bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fabrication of silver nanorods embedded in PDMS film and its application for strain sensing
Authors: Goel Pratibha , Singh J P 
Published: October 2015

Abstract
Highly reflective and surface conductive strain gauges have been prepared by embedding the silver nanorods (AgNRs) into polydimethylsiloxane (PDMS). Thermal curing of PDMS on AgNRs grown Si wafer leads to a flexible, reflective and conductive silver surface. The reflectance of the as prepared films were observed to be 60% with a low value of sheet resistance. The reflectance of the film was able to be tuned from 60% to 15% in the visible region. The fabrication of a parallel plate capacitor strain sensor from AgNRs embedded PDMS, and tuning of the capacitance with respect to the applied strain, leads to a gauge factor of ~1. These mechanically tunable AgNRs/PDMS films demonstrate potential application as a strain sensor.
Pedestal confinement and stability in JET-ILW ELMy H-modes
Authors: Maggi C.F. , Saarelma S. , Casson F.J. , Challis C. , de la Luna E. , Frassinetti L. , Giroud C. , Joffrin E. , Simpson J. , Beurskens M. , Chapman I. , Hobirk J. , Leyland M. , Lomas P. , Lowry C. , Nunes I. , Rimini F. , Sips A.C.C. , Urano H. 
Published: October 2015

Abstract
New experiments in 2013–2014 have investigated the physics responsible for the decrease in H-mode pedestal confinement observed in the initial phase of JET-ILW operation (2012 Experimental Campaigns). The effects of plasma triangularity, global beta and neutrals on pedestal confinement and stability have been investigated systematically. The stability of JET-ILW pedestals is analysed in the framework of the peeling–ballooning model and the model assumptions of the pedestal predictive code EPED. Low D neutrals content in the plasma, achieved either by low D2 gas injection rates or by divertor configurations with optimum pumping, and high beta are necessary conditions for good pedestal (and core) performance. In such conditions the pedestal stability is consistent with the peeling–ballooning paradigm. Moderate to high D2 gas rates, required for W control and stable H-mode operation with the ILW, lead to increased D neutrals content in the plasma and additional physics in the pedestal models may be required to explain the onset of the ELM instability. The changes in H-mode performance associated with the change in JET wall composition from C to Be/W point to D neutrals and low-Z impurities playing a role in pedestal stability, elements which are not currently included in pedestal models. These aspects need to be addressed in order to progress towards full predictive capability of the pedestal height.
The new protein topology graph library web server
Authors: Schäfer Tim , Scheck Andreas , Bruneß Daniel , May Patrick , Koch Ina 
Published: October 2015

Abstract
Summary: We present a new, extended version of the Protein Topology Graph Library web server. The Protein Topology Graph Library describes the protein topology on the super-secondary structure level. It allows to compute and visualize protein ligand graphs and search for protein structural motifs. The new server features additional information on ligand binding to secondary structure elements, increased usability and an application programming interface (API) to retrieve data, allowing for an automated analysis of protein topology.
Availability and implementation: The Protein Topology Graph Library server is freely available on the web at http://ptgl.uni-frankfurt.de. The website is implemented in PHP, JavaScript, PostgreSQL and Apache. It is supported by all major browsers. The VPLG software that was used to compute the protein ligand graphs and all other data in the database is available under the GNU public license 2.0 from http://vplg.sourceforge.net.
Contact: tim.schaefer@bioinformatik.uni-frankfurt.de; ina.koch@bioinformatik.uni-frankfurt.de
Supplementary information: Supplementary data are available at Bioinformatics online.
SIMToolbox: a MATLAB toolbox for structured illumination fluorescence microscopy
Authors: Křížek Pavel , Lukeš Tomáš , Ovesný Martin , Fliegel Karel , Hagen Guy M. 
Published: October 2015

Abstract
Summary: SIMToolbox is an open-source, modular set of functions for MATLAB equipped with a user-friendly graphical interface and designed for processing two-dimensional and three-dimensional data acquired by structured illumination microscopy (SIM). Both optical sectioning and super-resolution applications are supported. The software is also capable of maximum a posteriori probability image estimation (MAP-SIM), an alternative method for reconstruction of structured illumination images. MAP-SIM can potentially reduce reconstruction artifacts, which commonly occur due to refractive index mismatch within the sample and to imperfections in the illumination.
Availability and implementation: SIMToolbox, example data and the online documentation are freely accessible at http://mmtg.fel.cvut.cz/SIMToolbox.
Contact: ghagen@uccs.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
PROSE Treatment for Ocular Chronic Graft-Versus-Host Disease as a Clinical Network Expands
Authors: DeLoss Karen S. , Le Hong-Gam , Gire Anisa , Chiu Gloria B. , Jacobs Deborah S. , Carrasquillo Karen G. 
Published: October 2015

Background:
Keratoconjunctivitis sicca occurs in 40% to 90% of patients with ocular chronic graft-versus-host disease (cGVHD). Ocular symptoms can have profound effects in both the visual function and quality of life of patients with GVHD. We report the impact of prosthetic replacement of the ocular surface ecosystem (PROSE) treatment in patients with cGVHD as a clinical network expands.

Methods:
We queried the BostonSight PROSE manufacturing database from January 2002 to December 2011. Patients treated for ocular cGVHD were reported by age, gender, year, and network site where the treatment was undertaken. The baseline and six-month follow-up scores of visual function using a standardized validated instrument, the National Eye Institute Visual Function Questionnaire (NEI VFQ-25), were evaluated for a period in 2006 and again in 2010 after network expansion had occurred.

Results:
A total of 407 patients with a male:female ratio of 226:181, mean age was 51 years with ocular cGVHD underwent PROSE treatment from January 2002 to December 2011. By 2011, 67% of all cases were treated at network clinics. Baseline characteristics of patients treated throughout the network in 2010 were similar to that of 2006 and 2010 cohorts from the main center. There was a significant improvement of 41 points (P<0.001) in composite NEI VFQ score among patients treated across the network in 2010, similar to the improvement of 30 points (P<0.001) seen among the patients treated at the main center in 2010. There was a trend toward lower baseline self-reported general health status (SRGHS) and VFQ scores among patients treated at network clinics, suggesting that expansion of the network allows treatment of sicker patients (lower general health status) or those more severely affected by ocular cGVHD.

Conclusions:
PROSE treatment of ocular cGVHD has increased in the last decade with the establishment of BostonSight network clinics across the United States. Patients treated at network clinics showed similar levels of baseline visual function and SRGHS, and achieved a similar high level of improvement in visual function as those treated at the main center. Patient-reported measures of functional status are useful in evaluating treatment options for patients with cGVHD. PROSE treatment has significant positive impact on the visual function of patients with ocular cGVHD regardless of whether the patient is treated at the main center or at a network site.
Distinguishing Classical Hodgkin Lymphoma, Gray Zone Lymphoma, and Large B-cell Lymphoma: A Proposed Scoring System
Authors: O’Malley Dennis P. , Fedoriw Yuri , Weiss Lawrence M. 
Published: October 2015

Background:
The diagnosis of “B-cell lymphoma, unclassifiable, with features intermediate between diffuse large B-cell lymphoma and classical Hodgkin lymphoma” represents an indeterminate or equivocal decision in relation to management because there remain differences in the management of Hodgkin and non-Hodgkin lymphomas. We developed a scoring system for this group of lymphomas using markers that are traditionally associated with diagnosis of classical Hodgkin lymphoma (CHL) and immunophenotypic markers associated with the “B-cell program” expressed in normal B cells.

Materials and Methods:
This system emphasized known criteria used to diagnose CHL that are rare in B-cell lymphoma (BCL) [CD15+, CD45−, CD20− or weak/variable, PAX5+ (weak or moderate), CD79a−, OCT-2−/BOB.1− or OCT-2+/BOB.1− or OCT-2−/BOB.1+, EBV+] versus findings that are common in BCL in contrast to CHL (CD15−, CD45+, CD20+ strong, PAX5+ strong, CD79a+, OCT-2+/BOB.1+, EBV−). After a preliminary test trial, MUM1 staining was also added. Results associated with CHL were assigned a score of +1 and score associated with BCL were assigned a score of −1. In the final grading system, a maximum score of +6 is possible for CHL and −6 for BCL.

Results:
An initial series of 38 cases was evaluated using a proprietary system that allows analysis of multiple stains on individual cells in a single section. An additional 23 cases were evaluated with results blinded until after scoring was performed. In general there was high concordance among cases originally diagnosed as CHL with high scores (score +4 to +6). Cases originally diagnosed as gray zone lymphomas exhibited a broader range of scores (+3 to −4). Cases of BCLs had low scores (−3 to −6).

Conclusions:
The primary goal of this study was to create a scoring system that allows a cumulative quantitative measure of immunohistochemical markers, based on expected results to compare cases that might have overlapping features. In most cases, scores that trend to one extreme or another are likely representative of CHL or BCL and do not lie in the gray zone. This scoring system allows for practical resolution of many borderline cases and provide some guidance in difficult cases.
Interaction of seed size with light quality and temperature regimes as germination cues in 10 temperate pioneer tree species
Authors: Xia Qingqing , Ando Mariko , Seiwa Kenji 
Published: October 2015

Summary

Pioneer species use temperature fluctuations and light level as gap detection signals, but the relative importance of these two factors may differ among species with differently sized seeds.

We monitored changes in these environmental signals at different soil and litter depths in gaps and the adjacent forest understorey. We conducted a seed germination experiment in growth chambers to test the effects of darkness and red to far‐red (R:FR) light ratios of 0·1, 0·4 and 1·0 under fluctuating (30/10 °C day/night) and constant (20 °C) temperatures; the experimental subjects belonged to 10 pioneer tree species with different seed sizes.

In forest gaps, light is a germination cue that is detectable only at or within 2 mm below the soil surface when litter is absent, whereas temperature signals can be detected in deeper soil.

The proportion of seeds germinating (percent germination) in small‐seeded species (seed mass ≤1·05 mg) was strongly promoted by higher R:FR ratios, thereby ensuring germination of seeds close to the soil or litter surface. In contrast, the percent germination of large‐seeded species (seed mass ≥200 mg) was strongly facilitated by temperature fluctuations, ensuring germination of seeds buried in even deep soil and litter. We detected interactive effects of the two signals in three species with medium‐sized seeds (2·84–9·50 mg).

Across the temperate pioneer trees tested, the relative importance of light versus temperature regimens (as germination cues for gap detection) was strongly related to seed size.
Role of cyclooxygenase‐1 and ‐2 in endothelium‐dependent contraction of atherosclerotic mouse abdominal aortas
Authors: Li Shasha , Liu Bin , Luo Wenhong , Zhang Yingzhan , Li Hui , Huang Dongyang , Zhou Yingbi 
Published: October 2015

SummaryThe objective of this study was to determine the role of cyclooxygenase (COX)‐1 or ‐2 in endothelium‐dependent contraction under atherosclerotic conditions. Atherosclerosis was induced in apoE knockout (apoE−/−) mice and those with COX‐1−/− (apoE−/−‐COX‐1−/−) by feeding with high fat and cholesterol food. Aortas (abdominal or the whole section) were isolated for functional and/or biochemical analyses. As in non‐atherosclerotic conditions, the muscarinic receptor agonist acetylcholine (ACh) evoked an endothelium‐dependent, COX‐mediated contraction following NO synthase (NOS) inhibition in abdominal aortic rings from atherosclerotic apoE−/− mice. Interestingly, COX‐1 inhibition not only abolished such a contraction in rings showing normal appearance, but also diminished that in rings with plaques. Accordingly, only a minor contraction (<30% that of apoE−/− counterparts) was evoked by ACh (following NOS inhibition) in abdominal aortic rings of atherosclerotic apoE−/−‐COX‐1−/− mice with plaques, and none was evoked in those showing normal appearance. Also, the contraction evoked by ACh in apoE−/−‐COX‐1−/− abdominal aortic rings with plaques was abolished by non‐selective COX inhibition, thromboxane‐prostanoid (TP) receptor antagonism, or endothelial denudation. Moreover, it was noted that ACh evoked a predominant production of the prostacyclin (PGI2, which mediates abdominal aortic contraction via TP receptors in mice) metabolite 6‐keto‐PGF1α, which was again sensitive to COX‐1 inhibition or COX‐1−/−. Therefore, in atherosclerotic mouse abdominal aortas, COX‐1 can still be the major isoform mediating endothelium‐dependent contraction, which probably results largely from PGI2 synthesis as in non‐atherosclerotic conditions. In contrast, COX‐2 may have only a minor role in such response limited to areas of plaques under the same pathological condition.
Dispersive Micro‐Solid‐Phase Extraction Based on Decanoic Acid Coated‐Fe3O4 Nanoparticles for HPLC Analysis of Phthalate Esters in Liquor Samples
Authors: Wang Juan , Zhang Lei , Xin Dingqiang , Yang Yaling 
Published: October 2015

AbstractA novel, simple and low cost through coating Fe3O4 magnetic nanoparticles (MNPs) with decanoic acid were synthesized. The functionalized MNPs showed excellent dispersibility in aqueous solution and were applied to dispersive micro‐solid‐phase extraction (D‐μ‐SPE) followed by high performance liquid chromatographic analysis for 4 phthalate esters (PAEs) including benzyl butyl phthalate (BBP), dicyclohexyl phthalate (DCHP), di‐n‐butyl phthalate (DBP), and di‐n‐octyl phthalate (DNOP) from liquor samples. The extraction equilibrium is achieved in 1 min. The MNPs allow easy and rapid isolation of PAEs by using an external magnet, which can be reused 5 times. The 4 PAEs linear dynamic ranges were in the range of 5 to 1000 ng/mL and the correlation coefficients values were 0.9999. The limits of detection were in the range of 0.91 to 2.43 ng/mL. The influences of the adsorbent dosage and the use frequency of adsorbent, the adsorption time, the solution pH and ionic strength were investigated and optimized. The proposed method was used to determine of PAEs in liquor samples and recoveries between 88.9% and 105.4%, with the relative standard deviations were below 4.0%.
Association between sensory dysfunction and pain 1 week after breast cancer surgery: a psychophysical study
Authors: Andersen K. G. , Duriaud H. M. , Aasvang E. K. , Kehlet H. 
Published: October 2015

BackgroundBreast cancer patients treated with axillary lymph node dissection (ALND) have a higher risk of both acute and persistent pain than those treated with sentinel lymph node biopsy (SLNB). This could be attributed to a higher risk of nerve injury with ALND. We hypothesized that (1) pain patients have more pronounced sensory dysfunction than pain‐free patients, (2) ALND have more sensory dysfunction and pain than SLNB patients and (3) patients with preserved intercostobrachial nerve (ICBN) preservation have less sensory dysfunction compared to a sectioned ICBN.MethodsTwenty‐seven patients treated with ALND and 27 with SLNB examined with a standardized Quantitative Sensory Testing (QST) protocol, including sensory mapping, mechanical and thermal thresholds, as well as recording intraoperative ICBN handling and pain status 1 week post‐operative.ResultsThe area of cold hypoaesthesia was significantly associated with movement‐related pain (P = 0.004), with a similar tendency for warmth (P = 0.018) and brush (P = 0.030) hypoaesthesia areas. 14 (26%) of the patients had moderate/severe pain at rest and 13 (24%) during movement without differences between ALND and SLNB, but ALND was associated with more sensory dysfunction than SLNB. Patients with sectioned ICBN reported lower pain intensity than those with preserved ICBN (P = 0.005), but without differences in sensory dysfunction.ConclusionPain was increased in patients having larger areas of hypoaesthesia and reduced in patients where ICBN‐section was done. Sensory dysfunction was related to extent of axillary surgery, but not with ICBN handling. Our data suggest that acute pain after breast cancer surgery may be related to nerve injury.
Measurements of nasal airflow and patency: a critical review with emphasis on the use of peak nasal inspiratory flow in daily practice
Authors: Ottaviano G. , Fokkens W. J. 
Published: October 2015

AbstractObjective measures can be used to assist the clinician to diagnose and treat nasal obstruction and also to quantify nasal obstruction in research. Objective measurements of nasal obstruction are as important as objective measurements of lung function. peak nasal inspiratory flow (PNIF), acoustic rhinometry (AR) and rhinomanometry (RM), with their specific peculiarity, assess different aspects of nasal obstruction. From the studies available in the literature, it seems that these methods roughly correlate with each other and that all of them can be alternatively utilized very well in research as well as in clinical practice. This review describes the various methods that can be used to measure nasal patency, airflow and resistance, mainly peak nasal inspiratory flow, rhinomanometry and acoustic rhinometry. PNIF has been demonstrated to be reproducible and as good an indication of objective nasal patency as formal rhinomanometry and has the advantage to be cheap, simple and suitable for serial measurements and for home use even in the paediatric population. PNIF normative data are available for children, adults and elderly subjects, and the availability of unilateral PNIF normal values allows evaluation of nasal sides separately. Just as in the lower airways, objective and subjective evaluation gives different information that together optimizes the diagnosis and the treatment of our patients. We argue that PNIF should be used regularly in every outpatient clinic that treats patients with nasal obstruction.
Neurotoxicity and low paclitaxel clearance associated with concomitant clopidogrel therapy in a 60‐year‐old Caucasian woman with ovarian carcinoma
Authors: Bergmann Troels K. , Filppula Anne M. , Launiainen Terhi , Nielsen Flemming , Backman Janne T. , Brosen Kim 
Published: October 2015

AimThe aim of the present case report was to describe a novel pharmacokinetic drug–drug interaction between the antiplatelet agent clopidogrel and the antineoplastic agent paclitaxel.MethodsThe patient was identified in a previously described cohort of 93 patients with ovarian carcinoma treated with paclitaxel. The effect of clopidogrel acyl‐β‐D‐glucuronide on the metabolism of paclitaxel was assessed in human liver microsomes. The analysis of clopidogrel in plasma and the quantification of paclitaxel and 6α‐hydroxypaclitaxel in in vitro samples were performed by liquid chromatography tandem mass spectrometry.ResultsThe patient was a 60‐year‐old female treated with an unknown dose of clopidogrel at the time of paclitaxel therapy. Clopidogrel was present in all three of the plasma samples obtained during paclitaxel dosing. Estimated unbound paclitaxel clearance was 238 l h−1, which was only 62% of the cohort geometric mean (385 l h−1; range 176–726). She was hospitalized three times, developed severe neuropathy and paclitaxel treatment was subsequently discontinued. In vitro, 30‐min preincubation with 100 μM clopidogrel acyl‐β‐D‐glucuronide inhibited the depletion rate of 0.5 μM paclitaxel by 51% and the formation rate of 6α‐hydroxypaclitaxel by 77%.ConclusionThis is the first report of a clopidogrel–paclitaxel interaction, suggesting that clinically used doses of clopidogrel can reduce the cytochrome P450 2C8 (CYP2C8)‐mediated systemic clearance of paclitaxel, leading to an increased risk of paclitaxel toxicity. Caution should be exercised whenever the simultaneous use of paclitaxel and clopidogrel cannot be avoided.
The gender gap in student engagement: The role of teachers’ autonomy support, structure, and involvement
Authors: Lietaert Sofie , Roorda Debora , Laevers Ferre , Verschueren Karine , De Fraine Bieke 
Published: October 2015

BackgroundThe gender gap in education in favour of girls is a widely known phenomenon. Boys generally have higher dropout rates, obtain lower grades, and show lower engagement. Insight into factors related to these academic outcomes could help to address the gender gap.AimsThis study investigated, for Dutch language classes, (1) how boys and girls differ in behavioural engagement, (2) which teacher support dimensions (autonomy support, structure, involvement) may explain gender differences in engagement (mediation hypothesis), and (3) whether and which of these teacher support dimensions matter more for boys’ as opposed to girls’ engagement (moderation or differential effects hypothesis).SampleA total of 385 Grade 7 students and their 15 language teachers participated in this study.MethodsTeacher support was assessed through student reports. Student engagement was measured using student, teacher, and observer reports. By means of structural equation modelling, the mediating role of the teacher support dimensions for gender differences in behavioural engagement was tested. The potential differential role of the teacher support dimensions for boys’ and girls’ engagement was investigated through multigroup analysis.ResultsBoys were less engaged than girls and reported lower support from their teacher. Autonomy support and involvement partially mediated the relationship between gender and behavioural engagement. Autonomy support was demonstrated to be a protective factor for boys’ engagement but not for girls’. Structure and involvement contributed equally to engagement for both sexes.ConclusionsAlthough involvement and autonomy support partly explained the gender gap in engagement (mediation hypothesis), more support was found for differential effects of autonomy support on boys’ versus girls’ engagement (differential effects hypothesis).