bluuebunny/crossref_metadata_2025_split huggingface dataset:
A New Approach Toward Metal‐Free Self‐Healing Ionomers Based on Phosphate and Methacrylate Containing Copolymers
Authors: Dahlke Jan , Bose Ranjita K. , Zechel Stefan , Garcia Santiago J. , van der Zwaag Sybrand , Hager Martin D. , Schubert Ulrich S. 
Published: October 2017

AbstractIn order to accelerate the progress of the development of new self‐healing ionomers, a new pathway toward fully organic ionomers containing methacrylic acid and phosphate‐based functional groups, respectively, as well as butyl methacrylate as comonomer is presented in the current study. The well‐defined copolymer structures are synthesized using the reversible addition‐fragmentation chain transfer polymerization and further characterized by NMR, size exclusion chromatography as well as titration. Two different metal‐free ionomers as well as one reference K+ based ionomer are created and tested. The results of the detailed investigation by NMR, thermal analysis, and rheology are correlated with the scratch‐healing performance in order to identify trends and dependencies leading to preconditions for further improvements.
Robust intensity‐modulated proton therapy to reduce high linear energy transfer in organs at risk
Authors: An Yu , Shan Jie , Patel Samir H. , Wong William , Schild Steven E. , Ding Xiaoning , Bues Martin , Liu Wei 
Published: October 2017

PurposeWe propose a robust treatment planning model that simultaneously considers proton range and patient setup uncertainties and reduces high linear energy transfer (LET) exposure in organs at risk (OARs) to minimize the relative biological effectiveness (RBE) dose in OARs for intensity‐modulated proton therapy (IMPT). Our method could potentially reduce the unwanted damage to OARs.MethodsWe retrospectively generated plans for 10 patients including two prostate, four head and neck, and four lung cancer patients. The “worst‐case robust optimization” model was applied. One additional term as a “biological surrogate (BS)” of OARs due to the high LET‐related biological effects was added in the objective function. The biological surrogate was defined as the sum of the physical dose and extra biological effects caused by the dose‐averaged LET. We generated nine uncertainty scenarios that considered proton range and patient setup uncertainty. Corresponding to each uncertainty scenario, LET was obtained by a fast LET calculation method developed in‐house and based on Monte Carlo simulations. In each optimization iteration, the model used the worst‐case BS among all scenarios and then penalized overly high BS to organs. The model was solved by an efficient algorithm (limited‐memory Broyden–Fletcher–Goldfarb–Shanno) in a parallel computing environment. Our new model was benchmarked with the conventional robust planning model without considering BS. Dose–volume histograms (DVHs) of the dose assuming a fixed RBE of 1.1 and BS for tumor and organs under nominal and uncertainty scenarios were compared to assess the plan quality between the two methods.ResultsFor the 10 cases, our model outperformed the conventional robust model in avoidance of high LET in OARs. At the same time, our method could achieve dose distributions and plan robustness of tumors assuming a fixed RBE of 1.1 almost the same as those of the conventional robust model.ConclusionsExplicitly considering LET in IMPT robust treatment planning can reduce the high LET to OARs and minimize the possible toxicity of high RBE dose to OARs without sacrificing plan quality. We believe this will allow one to design and deliver safer proton therapy.
Automated detection of foveal center in SD‐OCT images using the saliency of retinal thickness maps
Authors: Niu Sijie , Chen Qiang , de Sisternes Luis , Leng Theodore , Rubin Daniel L. 
Published: October 2017

PurposeTo develop an automated method based on saliency map of the retinal thickness map to determine foveal center in spectral‐domain optical coherence tomography (SD‐OCT) images.MethodsThis paper proposes an automatic method for the detection of the foveal center in SD‐OCT images. Initially, a retinal thickness map is generated by considering the axial distance between the internal limiting membrane (ILM) and the Bruch's membrane (BM). Both the ILM and BM boundaries are automatically segmented by a known retinal segmentation technique. The macular foveal region is identified as a salient feature in the retinal thickness map, and segmented by the saliency detection method based on a human vision attention model. Finally, the foveal center is identified by searching for the lowest point from the determined macular fovea region.ResultsExperimental results in 39 scans from 35 healthy eyes and 58 scans from 29 eyes diagnosed with several stages of age‐related macular degeneration (AMD), from mild or intermediate stages to severe dry or wet stages, demonstrated that the proposed method achieves good performance. The mean radial distance error of the automatically detected foveal center locations when compared to consensus manual determination established by repeated sessions from two expert readers was 52 ± 56 μm for the normal eyes and 73 ± 63 μm for AMD eyes.ConclusionsThe proposed algorithm was more effective for detecting the foveal center automatically in SD‐OCT images than the state‐of‐art methods.
Evaluating the 8‐item overactive bladder questionnaire (OAB‐v8) using item response theory
Authors: Peterson Alexander C. , Sehgal Anika , Crump R. Trafford , Baverstock Richard , Sutherland Jason M. , Carlson Kevin 
Published: October 2017

AimsThe OAB‐v8 is a patient‐reported outcome questionnaire used to screen for overactive bladder and measure symptom bother. This study uses modern validation methods to assess the item and test characteristics of the OAB‐v8, and determine whether it should be scored differently for men and women.MethodsA secondary analysis of data from patients with lower urinary tract symptoms prospectively recruited from a urology clinic in Calgary, Canada. Item‐response theory (IRT) was used to evaluate the dimensionality, reliability, and validity of the OAB‐v8, and differential functioning analysis (DIF) was used to determine whether the OAB‐v8 should be scored differently for men and women.ResultsA total of 1128 patients were included for analysis, of which 28% were female. Mean OAB‐v8 scores indicated meaningful levels of symptom bother, and women scored 2 points higher, on average, than men (P = 0.005). Reliability was high (Cronbach's alpha = 0.901) for a wide range of patients (between −2 and 2.5 standard deviations of the mean). Samejima's graded response model best fit the data, and the scale demonstrated essential unidimensionality. Items #5 and #6 were excessively correlated. There was no evidence of differential functioning.ConclusionsOAB‐v8 demonstrated high reliability and would be appropriate for a wide range of patients. Items #5 and #6 may need to be re‐worded. The OAB‐v8 should not be scored differently for men and women, although women do appear to experience higher average levels of symptom bother from OAB than men.
A Comparison of Insulin Doses for the Treatment of Hyperkalemia in Patients with Renal Insufficiency
Authors: LaRue Heather A. , Peksa Gary Daniel , Shah Shital C. 
Published: October 2017

Study ObjectiveTo compare the safety and efficacy of 5 units versus 10 units of insulin for the treatment of hyperkalemia in patients with renal insufficiency.DesignRetrospective cohort study.SettingLarge academic medical center emergency department.PatientsBetween March 1, 2008, and February 29, 2016, 675 patients met the inclusion criteria of age 18 years and older, serum potassium greater than 5 mEq/L, renal insufficiency, 5 units or 10 units of intravenous regular insulin administered in the emergency department, and blood glucose documented within 5 hours after insulin administration. Of these patients, 133 (19.7%) received 5 units of insulin and 542 (80.3%) received 10 units of insulin.Measurements and ResultsThe primary outcome was incidence of hypoglycemia (blood glucose < 70 mg/dl). Secondary outcomes were incidence of severe hypoglycemia (blood glucose < 40 mg/dl) and change in serum potassium after insulin therapy. Hypoglycemia occurred in 26 of 133 patients receiving 5 units of insulin (19.5%) and in 155 of 542 patients receiving 10 units (28.6%) (difference = −9.1%, 95% confidence interval [CI] −16.8% to −1.3%). Severe hypoglycemia occurred in 4 of 133 patients (3.0%) and 37 of 542 patients (6.8%) receiving insulin 5 units and 10 units, respectively (difference = −3.8%, 95% CI −7.4% to 0%). Change in serum potassium was similar between groups (−1.0 ± 0.8 vs −1.0 ± 0.7 mEq/L, difference = 0, 95% CI −0.1 to 0.1).ConclusionIn patients with renal insufficiency and hyperkalemia, 5 units of insulin reduced serum potassium to the same extent as 10 units of insulin but with a lower rate of hypoglycemia. Further controlled studies are needed to confirm these findings.
What makes it difficult to refine protein models further via molecular dynamics simulations?
Authors: Heo Lim , Feig Michael 
Published: October 2017

AbstractProtein structure refinement remains a challenging yet important problem as it has the potential to bring already accurate template‐based models to near‐native resolution. Refinement based on molecular dynamics simulations has been a highly promising approach and the performance of MD‐based refinement in the Feig group during CASP12 is described here. During CASP12, sampling was extended well into the microsecond scale, an improved force field was applied, and new protocol variations were tested. Progress over previous rounds of CASP was found to be limited which is analyzed in terms of the quality of the initial models and dependency on the amount of sampling and refinement protocol variations. As current MD‐based refinement protocols appear to be reaching a plateau, detailed analysis is presented to provide new insight into the major challenges towards more extensive structure refinement, focusing in particular on sampling with and without restraints.
Methods for estimation of model accuracy in CASP12
Authors: Elofsson Arne , Joo Keehyoung , Keasar Chen , Lee Jooyoung , Maghrabi Ali H. A. , Manavalan Balachandran , McGuffin Liam J. , Ménendez Hurtado David , Mirabello Claudio , Pilstål Robert , Sidi Tomer , Uziela Karolis , Wallner Björn 
Published: October 2017

AbstractMethods to reliably estimate the quality of 3D models of proteins are essential drivers for the wide adoption and serious acceptance of protein structure predictions by life scientists. In this article, the most successful groups in CASP12 describe their latest methods for estimates of model accuracy (EMA). We show that pure single model accuracy estimation methods have shown clear progress since CASP11; the 3 top methods (MESHI, ProQ3, SVMQA) all perform better than the top method of CASP11 (ProQ2). Although the pure single model accuracy estimation methods outperform quasi‐single (ModFOLD6 variations) and consensus methods (Pcons, ModFOLDclust2, Pcomb‐domain, and Wallner) in model selection, they are still not as good as those methods in absolute model quality estimation and predictions of local quality. Finally, we show that when using contact‐based model quality measures (CAD, lDDT) the single model quality methods perform relatively better.
Biological and functional relevance of CASP predictions
Authors: Liu Tianyun , Ish‐Shalom Shirbi , Torng Wen , Lafita Aleix , Bock Christian , Mort Matthew , Cooper David N , Bliven Spencer , Capitani Guido , Mooney Sean D. , Altman Russ B. 
Published: October 2017

AbstractOur goal is to answer the question: compared with experimental structures, how useful are predicted models for functional annotation? We assessed the functional utility of predicted models by comparing the performances of a suite of methods for functional characterization on the predictions and the experimental structures. We identified 28 sites in 25 protein targets to perform functional assessment. These 28 sites included nine sites with known ligand binding (holo‐sites), nine sites that are expected or suggested by experimental authors for small molecule binding (apo‐sites), and Ten sites containing important motifs, loops, or key residues with important disease‐associated mutations. We evaluated the utility of the predictions by comparing their microenvironments to the experimental structures. Overall structural quality correlates with functional utility. However, the best‐ranked predictions (global) may not have the best functional quality (local). Our assessment provides an ability to discriminate between predictions with high structural quality. When assessing ligand‐binding sites, most prediction methods have higher performance on apo‐sites than holo‐sites. Some servers show consistently high performance for certain types of functional sites. Finally, many functional sites are associated with protein‐protein interaction. We also analyzed biologically relevant features from the protein assemblies of two targets where the active site spanned the protein‐protein interface. For the assembly targets, we find that the features in the models are mainly determined by the choice of template.
DFT study of the acid‐catalyzed esterification reaction mechanism of methanol with carboxylic acid and its halide derivatives
Authors: Lawal Monsurat M. , Govender Thavendran , Maguire Glenn E. M. , Kruger Hendrik G. , Honarparvar Bahareh 
Published: October 2017

AbstractExtensive experimental studies have been dedicated to the esterification mechanisms from carboxylic acids and acid halides. However, attention on the theoretical aspect of the mechanism has been scarcely addressed. Herein, the acid‐catalyzed esterification mechanism of methanol with acetic acid and its halide derivatives is described using density functional theoretical method and solvation model based on density. The mechanistic investigation involved formation of cyclic prereaction and 6‐membered ring transition structures, which favors the esterification process and product formation. A good comparison with experimental data from literature for the esterification reaction of acetic acid with methanol was achieved through this in silico approach. Density Functional Theory‐based quantum descriptors were applied to provide a better understanding on the reactivity, selectivity, and stability of this reaction. This theoretical results provide a crucial guide to study classical acid‐catalyzed reaction mechanisms and applying a reasonable theoretical model to study similar organic reactions. In addition, it can be applied to larger systems such as enzymatic mechanism.
Formation control for a class of nonlinear multiagent systems using model‐free adaptive iterative learning
Authors: Bu Xuhui , Cui Lizhi , Hou Zhongsheng , Qian Wei 
Published: October 2017

SummaryIn this paper, the problem of formation control is considered for a class of unknown nonaffine nonlinear multiagent systems under a repeatable operation environment. To achieve the formation objective, the unknown nonlinear agent's dynamic is first transformed into a compact form dynamic linearization model along the iteration axis. Then, a distributed model‐free adaptive iterative learning control scheme is designed to ensure that all agents can keep their desired deviations from the reference trajectory over the whole time interval. The main results are given for the multiagent systems with fixed communication topologies and the extension to the switching topologies case is also discussed. The feature of this design is that formation control can be solved only depending on the input/output data of each agent. An example is given to demonstrate the effectiveness of the proposed method.
Recent Progress in Micro‐Supercapacitors with In‐Plane Interdigital Electrode Architecture
Authors: Liu Nishuang , Gao Yihua 
Published: October 2017

AbstractDue to the boom of miniaturized electronic devices in the last decade, there are great demands for ultrathin and flexible on‐chip rechargeable energy storage microdevices. Supercapacitor, as one of the most hopeful appearing energy storage devices, can provide a wonderful alternative to batteries or electrolytic capacitors, owing to its fast charge and discharge rates, high power density, and long cycling stability. Especially for the recently developed micro‐supercapacitors, the unique in‐plane interdigital electrode architecture can fully meet the integration requirements of rapidly developed miniaturized electronic devices, and improve the power density of the unit via shortening the ionic diffusion distance between the interdigital electrodes. This concept introduces the recent advances on the design, fabrication, and application of planar micro‐supercapacitors for on‐chip energy storage from an overall perspective. Moreover, challenges and future development trends are discussed.
Whole exome sequencing as a diagnostic adjunct to clinical testing in fetuses with structural abnormalities
Authors: Fu F. , Li R. , Li Y. , Nie Z.‐Q. , Lei T. , Wang D. , Yang X. , Han J. , Pan M. , Zhen L. , Ou Y. , Li J. , Li F.‐T. , Jing X. , Li D. , Liao C. 
Published: October 2017

AbstractObjectivesTo evaluate the diagnostic yield of prenatal whole exome sequencing (WES) for monogenic disorders in fetuses with structural malformations and normal results on cytogenetic testing, and to describe information on pathogenic variants that is provided by WES.MethodsKaryotyping, chromosomal microarray analysis (CMA) and WES were performed sequentially on stored samples from a cohort of 3949 pregnancies with fetal structural abnormalities detected on ultrasound and/or magnetic resonance imaging, referred between January 2011 and December 2015. Diagnostic rates of the three techniques were investigated overall, for phenotypic subgroups and for proband‐only vs fetus–mother–father samples. Information on pathogenic variants was identified by WES.ResultsOverall, 18.2% (720/3949) of fetuses had an abnormal karyotype. Pathogenic copy number variants were detected on CMA in 8.2% (138/1680) of fetuses that had a normal karyotype result. WES performed on a subgroup of 196 fetuses with normal CMA and karyotype results revealed the putative genetic variants responsible for the abnormal phenotypes in 47 cases (24%). The molecular diagnosis rates for fetus–mother–father and proband‐only samples were 26.5% (13/49) and 23.1% (34/147), respectively. Variants of uncertain significance were detected in 12.8% (25/196) of fetuses, of which 22 were identified in the fetal proband‐only group (15%; 22/147) and three in the fetus–mother–father group (6.1%; 3/49). The incidental finding rate was 6.1% (12/196).ConclusionsWES is a promising method for the identification of genetic variants that cause structural abnormalities in fetuses with normal results on karyotyping and CMA. This enhanced diagnostic yield has the potential to improve the clinical management of pregnancies and to inform better the reproductive decisions of affected families. Copyright © 2017 ISUOG. Published by John Wiley & Sons Ltd.
Expression of STK11 gene and its promoter activity in MCF control and cancer cells
Authors: Alkaf Asma , Al-Jafari Abdulaziz , Wani Tanveer A. , Alqattan Somaya , Zargar Seema 
Published: October 2017

Abstract
Serine/threonine kinase gene (STK11) is identified as tumor suppressor gene whose mutation can lead to Peutz–Jeghers syndrome (PJS). STK11 is emerging as a multifunctional protein, it activates 14 different AMP-activated protein kinase (AMPK) family members, important in the regulation of cell polarity, cell cycle arrest, energy and hemostasis. Present study was designed to evaluate STK11 mRNA expression in MCF-7 cancer and MCF-10 normal breast cells lines. mRNA expression was studied by real-time PCR. Further, human STK11 promoter construct was fused to a luciferase reporter and transfected into both MCF-7 and MCF-10 cells to identify the promoter activity in these cells. STK11 mRNA was found significantly higher in MCF-7 compared to MCF-10 cells (p value < 0.0005) indicating its role in the onset of breast cancer. Interestingly, it was found that the promoter activity of STK11 gene in MCF-7 cells was also significantly higher when compared to MCF-10 cells (p value < 0.005). Positive correlation was observed in promoter activity and gene expression (p = 0.048, r
2 = 0.587). This study for the first time relates the altered STK11 gene expression in breast cancer cells with altered promoter activity. The present finding may shed light on the new therapeutic approaches against breast cancer by targeting gene or its promoter.
Evaluating the contribution of avalanching to the mass balance of Himalayan glaciers
Authors: Laha Sourav , Kumari Reshama , Singh Sunil , Mishra Aditya , Sharma Tushar , Banerjee Argha , Nainwal Harish Chandra , Shankar R. 
Published: October 2017

ABSTRACT
Avalanching is a prominent source of accumulation on glaciers that have high and steep valley-walls surrounding their accumulation zones. These glaciers are typically characterised by an extensive supraglacial debris cover and a low accumulation area ratio. Despite an abundance of such glaciers in the rugged landscapes of the High Himalaya, attempts to quantify the net avalanche contribution to mass balance and its long-term variation are almost missing. We first discuss diagnostic criteria to identify strongly avalanche-fed glaciers. Second, we develop an approximate method to quantify the magnitude of the avalanche accumulation exploiting its expected control on the dynamics of these glaciers. The procedure is based on a simplified flowline model description of the glacier concerned and utilises the known glaciological mass-balance, velocity and surface-elevation profiles of the glacier. We apply the method to three Himalayan glaciers and show that the data on the recent dynamics of these glaciers are consistent with a dominant contribution of avalanches to the total accumulation. As a control experiment, we also simulate another Himalayan glacier where no significant avalanche contribution is expected, and reproduce the recent changes in that glacier without any additional avalanche contribution.
Pre-pregnancy adherences to empirically derived dietary patterns and gestational diabetes risk in a Mediterranean cohort: the Seguimiento Universidad de Navarra (SUN) project
Authors: Donazar-Ezcurra Mikel , Lopez-del Burgo Cristina , Martinez-Gonzalez Miguel A. , Basterra-Gortari Francisco J. , de Irala Jokin , Bes-Rastrollo Maira 
Published: October 2017

AbstractThe aim of this study was to investigate the association between the adherence to empirically derived dietary patterns and gestational diabetes mellitus (GDM) risk and of healthy lifestyles with the prevention of GDM defining an overall healthy score. The Seguimiento Universidad de Navarra project is a Mediterranean cohort of university graduates started in 1999. We included 3455 pregnant women. During a mean follow-up of 10·3 (sd 3·3) years, we identified 173 incident GDM cases. Two major dietary patterns were identified using principal component analysis: the Western dietary pattern (WDP) (characterised by a high consumption of meat-based products and processed foods) and the Mediterranean dietary pattern (MDP) (characterised by a high consumption of vegetables, fruits, fish and non-processed foods). A low-risk score for GDM was defined taking into account important risk factors (age, BMI and unhealthy dietary pattern) for GDM. Positive association was found in the multivariable model between the highest quartile of adherence to WDP and GDM incidence compared with the lowest quartile (OR 1·56; 95 % CI 1·00, 2·43). No association was found between adherence to the MDP and GDM incidence (OR 1·08; 95 % CI 0·68, 1·70 for the highest quartile compared with the lowest). Women who adhered to all three low-risk factors had a 76 % lower risk of GDM (OR 0·24; 95 % CI 0·10, 0·55) compared with women who did not adhere to any factor before pregnancy. In conclusion, our results reinforce the importance of dietary recommendations and other two factors (low BMI and young age at pregnancy) in pre-gravid women.