bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative T1 and proton density mapping with direct calculation of radiofrequency coil transmit and receive profiles from two‐point variable flip angle data
Authors: Baudrexel Simon , Reitz Sarah C. , Hof Stephanie , Gracien René‐Maxime , Fleischer Vinzenz , Zimmermann Hilga , Droby Amgad , Klein Johannes C. , Deichmann Ralf
Published: January 2016

Quantitative T1 mapping of brain tissue is frequently based on the variable flip angle (VFA) method, acquiring spoiled gradient echo (GE) datasets at different excitation angles. However, accurate T1 calculation requires a knowledge of the sensitivity profile B1 of the radiofrequency (RF) transmit coil. For an additional derivation of proton density (PD) maps, the receive coil sensitivity profile (RP) must also be known. Mapping of B1 and RP increases the experiment duration, which may be critical when investigating patients. In this work, a method is presented for the direct calculation of B1 and RP from VFA data. Thus, quantitative maps of T1, PD, B1 and RP can be obtained from only two spoiled GE datasets. The method is based on: (1) the exploitation of the linear relationship between 1/PD and 1/T1 in brain tissue and (2) the assumption of smoothly varying B1 and RP, so that a large number of data points can be fitted across small volume elements where B1 and RP are approximately constant. The method is tested and optimized on healthy subjects. Copyright © 2016 John Wiley & Sons, Ltd.
Towards higher sensitivity and stability of axon diameter estimation with diffusion‐weighted MRI
Authors: Sepehrband Farshid , Alexander Daniel C. , Kurniawan Nyoman D. , Reutens David C. , Yang Zhengyi
Published: January 2016

Diffusion‐weighted MRI is an important tool for in vivo and non‐invasive axon morphometry. The ActiveAx technique utilises an optimised acquisition protocol to infer orientationally invariant indices of axon diameter and density by fitting a model of white matter to the acquired data. In this study, we investigated the factors that influence the sensitivity to small‐diameter axons, namely the gradient strength of the acquisition protocol and the model fitting routine. Diffusion‐weighted ex. vivo images of the mouse brain were acquired using 16.4‐T MRI with high (Gmax of 300 mT/m) and ultra‐high (Gmax of 1350 mT/m) gradient strength acquisitions. The estimated axon diameter indices of the mid‐sagittal corpus callosum were validated using electron microscopy. In addition, a dictionary‐based fitting routine was employed and evaluated. Axon diameter indices were closer to electron microscopy measures when higher gradient strengths were employed. Despite the improvement, estimated axon diameter indices (a lower bound of ~ 1.8 μm) remained higher than the measurements obtained using electron microscopy (~1.2 μm). We further observed that limitations of pulsed gradient spin echo (PGSE) acquisition sequences and axonal dispersion could also influence the sensitivity with which axon diameter indices could be estimated. Our results highlight the influence of acquisition protocol, tissue model and model fitting, in addition to gradient strength, on advanced microstructural diffusion‐weighted imaging techniques. © 2016 The Authors. NMR in Biomedicine published by John Wiley & Sons Ltd.
Oxygen‐dependent hyperpolarized 129Xe brain MR
Authors: Li Haidong , Zhang Zhiying , Zhong Jianping , Ruan Weiwei , Han Yeqing , Sun Xianping , Ye Chaohui , Zhou Xin
Published: January 2016

Hyperpolarized (HP) 129Xe MR offers unique advantages for brain functional imaging (fMRI) because of its extremely high sensitivity to different chemical environments and the total absence of background noise in biological tissues. However, its advancement and applications are currently plagued by issues of signal strength. Generally, xenon atoms found in the brain after inhalation are transferred from the lung via the bloodstream. The longitudinal relaxation time (T1) of HP 129Xe is inversely proportional to the pulmonary oxygen concentration in the lung because oxygen molecules are paramagnetic. However, the T1 of 129Xe is proportional to the pulmonary oxygen concentration in the blood, because the higher pulmonary oxygen concentration will result in a higher concentration of diamagnetic oxyhemoglobin. Accordingly, there should be an optimal pulmonary oxygen concentration for a given quantity of HP 129Xe in the brain. In this study, the relationship between pulmonary oxygen concentration and HP 129Xe signal in the brain was analyzed using a theoretical model and measured through in vivo experiments. The results from the theoretical model and experiments in rats are found to be in good agreement with each other. The optimal pulmonary oxygen concentration predicted by the theoretical model was 21%, and the in vivo experiments confirmed the presence of such an optimal ratio by reporting measurements between 25% and 35%. These findings are helpful for improving the 129Xe signal in the brain and make the most of the limited spin polarization available for brain experiments. Copyright © 2016 John Wiley & Sons, Ltd.
Stroke assessment with intravoxel incoherent motion diffusion‐weighted MRI
Authors: Suo Shiteng , Cao Mengqiu , Zhu Wanqiu , Li Lei , Li Jun , Shen Fei , Zu Jinyan , Zhou Zien , Zhuang Zhiguo , Qu Jianxun , Chen Zengai , Xu Jianrong
Published: January 2016

Intravoxel incoherent motion (IVIM) diffusion‐weighted MRI can simultaneously measure diffusion and perfusion characteristics in a non‐invasive way. This study aimed to determine the potential utility of IVIM in characterizing brain diffusion and perfusion properties for clinical stroke. The multi‐b‐value diffusion‐weighted images of 101 patients diagnosed with acute/subacute ischemic stroke were retrospectively evaluated. The diffusion coefficient D, representing the water apparent diffusivity, was obtained by fitting the diffusion data with increasing high b‐values to a simple mono‐exponential model. The IVIM‐derived perfusion parameters, pseudodiffusion coefficient D*, vascular volume fraction f and blood flow‐related parameter fD*, were calculated with the bi‐exponential model. Additionally, the apparent diffusion coefficient (ADC) was fitted according to the mono‐exponential model using all b‐values. The diffusion parameters for the ischemic lesion and normal contralateral region were measured in each patient. Statistical analysis was performed using the paired Student t‐test and Pearson correlation test. Diffusion data in both the ischemic lesion and normal contralateral region followed the IVIM bi‐exponential behavior, and the IVIM model showed better goodness of fit than the mono‐exponential model with lower Akaike information criterion values. The paired Student t‐test revealed significant differences for all diffusion parameters (all P < 0.001) except D* (P = 0.218) between ischemic and normal areas. For all patients in both ischemic and normal regions, ADC was significantly positively correlated with D (both r = 1, both P < 0.001) and f (r = 0.541, P < 0.001; r = 0.262, P = 0.008); significant correlation was also found between ADC and fD* in the ischemic region (r = 0.254, P = 0.010). For all pixels within the region of interest from a representative subject in both ischemic and normal regions, ADC was significantly positively correlated with D (both r = 1, both P < 0.001), f (r = 0.823, P < 0.001; r = 0.652, P < 0.001) and fD* (r = 0.294, P < 0.001; r = 0.340, P < 0.001). These findings may have clinical implications for the use of IVIM imaging in the assessment and management of acute/subacute stroke patients. Copyright © 2016 John Wiley & Sons, Ltd.
3D spatially encoded and accelerated TE‐averaged echo planar spectroscopic imaging in healthy human brain
Authors: Iqbal Zohaib , Wilson Neil E. , Thomas M. Albert
Published: January 2016

Several different pathologies, including many neurodegenerative disorders, affect the energy metabolism of the brain. Glutamate, a neurotransmitter in the brain, can be used as a biomarker to monitor these metabolic processes. One method that is capable of quantifying glutamate concentration reliably in several regions of the brain is TE‐averaged 1H spectroscopic imaging. However, this type of method requires the acquisition of multiple TE lines, resulting in long scan durations. The goal of this experiment was to use non‐uniform sampling, compressed sensing reconstruction and an echo planar readout gradient to reduce the scan time by a factor of eight to acquire TE‐averaged spectra in three spatial dimensions. Simulation of glutamate and glutamine showed that the 2.2–2.4 ppm spectral region contained 95% glutamate signal using the TE‐averaged method. Peak integration of this spectral range and home‐developed, prior‐knowledge‐based fitting were used for quantitation. Gray matter brain phantom measurements were acquired on a Siemens 3 T Trio scanner. Non‐uniform sampling was applied retrospectively to these phantom measurements and quantitative results of glutamate with respect to creatine 3.0 (Glu/Cr) ratios showed a coefficient of variance of 16% for peak integration and 9% for peak fitting using eight‐fold acceleration. In vivo scans of the human brain were acquired as well and five different brain regions were quantified using the prior‐knowledge‐based algorithm. Glu/Cr ratios from these regions agreed with previously reported results in the literature. The method described here, called accelerated TE‐averaged echo planar spectroscopic imaging (TEA‐EPSI), is a significant methodological advancement and may be a useful tool for categorizing glutamate changes in pathologies where affected brain regions are not known a priori. Copyright © 2016 John Wiley & Sons, Ltd.
Level‐set topology optimization with many linear buckling constraints using an efficient and robust eigensolver
Authors: Dunning Peter D. , Ovtchinnikov Evgueni , Scott Jennifer , Kim H. Alicia
Published: January 2016

Linear buckling constraints are important in structural topology optimization for obtaining designs that can support the required loads without failure. During the optimization process, the critical buckling eigenmode can change; this poses a challenge to gradient‐based optimization and can require the computation of a large number of linear buckling eigenmodes. This is potentially both computationally difficult to achieve and prohibitively expensive. In this paper, we motivate the need for a large number of linear buckling modes and show how several features of the block Jacobi conjugate gradient (BJCG) eigenvalue method, including optimal shift estimates, the reuse of eigenvectors, adaptive eigenvector tolerances and multiple shifts, can be used to efficiently and robustly compute a large number of buckling eigenmodes. This paper also introduces linear buckling constraints for level‐set topology optimization. In our approach, the velocity function is defined as a weighted sum of the shape sensitivities for the objective and constraint functions. The weights are found by solving an optimization sub‐problem to reduce the mass while maintaining feasibility of the buckling constraints. The effectiveness of this approach in combination with the BJCG method is demonstrated using a 3D optimization problem. Copyright © 2016 John Wiley & Sons, Ltd.
A transformation approach for efficient evaluation of oscillatory surface integrals arising in three‐dimensional boundary element methods
Authors: Hargreaves Jonathan A. , Lam Yiu W. , Langdon Stephen
Published: January 2016

We propose a method for efficient evaluation of surface integrals arising in boundary element methods for three‐dimensional Helmholtz problems (with real positive wavenumber k), modelling wave scattering and/or radiation in homogeneous media. To reduce the number of degrees of freedom required when k is large, a common approach is to include in the approximation space oscillatory basis functions, with support extending across many wavelengths. A difficulty with this approach is that it leads to highly oscillatory surface integrals whose evaluation by standard quadrature would require at least O(k2) quadrature points. Here, we use equivalent contour integrals developed for aperture scattering in optics to reduce this requirement to O(k), and possible extensions to reduce it further to O(1) are identified. The contour integral is derived for arbitrary shaped elements, but its application is limited to planar elements in many cases. In addition, the transform regularises the singularity in the surface integrand caused by the Green's function, including for the hyper‐singular case under appropriate conditions. An open‐source Matlab™code library is available to demonstrate our routines. © 2016 The Authors International Journal for Numerical Methods in Engineering Published by John Wiley & Sons Ltd.
Pore‐scale modeling of deformation and shear band bifurcation in porous crystalline rocks
Authors: Tjioe Martin , Borja Ronaldo I.
Published: January 2016

We develop a computational framework that captures the microfracture processes leading to shear band bifurcation in porous crystalline rocks. The framework consists of computational homogenization on a representative elementary volume that upscales the pore‐scale microfracture processes to the continuum scale. The assumed enhanced strain finite element approach is used to capture the discontinuous displacement field generated by the microfractures. Homogenization at the continuum scale results in incrementally nonlinear material response, in which the overall constitutive tangent tensor varies with the stress state and with the loading direction. Continuum bifurcation detects the formation of a shear band on the representative elementary volume level; multi‐dimensional strain probes, necessitated by the incremental nonlinearity of the overall constitutive response, determine the most critical orientation of shear band bifurcation. Numerical simulations focus on microfracturing at the pore scale with either predominant interface separation or predominant interface contact modes. Results suggest a non‐associative overall plastic flow and shear band bifurcation that depends on the microfracture length and the characteristic sliding distance related to slip weakening. Copyright © 2016 John Wiley & Sons, Ltd.
How well does the standard body mass index or variations with a different exponent predict human lifespan?
Authors: Foster Dean , Karloff Howard , Shirley Kenneth E.
Published: January 2016

Objective

The objective was twofold: (1) to estimate for each individual the body mass index (BMI) which is associated with the lowest risk of death, and (2) to study variants of the BMI formula to determine which gives the best predictions of death.

Methods

Treating BMI = mass/height2 as a continuous variable and estimating its interaction effects with several other variables, this study analyzed the NIH‐AARP study data set of approximately 566,000 individuals and fit Cox proportional hazards models to the survival times.

Results

For each individual, a “personalized optimal BMI,” the BMI for that individual which, according to the model, is associated with the lowest risk of death, is estimated. The average personalized optimal BMI is approximately 26, which is in the current “overweight” category. In fact, mass/height is a better predictor of death on the data set than BMI itself.

Conclusions

The model suggests that an individual's “optimal” BMI depends on his or her features; “one‐size‐fits‐all” recommendations may be not best.
Development of tools to study personal weight control strategies: OxFAB taxonomy
Authors: Hartmann‐Boyce Jamie , Aveyard Paul , Koshiaris Constantinos , Jebb Susan A.
Published: January 2016

Objective

To describe the development of the Oxford Food and Activity Behaviors (OxFAB) taxonomy and questionnaire to explore the cognitive and behavioral strategies used by individuals during weight management attempts.

Methods

The taxonomy was constructed through a qualitative analysis of existing resources and a review of existing behavior change taxonomies and theories. The taxonomy was translated into a questionnaire to identify strategies used by individuals. Think‐aloud interviews were conducted to test the face/concept validity of the questionnaire, and test–retest reliability was assessed in a sample of 138 participants.

Results

The OxFAB taxonomy consists of 117 strategies grouped into 23 domains. Compared to taxonomies used to describe interventions, around half of the domains and strategies identified are unique to the OxFAB taxonomy. The OxFAB questionnaire consists of 117 questions, one for each strategy from the taxonomy. Test–retest resulted in a mean PABAK score of 0.61 (SD 0.15). Questions were revised where appropriate.

Conclusions

The OxFAB taxonomy and questionnaire provide a conceptual framework to identify the cognitive and behavioral strategies used by individuals during attempts at weight control.
Marginal Pricing and Student Investment in Higher Education
Authors: Hemelt Steven W. , Stange Kevin M.
Published: January 2016

This paper examines the effect of marginal price on students’ educational investments using rich administrative data on students at Michigan public universities. Marginal price refers to the amount colleges charge for each additional credit taken in a semester. Institutions differ in how they price credits above the full‐time minimum (of 12 credits), with many institutions reducing the marginal price of such credits to zero. We find that a zero marginal price induces a modest share of students (i.e., 7 percent) to attempt up to one additional class (i.e., three credits) but also increases withdrawals and lowers course performance. The analysis generally suggests minimal impacts on credits earned and the likelihood of meeting “on‐time” benchmarks toward college completion, though estimates for these outcomes are less precise and more variable across specifications. Consistent with theory, the effect on attempted credits is largest among students who would otherwise locate at the full‐time minimum, which includes lower‐achieving and socioeconomically disadvantaged students.
Cell adhesion and polarity in squamous cell carcinoma of the lung
Authors: Bonastre Ester , Brambilla Elisabeth , Sanchez‐Cespedes Montse
Published: January 2016

Lung cancer is a deadly disease that can roughly be classified into three histopathological groups: lung adenocarcinomas, lung squamous cell carcinomas (LSCCs), and small cell carcinomas. These types of lung cancer are molecularly, phenotypically, and regionally diverse neoplasms, reflecting differences in their cells of origin. LSCCs commonly arise in the airway epithelium of a main or lobar bronchus, which is an important line of defence against the external environment. Furthermore, most LSCCs are characterized histopathologically by the presence of keratinization and/or intercellular bridges, consistent with the molecular features of these tumours, characterized by high levels of transcripts encoding keratins and proteins relevant to intercellular junctions and cell polarity. In this review, the relationships between the molecular features of LSCCs and the types of cell and epithelia of origin are discussed. Recurrent alterations in genes involved in intercellular adhesion and cell polarity in LSCCs are also reviewed, emphasizing the importance of the disruption of PAR3 and the PAR complex. Finally, the possible functional effects of these alterations on epithelial homeostasis, and how they contribute to the development of LSCC, are discussed. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Effectiveness of bevacizumab exposure beyond disease progression in patients with non–small‐cell lung cancer: analyses of the ARIES observational cohort study
Authors: Leon Larry , Kosty Michael , Jahanzeb Mohammad , Spigel David , Wozniak Antoinette J. , Brahmer Julie , Fish Susan , Flick E. Dawn , Hazard Sebastien J. , Lynch Thomas J.
Published: January 2016

Purpose

Bevacizumab used in combination with first‐line chemotherapy confers an overall survival (OS) benefit for patients with non‐squamous non–small‐cell lung cancer (NSCLC). This analysis from the ARIES observational cohort study (OCS) was initiated to evaluate the effect of bevacizumab use beyond disease progression (BBP) on clinical outcomes in patients with NSCLC receiving first‐line treatment with bevacizumab and chemotherapy.

Methods

The ARIES OCS prospectively enrolled patients from 2006 to 2009 in the United States who had advanced non‐squamous NSCLC, received bevacizumab with chemotherapy in the first‐line setting, and survived progressive disease (PD). A dichotomous landmark analysis examined post‐PD OS (ppOS) in patients who received BBP versus no BBP within 30 days post PD. A time‐dependent Cox model assessed the effect of cumulative BBP exposure on ppOS.

Results

The ARIES OCS enrolled 1967 patients with first‐line NSCLC; 1358 patients had first PD and were alive at the 30‐day landmark (351 patients with BBP and 1007 patients with no BBP). The landmark analysis showed that BBP was associated with a lower risk of death (BBP versus No‐BBP); hazard ratio [HR], 0.75; 95% confidence interval 0.65–0.86. In the cumulative exposure analysis of 1461 patients who had PD, HRs for ppOS decreased by approximately 4% for each additional 21‐day interval of bevacizumab received. Protocol‐specified bevacizumab‐select adverse events occurred in 14% of BBP patients.

Conclusions

BBP was associated with a lower risk of death in patients with NSCLC treated with first‐line bevacizumab and chemotherapy. Copyright © 2016 John Wiley & Sons, Ltd.
Pain medication in German nursing homes: a whole lot of metamizole
Authors: Hoffmann Falk , Schmiemann Guido
Published: January 2016

Purpose

Prescribing of metamizole (dipyrone), an analgesic that has been withdrawn from the market or never approved in many countries owing to safety concerns, is high in elder persons in Germany. This study assessed the use of pain medications in German nursing homes with a special focus on prescribing patterns of metamizole.

Methods

Using data of the ‘Inappropriate Medication in Patients with Renal Insufficiency in Nursing Homes’ (IMREN) study conducted between October 2014 and April 2015 in nursing homes in Bremen and Lower Saxony, we studied prescribing of analgesics including both scheduled and as‐needed medications. For residents with scheduled medication, dosage and duration of use were analysed.

Results

A total of 852 residents from 21 nursing homes were included. They were on average 83.5 years old, and 76.5% were women; 73.8% received at least one analgesic with 70.3% obtaining World Health Organization step I drugs. The most frequently prescribed substances were metamizole (for 40.6%) and paracetamol (acetaminophen; 35.6%), with paracetamol given mostly as‐needed. The proportion of residents receiving metamizole increased with age (up to 47.4% in persons aged 90 years and over). Of 143 residents with scheduled metamizole (16.8%), the mean daily dosage was 1843 mg (interquartile range [IQR]: 1500–2250); 66.9% received metamizole for at least 90 days and 23.2% for at least 365 days (mean duration 276 days; IQR: 59–314).

Discussion

There is a discrepancy between prescribing of metamizole for older persons, on the one hand, and evidence on comparative effectiveness and safety as well as approval and recommendations, on the other hand. Copyright © 2016 John Wiley & Sons, Ltd.
Instrumental variable analysis as a complementary analysis in studies of adverse effects: venous thromboembolism and second‐generation versus third‐generation oral contraceptives
Authors: Boef Anna G. C. , Souverein Patrick C. , Vandenbroucke Jan P. , van Hylckama Vlieg Astrid , de Boer Anthonius , le Cessie Saskia , Dekkers Olaf M.
Published: January 2016

Purpose

A potentially useful role for instrumental variable (IV) analysis may be as a complementary analysis to assess the presence of confounding when studying adverse drug effects. There has been discussion on whether the observed increased risk of venous thromboembolism (VTE) for third‐generation oral contraceptives versus second‐generation oral contraceptives could be (partially) attributed to confounding. We investigated how prescribing preference IV estimates compare with conventional estimates.

Methods

Women in the Clinical Practice Research Database who started a second‐generation or third‐generation oral contraceptive from 1989 to 2013 were included. Ordinary least squares and two‐stage least squares regression were used to estimate risk differences in VTE. Cox regression and IV for Cox proportional hazards regression were used to calculate hazard ratios (HR). The instrument used was the proportion of prescriptions for third‐generation oral contraceptives by the general practitioner in the year preceding the current prescription.

Results

All analyses pointed in the direction of an increased VTE risk for third‐generation oral contraceptives. The adjusted HR from the conventional Cox regression was 1.62 (95% confidence interval 1.16–2.27) and the fully adjusted HR from the IV Cox regression was 3.45 (95% confidence interval; 0.97–11.7), showing a larger risk and wider confidence intervals in the IV analysis.

Conclusions

The similarity in direction of results from the IV analyses and conventional analyses suggests that major confounding is unlikely. IV analysis can be a useful complementary analysis to assess the presence of confounding in studies of adverse drug effects in very large databases. Copyright © 2016 John Wiley & Sons, Ltd.
Effects of Medical Marijuana on Migraine Headache Frequency in an Adult Population
Authors: Rhyne Danielle N. , Anderson Sarah L. , Gedde Margaret , Borgelt Laura M.
Published: January 2016

Study Objective

No clinical trials are currently available that demonstrate the effects of marijuana on patients with migraine headache; however, the potential effects of cannabinoids on serotonin in the central nervous system indicate that marijuana may be a therapeutic alternative. Thus, the objective of this study was to describe the effects of medical marijuana on the monthly frequency of migraine headache.

Design

Retrospective chart review.

Setting

Two medical marijuana specialty clinics in Colorado.

Patients

One hundred twenty‐one adults with the primary diagnosis of migraine headache who were recommended migraine treatment or prophylaxis with medical marijuana by a physician, between January 2010 and September 2014, and had at least one follow‐up visit.

Measurements and Results

The primary outcome was number of migraine headaches per month with medical marijuana use. Secondary outcomes were the type and dose of medical marijuana used, previous and adjunctive migraine therapies, and patient‐reported effects. Migraine headache frequency decreased from 10.4 to 4.6 headaches per month (p<0.0001) with the use of medical marijuana. Most patients used more than one form of marijuana and used it daily for prevention of migraine headache. Positive effects were reported in 48 patients (39.7%), with the most common effects reported being prevention of migraine headache with decreased frequency of migraine headache (24 patients [19.8%]) and aborted migraine headache (14 patients [11.6%]). Inhaled forms of marijuana were commonly used for acute migraine treatment and were reported to abort migraine headache. Negative effects were reported in 14 patients (11.6%); the most common effects were somnolence (2 patients [1.7%]) and difficulty controlling the effects of marijuana related to timing and intensity of the dose (2 patients [1.7%]), which were experienced only in patients using edible marijuana. Edible marijuana was also reported to cause more negative effects compared with other forms.

Conclusion

The frequency of migraine headache was decreased with medical marijuana use. Prospective studies should be conducted to explore a cause‐and‐effect relationship and the use of different strains, formulations, and doses of marijuana to better understand the effects of medical marijuana on migraine headache treatment and prophylaxis.
Click‐coupling of anthraquinone dyes with β‐cyclodextrin: formation of polymeric superstructures
Authors: Lievenbrück Melanie , Hartlaub Benjamin , Ritter Helmut
Published: January 2016

Two novel cyclodextrin‐modified anthraquinone dyes were synthesized and investigated for their complexation behaviour and formation of superstructures. Therefore, 1‐fluoro‐4‐N‐(propargylamino)anthraquinone and 1,4‐bis(propargyloxy)anthraquinone were prepared via nucleophilic aromatic displacement and subsequently covalently ‘click‐coupled’ in a copper(I)‐catalysed azide–alkyne cycloaddition with β‐cyclodextrin monoazide. Both the propargyl‐modified precursor and the click‐coupled anthraquinone dyes were evaluated as hosts and guests, respectively, in β‐cyclodextrin interactions. The anthraquinone dye bearing two cyclodextrins, 1,4‐bis((1‐β‐cyclodextrin‐1H‐1,2,3‐triazol‐5‐yl)methoxy)anthraquinone, enables the reversible formation of supramolecular crosslinked poly[(N,N‐dimethyl acrylamide)‐co‐(N‐(ferrocenoylmethyl)acrylamide)] (11), whereas the monofunctionalized compound 1‐fluoro‐4‐(((1‐β‐cyclodextrin‐1H‐1,2,3‐triazol‐5‐yl)methyl)amino)anthraquinone can be supramolecularly linked to 11 resulting in coloured polymers. These features of β‐cyclodextrin‐linked anthraquinone dyes can be verified with either 1H 1H NMR rotating frame nuclear Overhauser effect spectroscopy or the naked eye. © 2016 Society of Chemical Industry
Soluble N‐substituted poly(benzimidazole imide)s via C−N coupling reaction
Authors: Shang Zhenfang , Yang Li , Chang Guanjun
Published: January 2016

Novel heat‐resistant N‐substituted poly(benzimidazole imide)s (PBIIs) with good solubility were synthesized via a C − N coupling reaction. A model reaction was carried out to assist in determining the optimal reaction conditions for the polymerization and to elucidate the chemical structures of the polymers. The structures of the resulting polymers were characterized by means of Fourier transform infrared and elemental analysis; the results showed good agreement with the proposed structures. The resulting PBIIs exhibited high glass transition temperatures (Tg > 290 oC) and good thermostability (T5% > 440 oC). The thermal behavior in air of the PBII polymers suggests that they can be considered as a new class of high performance polyimides. © 2016 Society of Chemical Industry
Enhanced crystallization of poly(lactide) stereocomplex by xylan propionate
Authors: Ishii Daisuke , Kimishima Misaki , Otake Katsuto , Iwata Tadahisa
Published: January 2016

The effect of xylan propionate (XylPr) as a novel biomass‐derived nucleating agent on the poly(lactide) sterecomplex was investigated. Addition of XylPr to an enantiomeric blend of poly(l‐lactide) (PLLA) and poly(d‐lactide) (PDLA) was performed in either the solution state or molten state. The solution blend of PLLA/PDLA with XylPr was prepared by mixing equal volumes of 1 wt% XylPr/PLLA and 1 wt% XylPr/PDLA solutions in chloroform and precipitating in methanol. The solution blend with XylPr showed shorter half‐time crystallization than the solution blend without XylPr in isothermal crystallization between 80 and 140 °C, although homocrystallization occurred. Enhanced stereocomplex crystallization in the solution blend with XylPr was observed at 180 °C, where no crystallization occurred in the solution blend without XylPr. Addition of XylPr to PLLA/PDLA blend in the molten state was performed at 240 °C. Thereafter, the melt blend of PLLA/PDLA with or without XylPr was either quenched in iced water or isothermally crystallized directly from the melt. Isothermal crystallization of the melt‐quenched blend with XylPr gave a similar result to the solution blend with XylPr. In contrast, the melt‐crystallized blend with XylPr formed only stereocomplex crystals after crystallization above 140 °C. Furthermore, the melt‐crystallized blend with XylPr showed a higher crystallinity index and melting temperature than the melt‐crystallized blend without XylPr. This shows that XylPr promotes stereocomplex crystallization only when the blend of PLLA/PDLA with XylPr is directly crystallized from the molten state just after blending. © 2016 Society of Chemical Industry
Integration of transcriptomic and proteomic analysis towards understanding the systems biology of root hairs
Authors: Wang Han , Lan Ping , Shen Ren Fang
Published: January 2016

Plants and other multicellular organisms consist of many types of specialized cells. Systems‐wide exploration of large‐scale information from singe cell level is essential to understand how cell works. Root hairs, tubular‐shaped outgrowths from root epidermal cells, play important roles in the acquisition of nutrients and water, in the interaction with microbe, and in plant anchorage, and represent an ideal model to study the biology of a single cell type. Single cell sampling combined with omics approaches has been applied to study plant root hairs. This review emphasizes the integration of omics approaches towards understanding the systems biology of root hairs, unraveling the common and plant species‐specific properties of root hairs, as well as the concordance of protein and transcript abundance. Understanding plant root hair biology by mining the integrated omics data will provide a way to know how a single cell differentiates, elongates, and functions, which might help molecularly modify crops for developing sustainable agriculture practices.
Advancing translational research with next‐generation protein microarrays
Authors: Yu Xiaobo , Petritis Brianne , LaBaer Joshua
Published: January 2016

Protein microarrays are a high‐throughput technology used increasingly in translational research, seeking to apply basic science findings to enhance human health. In addition to assessing protein levels, posttranslational modifications, and signaling pathways in patient samples, protein microarrays have aided in the identification of potential protein biomarkers of disease and infection. In this perspective, the different types of full‐length protein microarrays that are used in translational research are reviewed. Specific studies employing these microarrays are presented to highlight their potential in finding solutions to real clinical problems. Finally, the criteria that should be considered when developing next‐generation protein microarrays are provided.
Manual evaluation of tissue microarrays in a high‐throughput research project: The contribution of Indian surgical pathology to the Human Protein Atlas (HPA) project
Authors: Navani Sanjay
Published: January 2016

The Human Protein Atlas (HPA) program (www.proteinatlas.org) is an international program that has been set up to allow for a systematic exploration of the human proteome using antibody‐based proteomics. This is accomplished by combining high‐throughput generation of affinity‐purified (mono‐specific) antibodies with protein profiling in a multitude of tissues/cell types assembled in tissue microarrays. Twenty‐six surgical pathologists over a seven‐and‐half year period have annotated and curated approximately sixteen million tissue images derived from immunostaining of normal and cancer tissues by approximately 23 000 antibodies. Web‐based annotation software that allows for a basic and rapid evaluation of immunoreactivity in tissues has been utilized. Intensity, fraction of immunoreactive cells and subcellular localization were recorded for each given cell population. A text comment summarizing the characteristics for each antibody was added. The methods used and the challenges encountered for this exercise, the largest effort ever by a single group of surgical pathologists, are discussed. Manual annotation of digital images is an important tool that may be successfully utilized in high‐throughput research projects. This is the first time an Indian private pathology laboratory has been associated with cutting‐edge research internationally providing a classic example of developed and emerging nation collaboration.
α‐1‐Antitrypsin detected by MALDI imaging in the study of glomerulonephritis: Its relevance in chronic kidney disease progression
Authors: Smith Andrew , L'Imperio Vincenzo , De Sio Gabriele , Ferrario Franco , Scalia Carla , Dell'Antonio Giacomo , Pieruzzi Federico , Pontillo Claudia , Filip Szymon , Markoska Katerina , Granata Antonio , Spasovski Goce , Jankowski Joachim , Capasso Giovambattista , Pagni Fabio , Magni Fulvio
Published: January 2016

Idiopathic glomerulonephritis (GN), such as membranous glomerulonephritis, focal segmental glomerulosclerosis (FSGS), and IgA nephropathy (IgAN), represent the most frequent primary glomerular kidney diseases (GKDs) worldwide. Although the renal biopsy currently remains the gold standard for the routine diagnosis of idiopathic GN, the invasiveness and diagnostic difficulty related with this procedure highlight the strong need for new diagnostic and prognostic biomarkers to be translated into less invasive diagnostic tools. MALDI‐MS imaging MALDI‐MSI was applied to fresh‐frozen bioptic renal tissue from patients with a histological diagnosis of FSGS (n = 6), IgAN, (n = 6) and membranous glomerulonephritis (n = 7), and from controls (n = 4) in order to detect specific molecular signatures of primary glomerulonephritis. MALDI‐MSI was able to generate molecular signatures capable to distinguish between normal kidney and pathological GN, with specific signals (m/z 4025, 4048, and 4963) representing potential indicators of chronic kidney disease development. Moreover, specific disease‐related signatures (m/z 4025 and 4048 for FSGS, m/z 4963 and 5072 for IgAN) were detected. Of these signals, m/z 4048 was identified as α‐1‐antitrypsin and was shown to be localized to the podocytes within sclerotic glomeruli by immunohistochemistry. α‐1‐Antitrypsin could be one of the markers of podocyte stress that is correlated with the development of FSGS due to both an excessive loss and a hypertrophy of podocytes.
Synthesis of bisphenol A‐free oligomeric phthalonitrile resins with sulfone and sulfone‐ketone containing backbones
Authors: Laskoski Matthew , Clarke Jadah S. , Neal Arianna , Ricks‐Laskoski Holly L. , Hervey W. Judson , Keller Teddy M.
Published: January 2016

Two new oligomeric sulfone and sulfone‐ketone containing phthalonitrile (PN) resins with excellent processability have been developed. The PN monomers were prepared from the reaction of an excess amount of bisphenol S with 4‐(chlorophenyl)sulfone or 4,4‐dichlorobenzophenone in the presence of a base in a solvent mixture (dimethylsulfoxide/toluene), followed by end‐capping with 4‐nitro‐PN in a two‐step, one‐pot reaction. These PN resins exhibited good viscosities and cure times for molding into various shapes. After being thermally cured to yield crosslinked polymers, these polymers demonstrated superb mechanical properties, thermo‐oxidative stability, and maintained good dielectric properties. Published 2016. J. Polym. Sci., Part A: Polym. Chem. 2016, 54, 1639–1646
Detrimental Ni(0) transfer in Kumada catalyst transfer polycondensation of benzo[2,1‐b:3,4‐b']dithiophene
Authors: Bedi Anjan , De Winter Julien , Gerbaux Pascal , Koeckelberghs Guy
Published: January 2016

This article deals with the Kumada Catalyst Transfer Polycondensation (KCTP) of 4,7‐dioctylbenzo[2,1‐b:3,4‐b']dithiophene (BDP‐Oct) using Ni(II) catalyst or In/cat combination. A combination of MALDI MS, GPC, and 31P NMR spectroscopy is used to reveal the failure of the KCTP of this particular monomer. Intermolecular transfer reactions to monomer appeared to prevent the formation of polymer. This result is remarkable, since isomeric benzo[1,2‐b:4,5‐b']dithiophene polymerizes in a controlled way. The presence of a “non‐aromatic double bond” in annulated monomers is discussed. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016, 54, 1706–1712
Synthesis of new Azo‐based liquid crystalline polymers and their selective sensing behaviors to alkali metal ions
Authors: Byun In‐Joon , Lee Minjae , Han Yang‐Kyoo
Published: January 2016

We report novel liquid crystalline (LC) polymers containing pendant azobenzene moieties with n‐dodecyl substituents and ethyleneoxy spacers of different lengths and describe their selective detection behaviors to alkali metal ions. The new azopolymers produce homogenous smectic phases with a typical fan‐shaped texture. UV‐Vis and 1H NMR studies confirm that the azopolymers selectively bind to Li+ and Na+, but do not complex with K+, Ba2+, Mg2+, or Ca2+. Both the ethyleneoxy spacer and azobenzene units participate in binding to Li+ and Na+ cations in solution. Interestingly, after formation of the complexed structure, the ratio of cis to trans conformer is considerably increased suggesting stronger interactions of the cis conformer with alkali metal ions. Irradiation of the complexed structure with 365 nm UV induces conversion of the uncomplexed trans to the cis. These findings suggest a great potential of the LC azopolymers as selective sensors or separation membranes for alkali metal ions. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016, 54, 1713–1723
Toward large tubular helices based on the polymerization of tri(benzamide)s
Authors: Schulze Maren , Kilbinger Andreas F. M.
Published: January 2016

Herein we present the synthesis and polycondensation of mono‐ and di‐N‐protected, bis‐substituted tri(benzamide)s with the aim to create large, tubular helices. We synthesized 2,4‐dimethoxy and 2,5‐bis‐TEGylated aminobenzoic acid derivatives as bent and linear monomers and introduced p‐methoxybenzyl (PMB) amide protecting groups to the oligobenzamide backbone. An iterative coupling strategy allowed for sequence control, giving rise to oligomers consisting of one bent and two linear monomers. The resulting meta‐para‐para‐linked aromatic trimers carried either one or two PMB‐protecting groups. With high organosolubility and flexibility, this synthetic strategy generated suitable precursors for subsequent polycondensation reactions. After polymerization, treatment with acid triggered the cleavage of the N‐protecting groups. We hypothesize that the hydrogen bonding pattern generated along the polyaramide backbone could lead to the formation of a helical polymer. A drastic change in hydrodynamic volume was observed by gel permeation chromatography and dissolution in a chiral solvent lead to the observation of a circular dichroism signal for this polymer. The results of the polycondensations of N‐protected oligobenzamides are reported herein. The formation of macrocycles as well as polymers could also be observed, giving a highly interesting insight into the underlying mechanism of the polycondensation of flexible, oligobenzamide‐based oligomers. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016, 54, 1731–1741
Architecture‐controlled synthesis of redox‐degradable hyperbranched polyglycerol block copolymers and the structural implications of their degradation
Authors: Son Suhyun , Park Haeree , Shin Eeseul , Shibasaki Yuji , Kim Byeong‐Su
Published: January 2016

We have successfully synthesized a series of redox‐degradable hyperbranched polyglycerols using a disulfide containing monomer, 2‐((2‐(oxiran‐2‐ylmethoxy)ethyl)disulfanyl) ethan‐1‐ol (SSG), to yield PSSG homopolymers and hyperbranched block copolymers, P(G‐b‐SSG) and P(SSG‐b‐G), containing nondegradable glycerol (G) monomers. Using these polymers, we have explored the structures of the hyperbranched block copolymers and their related degradation products. Furthermore, side reaction such as reduction of disulfide bond during the polymerization was investigated by employing the free thiol titration experiments. We elucidated the structures of the degradation products with respect to the architecture of the hyperbranched block copolymer under redox conditions using 1H NMR and GPC measurements. For example, the degradation products of P(G‐b‐SSG) and P(SSG‐b‐G) are clearly different, demonstrating the clear distinction between linear and hyperbranched block copolymers. We anticipate that this study will extend the structural diversity of PG based polymers and aid the understanding of the structures of degradable hyperbranched PG systems. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016, 54, 1752–1761
Sulfonated polyaniline‐graphene oxide hybrids: Synthesis and effect of monomer composition on the electrochemical signal for direct DNA detection
Authors: Meng Le , Chen Huaiyin , Ge Tong , Yang Tao , Jiao Kui
Published: January 2016

A variety of sulfonated polyaniline‐graphene oxide (SPAN‐GNO) nanocomposites based on GNO, aniline (ANI) and m‐aminobenzenesulfonic acid (ABSA) are prepared via changing the mole ratio of ANI to ABSA for the comparison of DNA sensing behavior. Self‐signals of SPAN‐GNO are employed for estimating the effect of preparation conditions [component, monomer composition (mole ratio of ANI to ABSA), and reaction time] on DNA immobilization and hybridization detection. Then, we find herein that the mole ratio of ANI to ABSA plays a lead role over other factors on hybridization efficiency. Meanwhile, the parallel experiments using methylene blue as the classic indicator verifies this conclusion. The results show that, by comparison with other mole ratio SPAN‐GNO nanocomposites‐modified electrodes, the mole ratio (2:3) exhibits the widest dynamic detection range from 1.0 × 10−14 to 1.0 × 10−6 M, as well as the lowest detection limit (3.06 × 10−15 M). © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016, 54, 1762–1773
Prediction of viscoelastic properties with coarse‐grained molecular dynamics and experimental validation for a benchmark polyurea system
Authors: Agrawal Vipin , Holzworth Kristin , Nantasetphong Wiroj , Amirkhizi Alireza V. , Oswald Jay , Nemat‐Nasser Sia
Published: January 2016

To explore the relationship between microscopic structure and viscoelastic properties of polyurea, a coarse‐grained (CG) model is developed by a structure matching method and validated against experiments conducted on a controlled, benchmark material. Using the Green‐Kubo method, the relaxation function is computed from the autocorrelation of the stress tensor, sampled over equilibrium MD simulations, and mapped to a real time scale established by matching self‐diffusion rates of atomistic and CG models. Master curves computed from the predicted stress relaxation function are then compared with dynamic mechanical analysis experiments mapped to a wide frequency range by time–temperature superposition, as well as measurements of ultrasonic shear wave propagation. Computational simulations from monodisperse and polydisperse configurations, representative of the benchmark polyurea, show excellent agreement with the experimental measurements over a multidecade range of loading frequency. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016, 54, 797–810
Tuning the π‐π stacking distance and J‐aggregation of DPP‐based conjugated polymer via introducing insulating polymer
Authors: Chen Liang , Wang Haiyang , Liu Jiangang , Xing Rubo , Yu Xinhong , Han Yanchun
Published: January 2016

The close π–π stacking and the high J‐aggregation during the formation of fibrillar morphology in films of the poly[[2,5‐bis(2‐octyldodecyl)−2,3,5,6‐tetrahydro‐3,6‐dioxopyrrolo[3,4‐c]pyrrole‐1,4‐diyl]‐alt–[[2,2′‐(2,5‐thiophene)bis‐thieno[3,2‐b]thiophen]‐5,5′‐diyl]] (PDPPTT‐T) are demonstrated via blending with polystyrene (PS). The hydrodynamic radius (Rh) of PDPPTT‐T is decreased from 16.7 nm in the neat solution to 12.7 nm in the blend solution at the ratio of 1/20(PDPPTT‐T/PS). This phenomenon suggests that blending PS is beneficial for the disentanglement of PDPPTT‐T. The disentanglement of PDPPTT‐T facilitates the formation of fibrillar morphology. The growth of the fibrils occurs along the molecular backbones and the width of the fibrils is parallel to the π–π stacking direction. The disentanglement of PDPPTT‐T helps the molecules adjust conformation to improve J‐aggregation and decrease the π–π stacking distance. The maximum absorption is red‐shifted from 825 nm to 849 nm and the relative intensity of J‐aggregation (the 0‐0/0‐1 ratio) is increased from 1.19 to 1.60. The π–π stacking distance decreases from 3.57 to 3.52 Å. The charge‐carrier mobility will be improved in the fibrillar morphology with close π–π stacking and high J‐aggregation. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016, 54, 838–847