bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the Misleading Use of for QSAR Model Comparison
Authors: Consonni Viviana , Todeschini Roberto , Ballabio Davide , Grisoni Francesca 
Published: August 2018

AbstractQuantitative Structure – Activity Relationship (QSAR) models play a central role in medicinal chemistry, toxicology and computer‐assisted molecular design, as well as a support for regulatory decisions and animal testing reduction. Thus, assessing their predictive ability becomes an essential step for any prospective application. Many metrics have been proposed to estimate the model predictive ability of QSARs, which have created confusion on how models should be evaluated and properly compared. Recently, we showed that the metric
is particularly well‐suited for comparing the external predictivity of different models developed on the same training dataset. However, when comparing models developed on different training data, this function becomes inadequate and only dispersion measures like the root‐mean‐square error (RMSE) should be used. The intent of this work is to provide clarity on the correct and incorrect uses of
, discussing its behavior towards the training data distribution and illustrating some cases in which
estimates may be misleading. Hereby, we encourage the usage of measures of dispersions when models trained on different datasets have to be compared and evaluated.
Autosegmentation for thoracic radiation treatment planning: A grand challenge at AAPM 2017
Authors: Yang Jinzhong , Veeraraghavan Harini , Armato Samuel G. , Farahani Keyvan , Kirby Justin S. , Kalpathy‐Kramer Jayashree , van Elmpt Wouter , Dekker Andre , Han Xiao , Feng Xue , Aljabar Paul , Oliveira Bruno , van der Heyden Brent , Zamdborg Leonid , Lam Dao , Gooding Mark , Sharp Gregory C. 
Published: August 2018

PurposeThis report presents the methods and results of the Thoracic Auto‐Segmentation Challenge organized at the 2017 Annual Meeting of American Association of Physicists in Medicine. The purpose of the challenge was to provide a benchmark dataset and platform for evaluating performance of autosegmentation methods of organs at risk (OARs) in thoracic CT images.
Methods
Sixty thoracic CT scans provided by three different institutions were separated into 36 training, 12 offline testing, and 12 online testing scans. Eleven participants completed the offline challenge, and seven completed the online challenge. The OARs were left and right lungs, heart, esophagus, and spinal cord. Clinical contours used for treatment planning were quality checked and edited to adhere to the RTOG 1106 contouring guidelines. Algorithms were evaluated using the Dice coefficient, Hausdorff distance, and mean surface distance. A consolidated score was computed by normalizing the metrics against interrater variability and averaging over all patients and structures.
Results
The interrater study revealed highest variability in Dice for the esophagus and spinal cord, and in surface distances for lungs and heart. Five out of seven algorithms that participated in the online challenge employed deep‐learning methods. Although the top three participants using deep learning produced the best segmentation for all structures, there was no significant difference in the performance among them. The fourth place participant used a multi‐atlas‐based approach. The highest Dice scores were produced for lungs, with averages ranging from 0.95 to 0.98, while the lowest Dice scores were produced for esophagus, with a range of 0.55–0.72.
Conclusion
The results of the challenge showed that the lungs and heart can be segmented fairly accurately by various algorithms, while deep‐learning methods performed better on the esophagus. Our dataset together with the manual contours for all training cases continues to be available publicly as an ongoing benchmarking resource.
Early diabetic retinopathy diagnosis based on local retinal blood vessel analysis in optical coherence tomography angiography (OCTA) images
Authors: Eladawi Nabila , Elmogy Mohammed , Khalifa Fahmi , Ghazal Mohammed , Ghazi Nicola , Aboelfetouh Ahmed , Riad Alaa , Sandhu Harpal , Schaal Shlomit , El‐Baz Ayman 
Published: August 2018

PurposeThis paper introduces a new computer‐aided diagnosis (CAD) system for detecting early‐stage diabetic retinopathy (DR) using optical coherence tomography angiography (OCTA) images.MethodsThe proposed DR‐CAD system is based on the analysis of new local features that describe both the appearance and retinal structure in OCTA images. It starts with a new segmentation approach that has the ability to extract the blood vessels from superficial and deep retinal OCTA maps. The high capability of our segmentation approach stems from using a joint Markov–Gibbs random field stochastic model integrating a 3D spatial statistical model with a first‐order appearance model of the blood vessels. Following the segmentation step, three new local features are estimated from the segmented vessels and the foveal avascular zone (FAZ): (a) vessels density, (b) blood vessel calibre, and (c) width of the FAZ. To distinguish mild DR patients from normal cases, the estimated three features are used to train and test a support vector machine (SVM) classifier with the radial basis function (RBF) kernel.ResultsOn a cohort of 105 subjects, the presented DR‐CAD system demonstrated an overall accuracy (ACC) of 94.3%, a sensitivity of 97.9%, a specificity of 87.0%, the area under the curve (AUC) of 92.4%, and a Dice similarity coefficient (DSC) of 95.8%. This in turn demonstrates the promise of the proposed CAD system as a supplemental tool for early detection of DR.ConclusionWe developed a new DR‐CAD system that is capable of diagnosing DR in its early stage. The proposed system is based on extracting three different features from the segmented OCTA images, which reflect the changes in the retinal vasculature network.
Growing disparities in an urban food desert: Downtown Albany longitudinal food environment studies
Authors: Hosler Akiko S. 
Published: August 2018

This paper presents findings from our longitudinal study of food environments in two exemplary, contrasting urban neighborhoods in Downtown Albany, New York. The “minority neighborhood” (74% racial/ethnic minority population) is a “food desert” by the United States Department of Agriculture's definition, whereas the adjacent “mixed neighborhood” (33% minority population) is not. The long‐term trend analysis (1970–2018) of the macro‐level food environment found that although the minority neighborhood lost all supermarkets and remains supermarket‐less since the late 1990s, the mixed neighborhood was able to retain several supermarkets and since 2008, it gained a new supermarket every 3–5 years. The medium‐term trend analysis (2003–2015) of the micro‐level food environment revealed a more complex picture of changing food environments. The total number of food stores in the minority neighborhood increased in much greater rates than the mixed neighborhood in the 12‐year period, and accordingly, the standardized availability measures for “any” fresh fruits and fresh vegetables increased significantly in the minority neighborhood. The standardized availability measure for adequate (five or more) varieties of nutritionally desirable fresh fruits and vegetables, however, did not increase in the minority neighborhood. Because the mixed neighborhood saw steady increases in such measures, disparities between the two neighborhoods grew incrementally and reached the highest point (rate ratio of over 5.0) in 2015. In this paper, there are also sections to provide historical and contextual background of our food environment research, as well as discussion on intervention ideas to address the disparities in fresh produce availability focusing on ethnic markets.
An Overview of Hyperinsulinemic‐Euglycemic Therapy in Calcium Channel Blocker and β‐blocker Overdose
Authors: Krenz James R. , Kaakeh Yaman 
Published: August 2018

Both calcium channel blockers (CCBs) and β blockers (BBs) are associated with fatal substance exposures within the United States. Cases of overdose with these agents have the potential to be both complex and difficult to manage. A variety of pharmacologic treatment options are available for clinicians to use to help mitigate harm from these poisonings. Hyperinsulinemic‐euglycemic therapy (HIET) was once regarded as a last‐ditch effort to treat patients in highly refractory cases. In recent years, this therapy has become a routine therapy in the treatment of CCB/BB overdose. This article provides a literature review regarding HIET in cases of overdose with CCB and BB agents. Relevant literature articles from 1997–2018 were identified and reviewed using the PubMed and Embase databases. The following search terms were used to identify potential articles: “hyperinsulinemic‐euglycemic therapy,” “overdose,” “calcium channel blocker,” “beta blocker,” and “insulin.” Articles published in the English language were included in this review. A manual search of reference lists was also conducted. Much of the literature is limited to case reports, series, retrospective chart reviews, and small prospective studies. The success rate observed in published case series ranged from 80.4–100%. Regular insulin is most commonly dosed at an initial bolus of 1 unit/kg followed by a regular insulin infusion of 0.5–1 unit/kg/hour. Euglycemia is often maintained using intravenous fluids containing dextrose. Hyperinsulinemic‐euglycemic therapy exhibited a promising safety profile, provided close monitoring is conducted. More research is needed to determine optimal strategies for maintaining euglycemia, ideal monitoring parameters, and consistent efficacy goals.
A 1‐year follow‐up study of capacity to love and work: What components of borderline personality disorder most impair interpersonal and vocational functioning?
Authors: Miller Caitlin E. , Lewis Kate L. , Huxley Elizabeth , Townsend Michelle L. , Grenyer Brin F.S. 
Published: August 2018

AbstractBackgroundFor individuals with borderline personality disorder (BPD), both the reduction in symptoms and the improvement of vocational and interpersonal function (psychosocial function) are important for recovery. Research suggests that some components of BPD make it harder to achieve functional recovery; however, findings are varied and inconclusive. The present study assesses recovery over time in BPD, investigates which symptoms make it harder to function and explores the relationships between these symptoms.MethodOne hundred ninety‐nine consecutively recruited individuals in psychological treatment for personality disorder were studied over 12 months. Measures of BPD symptom severity at intake were used to predict improvements in social and vocational function at follow‐up. Exploratory modelling was conducted to understand the relationships between symptoms and function.ResultsFollowing 12 months of treatment, symptoms and functioning improved. Those who experienced more severe emptiness, impulsivity and self‐harm had worse outcomes. A relationship between chronic emptiness at intake and impaired vocational outcome (days out of work) at follow‐up was found, mediated by severity of impulsivity and frequency of self‐harm.ConclusionChronic emptiness is associated with dysfunctional behaviours such as impulsivity and self‐harm, and poor psychosocial improvement. Interventions targeting chronic emptiness in those most vulnerable may improve functional outcomes. © 2018 John Wiley & Sons, Ltd.
Interactions between the Intrinsically Disordered Proteins β‐Synuclein and α‐Synuclein
Authors: Williams Jonathan K. , Yang Xue , Baum Jean 
Published: August 2018

AbstractSeveral intrinsically disordered proteins have been implicated in the process of amyloid fibril formation in neurodegenerative disease, and developing approaches to inhibit the aggregation of these intrinsically disordered proteins is critical for establishing effective therapies against disease progression. The aggregation pathway of the intrinsically disordered protein alpha‐synuclein, which is implicated in several neurodegenerative diseases known as synucleinopathies, has been extensively characterized. Less attention has been leveraged on beta‐synuclein, a homologous intrinsically disordered protein that co‐localizes with alpha‐synuclein and is known to delay alpha‐synuclein fibril formation. In this review, we focus on beta‐synuclein and the molecular‐level interactions between alpha‐synuclein and beta‐synuclein that underlie the delay of fibril formation. We highlight studies that begin to define alpha‐synuclein and beta‐synuclein interactions at the monomer, oligomer, and surface levels, and suggest that beta‐synuclein plays a role in regulation of inhibition at many different stages of alpha‐synuclein aggregation.
Se Atom‐Induced Synthesis of Concave Spherical Fe3O4@Cu2O Nanocrystals for Highly Efficient MRI–SERS Imaging‐Guided NIR Photothermal Therapy
Authors: Wang Zhiyi , Zhang Jie , Wang Hao , Hai Jun , Wang Baodui 
Published: August 2018

AbstractDeveloping multifunctional nanoplatform, which generally integrates multimodality imaging and therapeutic functions into a single nanocarrier, is of great importance for biomedicine and nanoscience. Herein, concave spherical Fe3O4@Cu2O nanocrystals (NCs) is first reported as a multifunctional diagnostic agent for in vitro magnetic resonance imaging (MRI) and surface‐enhanced Raman scattering (SERS) imaging‐guided photothermal therapy (PTT) based on Se atom‐induced transformation of core–shell Fe3O4@Cu2O NCs. Notably, a remarkable increase is found in SERS enhancement from rhodamine 123 (R123) molecules adsorbed on concave spherical Fe3O4@Cu2O NCs with a detection limit of 3 × 10−8m and enhancement factor up to 6.62 × 105. Due to it containing MRI‐active Fe3O4 nanoparticles, the synthesized probe could be used as a MRI‐SERS imaging in vitro (r2 relaxivity value: 72.37 mm−1 s−1). The detection limit is as low as 50 cells mL−1 based on SERS detection. Moreover, due to its high photothermal conversion efficiency (31.5%), the concave spherical Fe3O4@Cu2O NCs could be used for PTT in cellular level. The studies illustrate for the first time integrating MRI‐SERS imaging‐guided PTT all in one based on noble metal free nanostructures, which have great potential for precision theranostic nanomedicines.
Safe chemical repellents to prevent the spread of invasive ants
Authors: Chen Siqi , Chen Hongyu , Xu Yijuan 
Published: August 2018

AbstractBACKGROUNDThe red imported fire ant, Solenopsis invicta, is one of the most dangerous invasive species in the world. Fire ants can spread by hiding among plant material and soil that are transported from infested areas in vehicles and vessels. Therefore, efficient repellents may be used to prevent fire ants from infesting transported goods. Although some fire ant repellants have been identified, novel, cost‐effective and environmentally friendly materials for fire ant control are still needed. Recent studies with other model insects have suggested readily available, non‐toxic alternatives (e.g., anthranilates) to commercial repellents.RESULTSWe measured the repellent effects of the food additives ethyl anthranilate and butyl anthranilate against nesting by fire ant workers, and the results demonstrated that extremely low concentrations of these compounds can prevent fire ant nesting in pots. The tested compounds remained active at concentrations < 100 µL/L, which is many times lower than the minimum active concentration of any other proposed compound, including the established insect repellent N,N‐diethyl‐3‐methylbenzamide (DEET).CONCLUSIONThese inexpensive chemicals are safely used by the food and cosmetics industries, and their high efficiency differentiates them as the most promising chemicals for use in preventing the spread of fire ants; thus, these chemicals should be evaluated for further potential applications. © 2018 Society of Chemical Industry
Antiviral activity of titanium dioxide nanostructures as a control strategy for broad bean strain virus in faba bean
Authors: Elsharkawy Mohsen M , Derbalah Aly 
Published: August 2018

ABSTRACTBACKGROUNDThis study fabricated titanium dioxide nanostructures (TDNS) to control broad bean stain virus (BBSV) in faba bean plants. Protection of faba bean against BBSV was evaluated biologically with respect to virus severity, reduction in BBSV accumulation and expression of a pathogenesis‐related gene.RESULTSThe results indicate that faba bean plants treated with TDNS show a significant reduction in disease severity relative to untreated plants. The regulatory and defense gene involved in the salicylic acid signaling pathway was highly expressed in faba bean plants treated with TDNS compared with untreated plants. The structural features of TDNS, such as the small particle size and suitable shape, contributed to its high efficacy against BBSV. Growth of faba bean plants treated with TDNS was significantly enhanced relative to untreated plants.CONCULSIONTDNS is an important, eco‐friendly and safe strategy for controlling BBSV in faba bean and this study is the first report of this control strategy. © 2018 Society of Chemical Industry
Unravelling the demographic dynamics of ethnic residential segregation
Authors: Kauppinen Timo M. , van Ham Maarten 
Published: August 2018

AbstractSelective intraurban migration of ethnic groups is often assumed to be the main microlevel mechanism reproducing ethnic residential segregation. However, other demographic processes, such as natural change and international migration, also matter. This paper contributes to the literature by unravelling the impacts of different demographic processes to changes in ethnic segregation. It uses longitudinal individual‐level register data on the complete population of the Helsinki region in Finland. We calculate observed changes in exposure indices, segregation indices in counterfactual scenarios, and decompositions of population changes. Results indicate that intraregional migration is the main process affecting segregation between Finnish‐origin and non‐Western‐origin populations, but whereas migration of the former increases segregation, migration of the latter decreases it. International migration and natural change among the non‐Western‐origin population are the main processes increasing exposure of the non‐Western‐origin population to other members of the group. No indication is found of a general tendency to “self‐segregate.”
Quantifiable Simulation of Quantum Computation beyond Stochastic Ensemble Computation
Authors: Bang Jeongho , Ryu Junghee , Lee Chang‐Woo , Yee Ki Hyuk , Lee Jinhyoung , Son Wonmin 
Published: August 2018

AbstractIn this study, a distinctive feature of quantum computation (QC) is characterized. To this end, a seemingly‐powerful classical computing model, called “stochastic ensemble machine (SEnM),” is considered. The SEnM runs with an ensemble consisting of finite copies of a single probabilistic machine, hence is as powerful as a probabilistic Turing machine (PTM). Then the hypothesis—that is, the SEnM can effectively simulate a general circuit model of QC—is tested by introducing an information‐theoretic inequality, named readout inequality. The inequality is satisfied by the SEnM and imposes a critical condition: if the hypothesis holds, the inequality should be satisfied by the probing model of QC. However, it is shown that the above hypothesis is not generally accepted with the inequality violation; namely, such a simulation necessarily fails, implying that PTM ⊆ QC.
A Cut‐Resistant and Highly Restorable Graphene Foam
Authors: Liang Yuan , Liu Feng , Deng Yaxi , Zhou Qinhan , Cheng Zhihua , Zhang Panpan , Xiao Yukun , Lv Lingxiao , Liang Hanxue , Han Qing , Shao Huibo , Qu Liangti 
Published: August 2018

AbstractHigh‐pressure resistant and multidirectional compressible materials enable various applications but are often hindered by structure‐derived collapse and weak elasticity. Here, a super‐robust graphene foam with ladder shape microstructure capable of withstanding high pressure is presented. The multioriented ladder arrays architecture of the foam, consisting of thousands of identically sized square spaces, endow it with a great deal of elastic units. It can easily bear an iterative and multidirectional pressure of 44.5 MPa produced by a sharp blade, and may completely recover to its initial state by a load of 180 000 times their own weight even under 95% strain. More importantly, the foam can also maintain structural integrity after experiencing a pressure of 2.8 GPa through siphoning. Computational modeling of the “buckling of shells” mechanism reveals the unique ladder‐shaped graphene foam contributes to the superior cut resistance and good resilience. Based on this finding, it can be widely used in cutting resistance sensors, monitoring of sea level, and the detection of oily contaminants in water delivery pipelines.
Bifunctional Au@Bi2Se3 Core–Shell Nanoparticle for Synergetic Therapy by SERS‐Traceable AntagomiR Delivery and Photothermal Treatment
Authors: Mohammadniaei Mohsen , Lee Taek , Bharate Bapurao G. , Yoon Jinho , Choi Hye Kyu , Park Soo‐jeong , Kim Junghoon , Kim Jungho , Choi Jeong‐Woo 
Published: August 2018

AbstractFor the first time, topological insulator bismuth selenide nanoparticles (Bi2Se3 NP) are core–shelled with gold (Au@Bi2Se3) i) to represent considerably small‐sized (11 nm) plasmonic nanoparticles, enabling accurate bioimaging in the near‐infrared region; ii) to substantially improve Bi2Se3 biocompatibility, iii) water dispersibility, and iv) surface functionalization capability through straightforward gold–thiol interaction. The Au@Bi2Se3 is subsequently functionalized for v) effective targeting of SH‐SY5Y cancer cells, vi) disrupting the endosome/lysosome membrane, vii) traceable delivery of antagomiR‐152 and further synergetic oncomiR knockdown and photothermal therapy (PTT). Unprecedentedly, it is observed that the Au shell thickness has a significant impact on evoking the exotic plasmonic features of Bi2Se3. The Au@Bi2Se3 possesses a high photothermal conversion efficiency (35.5%) and a remarkable surface plasmonic effect (both properties are approximately twofold higher than those of 50 nm Au nanoparticles). In contrast to the siRNA/miRNA delivery methods, the antagomiR delivery is based on strand displacement, in which the antagomiR‐152 is displaced by oncomiR‐152 followed by a surface‐enhanced Raman spectroscopy signal drop. This enables both cancer cell diagnosis and in vitro real‐time monitoring of the antagomiR release. This selective PTT nanoparticle can also efficiently target solid tumors and undergo in vivo PTT, indicating its potential clinical applications.
Hierarchy Design in Metal Oxides as Anodes for Advanced Lithium‐Ion Batteries
Authors: Jin Jun , Wu Liang , Huang Shaozhuan , Yan Min , Wang Hongen , Chen Lihua , Hasan Tawfique , Li Yu , Su Bao‐Lian 
Published: August 2018

AbstractHierarchical structures are ubiquitous in both animals and plants. The coordination of the hierarchical structures and functions makes living organisms function efficiently. This explains why hierarchical metal oxide (HMO)‐based micro/nanostructures have recently received huge attention as anodes for application in highly efficient lithium‐ion batteries (LIBs). Indeed, hierarchy in such micro/nanostructured HMOs offers high specific surface area, stable structure, short path length, and improved higher packing density to improve the reaction kinetics and Li+/e− transport kinetics, resulting in highly enhanced rate capability and cycling stability for LIBs. This report focuses on the hierarchical design from structural, morphological, porous, and component levels to engineer the HMOs as anodes for LIBs. The advantages of micro/nanostructured HMO‐based on three reaction mechanisms (intercalation/deintercalation, conversion, and alloying/dealloying), important challenges ahead, and future perspectives on designing advanced electrode materials for next‐generation high‐performance LIBs are discussed.