bluuebunny/crossref_metadata_2025 huggingface dataset:
Validation of the yale‐brown obsessive compulsive scale modified for binge eating
Authors: Deal Linda S. , Wirth R.J. , Gasior Maria , Herman Barry K. , McElroy Susan L.
Published: June 2015

Objective

Establish the Yale–Brown obsessive compulsive scale modified for binge eating (YBOCS‐BE) as a fit for purpose measure of treatment benefit in clinical trials of binge eating disorder (BED).

Methods

YBOCS‐BE psychometric properties were evaluated with data from a Phase 2 randomized controlled trial of lisdexamfetamine dimesylate in 260 adults with BED. Assessments included: Cohen's effect size estimates of item‐level sensitivity and scale‐level external responsiveness; item‐to‐total correlations; Cronbach's alpha for internal consistency reliability; Spearman correlations against reference measures for construct validity; known‐groups analyses for discriminating ability; t tests of within‐group differences between baseline and post baseline visits for internal responsiveness; and multiple anchor‐based approaches to estimate minimum clinically important change (MCIC).

Results

No significant distribution anomalies were seen. Items appear sensitive to treatment group differences. Item‐to‐total correlations were positive. Internal consistency is 0.81. Large correlations (>0.50) were seen between YBOCS‐BE score change and the Clinical Global Impression–Improvement (CGI‐I; 0.58) and score changes for the following; number of binge days (0.38), Clinical Global Impression–Severity (CGI‐S; 0.57), the disinhibition (0.57) and hunger (0.52) subscales of the Three‐Factor Eating Questionnaire (TFEQ), and the Barratt Impulsiveness Scale (BIS‐11; 0.58). MCIC estimates range from −4 to −17.

Discussion

The YBOCS‐BE was found to be a reliable and valid measure of an important and unique concept in BED‐related clinical studies. Study limitations include using protocol‐defined BED severity level and the exclusion of psychiatric comorbidities. © 2015 Wiley Periodicals, Inc. (Int J Eat Disord 2015; 48:994–1004).
Brown trout thermal niche and climate change: expected changes in the distribution of cold‐water fish in central Spain
Authors: Santiago José M. , García de Jalón Diego , Alonso Carlos , Solana Joaquín , Ribalaygua Jaime , Pórtoles Javier , Monjo Robert
Published: June 2015

This paper addresses the determination of the realized thermal niche and the effects of climate change on the range distribution of two brown trout populations inhabiting two streams in the Duero River basin (Iberian Peninsula) at the edge of the natural distribution area of this species. For reaching these goals, new methodological developments were applied to improve reliability of forecasts. Water temperature data were collected using 11 thermographs located along the altitudinal gradient, and they were used to model the relationship between stream temperature and air temperature along the river continuum. Trout abundance was studied using electrofishing at 37 sites to determine the current distribution. The Representative Concentration Pathways RCP4·5 and RCP8·5 change scenarios adopted by the International Panel of Climate Change for its Fifth Assessment Report were used for simulations and local downscaling in this study. We found more reliable results using the daily mean stream temperature than maximum daily temperature and their respective 7 days moving average to determine the distribution thresholds. Thereby, the observed limits of the summer distribution of brown trout were linked to thresholds between 18·1 and 18·7 °C. These temperatures characterize a realized thermal niche narrower than the physiological thermal range. In the most unfavourable climate change scenario, the thermal habitat loss of brown trout increased to 38% (Cega stream) and 11% (Pirón stream) in the upstream direction at the end of the century; however, at the Cega stream, the range reduction could reach 56% due to the effect of a ‘warm‐window’ opening in the piedmont reach. Copyright © 2015 John Wiley & Sons, Ltd.
Computer simulations of sample preconcentration in carrier‐free systems and isoelectric focusing in microchannels using simple ampholytes
Authors: Mikkonen Saara , Thormann Wolfgang , Emmer Åsa
Published: June 2015

In this work, electrophoretic preconcentration of protein and peptide samples in microchannels was studied theoretically using the 1D dynamic simulator GENTRANS, and experimentally combined with MS. In all configurations studied, the sample was uniformly distributed throughout the channel before power application, and driving electrodes were used as microchannel ends. In the first part, previously obtained experimental results from carrier‐free systems are compared to simulation results, and the effects of atmospheric carbon dioxide and impurities in the sample solution are examined. Simulation provided insight into the dynamics of the transport of all components under the applied electric field and revealed the formation of a pure water zone in the channel center. In the second part, the use of an IEF procedure with simple well defined amphoteric carrier components, i.e. amino acids, for concentration and fractionation of peptides was investigated. By performing simulations a qualitative description of the analyte behavior in this system was obtained. Neurotensin and [Glu1]‐Fibrinopeptide B were separated by IEF in microchannels featuring a liquid lid for simple sample handling and placement of the driving electrodes. Component distributions in the channel were detected using MALDI‐ and nano‐ESI‐MS and data were in agreement with those obtained by simulation. Dynamic simulations are demonstrated to represent an effective tool to investigate the electrophoretic behavior of all components in the microchannel.
Interactions between water temperature and contaminant toxicity to freshwater fish
Authors: Patra Ronald W. , Chapman John C. , Lim Richard P. , Gehrke Peter C. , Sunderam Ramasamy M.
Published: June 2015

Warming of freshwaters as a result of climate change is expected to have complex interactions with the toxicity of contaminants to aquatic organisms. The present study evaluated the effects of temperature on the acute toxicity of endosulfan, chlorpyrifos, and phenol to 3 warm water species of fish—silver perch, rainbowfish, and western carp gudgeon—and 1 cold water species, rainbow trout. Endosulfan was more toxic to silver perch at 30 °C and 35 °C than at 15 °C, 20 °C and 25 °C during short exposures of 24 h, but at 96 h, temperature had no effect on toxicity. Toxicity to rainbow trout increased with increasing temperature, whereas warm water species exhibited maximum toxicity at around 30 °C, decreasing again toward 35 °C. Chlorpyrifos became more toxic to all species with increasing temperature. Phenol toxicity to all species decreased at low to intermediate temperatures; but as temperatures increased further toward the upper thermal limit, phenol became more toxic. Increasing toxicity in the upper thermal range of cold water species may contribute to upstream range contraction in rivers with high toxicant loads. In contrast, warm water species may not exhibit a range shift within rivers as a result of interactions between temperature and toxicity. Catchment management to offset global warming at local scales may present opportunities to mitigate increased toxicity of contaminants to fish. Environ Toxicol Chem 2015;34:1809–1817. © 2015 SETAC
Soil water dynamics and hydrophysical properties of regenerating Sphagnum layers in a cutover peatland
Authors: Taylor Neil , Price Jonathan
Published: June 2015

The physical and hydrological conditions in extracted peatlands often act as barriers to the regeneration of the keystone peat‐forming genus Sphagnum. Although previous work has suggested that Sphagnum mosses regenerating on cutover peat surfaces quickly become vulnerable to water stress as the thickness of the regenerated layer increases, uncertainties regarding the storage and transmission properties of this layer and how these might evolve over time have made this assertion difficult to evaluate. This study investigates the hydrophysical properties and hydrological behaviour of regenerating Sphagnum layers ranging from 3 to 43 years in age using both field and laboratory methods. The >40‐year‐old regenerated layers had significantly (p < 0.001) higher bulk density and retention capacity in the 5‐cm‐thick basal layer directly overlying the cutover peat than the newer (<10 year old) regenerated layers. Capillarity was a much stronger control on surficial water content (θ) than precipitation, which was poorly retained in the Sphagnum canopy, suggesting that regulation of water table position is an effective method of controlling θ as a means of optimizing productivity. In general, the θ sustained at a given water table position decreased as regenerated layer thickness increased. Analysis of water table position relative to the former cutover peat surface in different areas of the site suggests that the soil water dynamics of the >40‐year‐old regenerated layers may be becoming increasingly similar to those of a natural bog peatland. Copyright © 2015 John Wiley & Sons, Ltd.
Assessment of trace element impacts on agricultural use of water from the Dan River following the Eden coal ash release
Authors: Hesterberg Dean , Polizzotto Matthew L , Crozier Carl , Austin Robert E
Published: June 2015

Catastrophic events require rapid, scientifically sound decision making to mitigate impacts on human welfare and the environment. The objective of this study was to analyze potential impacts of coal ash-derived trace elements on agriculture following a 35 000-tonne release of coal ash into the Dan River at the Duke Energy Steam Station in Eden, North Carolina. We performed scenario calculations to assess the potential for excessive trace element loading to soils via irrigation and flooding with Dan River water, uptake of trace elements by crops, and livestock consumption of trace elements via drinking water. Concentrations of 13 trace elements measured in Dan River water samples within 4 km of the release site declined sharply after the release and were equivalent within 5 d to measurements taken upriver. Mass–balance calculations based on estimates of soil trace-element concentrations and the nominal river water concentrations indicated that irrigation or flooding with 25 cm of Dan River water would increase soil concentrations of all trace elements by less than 0.5%. Calculations of potential increases of trace elements in corn grain and silage, fescue, and tobacco leaves suggested that As, Cr, Se, Sr, and V were elements of most concern. Concentrations of trace elements measured in river water following the ash release never exceeded adopted standards for livestock drinking water. Based on our analyses, we present guidelines for safe usage of Dan River water to diminish negative impacts of trace elements on soils and crop production. In general, the approach we describe here may serve as a basis for rapid assessment of environmental and agricultural risks associated with any similar types of releases that arise in the future. Integr Environ Assess Manag 2016;12:353–363. © 2015 SETAC

Key Points

Following a 35,000-tonne release of coal ash into the Dan River in North Carolina, total concentrations of 13 trace elements measured in river water within 4 kilometers of the release site declined sharply after the release and were equivalent to measurements taken upriver within 4 days. Trace-element concentrations in river water exceeded standards for surface water used as a drinking water source in <10% of samples, and no samples exceeded guidelines for cattle drinking water. Irrigation or flooding with 25 cm of river water would increase soil trace-element concentrations by <0.5%, indicating that river water is now suitable for use as irrigation water, and trace-element influx during flooding of agricultural areas will have only a marginal impact on soils and crops. Because the mobility and plant-availability of trace elements is difficult to accurately model on a site-by-site basis, a mass-balance approach provides a means to quickly assess the potential impacts of any future coal-ash spills or other similar events on agricultural operations.
Effects of perceived social support and family demands on college students' mental well‐being: A cross‐cultural investigation
Authors: Khallad Yacoub , Jabr Fares
Published: June 2015

The effects of perceived social support and family demands on college students' mental well‐being (perceived stress and depression) were assessed in 2 samples of Jordanian and Turkish college students. Statistically significant negative correlations were found between perceived support and mental well‐being. Multiple regression analyses showed that perceived family support was a better predictor of mental well‐being for Jordanian students, while perceived support from friends was a better predictor of mental well‐being for Turkish students. Perceived family demands were stronger predictors of mental well‐being for participants from both ethnic groups. Jordanian and Turkish participants who perceived their families to be too demanding were more likely to report higher depression and stress levels. None of the interactions between social support or family demands and either of the 2 demographic variables were statistically significant. These findings provide a more nuanced view of the relationship between social support and mental health among college students, and point to the relevance of some cultural and situational factors. They also draw further attention to the detrimental effects of unrealistic family demands and pressures on the mental health of college youths.
Calcium hypochlorite as a dentin deproteinization agent: Microleakage, scanning electron microscopy and elemental analysis
Authors: Bortoluzzi de Conto Ferreira Michele , Carlini Júnior Bruno , Galafassi Daniel , Gobbi Delton Luiz
Published: June 2015

Purpose: This study investigated the influence of collagen removal with calcium hypochlorite on the surface morphology of acid‐etched dentin and on the microleakage of composite restorations. In addition, the elemental composition (EC) of dentin after removal of the collagen fibrils was analyzed. Materials and Methods: Forty third molars received two cavities and were divided into four groups according to dentin treatment: CTRL—no pre‐treatment; Na10—10% NaOCl for 30 s; Ca10—10% CaOCl for 30 s, and Ca15—15% CaOCl for 30 s. The cavities were filled using an acetone‐based adhesive system and a resin composite; they were then subjected to thermal cycling for 5,000 cycles, immersed in methylene blue for 4 h and sectioned into 1‐mm thick slabs. Two examiners evaluated two slices per tooth using a stereomicroscope and assigned the degree of infiltration (scores 0–3). The data were analyzed using the Kruskal–Wallis (α = 0.05). Four teeth received surface treatment according to the groups and were submitted to SEM and EDS to carry at the EC. Results: There was no significant difference between the experimental groups (P = 0.533). CaOCl alters the morphology and surface composition of the dentin, resulting in an increase in the amount of calcium in the interface. Conclusions: When used prior to an acetone‐based adhesive system, CaOCl did not produce any differences in microleakage when compared to the CTRL group or to the Na10 group. Microsc. Res. Tech. 78:676–681, 2015. © 2015 Wiley Periodicals, Inc.
Three‐dimensional Co‐culture of hepatic progenitor cells and mesenchymal stem cells in vitro and in vivo
Authors: Zhong Li , Gou Juhua , Deng Nian , Shen Hao , He Tongchuan , Zhang Bing‐Qiang
Published: June 2015

Introduction: Here we co‐cultured hepatic progenitor cells (HPCs) and mesenchymal stem cells (MSCs) to investigate whether the co‐culture environments could increase hepatocytes form. Methods: Three‐dimensional (3D) co‐culture model of HPCs and MSCs was developed and morphological features of cells were continuously observed. Hepatocyte specific markers Pou5f1/Oct4, AFP, CK‐18 and Alb were analyzed to confirm the differentiation of HPCs. The mRNA expression of CK‐18 and Alb was analyzed by RT‐PCR to investigate the influence of co‐culture model to the terminal differentiation process of mature hepatocytes. The functional properties of hepatocyte‐like cells were detected by continuously monitoring the albumin secretion using Gaussia luciferase assays. Scaffolds with HPCs and MSCs were implanted into nude mouse subcutaneously to set up the in vivo co‐culture model. Results: Although two groups formed smooth spheroids and high expressed of CK‐18 and Alb, hybrid spheroids had more regular structures and higher cell density. CK‐18 and Alb mRNA were at a relatively higher expression level in co‐culture system during the whole cultivation time (P < 0.05). Albumin secretion rates in the hybrid spheroids had been consistently higher than that in the mono‐culture spheroids (P < 0.05). In vivo, the hepatocyte‐like cells were consistent with the morphological features of mature hepatocytes and more well‐differentiated hepatocyte‐like cells were observed in the co‐culture group. Conclusions: HPCs and MSCs co‐culture system is an efficient way to form well‐differentiated hepatocyte‐like cells, hence, may be helpful to the cell therapy of hepatic tissues and alleviate the problem of hepatocytes shortage. Microsc. Res. Tech. 78:688–696, 2015. © 2015 Wiley Periodicals, Inc.
Heat waves in Central Europe and their circulation conditions
Authors: Tomczyk Arkadiusz M. , Bednorz Ewa
Published: June 2015

The research objectives were to describe heat waves (HWs) in Central Europe and define the synoptic situations that cause their occurrence. In this article, a hot day was defined as a day when the maximum temperature was above the 95th annual percentile and an HW was considered a sequence of at least five hot days. In the analysed multi‐year period and study area, 11 HWs were observed in the north and 51 HWs were observed in the south. The occurrence of HWs was mainly connected with positive anomalies of sea level pressure and with the 500 hPa level, which shows the presence of high‐pressure systems. HWs were also accompanied by positive T850 and precipitable water (PW) anomalies.
Future changes of wind energy potentials over Europe in a large CMIP5 multi‐model ensemble
Authors: Reyers Mark , Moemken Julia , Pinto Joaquim G.
Published: June 2015

A statistical‐dynamical downscaling method is used to estimate future changes of wind energy output (Eout) of a benchmark wind turbine across Europe at the regional scale. With this aim, 22 global climate models (GCMs) of the Coupled Model Intercomparison Project Phase 5 (CMIP5) ensemble are considered. The downscaling method uses circulation weather types and regional climate modelling with the COSMO‐CLM model. Future projections are computed for two time periods (2021–2060 and 2061–2100) following two scenarios (RCP4.5 and RCP8.5). The CMIP5 ensemble mean response reveals a more likely than not increase of mean annual Eout over Northern and Central Europe and a likely decrease over Southern Europe. There is some uncertainty with respect to the magnitude and the sign of the changes. Higher robustness in future changes is observed for specific seasons. Except from the Mediterranean area, an ensemble mean increase of Eout is simulated for winter and a decreasing for the summer season, resulting in a strong increase of the intra‐annual variability for most of Europe. The latter is, in particular, probable during the second half of the 21st century under the RCP8.5 scenario. In general, signals are stronger for 2061–2100 compared to 2021–2060 and for RCP8.5 compared to RCP4.5. Regarding changes of the inter‐annual variability of Eout for Central Europe, the future projections strongly vary between individual models and also between future periods and scenarios within single models. This study showed for an ensemble of 22 CMIP5 models that changes in the wind energy potentials over Europe may take place in future decades. However, due to the uncertainties detected in this research, further investigations with multi‐model ensembles are needed to provide a better quantification and understanding of the future changes.
Multiscale strain analysis of tendon subjected to shear and compression demonstrates strain attenuation, fiber sliding, and reorganization
Authors: Fang Fei , Lake Spencer P.
Published: June 2015

The manner in which strains are passed down the hierarchical length scales of tendons dictates how cells within the collagen network regulate the tissue response to loading. How tendons deform in different hierarchical levels under shear and compression is unknown. The aims of this study were: (i) to evaluate whether specific regions of bovine deep digital flexor tendons exhibited different strain attenuation from macro to micro length scales, and (ii) to elucidate mechanisms responsible for tendon deformation under shear and compression. Samples from distal and proximal regions of flexor tendons were subjected to three‐step incremental stress‐relaxation tests. Images of tissue markers, photobleached lines on collagen fibers, and nuclei locations were collected before and after loading. Results showed that strain transfer was attenuated from tissue to local matrix under both shear and compression. Nuclear aspect ratios exhibited smaller changes for distal samples, suggesting that cells are more shielded from deformation in the distal region. Collagen fiber sliding was observed to contribute significantly in response to shear, while uncrimping and fiber reorganization were the predominant mechanisms under compression. This study provides insight into microscale mechanisms responsible for multiscale strain attenuation of tendons under non‐tensile macroscale loading. © 2015 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 33:1704–1712, 2015.
Anti‐inflammatory effect of water extracts of Graptopetalum paraguayense supplementation in subjects with metabolic syndrome: a preliminary study
Authors: Chen Shu‐Ju , Yen Chi‐Hua , Liu Jen‐Tzu , Tseng Yu‐Fen , Lin Ping‐Ting
Published: June 2015

BACKGROUND

Many studies have demonstrated that Graptopetalum paraguayense has good antioxidant ability; however, few studies have examined its anti‐inflammatory effect. The study aimed to investigate the anti‐inflammatory effects of water extracts of G. paraguayense (WGP, 4 g day−1) in subjects with metabolic syndrome (MS). Intervention was administered for 12 weeks. Levels of inflammatory markers [high sensitivity C‐reactive protein (CRP), tumour necrosis factor‐α (TNF‐α), and interleukin‐6 (IL‐6)] and antioxidant enzymes activities were measured.

RESULTS

Forty‐two subjects completed the 12 week intervention study (placebo, n = 19; WGP, n = 23). After 12 weeks supplementation, subjects in WGP group had significantly lower levels of inflammatory markers than the baseline (P < 0.05) and the placebo group (CRP, P = 0.07; TNF‐α, P = 0.04; IL‐6, P = 0.03). The changes in levels of the inflammatory markers were significantly decreased in WGP group (CRP, P = 0.04; TNF‐α, P = 0.06; IL‐6, P = 0.01) compared to the placebo group. Levels of inflammatory markers were significantly negatively correlated with the antioxidant enzymes activities after supplementation.

CONCLUSION

This study demonstrated a significant reduction in inflammatory status in MS after WGP supplementation. WGP may exert an anti‐inflammatory effect on MS in addition to its antioxidant ability. © 2015 Society of Chemical Industry
Fatty acid composition of the ovine longissimus dorsi muscle: effect of feed restriction in three breeds of different origin
Authors: van Harten Sofia , Kilminster Tanya , Scanlon Timothy , Milton John , Oldham Chris , Greeff Johann , Almeida André M
Published: June 2015

BACKGROUND

Muscle fatty acid profile reflects the body condition of animals and has a noticeable effect on meat quality. Herein, longissimus dorsi muscle of three different sheep breeds, Damara (a fat‐tailed breed), Dorper and Australian Merino sheep, was analysed for fatty acid composition. The three breeds were subjected to two distinctive feeding levels (ad libitum and restricted feeding) over 42 days.

RESULTS

The Damara sheep revealed several differences compared to the other two breeds, namely a higher concentration of polyunsaturated fatty acids, which can be related to being a fat‐tailed breed. Even in restricted feeding conditions, this breed revealed the highest levels compared to Merino and Dorper sheep respectively, of linoleic acid (+31% and +28%), linolenic acid (+97% and +51%), eicosapentaenoic acid (EPA) (+65% and +37%), docosapentanenoic acid (DPA) (+31% Merino) and dodosahexanenoic acid (DHA) (+63% and +77%). EPA, DPA and DHA are three omega‐3 fatty acids, with described beneficial characteristics.

CONCLUSION

With this work we show other qualities (higher levels of the omega‐3 fatty acids, EPA, DPA and DHA) of Damara meat that might present this breed as an interesting alternative for animal production in semi‐arid climates. © 2015 Society of Chemical Industry
Modified olfactory training in patients with postinfectious olfactory loss
Authors: Altundag Aytug , Cayonu Melih , Kayabasoglu Gurkan , Salihoglu Murat , Tekeli Hakan , Saglam Omer , Hummel Thomas
Published: June 2015

Objectives/Hypothesis

Patients with olfactory dysfunction benefit from repeated exposure to odors, so‐called olfactory training (OT). This does not mean occasional smelling but the structured sniffing of a defined set of odors, twice daily, for a period of 4 months or longer. In this prospective study, we investigated whether the effect of OT might increase through the use of more odors and extension of the training period.

Study Design and Methods

This study shows OT results when performed with four or 12 odors for 36 weeks in patients with postinfectious olfactory dysfunction. A total of 85 subjects participated (mean age 45.6 ± 10.5 years, range 24–68 years). Three groups were formed: 1) In the modified olfactory training (MOT) group, patients used three sets of four different odors sequentially. 2) Participants in the classical odor training (COT) group used four odors. 3) Participants in the control group did not perform OT. All groups were matched for age and sex distribution of participants.

Results

Both participants in the COT and MOT groups reached better scores than controls in terms of odor discrimination and odor identification. Continuing OT with four different odors after the 12th and 24th weeks produced better results in terms of odor discrimination and odor identification scores as compared to using the same four odors throughout the entire study.

Conclusion

This study confirmed the effectiveness of OT. Increasing the duration of OT and changing the odors enhances the success rate of this therapy.

Level of Evidence

2b. Laryngoscope, 125:1763–1766, 2015
Thermoresponsive AuNPs Stabilized by Pillararene‐Containing Polymers
Authors: Liao Xiaojuan , Guo Lei , Chang Junxia , Liu Sha , Xie Meiran , Chen Guosong
Published: June 2015

Pillararene‐containing thermoresponsive polymers are synthesized via reversible addition–fragmentation chain transfer polymerization using pillararene derivatives as the effective chain transfer agents for the first time. These polymers can self‐assemble into micelles and form vesicles after guest molecules are added. Furthermore, such functional polymers can be further applied to prepare hybrid gold nanoparticles, which integrate the thermoresponsivity of polymers and molecular recognition of pillararenes.

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Molecular Weight Effects on the Glass Transition and Confinement Behavior of Polymer Thin Films
Authors: Xia Wenjie , Hsu David D. , Keten Sinan
Published: June 2015

Nanoscale polymer thin films exhibit strong confinement effects onTgarising from free surfaces. However, the coupled influence of molecular weight (MW) and surface effects onTgis not well understood for low MW film systems below the entanglement length. Utilizing atomistically informed coarse‐grained molecular dynamics simulations for poly(methyl methacrylate) (PMMA), it is demonstrated that the decrease in free‐standing filmTgwith respect to bulk is more significant for low MW compared to high MW systems. Investigation of the local interfacial properties reveals that the increase in the local free volume near the free surface is greater for low MW, explaining the MW dependence ofTg‐confinement behaviors. These findings corroborate recent experiments on low MW films, and highlight the relationship between nanoconfinement phenomena and local free volume effects arising from free surfaces.

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Coarse‐Grained and Atomistic Simulations for the G = 4 PAMAM‐EDA Dendrimer
Authors: Freire Juan J. , Rubio Ana M. , McBride Carl
Published: June 2015

Extensive fully‐atomistic molecular dynamics simulations have been performed for the G = 4 generation of the dendrimer PAMAM‐EDA in water, with fully protonated and non‐protonated amine groups. Some parameters from these results have been incorporated into a coarse‐grained model suitable for Monte Carlo simulations. Satisfactory agreement is found between the dendrimer density profiles obtained from the Monte Carlo and the molecular dynamics simulations, both for the protonated and neutral molecules. The Monte Carlo and molecular dynamics trajectories have also been employed to calculate binary interactions between pairs of dendrimers. The interactions between G = 4 PAMAM‐EDA dendrimers can be satisfactorily described by a theoretically proposed Gaussian potential.
The mzqLibrary – An open source Java library supporting the HUPO‐PSI quantitative proteomics standard
Authors: Qi Da , Zhang Huaizhong , Fan Jun , Perkins Simon , Pisconti Addolorata , Simpson Deborah M. , Bessant Conrad , Hubbard Simon , Jones Andrew R.
Published: June 2015

The mzQuantML standard has been developed by the Proteomics Standards Initiative for capturing, archiving and exchanging quantitative proteomic data, derived from mass spectrometry. It is a rich XML‐based format, capable of representing data about two‐dimensional features from LC‐MS data, and peptides, proteins or groups of proteins that have been quantified from multiple samples. In this article we report the development of an open source Java‐based library of routines for mzQuantML, called the mzqLibrary, and associated software for visualising data called the mzqViewer. The mzqLibrary contains routines for mapping (peptide) identifications on quantified features, inference of protein (group)‐level quantification values from peptide‐level values, normalisation and basic statistics for differential expression. These routines can be accessed via the command line, via a Java programming interface access or a basic graphical user interface. The mzqLibrary also contains several file format converters, including import converters (to mzQuantML) from OpenMS, Progenesis LC‐MS and MaxQuant, and exporters (from mzQuantML) to other standards or useful formats (mzTab, HTML, csv). The mzqViewer contains in‐built routines for viewing the tables of data (about features, peptides or proteins), and connects to the R statistical library for more advanced plotting options. The mzqLibrary and mzqViewer packages are available from https://code.google.com/p/mzq‐lib/.
Microparticles released from Mycobacterium tuberculosis‐infected human macrophages contain increased levels of the type I interferon inducible proteins including ISG15
Authors: Hare Nathan J. , Chan Brian , Chan Edwina , Kaufman Kimberley L. , Britton Warwick J. , Saunders Bernadette M.
Published: June 2015

Microparticles (MPs) are small membranous particles (100–1000 nm) released under normal steady‐state conditions and are thought to provide a communication network between host cells. Previous studies demonstrated that Mycobacterium tuberculosis (M. tb) infection of macrophages increased the release of MPs, and these MPs induced a proinflammatory response from uninfected macrophages in vitro and in vivo following their transfer into uninfected mice. To determine how M. tb infection modulates the protein composition of the MPs, and if this contributes to their proinflammatory properties, we compared the proteomes of MPs derived from M. tb‐infected (TBinf‐MP) and uninfected human THP‐1 monocytic cells. MP proteins were analyzed by GeLC‐MS/MS with spectral counting revealing 68 proteins with statistically significant differential abundances. The 42 proteins increased in abundance in TBinf‐MPs included proteins associated with immune function (7), lysosomal/endosomal maturation (4), vesicular formation (12), nucleosome proteins (4), and antigen processing (9). Prominent among these were the type I interferon inducible proteins, ISG15, IFIT1, IFIT2, and IFIT3. Exposure of uninfected THP‐1 cells to TBinf‐MPs induced increased gene expression of isg15, ifit1, ifit2, and ifit3 and the release of proinflammatory cytokines. These proteins may regulate the proinflammatory potential of the MPs and provide candidate biomarkers for M. tb infection.
Single‐residue posttranslational modification sites at the N‐terminus, C‐terminus or in‐between: To be or not to be exposed for enzyme access
Authors: Sirota Fernanda L. , Maurer‐Stroh Sebastian , Eisenhaber Birgit , Eisenhaber Frank
Published: June 2015

Many protein posttranslational modifications (PTMs) are the result of an enzymatic reaction. The modifying enzyme has to recognize the substrate protein's sequence motif containing the residue(s) to be modified; thus, the enzyme's catalytic cleft engulfs these residue(s) and the respective sequence environment. This residue accessibility condition principally limits the range where enzymatic PTMs can occur in the protein sequence. Non‐globular, flexible, intrinsically disordered segments or large loops/accessible long side chains should be preferred whereas residues buried in the core of structures should be void of what we call canonical, enzyme‐generated PTMs. We investigate whether PTM sites annotated in UniProtKB (with MOD_RES/LIPID keys) are situated within sequence ranges that can be mapped to known 3D structures. We find that N‐ or C‐termini harbor essentially exclusively canonical PTMs. We also find that the overwhelming majority of all other PTMs are also canonical though, later in the protein's life cycle, the PTM sites can become buried due to complex formation. Among the remaining cases, some can be explained (i) with autocatalysis, (ii) with modification before folding or after temporary unfolding, or (iii) as products of interaction with small, diffusible reactants. Others require further research how these PTMs are mechanistically generated in vivo.
Improving the quality of genome, protein sequence, and taxonomy databases: A prerequisite for microbiome meta‐omics 2.0
Authors: Pible Olivier , Armengaud Jean
Published: June 2015

High‐throughput shotgun metaproteomic approaches on environmental or medical microbiomes are producing huge amounts of tandem mass spectrometry data. These can be interpreted either with a general protein sequence database comprising tens of thousands of sequenced genomes or with a more customized database such as those obtained after metagenome sequencing of the DNA extracted from the same sample. However, not all entries in a nucleotide or protein sequence database are of equal quality and this can critically impact metaproteomic data interpretation. In this viewpoint article, we exemplify several key issues. First, either genome or transcriptome data interpretation due to inaccurate contig assembly and gene prediction may be erroneous, for its mitigation the metaproteogenomic strategies could have an interesting perspective. Errors in sample handling and taxonomical characterization may also be problematic. Cross‐contamination of genome sequences is also underestimated while frequent. As a consequence of these structural errors regarding protein sequences and additional problems due to homology‐based functional annotation of proteins, specific efforts for better interpretation of metaproteomic data are required. We propose the development of new bioinformatic pipelines devoted to detection and correction of errors and contaminations to improve the overall quality of sequence and taxonomy databases for metaproteomics.
Influence of DBD Inlet Geometry on the Homogeneity of Plasma‐Polymerized Acrylic Acid Films: The Use of a Microplasma–Electrode Inlet Configuration
Authors: Cools Pieter , Sainz‐García Elisa , Geyter Nathalie De , Nikiforov Anton , Blajan Marius , Shimizu Kazuo , Alba‐Elías Fernando , Leys Christophe , Morent Rino
Published: June 2015

Multiple vapor inlet systems have been developed to enhance the homogeneity of deposited polyacrylic acid films via medium and atmospheric pressure plasma technology. Different inlet systems were experimentally tested and optical reflectance spectrometry (OPS) was used to measure the differences in thickness of the films along the exposed surface. Standard deviations of more than 65% were reduced to less than 10%. COMSOL models point to the gas flow as the main contributor to the film homogeneity. OPS analysis of the best set‐up shows a linear relationship between thickness and exposure time (100–200 nm/min). XPS C1s deconvolution indicates a preservation of +50% of the –COOH groups and a significant incorporation of other oxygen containing groups.
Multiculture and Public Parks: Researching Super‐diversity and Attachment in Public Green Space
Authors: Neal Sarah , Bennett Katy , Jones Hannah , Cochrane Allan , Mohan Giles
Published: June 2015

Situating itself in encounter and public space debates and borrowing from non‐representational theory approaches, this paper uses data from the authors' 2‐year Economic and Social Research Council research project to consider how local urban parks can work as sites of routine encounter, mixity, and place belonging. The paper explores how parks as green public spaces are important as sites of inclusive openness while the materiality of parks is a key dynamic in affective encounter processes. Parks can work as animators of social interactions, participatory practices, and place affinities across ethnic and cultural difference. The paper concludes that the concept of convivial encounter can be extended to incorporate the concept of elective practices – choosing to be in shared public space can generate connective sensibilities that are not necessarily contingent on exchange. In using parks as a lens to examine localities and diversity, the paper critically reflects on research practices for understanding and describing heterogeneous formations of multiculture and outlines how the project's research design and the fieldwork methods sought to carefully and appropriately undertake research with complexly different places and populations Copyright © 2015 John Wiley & Sons, Ltd.
Compression and encryption for remote sensing image using chaotic system
Authors: Huang Xiaoling , Ye Guodong , Chai Huajin , Xie Ou
Published: June 2015

In this paper, because of the acquisition principle and big data of remote sensing image, we suggest an encryption scheme using chaotic system to build up the compressed sensing framework. A two‐dimensional generalized Arnold map is adopted here to generate the entries of the Toeplitz matrix used as measurement matrix. Then, the selecting row of the Toeplitz matrix is also decided by the chaotic sequence generated randomly by the Arnold map. With a further function of permutation operation, we can also encrypt remote sensing image after compression. The key space is constructed by the initial conditions in chaotic system. Experiment results show that the proposed method can be suitable to compressed sensing when the random measurement matrix is generated using chaotic system. Additionally, although the permutation operation is adopted, it is mainly used to enhance the security of cipher‐image. The reconstruction result is only dependent on the standard recovery algorithm. Copyright © 2015 John Wiley & Sons, Ltd.
The prediction of the small for gestational age fetus with the head circumference to abdominal circumference (HC/AC) ratio: a new look at an old measurement
Authors: Quinton Ann , Cook Colleen , Peek Michael
Published: June 2015

Introduction

The small for gestational age (SGA) fetus is at a higher risk of adverse events throughout life. Third trimester ultrasound measurements are poor at predicting SGA at delivery. We aimed to determine if ultrasound biometric growth parameters at 28–32 weeks of gestation could predict SGA, defined as birth weight below the 10th percentile.

Method

The relationship between fetal biometry and SGA at birth was examined using various statistical analyses. This prospective cross‐sectional study of 41 women (smokers n = 21; non‐smokers n = 20) had a 20% SGA incidence (8/41).

Results

We demonstrated an increase in the head circumference (HC)/abdominal circumference (AC) ratio correlated with a decrease in birth weight percentile (r = −0.528, P < 0.001). The HC/AC ratio was the best predictor of SGA and was significantly higher at 1.105 ± 0.037 (mean ± SD) for SGA neonates compared with 1.067 ± 0.039 for appropriate‐for‐gestational‐age neonates (P = 0.02). A cutoff value of 1.067 derived from the receiver operating characteristic curve gave a sensitivity of 88% and specificity of 52% with area under the curve equal to 0.742 (P = 0.04, Chi‐square).

Discussion

An increased HC/AC ratio at 28–32 weeks was a sensitive predictor of SGA at delivery. The HC/AC ratio may prove to be a useful marker for SGA with larger studies necessary to confirm these findings.
Human Induced Pluripotent Stem Cell-Derived Microvesicles Transmit RNAs and Proteins to Recipient Mature Heart Cells Modulating Cell Fate and Behavior
Authors: Bobis-Wozowicz Sylwia , Kmiotek Katarzyna , Sekula Malgorzata , Kedracka-Krok Sylwia , Kamycka Elzbieta , Adamiak Marta , Jankowska Urszula , Madetko-Talowska Anna , Sarna Michal , Bik-Multanowski Miroslaw , Kolcz Jacek , Boruczkowski Dariusz , Madeja Zbigniew , Dawn Buddhadeb , Zuba-Surma Ewa K.
Published: June 2015

Microvesicles (MVs) are membrane-enclosed cytoplasmic fragments released by normal and activated cells that have been described as important mediators of cell-to-cell communication. Although the ability of human induced pluripotent stem cells (hiPSCs) to participate in tissue repair is being increasingly recognized, the use of hiPSC-derived MVs (hiPSC-MVs) in this regard remains unknown. Accordingly, we investigated the ability of hiPSC-MVs to transfer bioactive molecules including mRNA, microRNA (miRNA), and proteins to mature target cells such as cardiac mesenchymal stromal cells (cMSCs), and we next analyzed effects of hiPSC-MVs on fate and behavior of such target cells. The results show that hiPSC-MVs derived from integration-free hiPSCs cultured under serum-free and feeder-free conditions are rich in mRNA, miRNA, and proteins originated from parent cells; however, the levels of expression vary between donor cells and MVs. Importantly, we found that transfer of hiPSC components by hiPSC-MVs impacted on transcriptome and proteomic profiles of target cells as well as exerted proliferative and protective effects on cMSCs, and enhanced their cardiac and endothelial differentiation potential. hiPSC-MVs also transferred exogenous transcripts from genetically modified hiPSCs that opens new perspectives for future strategies to enhance MV content. We conclude that hiPSC-MVs are effective vehicles for transferring iPSC attributes to adult somatic cells, and hiPSC-MV-mediated horizontal transfer of RNAs and proteins to injured tissues may be used for therapeutic tissue repair. In this study, for the first time, we propose a new concept of use of hiPSCs as a source of safe acellular bioactive derivatives for tissue regeneration. Stem Cells  2015;33:2748–2761
Use of genomic markers to risk stratify men with prostate cancer
Authors: Davis John W.
Published: June 2015

New genomic biomarkers are being developed to refine the risk for men with prostate cancer, but for healthcare professionals to believe in them, they must be both valid and of clinical utility. John Davis reviews three of these biomarkers, providing advice on how to interpret results and make decisions.
Olecranon Tip Osteoarticular Autograft Transfer for Irreparable Coronoid Process Fracture: A Biomechanical Study
Authors: Ramirez Miguel A. , Ramirez Jose M. , Parks Brent G. , Tsai Michael A. , Murthi Anand M.
Published: June 2015

Background

We hypothesized that transfer of the olecranon tip for simulated type III coronoid fracture would restore posterior ulnohumeral translation to a level not different from that in the intact state.

Methods

The collateral ligaments were left intact in 12 fresh-frozen cadaveric elbows, and all other soft tissues were removed. The entire coronoid process was osteotomized flush with the ventral aspect of the ulna and was reconstructed using the tip of the olecranon process. Specimens were tested with an axial load of 100 N at 0.25 mm/s in 15° increments from 15 to 120° of flexion. Intact, osteotomized, and reconstructed posterior ulnohumeral displacement was measured.

Results

The bony reconstruction did not obstruct range of motion of the elbow. Intact translation (mean±SD) ranged from 0.3±0.1 to 1.1±0.6 mm, and translation in the osteotomized state ranged from 1.3±1.0 to 2.0±1.0 mm. Resection of the coronoid resulted in a significant increase in posterior ulnar translation compared with intact at all flexion angles ( p<.05) except at 75°. Reconstruction decreased translation versus the osteotomized state at all flexion angles, significantly at 60 and 120°. No significant difference in translation was found between reconstructed and intact states at five of eight positions tested.

Conclusions

In this biomechanical study of irreparable coronoid fracture, autograft olecranon tip transfer restored posterior elbow stability to a level not significantly different from the intact elbow in five of eight elbow positions tested.
Why it is Time to Redesign Our Political System
Authors: Mancini Pia
Published: June 2015

Modern political systems are out of sync with the times we are living in. While the Internet allows us unprecedented access to information, low costs for collaborating and participating, and the ability to express our desires, demands and concerns, our input in policymaking is limited to voting once every two to five years. Innovative tools, both online and offline, are needed to upgrade our democracies. Society needs instruments and processes that allow it to choose how it is governed. Institutions have to be established that reflect today's technological, cultural and social realities and values. These institutions must be able to generate trust and provide mechanisms for social debate and collaboration, as well as social feedback loops that can accelerate institutionalised change.
Actitudes lingüísticas hacia la maya y la elección del aprendizaje de un idioma en un sector de población joven de la ciudad de Mérida
Authors: Sima Lozano Eyder Gabriel , Perales Escudero Moisés Damián
Published: June 2015

La población juvenil monolingüe de español de la ciudad de Mérida afirma que actualmente la lengua maya tiene mucho valor y prestigio. A pesar de ello, cuando eligen aprender un segundo idioma, la preferencia se inclina hacia el inglés u otra lengua. Este estudio explora cuáles son las actitudes que inciden en las decisiones de los hablantes para valorar una lengua y estudiar otra.
Institucionalización de un Nuevo Movimiento Religioso Japonés en Yucatán. Historia y organización de la Soka Gakkai
Authors: May May Ezer R.
Published: June 2015

En este artículo exploro la historia de la Soka Gakkai de Mérida, un nuevo movimiento religioso laico budista con sede en Japón. El objetivo principal es analizar el proceso de institucionalización para comprender su establecimiento en un contexto ajeno, reconociendo las fuerzas disruptivas que surgen como parte de la complejización organizacional. En primer lugar, presento una síntesis histórica de la Soka Gakkai y sus antecedentes religiosos, procedentes del budismo de Nichiren. Posteriormente divido en fases (organización incipiente, eficiencia y formalismo) el desarrollo de la agrupación para ubicar las coyunturas históricas que expliquen la condición actual de la Soka Gakkai en Mérida. Finalmente, expongo una visión en conjunto proveniente del análisis.