bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Rosetta flexible‐backbone computational protein design methods on binding interactions
Authors: Loshbaugh Amanda L. , Kortemme Tanja 
Published: July 2019

AbstractComputational design of binding sites in proteins remains difficult, in part due to limitations in our current ability to sample backbone conformations that enable precise and accurate geometric positioning of side chains during sequence design. Here we present a benchmark framework for comparison between flexible‐backbone design methods applied to binding interactions. We quantify the ability of different flexible backbone design methods in the widely used protein design software Rosetta to recapitulate observed protein sequence profiles assumed to represent functional protein/protein and protein/small molecule binding interactions. The CoupledMoves method, which combines backbone flexibility and sequence exploration into a single acceptance step during the sampling trajectory, better recapitulates observed sequence profiles than the BackrubEnsemble and FastDesign methods, which separate backbone flexibility and sequence design into separate acceptance steps during the sampling trajectory. Flexible‐backbone design with the CoupledMoves method is a powerful strategy for reducing sequence space to generate targeted libraries for experimental screening and selection.
Physiologically‐Based Pharmacokinetic Modeling vs. Allometric Scaling for the Prediction of Infliximab Pharmacokinetics in Pediatric Patients
Authors: Malik Paul R. V. , Edginton Andrea N. 
Published: July 2019

The comparative performances of physiologically‐based pharmacokinetic (PBPK) modeling and allometric scaling for predicting the pharmacokinetics (PKs) of large molecules in pediatrics are unknown. Therefore, both methods were evaluated for accuracy in translating knowledge of infliximab PKs from adults to children. PBPK modeling was performed using the base model for large molecules in PK‐Sim version 7.4 with modifications in Mobi. Eight population PK models from literature were reconstructed and scaled by allometry to pediatrics. Evaluation data included seven pediatric studies (~4–18 years). Both methods performed comparably with 66.7% and 68.6% of model‐predicted concentrations falling within twofold of the observed concentrations for PBPK modeling and allometry, respectively. Considerable variability was noted among the allometric models. Therefore, pediatric clinical trial planning would benefit from using approaches that require predictions depending on the specific question i.e., PBPK modeling and allometry.
The effects of Cernitin® on inflammatory parameters and benign prostatic hyperplasia: An in vitro study
Authors: Dizeyi Nishtman , Mattisson Ingrid Yao , Ramnemark Lena , Grabe Magnus , Abrahamsson Per‐Anders 
Published: July 2019

The pollen extract Cernitin® is widely used for treatment of benign prostatic hyperplasia (BPH) and non‐bacterial chronin prostatitis. However, little is known about the underlying molecular mechanisms to explain the clinical effects of Cernitin®. In this study, we sought to investigate the cellular mechanisms by which Cernitin® induces its effects on human prostatic cell lines BPH‐1 and WPMY‐1 and primary human peripheral blood mononuclear cells (hPBMCs) in vitro. We examined the effects of Cernitin® formulas T60 and GBX on the protein expression, proliferation, and cytokines production. Results revealed that Cernitin® upregulated antiinflammatory cytokine interleukin (IL)‐10 and its receptors IL‐10RA and IL‐10B in addition to the upregulation of tumour necrosis factor‐related apoptosis‐inducing ligand in hPBMC. Interestingly, the levels of proinflammatory cytokines IL‐6 and IL‐8 were also increased. Furthermore, Cernitin® had significantly increased the level of IL‐10 in BPH‐1 and WPMY‐1 cells. The level of IL‐6 was also significantly increased in these cells although both T60 and GBX inhibited STAT‐3 phosphorylation. Moreover, Cernitin® formulas had significantly reduced androgen receptor and prostate‐specific antigen protein expression in stromal cells (p < .05). Treatment with GBX and T60 had significantly inhibited proliferation of BPH (p < .001) and stromal cells (p < .05), in a dose‐dependent manner. Taken together, treatment with Cernitin® showed to regulate cytokines level in both prostatic cell lines and hPBMCs and it was associated with decreased androgen receptor and prostate‐specific antigen levels WPMY‐1 cells.
Energetically consistent scale‐adaptive stochastic and deterministic energy backscatter schemes for an atmospheric model
Authors: Dwivedi Suneet , Franzke Christian L. E. , Lunkeit Frank 
Published: July 2019

AbstractCurrent climate models still suffer from many biases which are partly due to excessive subgrid‐scale dissipation. Here we systematically develop energetically consistent stochastic energy backscatter (SEB) and deterministic energy backscatter (DEB) parametrization schemes. We implement our schemes in a simplified spectral atmospheric General Circulation Model (GCM). It is shown that the SEB scheme performs better than the DEB scheme at low horizontal resolutions (T21 and T31), whereas the performance of both schemes becomes comparable as the resolution increases to T42 when comparing with our reference simulation at T127 resolution. The energy backscatter parametrization schemes improve eddy variability in low‐resolution models and correctly capture the dominant mode of zonal‐mean zonal wind variability. The autocorrelation time‐scale of low‐resolution models is also found to be more consistent with the reference simulation when applying the SEB and DEB parametrizations. Our schemes are scale‐adaptive and computationally efficient.
Markov chain‐based cost‐optimal control charts for health care data
Authors: Dobi Balázs , Zempléni András 
Published: July 2019

AbstractControl charts have traditionally been used in industrial statistics but are constantly seeing new areas of application, especially in the age of Industry 4.0. This paper introduces a new method, which is suitable for applications in the health care sector, especially for monitoring the health characteristic of a patient. We adopt a Markov chain‐based approach and develop a method in which not only the shift size (ie, the degradation of the patient's health) can be random, but the effect of the repair (ie, treatment) and time between samplings (ie, visits) too. This means that we do not use many often‐present assumptions that are usually not applicable for medical treatments. The average cost of the protocol, which is determined by the time between samplings and the control limit, can be estimated using the stationary distribution of the Markov chain.Furthermore, we incorporate the standard deviation of the cost into the optimisation procedure, which is often very important from a process control viewpoint. The sensitivity of the optimal parameters and the resulting average cost and cost standard deviation on different parameter values is investigated. We demonstrate the usefulness of the approach for real‐life data of patients treated in Hungary, namely the monitoring of cholesterol level of patients with cardiovascular event risk. The results showed that the optimal parameters from our approach can be somewhat different from the original medical parameters.
Observer‐based finite‐time output‐feedback controller for DC‐DC buck converters with unknown load variations
Authors: Cheng Yingying , Jin Qingchun , Du Haibo , Xu Yeyuan , Zhu Wenwu , Jiang Congrang 
Published: July 2019

SummaryThe output voltage regulation problem of a DC‐DC buck converter is investigated in this paper via an observer‐based finite‐time output‐feedback control approach. Considering the effects of unknown load variations and the case without current sensor, by using the technique of adding a power integrator and the idea of nonseparation principle, a finite‐time voltage regulation control algorithm via dynamic output feedback is designed. The main feature of the designed observer and controller does not need any load's information. Theoretically, it is proven that the output voltage can reach the desired voltage in a finite time under the proposed controller. The effectiveness of the proposed control method is illustrated by numerical simulations and experimental results.
Gaussian mixture models as automated particle classifiers for fast neutron detectors
Authors: Blair Brenton , Chen Cliff , Glenn Andrew , Kaplan Alan , Ruz Jaime , Simms Lance , Wurtz Ron 
Published: July 2019

AbstractPulse shape discrimination (PSD) is the task of classifying electronic pulse shapes for different particle types such as gamma rays and fast neutrons interacting in scintillators and read out by photo sensitive detectors. This field has been limited in its adoption of techniques found in the statistical learning community. Methods initially employed in the 1960s for analog electronic circuitry persist in the current PSD literature describing operations performed on digitized pulses, which are amenable to statistical rigor. Despite vast amounts of data collected at low energy levels, traditional PSD methods are unable to discriminate particles below a certain threshold. In this work, Gaussian mixture models (GMMs) are used as a clustering technique for fast neutron detection in the absence of labeled data. GMMs yield improvements spanning the energy spectrum in a desirably efficient, unsupervised fashion. An extension, the Dirichlet Process GMM, provides further flexibility and classification improvement.
A dynamic CSFICA and feature‐based collision detection method in multichannel space‐based AIS
Authors: Zhang Peixin , Wang Jianxin , Tian Da , Ren Peng 
Published: July 2019

SummaryTo detect message collisions in multichannel spaced‐based automatic identification system (AIS), a dynamic complex symmetric fast independent component analysis (CSFICA) and feature‐based collision detection method is proposed in this paper. A fast and stable blind source separation algorithm, dynamic CSFICA, is utilized to separate signals dynamically and improve the signal‐to‐interference ratio (SIR) in each channel. A frequency and phase offset insensitive feature detection algorithm is used to calculate the test statistics in each channel. The false alarm is suppressed by applying the arithmetic to geometric mean (AGM) method, and test statistics of channels with sufficient signal quality are extracted to detect the preamble. Simulation results show that the proposed algorithm outperforms the reference feature detection algorithm under collision conditions and is insensitive to the SIR. The proposed algorithm is more resistant to false alarm caused by signal (FAS) than the differential correlation (DC) algorithm.
Organizational design choices of high‐tech startups: How middle management drives innovation performance
Authors: Grimpe Christoph , Murmann Martin , Sofka Wolfgang 
Published: July 2019

AbstractResearch SummaryInnovative products and services are the inspiration for many startups. However, founders find that the management of existing operations competes with the attention that they can devote to innovation. We investigate whether and how establishing a middle management level frees up attention for innovation when firms are newly started. We argue that middle management is positively related to introducing product innovations and that the effect is stronger when founders have larger stocks of pre‐existing knowledge and when the startup's industry provides more innovation opportunities. These hypotheses are supported by an analysis of 2,431 German high‐tech startups founded between 2005 and 2012.
Managerial SummaryMost high‐tech entrepreneurs acknowledge that an overload of managerial tasks keeps them from advancing innovation in their startups. However, they are often times reluctant to introduce middle management because of a fear that the resulting bureaucratization will stifle innovation. Our study shows that these fears are not justified. Instead, we find for 2,431 high‐tech startups in Germany that startups with middle managers are significantly more innovative than those without. While middle managers might be a roadblock for innovation in large firms, startups benefit from having them. Founders are the central decision makers in startups and can easily be overburdened with management tasks. Middle managers can alleviate parts of this workload and allow founders to focus on creating innovative products and services.
First‐principles study of the atomic structures, electronic properties, and surface stability of BaTiO3 (001) and (011) surfaces
Authors: Zhong Mi , Zeng Wei , Liu Fu‐Sheng , Tang Bin , Liu Qi‐Jun 
Published: July 2019

The atomic structures, electronic properties, and surface stability of (001) and (011) surfaces of BaTiO3 are studied by first‐principles calculations. Four differently terminated BaTiO3 surfaces are considered in this study, including (001)‐BaO, (001)‐TiO2, (011)‐BaTiO, and (011)‐O2 terminations. The relaxations and rumplings are calculated and discussed, finding that the first layer relaxes inwards, while the second layer relaxes outwards for (001) and (110) surfaces. The data obtained for electronic properties show that O2p states in (001)‐BaO/(001)‐TiO2 termination shift to the lower/higher energy region, leading to a wide/narrow band gap. And the new produced surface states are observed in (011) surface terminations, which is mainly attributed to the supplied electrons from outermost surface atoms, even O atoms are oxidized. Furthermore, the (001) surface of BaTiO3 is found to be more stable than the (011) surface according to the predicted surface energy which is 0.86 and 2.92 J/m2 for (001) and (011) surfaces, respectively. Of which, BaO termination is predicted to be more likely to cleavage from the (001) direction than the TiO2 termination is.
Self‐Assembled Metalloporphyrins–Magnesium Phosphate Hybrid Spheres as Efficient Catalysts for Cycloaddition of Carbon Dioxide
Authors: Gan Tao , Zhang Hao , Liu Yifei , He Qian , Zhang Ying , He Xiaohui , Ji Hongbing 
Published: July 2019

AbstractDue to the unique microstructure and superior catalytic properties, organic‐inorganic hybrid materials attract extensive attention. Herein, we report a facile coprecipitation method for the fabrication of metalloporphyrin–metal phosphate salt hybrid spheres, and the cycloaddition of carbon dioxide with epoxides is employed as probe reaction to evaluate the catalytic performance of our as‐synthesized catalysts. The hybrid spheres composed of meso‐tetra‐(4‐N‐pyridyl) zinc porphyrin (ZnTPyP)–magnesium phosphate exhibited superior catalytic performance, and the conversion was much higher than that of individual ZnTPyP and magnesium phosphate, probably because of the acid‐base synergistic effect. Meanwhile, the spheres showed excellent stability during the circulation experiments as well as compatibility with a wide scope of substrates. This work provides a valuable approach for the preparation of novel and efficient heterogeneous catalytic composites.
Citrate Stabilized Au‐FexOy Nanocomposites for Variable Exchange Bias, Catalytic Properties and Reversible Interaction with Doxorubicin
Authors: Lone Shahbaz Ahmad , Sanyal Prabuddha , Das Pintu , Sadhu Kalyan K. 
Published: July 2019

AbstractExchange bias effect in Au‐FexOy nanocomposites, prepared with regulated Au:Fe content, has been controlled using the variable iron content and the composition of FexOy. A green synthetic route has been adapted at room temperature in aqueous medium for such Au−Fe oxide nanocomposites. Diversity in FexOy compositions has been achieved through Au(III) reduction by Fe powder to obtain Au‐FexOy nanocomposites in presence of gold nanoparticles as seed and threshold amount of sodium citrate as stabilizing agent. The exchange bias effect in selective Au‐FexOy nanocomposites (5Fe, 6Fe, 7Fe and 9Fe) arises from the ferromagnetic‐antiferromagnetic (FM‐AFM) interaction between Fe3O4 and α‐Fe2O3 present in the samples. A theoretical model is used to explain the variation of the exchange bias, coercivity and magnetization for the different samples at various temperatures. These Au‐FexOy nanocomposites have been compared in terms of their catalytic activities for nitroarene reductions and reversible surface interaction with cancer drug doxorubicin.
A systematic literature review of software effort prediction using machine learning methods
Authors: Ali Asad , Gravino Carmine 
Published: July 2019

AbstractMachine learning (ML) techniques have been widely investigated for building prediction models, able to estimate software development effort as well as to improve the accuracy of other estimation techniques. The objective of this paper is to systematically review the recent studies which used and discussed the software effort estimation models built using ML techniques. The performed literature review is based on the empirical studies published in the time period of January 1991 to December 2017, by employing widely used guidelines. The review has selected a total of 75 primary studies after the careful filtering of inclusion/exclusion and quality assessment criteria. The performed analysis reveals that artificial neural network (ANN) as ML model, NASA as dataset, and mean magnitude of relative error (MMRE) as accuracy measure are widely used in the selected studies. ANN and support vector machine (SVM) are the two techniques which have outperformed other ML techniques in more studies. Regression techniques are the mostly used among the non‐ML techniques, which outperformed other ML techniques in about 19 studies. Moreover, SVM and regression techniques in combination are characterized by better predictions when compared with other ML and non‐ML techniques.
Highly Transparent Organic Solar Cells with All‐Near‐Infrared Photoactive Materials
Authors: Xie Yuanpeng , Xia Ruoxi , Li Tengfei , Ye Linglong , Zhan Xiaowei , Yip Hin‐Lap , Sun Yanming 
Published: July 2019

AbstractTransparent organic photovoltaics are identified as important components for building‐integrated photovoltaics and smart window technologies. In this work, highly transparent organic solar cells (T‐OSCs) based on all‐near‐infrared (NIR) harvesting materials (optical bandgap, < 1.4 eV) are first fabricated. Both donor and acceptor materials used in T‐OSCs exhibit great transparency in the visible region. After combining MoO3/Ag or MoO3/Ag/MoO3 transparent electrode, T‐OSCs show excellent visible light transmittance (VLT) of 52–61.5% with power conversion efficiencies of 3.5–4.2%. As far as it is known, this all‐NIR active layer represents the most visible transparent donor–acceptor combination in OSCs. In addition to high VLT, T‐OSCs have great aesthetic value, good color‐rendering index (CRI > 90), and high light energy utilization properties. This work highlights great potential of NIR photoactive materials for T‐OSCs.
Decoupling and analysis of the deformation of flanged reinforced concrete shear walls
Authors: Wang Bin , Shi Qing‐Xuan , Cai Wen‐Zhe 
Published: July 2019

SummaryCompared with rectangular walls, a relatively large proportion of shear deformations are expected for flanged walls due to their larger flexural capacity. As few well‐documented experimental data are available to assess the attributes of the various deformation components of flanged walls, the feasibility of using established models to predict the deformation capacity of flanged walls is debatable. This study presents experimental results for three large‐scale T‐shaped reinforced concrete walls under cyclic loading to examine the relative contributions of flexural, shear, and sliding deformations to lateral displacement. By using a high‐precision and noninterference measurement method based on particle image velocimetry, the deformation components were decoupled to investigate the variation in each deformation component with the total deformation corresponding to the damage evolution process. For flexure‐dominant T‐shaped walls, the ratio of shear‐to‐total deformations in the plastic hinge region slowly increases over the entire plastic range, whereas the ratio of shear‐to‐total top displacements remains approximately constant. When predicting the deformation capacity of flanged walls, shear deformations but not the contribution of sliding deformations should be considered. Based on the proportional relationship between shear strain and curvature, a simple model for estimating the shear deformations of flexure‐dominant flanged walls is proposed.
“In Search of Peace”: Refugee Experiences in Children's Literature
Authors: A. Ward Natalia , N. Warren Amber 
Published: July 2019

AbstractThe authors closely analyzed 45 children's books featuring characters with refugee backgrounds that had been published since 2013. With the concept of culturally sustaining pedagogy underpinning the review, analysis revealed that these texts are rich and detailed, providing a starting point for discussing the global refugee crisis with students, but they occasionally fall short in providing complex, multidimensional representations of characters’ lives and experiences. A majority of the texts analyzed focus on the journey in search of a safe place to live, whereas very few focus on the complexity of making a life in a new place. The findings highlight the importance of identifying texts that provide complexity, dimension, and specificity in depicting experiences of refugee‐background characters across settings. Opening classrooms to texts about the diversity of refugee experiences invites teachers and their students to critically explore the important global issues of migration, equity, and ways of being human.