect of labour market conditions, attraction to co‐ethnic communities, and spatial distribution of marital opportunities) are confirmed to a similar extent in this study as in the previous period. Second, the pull effect of the service industry is much larger than that of the manufacturing industry, for both new immigration and internal migration. Finally, although there is an obvious distance–decay tendency in internal migration, foreign residents (particularly Chinese residents) have shown the tendency of dispersal, including suburbanization. However, if the destination choices of foreign residents observed in 2005–2010 as a whole continue into the future, they would eventually worsen rather than alleviate the disparity. Copyright © 2015 John Wiley & Sons, Ltd.
The importance of edges in reactive ion etched graphene nanodevices
Authors: Bischoff Dominik , Simonet Pauline , Varlet Anastasia , Overweg Hiske C. , Eich Marius , Ihn Thomas , Ensslin Klaus
Published: August 2015

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Patterned graphene nanodevices are promising candidates for nano‐ and quantum‐electronics. Low temperature electronic transport in reactive ion etched graphene nanodevices is typically governed by charge localization manifesting itself in the appearance of Coulomb blockade. The disorder originating from non‐perfect graphene edges was identified as being the dominant reason for the stochastic charge localization in graphene nanoribbons. It was found that electrons can localize along the edges on length scales much longer than the physical disorder length. Such states localized along the edge can even leak out of the nanoribbon into adjacent wide graphene leads suggesting that a possibly existing confinement gap is not required to explain transport properties of etched graphene nanodevices. These insights are then used to improve the understanding of transport in graphene quantum dots where Coulomb blockade is typically more regular than in nanoribbons. It is shown that non‐overlapping Coulomb diamonds can be observed even in a regime where three states of localized charge need to be passed in series by an electron traveling from source to drain contact. This counter‐intuitive observation is explained by higher order co‐tunneling through the localized states in the nanoribbons connecting the graphene dot to the leads.

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(© 2015 WILEY‐VCH Verlag GmbH &Co. KGaA, Weinheim)
Potential energy surface as a key to understanding the structure and properties of short‐living radical ions of cyclic organic molecules
Authors: Shchegoleva Lyudmila N. , Beregovaya Irina V.
Published: August 2015

The review proposed summarizes the results of investigations on the adiabatic potential energy surfaces (PESes) for the radical ions of some derivatives of highly symmetric organic molecules such as benzene and cyclohexane. The results obtained show that the main feature of the PESes of highly symmetric Jahn–Teller ions, namely conical intersection, may persist for their low‐symmetric derivatives. Hence, their PESes have a pseudorotational shape resulting from the intersection avoidance. A distinctive feature of radical anions of fluorine containing aromatic compounds is the planar structure disturbance due to the vibronic coupling of the ground π and low‐lying excited σ states. The data on the PES structure including the positions and relative energies of its extrema, curvature in their vicinity, and stationary point interrelations provide the foundation for understanding the spectral properties and reactivity of radical ionic species. Examples of applying the PES study results to experimental data interpretation are given. © 2015 Wiley Periodicals, Inc.
Generation of (M = K, Rb, Cs, 2n = 80–220) by laser ablation of graphene
Authors: Bao Xiaodi , Kong Xianglei
Published: August 2015

Rationale

The yield of endohedral metallofullerene (EMF) ions is greatly related to the encaged metal atoms. For alkali metals, the generation of corresponding large‐sized monometallofullerene ions by traditional methods is still difficult. The aim of this work is to study the generation and the distribution of alkali‐metallofullerene ions by the method of laser ablation with graphene as the precursor.

Methods

The experiment was performed with a Fourier transform ion cyclotron (FTICR) mass spectrometer. Mass spectra were obtained by laser ablation of the mixtures of graphene and KCl, RbCl or CsCl in the positive ion mode. Collision‐induced dissociation (CID) experiments were also performed for some selected ions.

Results

EMF ions of
(M = K, Rb, Cs, 2n = 80–220) can be generated by using graphene as the precursor. Other EMF ions with smaller sizes, including
, were also observed under the optimized experimental conditions. CID experiments of some selected ions confirmed their endohedral structures.

Conclusions

Metallofullerene ions of
(M = K, Rb, Cs, 2n = 80–220) were generated by laser ablation of graphene and corresponding metal salts. Compared with previous results of alkaline earth metals, the yields of EMF ions are generally lower. However, for large‐sized EMF ions, the relative intensities of EMF ions to their corresponding fullerene ions
/
generally increase with the increase in cluster sizes, which is opposite to the trend observed for alkaline earth metals. Copyright © 2015 John Wiley & Sons, Ltd.
The in situ gas‐phase formation of a C‐glycoside ion obtained during electrospray ionization tandem mass spectrometry. A unique intramolecular mechanism involving an ion‐molecule reaction
Authors: Banoub Joseph H. , Demian Wael L. L. , Piazzetta Paolo , Sarkis George , Kanawati Basem , Lafont Dominique , Laurent Nicolas , Vaillant Celine , Randell Edward , Giorgi Gianluca , Fridgen Travis D.
Published: August 2015

Rationale

This study examines the electrospray ionization mass spectrometry (ESI‐MS), in‐source collision‐induced dissociation (CID) fragmentation and low‐energy collision‐induced dissociation tandem mass spectrometry (CID‐MS/MS) of a synthetic pair of β‐ and α‐anomers of the amphiphilic cholesteryl polyethoxy neoglycolipids containing the 2‐azido‐2‐deoxy‐D‐galactosyl‐D‐GalN3 moiety. We describe the novel and unique in situ gas‐phase formation of a C‐glycoside ion formed during all these gas‐phase processes and propose a reasonable mechanism for its formation.

Methods

The synthetic amphiphilic glycolipids were composed of the 2‐deoxy‐2‐azido‐D‐galactosyl moiety (GalN3, the hydrophilic part) covalently attached to a polyethoxy spacer which is covalently linked to the cholesteryl moiety (hydrophobic part). The 2‐azido‐2‐deoxy‐α‐ and β‐D‐galactosyl‐containing glycolipids were studied by in‐time and in‐space ESI‐MS and CID‐MS/MS in positive ion mode, with quadrupole ion trap (QIT), quadrupole‐quadrupole‐time‐of‐flight (QqTOF), and Fourier transform ion cyclotron resonance (FTICR) instruments.

Results

Conventional single‐stage ESI‐MS analysis showed the formation of the protonated molecule. During the single‐stage ESI‐MS analysis and the CID‐MS/MS of the [M+H]+ and [M+NH4]+ adducts obtained from both glycolipid anomers, the presence of a series of specific product ions with different intensities was observed, consistent with the [C‐glycoside+H–N2]+, [cholestadiene+H]+, 2‐deoxy‐2‐D‐azido‐galactosyl [GalN3]+, [GalNH]+ and [sugar−Spacer+H]+ ions.

Conclusions

The gas‐phase formation of the [C‐glycoside+H–N2]+ ion isolated from the glycolipid anomers was observed during both the ESI‐MS of the glycolipids and the CID‐MS/MS analyses of the [M+H]+ ions and it was found to occur by an intramolecular rearrangement involving an ion‐molecule complex. CID‐QqTOF‐MS/MS and CID‐FTICR‐MS2 analysis allowed the differentiation of the two glycolipid anomers and showed noticeable variation in the intensities of the product ions. Copyright © 2015 John Wiley & Sons, Ltd.
MZDASoft: a software architecture that enables large‐scale comparison of protein expression levels over multiple samples based on liquid chromatography/tandem mass spectrometry
Authors: Ghanat Bari Mehrab , Ramirez Nelson , Wang Zhiwei , Zhang Jianqiu (Michelle)
Published: August 2015

Rationale

Without accurate peak linking/alignment, only the expression levels of a small percentage of proteins can be compared across multiple samples in Liquid Chromatography/Mass Spectrometry/Tandem Mass Spectrometry (LC/MS/MS) due to the selective nature of tandem MS peptide identification. This greatly hampers biomedical research that aims at finding biomarkers for disease diagnosis, treatment, and the understanding of disease mechanisms. A recent algorithm, PeakLink, has allowed the accurate linking of LC/MS peaks without tandem MS identifications to their corresponding ones with identifications across multiple samples collected from different instruments, tissues and labs, which greatly enhanced the ability of comparing proteins. However, PeakLink cannot be implemented practically for large numbers of samples based on existing software architectures, because it requires access to peak elution profiles from multiple LC/MS/MS samples simultaneously.

Methods

We propose a new architecture based on parallel processing, which extracts LC/MS peak features, and saves them in database files to enable the implementation of PeakLink for multiple samples. The software has been deployed in High‐Performance Computing (HPC) environments. The core part of the software, MZDASoft Parallel Peak Extractor (PPE), can be downloaded with a user and developer's guide, and it can be run on HPC centers directly. The quantification applications, MZDASoft TandemQuant and MZDASoft PeakLink, are written in Matlab, which are compiled with a Matlab runtime compiler. A sample script that incorporates all necessary processing steps of MZDASoft for LC/MS/MS quantification in a parallel processing environment is available. The project webpage is http://compgenomics.utsa.edu/zgroup/MZDASoft.

Results

The proposed architecture enables the implementation of PeakLink for multiple samples. Significantly more (100%–500%) proteins can be compared over multiple samples with better quantification accuracy in test cases.

Conclusion

MZDASoft enables large‐scale comparison of protein expression levels over multiple samples with much larger protein comparison coverage and better quantification accuracy. It is an efficient implementation based on parallel processing which can be used to process large amounts of data. Copyright © 2015 John Wiley & Sons, Ltd.