bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acrylate Network Formation by Free‐Radical Polymerization Modeled Using Random Graphs
Authors: Schamboeck Verena , Kryven Ivan , Iedema Pieter D. 
Published: September 2017

AbstractA novel technique is developed to predict the evolving topology of a diacrylate polymer network under photocuring conditions, covering the low‐viscous initial state to full transition into polymer gel. The model is based on a new graph theoretical concept being introduced in the framework of population balance equations (PBEs) for monomer states (mPBEs). A trivariate degree distribution that describes the topology of the network locally is obtained from the mPBE, which serves as an input for a directional random graph model. Thus, access is granted to global properties of the acrylate network which include molecular size distribution, distributions of molecules with a specific number of crosslinks/radicals, gelation time/conversion, and gel/sol weight fraction. Furthermore, an analytic criterion for gelation is derived. This criterion connects weight fractions of converted monomers and the transition into the gel regime. Valid results in both sol and gel regimes are obtained by the new model, which is confirmed by a comparison with a “classical” macromolecular PBE model. The model predicts full transition of polymer into gel at very low vinyl conversion (<2%). Typically, this low‐conversion network is very sparse, as becomes apparent from the predicted crosslink distribution.
Simulating Light Scattering Behavior of Branched Molecules
Authors: Tacx Jacques C. J. F. , Iedema Piet D. 
Published: September 2017

AbstractMonte Carlo simulations reveal long chain branching (LCB) topology based on kinetics of systems like low‐density polyethylene (ldPE). Examining the topologies computed shows the majority of branch arms to be short as compared to backbone length, while also a significant branch‐on‐branch fine structure is observed. Until now, predicting scattering functionP−1(θ) from LCB has only been successful for structures like simple combs or stars. Topologies in graph theoretical form are used to predict scattering functionP−1(θ) andby summating intramolecular distances, accounting for branching and excluded volume. Experimental size exclusion chromatography with multiangle light scattering can be brought in line with the predicted branching character. Branching is less than predicted due to a different fine structure in ldPE leading to stronger size contraction.
Technical Note: A simple algorithm to convert EPID gray values into absorbed dose to water without prior knowledge
Authors: Boutry Christine , Sors Aurélie , Fontaine Jimmy , Delaby Nolwenn , Delpon Gregory 
Published: September 2017

PurposeFull integration of EPID‐based dosimetry in a global quality control workflow is still complicated. All the actual solutions are based on a relation between image gray‐level signal and total linac‐delivered dose. In this study, we propose a simple algorithm relying pixel gray‐level of EPID image with average linac delivered dose per acquisition frame.MethodsCalibration models are constructed for Varian and Elekta linacs including scattering conditions and EPID‐arm backscatter‐specific corrections. Only simple homogeneous fields are required to establish the EPID dose conversion model for each x‐ray beam. Then, the model was evaluated by comparing calculated and converted dose distributions for homogeneous and modulated beams using gamma maps.ResultsTo fit average dose per frame (Dfnorm) vs pixel gray value (Ngnorm) of each EPID image, a logarithmic curve , has been chosen where A, B and C are constants depending on beam energy. Gamma comparison (2%, 2 mm, threshold 15%) between converted images and calculated dose distributions for linac control and pretreatment patient fields led to a gamma pass rate higher than 97% for all the analyzed fields.ConclusionsWithout a prior irradiation settings knowledge except the incident energy beam, we use EPID as a reliable dose to water detector for both homogeneous and modulated beams.
Machine‐specific quality assurance procedure for stereotactic treatments with dynamic couch rotations
Authors: Wilson Byron , Gete Ermias 
Published: September 2017

ObjectiveWe present a method in which the treatment couch's accuracy is measured using the electronic portal imaging device (EPID) and a phantom of our own construction. Using this phantom, we were able to quantify the treatment couch walkout, and the rotation angle accuracy for both static and dynamic couch treatments. These measurements were used to provide an accurate measure of the treatment couch isocenter as well as to verify the couch rotation angle recorded in the trajectory log.MethodsThe phantom was constructed using a polystyrene slab in which five ball bearings of 4 mm diameter are placed on the same plane at varying radii (0, 2.8, 4.4, 5.6, and 6.7 cm). The couch was rotated through its full extent (‐90, 90 degrees) while MV images were acquired continuously. The couch rotational accuracy was calculated using a least squares minimization which fit the locations of the BBs to their expected locations relative to reference setup conditions. Using this approach, rotation angle and isocenter walkout was calculated in three dimensions. These measurements were used to quantify the accuracy of the couch as well as to validate the Varian TrueBeam trajectory logs. Additionally, a method for an EPID‐based couch star‐shot measurement was developed and compared with the traditional film‐based method.ResultsThe measured couch center of rotation consisted of a cloud of points clustered around the room isocenter within 0.7 mm distance. The trajectory log couch angle values agreed with those recorded in the DICOM header of the EPID images to the third significant digit and the couch rotation angles recorded in the trajectory log and DICOM header agreed with the calculated values to 0.08 degrees. Comparison of couch star‐shot measurement developed in this study with film‐based star‐shot measurements gave an agreement to within 0.2 mm.ConclusionWe have developed a quality assurance method for the treatment couch which is simple, accurate, and enables the user to access a multitude of consistent data with a single measurement. Using this method, we have shown that the treatment couch is accurate for both static and dynamic stereotactic deliveries.
A fast inverse treatment planning strategy facilitating optimized catheter selection in image‐guided high‐dose‐rate interstitial gynecologic brachytherapy
Authors: Guthier Christian V. , Damato Antonio L. , Hesser Juergen W. , Viswanathan Akila N. , Cormack Robert A. 
Published: September 2017

PurposeInterstitial high‐dose rate (HDR) brachytherapy is an important therapeutic strategy for the treatment of locally advanced gynecologic (GYN) cancers. The outcome of this therapy is determined by the quality of dose distribution achieved. This paper focuses on a novel yet simple heuristic for catheter selection for GYN HDR brachytherapy and their comparison against state of the art optimization strategies. The proposed technique is intended to act as a decision‐supporting tool to select a favorable needle configuration.MaterialsThe presented heuristic for catheter optimization is based on a shrinkage‐type algorithm (SACO). It is compared against state of the art planning in a retrospective study of 20 patients who previously received image‐guided interstitial HDR brachytherapy using a Syed Neblett template. From those plans, template orientation and position are estimated via a rigid registration of the template with the actual catheter trajectories. All potential straight trajectories intersecting the contoured clinical target volume (CTV) are considered for catheter optimization. Retrospectively generated plans and clinical plans are compared with respect to dosimetric performance and optimization time.ResultsAll plans were generated with one single run of the optimizer lasting 0.6–97.4 s. Compared to manual optimization, SACO yields a statistically significant (P ≤ 0.05) improved target coverage while at the same time fulfilling all dosimetric constraints for organs at risk (OARs). Comparing inverse planning strategies, dosimetric evaluation for SACO and “hybrid inverse planning and optimization” (HIPO), as gold standard, shows no statistically significant difference (P > 0.05). However, SACO provides the potential to reduce the number of used catheters without compromising plan quality.ConclusionThe proposed heuristic for needle selection provides fast catheter selection with optimization times suited for intraoperative treatment planning. Compared to manual optimization, the proposed methodology results in fewer catheters without a clinically significant loss in plan quality. The proposed approach can be used as a decision support tool that guides the user to find the ideal number and configuration of catheters.
“Metabolically Healthy” Obesity and Hyperuricemia Increase Risk for Hypertension and Diabetes: 5‐year Japanese Cohort Study
Authors: Kuwabara Masanari , Kuwabara Remi , Hisatome Ichiro , Niwa Koichiro , Roncal‐Jimenez Carlos A. , Bjornstad Petter , Andres‐Hernando Ana , Sato Yuka , Jensen Thomas , Garcia Gabriela , Ohno Minoru , Hill James O. , Lanaspa Miguel A. , Johnson Richard J. 
Published: September 2017

ObjectiveWhether obesity without metabolic syndrome (i.e., “metabolically healthy” obesity) confers similar or less metabolic risk remains controversial.MethodsA retrospective 5‐year cohort study of 9,721 Japanese subjects (48.5 ± 10.5 years, 4,160 men) was conducted in 2004 and reevaluated 5 years later. Subjects were excluded if they were hypertensive or diabetic or were receiving medications for dyslipidemia and/or gout or hyperuricemia in 2004. Study subjects were categorized according to baseline BMI  ≥ 25 kg/m2 (overweight/obesity) and < 25 kg/m2 (lean/normal weight) and also whether they had metabolic syndrome. The cumulative incidence of hypertension and diabetes over 5 years between groups was assessed. A second analysis evaluated whether baseline hyperuricemia provided additional risk.ResultsSubjects with overweight/obesity but without metabolic syndrome carried increased cumulative incidence of hypertension (14.6% vs. 7.2%, P < 0.001) and diabetes (2.6% vs. 1.1%, P = 0.004) over 5 years compared to lean/normal subjects without metabolic syndrome. Overweight/obesity conferred an increased risk for diabetes even in individuals with normal fasting blood glucose. Hyperuricemia became an independent risk factor for developing hypertension over 5 years in lean/normal subjects without metabolic syndrome. A 1 mg/dL increase in serum uric acid carried increased risk for hypertension (19%) and diabetes (27%).ConclusionsMetabolically healthy obesity and hyperuricemia confer increased risk for hypertension and diabetes.
Patient–provider relationship and perceived provider weight bias among American Indians and Alaska Natives
Authors: Gonzales K. L. , Garcia G. E. , Jacob M. M. , Muller C. , Nelson L. , Manson S. M. 
Published: September 2017

SummaryObjectiveThe objective of this study was to examine patient–provider relationships among American Indians and Alaska Native (AI/AN) patients by examining associations between patient activation, perceived provider weight bias and working alliance. Patient activation is generally defined as having the knowledge, skills and confidence to manage one's health.MethodsAmong a sample of 87 AI/AN adults presenting for general medical care at an urban clinic in the north‐west region of the USA, ordinary least squares regression analysis was completed to examine associations.ResultsBetter working alliance scores were associated with increased patient activation, while perceived provider weight bias was associated with reduced patient activation. In addition, those with class II obesity had decreased patient activation.ConclusionThese findings point to the importance of a positive patient–provider relationship in AI/ANs. Optimal patient engagement and subsequent health outcomes warrant additional consideration of patients' perceptions of provider weight bias within the context of health promotion and interventions.
Proteomic Response of Human Umbilical Vein Endothelial Cells to Histamine Stimulation
Authors: Emirbayer Pelin Esma , Sinha Ankit , Ignatchenko Vladimir , Hoyer Stefanie , Dörrie Jan , Schaft Niels , Pischetsrieder Monika , Kislinger Thomas 
Published: September 2017

AbstractThe histamine receptors (HRs) represent a subclass of G protein‐coupled receptors (GPCRs) and comprise four subtypes. Due to their numerous physiological and pathological effects, HRs are popular drug targets for the treatment of allergic reactions or the regulation of gastric acid secretion. Hence, an understanding of the functional selectivity of HR ligands has gained importance. These ligands can bind to specific GPCRs and selectively activate defined pathways. Supporting the activation of a therapeutically necessary pathway without the activation of other signaling cascades can result in drugs with more specific activity and fewer side effects. To evaluate the cellular consequences resulting from receptor binding, comprehensive analyses of cellular protein alterations upon incubation with ligands are required. For this purpose, endothelial cells are treated with histamine, as the endogenous ligand of HRs, to obtain a global overview of its cellular effects. Quantitative proteomics and pathway analyses of histamine‐treated and untreated cells reveal enrichment of the nuclear factor‐κB and tumor necrosis factor signaling pathways, cytokine‒cytokine receptor interactions, complement and coagulation cascades, and acute inflammatory processes upon histamine treatment. This strategy offers the opportunity to monitor HR‐mediated signaling in a multidimensional manner.
Spectral Libraries for SWATH‐MS Assays for Drosophila melanogaster and Solanum lycopersicum
Authors: Fabre Bertrand , Korona Dagmara , Mata Clara I. , Parsons Harriet T. , Deery Michael J. , Hertog Maarten L. A. T. M. , Nicolaï Bart M. , Russell Steven , Lilley Kathryn S. 
Published: September 2017

AbstractQuantitative proteomics methods have emerged as powerful tools for measuring protein expression changes at the proteome level. Using MS‐based approaches, it is now possible to routinely quantify thousands of proteins. However, prefractionation of the samples at the protein or peptide level is usually necessary to go deep into the proteome, increasing both MS analysis time and technical variability. Recently, a new MS acquisition method named SWATH is introduced with the potential to provide good coverage of the proteome as well as a good measurement precision without prior sample fractionation. In contrast to shotgun‐based MS however, a library containing experimental acquired spectra is necessary for the bioinformatics analysis of SWATH data. In this study, spectral libraries for two widely used models are built to study crop ripening or animal embryogenesis, Solanum lycopersicum (tomato) and Drosophila melanogaster, respectively. The spectral libraries comprise fragments for 5197 and 6040 proteins for S. lycopersicum and D. melanogaster, respectively, and allow reproducible quantification for thousands of peptides per MS analysis. The spectral libraries and all MS data are available in the MassIVE repository with the dataset identifiers MSV000081074 and MSV000081075 and the PRIDE repository with the dataset identifiers PXD006493 and PXD006495.
Mannose‐based graft polyesters with tunable binding affinity to concanavalin A
Authors: Xie Yixuan , Peng Chao , Gao Yunyi , Liu Xiaohong , Liu Tianbo , Joy Abraham 
Published: September 2017

ABSTRACTGlycopolymers have been widely used to understand the interactions between carbohydrates and lectins, which facilitate the diagnosis and detection of disease and pathogens as well as the development of vaccines. While studies have been focused on the correlation of glycopolymer structure and their binding to lectins, graft‐type glycopolyesters are uncommon. Herein, we report the design and synthesis of mannose‐based graft polyesters by “grafting‐from” method and investigate their interactions with Concanavalin A (Con A). As confirmed by 1H NMR spectroscopy and sulfuric acid‐UV method, graft polyesters with different lengths of mannose graft were successfully synthesized. Our results from turbidimetry binding assay showed that graft polyesters with longer mannose graft exhibit higher initial binding rate (ki). Isothermal titration calorimetry measurements of these graft polyesters with Con A showed that polymers exhibit higher binding affinity (ka) with the number of side chain mannose. This study provides understanding of the interaction between Con A and mannose‐based graft polyesters, which can be employed for the development of glycopolymeric therapeutics. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017, 55, 3908–3917
Polymersomes as protocellular constructs
Authors: Mason Alexander F. , Thordarson Pall 
Published: September 2017

ABSTRACTDespite the rapidly growing amount of knowledge on the structure and function of cells, they remain a distant bottom‐up synthetic target due to their overwhelming complexity. A path to this goal is the development of protocellular systems that approximate one or more aspects of a natural cell. Polymer vesicles, or polymersomes, are an attractive scaffold for protocellular constructs, due to our ability to engineer the polymer membrane and generate a wide range of properties. This article summarizes the current state of polymersome science with respect to the properties and functions that lend these polymer‐based systems to applications in synthetic cell research. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017, 55, 3817–3825
AnchorQuery: Rapid online virtual screening for small‐molecule protein–protein interaction inhibitors
Authors: Koes David R. , Dömling Alexander , Camacho Carlos J. 
Published: September 2017

AbstractAnchorQuery (http://anchorquery.csb.pitt.edu) is a web application for rational structure‐based design of protein–protein interaction (PPI) inhibitors. A specialized variant of pharmacophore search is used to rapidly screen libraries consisting of more than 31 million synthesizable compounds biased by design to preferentially target PPIs. Every library compound is accessible through one‐step multi‐component reaction (MCR) chemistry and contains an anchor motif that is bioisosteric to an amino acid residue. The inclusion of this anchor not only biases the compounds to interact with proteins, it also enables a rapid, sublinear time pharmacophore search algorithm. AnchorQuery provides all the tools necessary for users to perform online interactive virtual screens of millions of compounds, including pharmacophore elucidation and search, and enrichment analysis.Accessibility: AnchorQuery is freely accessible at http://anchorquery.csb.pitt.edu.
An integrative modeling approach to mapping wetlands and riparian areas in a heterogeneous Rocky Mountain watershed
Authors: Chignell Stephen M. , Luizza Matthew W. , Skach Sky , Young Nicholas E. , Evangelista Paul H. 
Published: September 2017

AbstractAccurate maps of wetlands and riparian areas are critical for targeting conservation and monitoring efforts. However, detailed inventories in mountain regions are largely non‐existent, as conventional mapping approaches are hindered by high costs, remoteness, and landscape variability. Contemporary modeling techniques can circumvent many of these issues, but are often difficult to interpret and tend to rely on specialized datasets that prevent their wider application. In this study, we used machine learning, Landsat 8 imagery and geomorphometric indices to map the distribution of wetlands and riparian areas in the Cache la Poudre River watershed, Colorado, USA. We used a presence‐background approach to develop and compare predictions from three popular algorithms: boosted regression trees, MaxEnt and random forests. In addition, we developed the models within three elevation‐based life zones to account for altitudinal changes in ecohydrology and land use. Our results showed strong predictive performance, with top‐performing models achieving area under the curve values as high as 0.98 and correctly classifying up to 95% of test data. Model performance varied by elevation zone, and no algorithm consistently outperformed the others. The boosted regression trees approach was uniquely able to differentiate wetlands from irrigated agriculture and residential areas in lower elevations. Multi‐seasonal greenness and wetness indices were highly influential predictors in all models, underscoring the importance of capturing local phenological characteristics and hydrological regimes. Dissection and roughness terrain metrics were key predictors for identifying valley bottom meadows and emergent wetlands in high‐elevation forests. We demonstrate how integrating ecological interpretation into the modeling workflow can inform conventional accuracy statistics and help bridge field‐based and remote sensing perspectives. We also show how continuous model outputs can facilitate this process by depicting nuances of the wetland‐upland continuum. Our approach requires only public data that are widely available, and can be easily adapted to other heterogeneous mountain settings.
Helical l–Leu‐Based Peptides Having Chiral Five‐Membered Carbocyclic Ring Amino Acids with an Ethylene Acetal Moiety
Authors: Koba Yurie , Ueda Atsushi , Oba Makoto , Doi Mitsunobu , Demizu Yosuke , Kurihara Masaaki , Tanaka Masakazu 
Published: September 2017

Abstractl–Leu‐based heteropeptides having (R)‐ or (S)‐chiral five‐membered carbocyclic ring amino acids (Ac5c3EG) with an ethylene acetal moiety were prepared. A conformational analysis using FT‐IR absorption, 1H NMR, and circular dichroism (CD) spectra revealed that l–Leu‐based hexapeptides and nonapeptides having (R)‐ or (S)‐Ac5c3EG formed right‐handed (P) helical structures in solution. An X‐ray crystallographic analysis of nonapeptides 5 a and 5 b showed similar right‐handed (P) α‐helical structures, without an intramolecular hydrogen bond of the peptide N–H⋅⋅⋅–O– (acetal) type.
Mercuric Ion Sensing by an Overlapping β‐turn Containing Peptide
Authors: Tomar Kalpana , Soni Satyendra , Bhadauriya Pratibha , Parihar Rashmi , Ganesh Subramaniam , Nair Nisanth N. , Ramanathan Gurunath 
Published: September 2017

AbstractA tetrapeptide containing dehydrophenylalanine residue exhibits unusual enhanced fluorescence emission intensity for Hg2+ ions selectively. In vivo studies on HeLa cells revealed that this peptide could be used to study Hg2+ trafficking in mammalian cells. The results demonstrate that Hg2+ can interact with sulfurless peptide backbones, if the latter provides the requisite geometry, especially a folded type III/III overlapping beta turn conformation.