bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cheminformatics in Drug Discovery, an Industrial Perspective
Authors: Chen Hongming , Kogej Thierry , Engkvist Ola 
Published: May 2018

AbstractCheminformatics has established itself as a core discipline within large scale drug discovery operations. It would be impossible to handle the amount of data generated today in a small molecule drug discovery project without persons skilled in cheminformatics. In addition, due to increased emphasis on “Big Data”, machine learning and artificial intelligence, not only in the society in general, but also in drug discovery, it is expected that the cheminformatics field will be even more important in the future. Traditional areas like virtual screening, library design and high‐throughput screening analysis are highlighted in this review. Applying machine learning in drug discovery is an area that has become very important. Applications of machine learning in early drug discovery has been extended from predicting ADME properties and target activity to tasks like de novo molecular design and prediction of chemical reactions.
Regulatory Roles of Flavonoids on Inflammasome Activation during Inflammatory Responses
Authors: Yi Young‐Su 
Published: May 2018

AbstractInflammation is an innate immune response to noxious stimuli to protect the body from pathogens. Inflammatory responses consist of two main steps: priming and triggering. In priming, inflammatory cells increase expressions of inflammatory molecules, while in triggering, inflammasomes are activated, resulting in cell death and pro‐inflammatory cytokine secretion. Inflammasomes are protein complexes comprising intracellular pattern recognition receptors (PRRs) (e.g., nucleotide‐binding oligomerization domain‐like receptors (NLRs), absent in melanoma 2 (AIM2), and caspases‐4/5/11) and pro‐caspase‐1 with or without a bipartite adaptor molecule ASC. Inflammasome activation induces pyroptosis, inflammatory cell death, and stimulates caspase‐1‐mediated secretion of interleukin (IL)‐1b and IL‐18. Flavonoids are secondary metabolites found in various plants and are considered as critical ingredients promoting health and ameliorating various disease symptoms. Anti‐inflammatory activity of flavonoids and underlying mechanisms have been widely studied. This review introduces current knowledge on different types of inflammasomes and their activation during inflammatory responses and discusses recent studies regarding anti‐inflammatory roles of flavonoids as suppressors of inflammasomes in inflammatory conditions. Understanding the regulatory effects of flavonoids on inflammasome activation will increase our knowledge of flavonoid‐mediated anti‐inflammatory activity and provide new insights into the development of flavonoid preparations to prevent and treat human inflammatory diseases.
Accelerated pre‐senile systemic amyloidosis in PACAP knockout mice – a protective role of PACAP in age‐related degenerative processes
Authors: Reglodi Dora , Jungling Adel , Longuespée Rémi , Kriegsmann Joerg , Casadonte Rita , Kriegsmann Mark , Juhasz Tamas , Bardosi Sebastian , Tamas Andrea , Fulop Balazs Daniel , Kovacs Krisztina , Nagy Zsuzsanna , Sparks Jason , Miseta Attila , Mazzucchelli Gabriel , Hashimoto Hitoshi , Bardosi Attila 
Published: May 2018

AbstractDysregulation of neuropeptides may play an important role in aging‐induced impairments. Among them, pituitary adenylate cyclase‐activating polypeptide (PACAP) is a potent cytoprotective peptide that provides an endogenous control against a variety of tissue‐damaging stimuli. We hypothesized that the progressive decline of PACAP throughout life and the well‐known general cytoprotective effects of PACAP lead to age‐related pathophysiological changes in PACAP deficiency, supported by the increased vulnerability to various stressors of animals partially or totally lacking PACAP. Using young and aging CD1 PACAP knockout (KO) and wild type (WT) mice, we demonstrated pre‐senile amyloidosis in young PACAP KO animals and showed that senile amyloidosis appeared accelerated, more generalized, more severe, and affected more individuals. Histopathology showed age‐related systemic amyloidosis with mainly kidney, spleen, liver, skin, thyroid, intestinal, tracheal, and esophageal involvement. Mass spectrometry‐based proteomic analysis, reconfirmed with immunohistochemistry, revealed that apolipoprotein‐AIV was the main amyloid protein in the deposits together with several accompanying proteins. Although the local amyloidogenic protein expression was disturbed in KO animals, no difference was found in laboratory lipid parameters, suggesting a complex pathway leading to increased age‐related degeneration with amyloid deposits in the absence of PACAP. In spite of no marked inflammatory histological changes or blood test parameters, we detected a disturbed cytokine profile that possibly creates a pro‐inflammatory milieu favoring amyloid deposition. In summary, here we describe accelerated systemic senile amyloidosis in PACAP gene‐deficient mice, which might indicate an early aging phenomenon in this mouse strain. Thus, PACAP KO mice could serve as a model of accelerated aging with human relevance. © 2018 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
Student engagement and mathematics achievement: Unraveling main and interactive effects
Authors: Fung Francis , Tan Cheng Yong , Chen Gaowei 
Published: May 2018

AbstractThe present study explored the relationships between student engagement and mathematics achievement for 295,416 15‐year‐old students from 11,767 secondary schools in 34 countries who participated in the Program for International Student Assessment (PISA) 2012. Affective engagement was measured by students’ mathematics interest (InterestMath) and perceived usefulness of schooling (PerceptionSch), behavioral engagement by behaviors facilitating mathematics learning (BehaviorMath) and participation in mathematics learning activities (ActivitiesMath), and cognitive engagement by openness (Openness) and perseverance (Perseverance) in problem‐solving. Results showed that students who were more engaged had higher levels of academic achievement, with cognitive engagement having the strongest association with achievement. Results also showed that students who were highly engaged in two domains had higher achievement levels than peers who were engaged in only one domain in six pairwise comparisons (InterestMath‐BehaviorMath, InterestMath‐Openness, InterestMath‐Perseverance, PerceptionSch‐BehaviorMath, PerceptionSch‐Openness, PerceptionSch‐Perseverance). These results highlighted the importance of a whole‐school based approach in enhancing student achievement.
Factors associated with self‐reported history of depression diagnosis among cancer survivors aged 18 years and over in the United States
Authors: Gerbi Gemechu B. , Ivory Stranjae , Archie‐Booker Elaine , Claridy Mechelle D. , Miles‐Richardson Stephanie 
Published: May 2018

AbstractObjectiveAccording to the American Cancer Society, 25% of cancer survivors in the United States develop depression. The objective of this study is to assess factors associated with self‐reported history of depression diagnosis among cancer survivors aged ≥18 years in the United States.MethodsData were analyzed from the 2014 Behavioral Risk Factor Surveillance System (N = 6079). The Behavioral Risk Factor Surveillance System collects data about US residents regarding their health‐related risk behaviors and events, chronic health conditions, and use of preventive services. Respondents were considered to have a history of depression diagnosis if they answered yes to the question “Has a doctor or other health care provider EVER told you that you have a depressive disorder, including depression, major depression, dysthymia, or minor depression?” Bivariate and multivariable logistic regression analyses were conducted to assess factors associated with depression in cancer survivors. Analyses were conducted using SAS 9.4.ResultsAfter adjusting for demographic and socioeconomic factors, females (AOR: 1.70; 95% CI, 1.50‐1.97); those with an annual household income of $24 999 or less (AOR: 2.48; 95% CI, 1.95‐3.16); $25 000 to $49 999 (AOR: 1.62; 95% CI, 1.31‐2.02), and $50 000 to $74 999 (AOR: 1.35; 95% CI, 1.10‐1.71); those who were not married (AOR = 1.37; 95% CI, 1.17‐1.60); and those who perceived their health as poor (AOR = 2.33; 95% CI, 2.01‐2.70), were significantly more likely to report a diagnosis of depression.ConclusionsThe results indicate that gender, income, marital status, and perceived health status were associated with self‐reported depression among cancer survivors aged ≥18 years in the United States.
Flame‐Engraved Nickel–Iron Layered Double Hydroxide Nanosheets for Boosting Oxygen Evolution Reactivity
Authors: Zhou Daojin , Xiong Xuya , Cai Zhao , Han Nana , Jia Yin , Xie Qixian , Duan Xinxuan , Xie Tianhui , Zheng Xiaolin , Sun Xiaoming , Duan Xue 
Published: May 2018

AbstractIntroducing oxygen vacancies to metal oxide materials would improve their catalytic activity but usually needs reductive reagents (e.g., H2) and high temperatures (e.g., >600 °C), which is unsafe, complex, and time consuming. Herein, a fast (30 s) and facile (operated at ambient conditions) flame‐engraved method is used to introduce abundant oxygen vacancies and well‐defined hexagonal cavities with (110) edges to nickel–iron layered double hydroxides (NiFe‐LDH). Abundant oxygen vacancies, lower coordination numbers, and electron‐rich structures of Ni and Fe sites emerge in the flame‐engraved NiFe‐LDH array electrode, leading to its onset potential as low as 1.40 V (vs reversible hydrogen electrode) for oxygen evolution reaction. This highlights the importance and convenience of flame‐engraving method in preparing metal hydroxides with abundant oxygen vacancies, which can be used as efficient electrochemical catalysts.
MMRUC3: A recommendation approach ofmove methodrefactoring using coupling, cohesion, and contextual similarity to enhance software design
Authors: Rahman Md. Masudur , Riyadh Rashed Rubby , Khaled Shah Mostafa , Satter Abdus , Rahman Md. Rayhanur 
Published: May 2018

SummaryPlacement of methods is one of the most important design activities for any object‐oriented application in terms of coupling and cohesion. Due to method misplacement, the application becomes tightly coupled and loosely cohesive, reflecting inefficient design. Therefore, a feature envy code smell emerges from the application, as many methods use more features of other classes than its current class. Hence, development and maintenance time, cost, and effort are increased. To refactor the code smell and enhance the design quality,move methodrefactoring plays a significant role through grouping similar behaviors of methods. This is because the manual refactoring process is infeasible due to the necessity of huge time and most of the existing techniques consider only coupling‐based and/or cohesion‐based information of nonstatic entities (methods and attributes) for the recommendation. However, this article proposes an approach that uses contextual information, based on information retrieval techniques, along with dependency (coupling and cohesion)‐based information of the application for the recommendation. In addition, the approach incorporates both static and nonstatic entities in the recommendation process. For validation, the approach is applied on seven well‐known open source projects. The results of the experimental evaluation indicate that the proposed approach provides better results with an average precision of 18.91%, a recall of 69.91%, and an F‐measure of 29.77% than the JDeodorant tool (a widely used eclipse plugin for refactorings). Moreover, this article establishes several relationships between the accuracy of the approach and project standards and sizes.
An investigation on the interaction of moment‐resisting frames and shear walls in RC dual systems using endurance time method
Authors: Estekanchi H.E. , Harati M. , Mashayekhi M.R. 
Published: May 2018

SummaryReinforced concrete (RC) dual systems are composed of RC moment‐resisting frames (MRFs) and RC shear walls, where MRFs are barely designed to handle gravity loads. Investigations have demonstrated that shear walls exert negative effects on the upper part of MRFs. In this paper, the interaction of shear walls and MRFs is inspected using endurance time (ET) method. ET is a dynamic time history‐based pushover procedure in which structures are exposed to a set of predefined intensifying ET acceleration functions. In this method, seismic performance of the considered structure is assessed based on earthquake return periods; during which, required predefined seismic performance objectives are fulfilled. In this study, several buildings with RC dual systems were designed based on the conventional codes. Next, their nonlinear duplicates were generated for the application of the ET analysis. It was revealed that shear wall elements impose considerable rotational demands—exceeding the criteria established by ASCE41‐13—on the beams and columns, especially those located on the upper parts of the buildings. This paper puts forth and reviews certain methods to cushion the negative effects brought about by RC shear walls, along with a detailed discussion on their merits and demerits.
Structural health monitoring for a 600 m high skyscraper
Authors: Li Qiusheng , He Yinghou , Zhou Kang , Han Xuliang , He Yuncheng , Shu Zhenru 
Published: May 2018

SummaryPing‐An Finance Center (PAFC), with a total height of 600 m, is the fourth tallest building in the world. An integrated structural health monitoring (SHM) system with total number of 553 sensors, which was designed based on the modular design methodology, is being installed in PAFC to monitor its structural performance and external excitations during both construction and service stages. This paper first gives a brief introduction of the architecture of the SHM system, followed by detailed descriptions on its 7 subsystems, including the components, functions, and interrelationship corresponding to each subsystem. The modular design of the SHM system ensures highly effective operation of the comprehensive monitoring system, and such an extensible system allows the subsystems to be deployed and augmented easily to meet the evolving monitoring needs. The second part of this paper introduces the research activities and selected results from the SHM system equipped in PAFC, including monitoring of vertical deformations of various structural components, verification of effectiveness of active tuned mass damper systems, and verification of numerous damage identification methods. Finally, representative monitoring results from the SHM system in PAFC during a typhoon are presented and discussed. This paper aims to provide useful information for the SHM, construction, and design of super‐tall buildings.
Fragility analysis of hillside buildings designed for modern seismic design codes
Authors: Surana Mitesh , Singh Yogendra , Lang Dominik H. 
Published: May 2018

SummaryThe structural configurations of hillside buildings are significantly different than those observed on flat terrain. To study the effect of often observed structural configurations of hillside buildings, collapse fragility of regular “flat land (FL)” and irregular “split‐foundation (SF)” and “step‐back (SB)” buildings is studied using incremental dynamic analysis. The effects of building height, seismic zone, and near‐ and far‐field sites on collapse fragility are investigated. It is observed that SF and SB hillside buildings exhibit significant torsional effects at the storey just above the uppermost foundation level. In case of FL buildings, collapse occurs due to the flexural failure of beams and columns. On the other hand, in SF and SB buildings, the collapse occurs due to the combined effects of shear failure of short columns and flexural failure of beams and columns in the storey just above the uppermost foundation level. In general, SF buildings are observed to be the most vulnerable, whereas FL buildings are the least vulnerable. It is observed that high‐rise SF and SB buildings show unacceptably high probability of collapse at maximum considered earthquake, in Seismic Zone V and for the near‐field site in Seismic Zone IV.
A review of quadratic discriminant analysis for high‐dimensional data
Authors: Qin Yingli 
Published: May 2018

Quadratic discriminant analysis (QDA) is a classical and flexible classification approach, which allows differences between groups not only due to mean vectors but also covariance matrices. Modern high‐dimensional data bring us opportunities and also challenges. In the framework of classical QDA, the inverse of each sample covariance matrix is essential, but high‐dimensionality causes singularity in sample covariance matrices. To overcome this technical difficulty, several high‐dimensional QDA approaches with desirable theoretical properties emerge in recent years. We are to discuss the challenges, some existing works, and possibly several future directions with regard to high‐dimensional QDA.This article is categorized under:

Statistical and Graphical Methods of Data Analysis > Bayesian Methods and Theory
Statistical and Graphical Methods of Data Analysis > Analysis of High Dimensional Data
Statistical and Graphical Methods of Data Analysis > Multivariate Analysis
Statistical Learning and Exploratory Methods of the Data Sciences > Clustering and Classification
Research Gaps in Wilderness Medicine
Authors: Tritz Daniel , Dormire Kody , Brachtenbach Travis , Gordon Joshua , Sanders Donald , Gearheart David , Crawford Julia , Vassar Matt 
Published: May 2018

Introduction Wilderness medicine involves the treatment of individuals in remote, austere environments. Given the high potential for injuries as well as the unique treatment modalities required in wilderness medicine, evidence-based clinical practice guidelines are necessary to provide optimal care. In this study, we identify evidence gaps from low-quality recommendations in wilderness medicine clinical practice guidelines and identify new/ongoing research addressing them. Methods We included relevant clinical practice guidelines from the Wilderness Medical Society and obtained all 1C or 2C level recommendations. Patient/Problem/Population, intervention, comparison, outcome (PICO) questions were created to address each recommendation. Using 24 search strings, we extracted titles, clinical trial registry number, and recruitment status for 8899 articles. We categorized the articles by trial design to infer the effect they may have on future recommendations. Results Twelve clinical practice guidelines met inclusion criteria. From these we located 275 low-quality recommendations and used them to create 275 PICO questions. Thirty-three articles were relevant to the PICO questions. Heat-related illness had the highest number of relevant articles (n=9), but acute pain and altitude sickness had the most randomized clinical trials (n=6). Conclusion Overall, few studies were being conducted to address research gaps in wilderness medicine. Heat-related illness had the most new or ongoing research, whereas no studies were being conducted to address gaps in eye injuries, basic wound management, or spine immobilization. Animals, cadavers, and mannequin research are useful in cases in which human evidence is difficult to obtain. Establishing research priorities is recommended for addressing research gaps identified by guideline panels.
Classification of volcanic ash particles using a convolutional neural network and probability
Authors: Shoji Daigo , Noguchi Rina , Otsuki Shizuka , Hino Hideitsu 
Published: May 2018

AbstractAnalyses of volcanic ash are typically performed either by qualitatively classifying ash particles by eye or by quantitatively parameterizing its shape and texture. While complex shapes can be classified through qualitative analyses, the results are subjective due to the difficulty of categorizing complex shapes into a single class. Although quantitative analyses are objective, selection of shape parameters is required. Here, we applied a convolutional neural network (CNN) for the classification of volcanic ash. First, we defined four basal particle shapes (blocky, vesicular, elongated, rounded) generated by different eruption mechanisms (e.g., brittle fragmentation), and then trained the CNN using particles composed of only one basal shape. The CNN could recognize the basal shapes with over 90% accuracy. Using the trained network, we classified ash particles composed of multiple basal shapes based on the output of the network, which can be interpreted as a mixing ratio of the four basal shapes. Clustering of samples by the averaged probabilities and the intensity is consistent with the eruption type. The mixing ratio output by the CNN can be used to quantitatively classify complex shapes in nature without categorizing forcibly and without the need for shape parameters, which may lead to a new taxonomy.
Two yellow luminescence bands in undoped GaN
Authors: Reshchikov M. A. , McNamara J. D. , Helava H. , Usikov A. , Makarov Yu. 
Published: May 2018

AbstractTwo yellow luminescence bands related to different defects have been revealed in undoped GaN grown by hydride vapor phase epitaxy (HVPE). One of them, labeled YL1, has the zero-phonon line (ZPL) at 2.57 eV and the band maximum at 2.20 eV at low temperature. This luminescence band is the ubiquitous yellow band observed in GaN grown by metalorganic chemical vapor deposition, either undoped (but containing carbon with high concentration) or doped with Si. Another yellow band, labeled YL3, has the ZPL at 2.36 eV and the band maximum at 2.09 eV. Previously, the ZPL and fine structure of this band were erroneously attributed to the red luminescence band. Both the YL1 and YL3 bands show phonon-related fine structure at the high-energy side, which is caused by strong electron-phonon coupling involving the LO and pseudo-local phonon modes. The shapes of the bands are described with a one-dimensional configuration coordinate model, and the Huang-Rhys factors are found. Possible origins of the defect-related luminescence bands are discussed.
Complex Hydrogels Composed of Chitosan with Ring-opened Polyvinyl Pyrrolidone as a Gastroretentive Drug Dosage Form to Enhance the Bioavailability of Bisphosphonates
Authors: Su Chia-Yu , Ho Hsiu-O , Chen Ying-Chen , Yu Yu-Ting , Liu Der-Zen , Chao Fang-Ching , Sheu Ming-Thau 
Published: May 2018

AbstractComplex hydrogels formed with chitosan (CS) and ring-opened polyvinyl pyrrolidone (roPVP) as a swellable mucoadhesive gastroretentive drug dosage form (smGRDDF) were prepared and characterized. CS/roPVP hydrogels were produced by blending CS with roPVP obtained by basic treatment of PVP. Effects of the heating time and NaOH concentration employed for preparing roPVP, and CS molecular weights (Mws), and roPVP/CS ratios on the swelling ability of the resultant hydrogels were characterized. Rheological characteristics were further examined. Results demonstrated that roPVP obtained in a 0.5 M NaOH solution heated to 50 °C for 4 h was suitable for producing complex hydrogels with CS. At a roPVP/CS ratio of 20:1, hydrogels composed of three different Mws of CS possessed optimal swelling and mucoadhesive abilities and rheological properties. In vitro dissolution revealed sustained drug release. A pharmacokinetic study exhibited that the plasma profile of alendronate followed a sustained manner with 3-fold enhancement of the oral bioavailability. In conclusion, the smGRDDF composed of CS/roPVP complex hydrogels was successfully developed and is potentially applicable to improve the clinical efficacy of bisphosphonates.