bluuebunny/crossref_metadata_2025_split huggingface dataset:
CASP13 target classification into tertiary structure prediction categories
Authors: Kinch Lisa N. , Kryshtafovych Andriy , Monastyrskyy Bohdan , Grishin Nick V. 
Published: July 2019

AbstractProtein target structures for the Critical Assessment of Structure Prediction round 13 (CASP13) were split into evaluation units (EUs) based on their structural domains, the domain organization of available templates, and the performance of servers on whole targets compared to split target domains. Eighty targets were split into 112 EUs. The EUs were classified into categories suitable for assessment of high accuracy modeling (or template‐based modeling [TBM]) and topology (or free modeling [FM]) based on target difficulty. Assignment into assessment categories considered the following criteria: (a) the evolutionary relationship of target domains to existing fold space as defined by the Evolutionary Classification of Protein Domains (ECOD) database; (b) the clustering of target domains using eight objective sequence, structure, and performance measures; and (c) the placement of target domains in a scatter plot of target difficulty against server performance used in the previous CASP. Generally, target domains with good server predictions had close template homologs and were classified as TBM. Alternately, targets with poor server predictions represent a mixture of fast evolving homologs, structure analogs, and new folds, and were classified as FM or FM/TBM overlap.
A deep dense inception network for protein beta‐turn prediction
Authors: Fang Chao , Shang Yi , Xu Dong 
Published: July 2019

AbstractBeta‐turn prediction is useful in protein function studies and experimental design. Although recent approaches using machine‐learning techniques such as support vector machine (SVM), neural networks, and K nearest neighbor have achieved good results for beta‐turn prediction, there is still significant room for improvement. As previous predictors utilized features in a sliding window of 4‐20 residues to capture interactions among sequentially neighboring residues, such feature engineering may result in incomplete or biased features and neglect interactions among long‐range residues. Deep neural networks provide a new opportunity to address these issues. Here, we proposed a deep dense inception network (DeepDIN) for beta‐turn prediction, which takes advantage of the state‐of‐the‐art deep neural network design of dense networks and inception networks. A test on a recent BT6376 benchmark data set shows that DeepDIN outperformed the previous best tool BetaTPred3 significantly in both the overall prediction accuracy and the nine‐type beta‐turn classification accuracy. A tool, called MUFold‐BetaTurn, was developed, which is the first beta‐turn prediction tool utilizing deep neural networks. The tool can be downloaded at http://dslsrv8.cs.missouri.edu/~cf797/MUFoldBetaTurn/download.html.
Increasing the discrimination power of rapid evaporative ionisation mass spectrometry (REIMS) in analytical control tissue quality screening and cell line sample identification
Authors: Abu‐Rabie Paul , Sheelan Denver , Laures Alice , Spaull John , Dowell Simon 
Published: July 2019

RationaleRapid Evaporative Ionisation Mass Spectrometry (REIMS) has been evaluated as a tool to improve analytical efficiency and add capability in areas within Pharmaceutical Research and Development (Pharma R&D). This article reports the comparison of single MS, and tandem MS/MS REIMS (REIMS and REIMS/MS) methodologies to investigate which mode produces maximum discrimination power for screening applications.MethodsControl tissue samples and cell line suspension samples were analysed using optimised REIMS and REIMS/MS to evaluate which technique produced optimal discrimination power for control tissue and cell line identification. The iKnife sampling tool and a prototype ‘cell sampler’ were utilised for tissue and cell analysis, respectively. The REIMS source was coupled to a hybrid Quadrupole‐Time Of Flight (QTOF) mass spectrometer. Multivariate Analysis (MVA) was utilised to evaluate the resulting Mass Spectrometry (MS) data and discriminate between sample types.ResultsProof of concept investigations demonstrating that REIMS/MS offered increased MVA discrimination for sample identification, compared with REIMS, is presented for the first time. Control tissue data showed discrimination by timepoint classification over 0‐144 h storage after removal from the host. Timepoint discrimination was optimised using REIMS/MS with a collision energy that effectively maximised ion fragmentation. Similar optimisation was observed when REIMS/MS was applied to the identification of cell lines.ConclusionsThe proof of concept results demonstrate that REIMS/MS can offer advantages over REIMS for control tissue quality screening, and cell line identification applications in Pharma R&D. Further work following this proof of concept investigation is being undertaken to implement the technology for these applications, utilising the optimised REIMS/MS methodology. REIMS/MS will also be used as an optimised tool for other applications.
Robust orientation control of multi‐DOF cell based on uncertainty and disturbance estimation
Authors: Xie Mingyang , Shakoor Adnan , Li Chuntao , Sun Dong 
Published: July 2019

SummaryMultiple degrees‐of‐freedom (multi‐DOF) cell orientation control is a vital important technique involved in single cell surgery applications. Currently, few studies have been performed toward automation of multi‐DOF cell orientation control using robotically controlled optical tweezers. In this paper, a robust control framework is developed to perform multi‐DOF cell rotational control with consideration of model uncertainties and external disturbances. Both simulation and experimental studies are presented to illustrate the performance of the proposed control strategy. The main contributions of this work lie in that this is the first time to develop a unified framework to achieve multi‐DOF cell orientation control without the need for accurate dynamic model parameters and/or any knowledge about uncertainty characteristic, which greatly enhances the robustness of the overall system.
Inkjet‐Printed High‐Performance Flexible Micro‐Supercapacitors with Porous Nanofiber‐Like Electrode Structures
Authors: Cheng Tao , Wu You‐Wei , Chen Ya‐Li , Zhang Yi‐Zhou , Lai Wen‐Yong , Huang Wei 
Published: July 2019

AbstractFlexible planar micro‐supercapacitors (MSCs) with unique loose and porous nanofiber‐like electrode structures are fabricated by combining electrochemical deposition with inkjet printing. Benefiting from the resulting porous nanofiber‐like structures, the areal capacitance of the inkjet‐printed flexible planar MSCs is obviously enhanced to 46.6 mF cm−2, which is among the highest values ever reported for MSCs. The complicated fabrication process is successfully averted as compared with previously reported best‐performing planar MSCs. Besides excellent electrochemical performance, the resultant MSCs also show superior mechanical flexibility. The as‐fabricated MSCs can be highly bent to 180° 1000 times with the capacitance retention still up to 86.8%. Intriguingly, because of the remarkable patterning capability of inkjet printing, various modular MSCs in serial and in parallel can be directly and facilely inkjet‐printed without using external metal interconnects and tedious procedures. As a consequence, the electrochemical performance can be largely enhanced to better meet the demands of practical applications. Additionally, flexible serial MSCs with exquisite and aesthetic patterns are also inkjet‐printed, showing great potential in fashionable wearable electronics. The results suggest a feasible strategy for the facile and cost‐effective fabrication of high‐performance flexible MSCs via inkjet printing.
Freestanding Lamellar Porous Carbon Stacks for Low‐Temperature‐Foldable Supercapacitors
Authors: Yang Yu , Ng Sze‐Wing , Chen Dongdong , Chang Jian , Wang Dongrui , Shang Jian , Huang Qiyao , Deng Yonghong , Zheng Zijian 
Published: July 2019

AbstractHigh‐performance supercapacitors (SCs) are important energy storage components for emerging wearable electronics. Rendering low‐temperature foldability to SCs is critically important when wearable devices are used in a cold environment. However, currently reported foldable SCs do not have a stable electrochemical performance at subzero temperatures, while those that are performing are not foldable. Herein, a freestanding pure‐carbon‐based porous electrode, namely, lamellar porous carbon stack (LPCS), is reported, which enables stable low‐temperature‐foldable SCs. The LPCS, which is fabricated with a simple vacuum filtration of a mixture of carbon fibers (CFs), holey reduced graphene oxides (HRGOs), and carbon nanotubes (CNTs), possesses a lamellar stacking of porous carbon thin sheets, in which the CFs act as the skeleton and the HRGOs and CNTs act as binders. The unique structure leads to excellent compression resilience, high foldability, and high electronic and ionic conductivity. SCs made with the LPCS electrodes and ionic liquid electrolyte show a high energy density (2.1 mWh cm−2 at 2 mA cm−2), low‐temperature long lifetime (95% capacity after 10 000 cycles at −30 °C), and excellent low‐temperature foldability (86% capacity after 1000 folding cycles at −30 °C).
Integrating qualitative system dynamics with accounting practices: The case of integrated reporting and resource mapping
Authors: Giorgino Maria Cleofe , Barnabè Federico , Kunc Martin 
Published: July 2019

AbstractThe article explores the role of qualitative system dynamics (SD) in evaluating the information presented in corporate accounting reports. Particularly, this study focuses on a recent corporate report called integrated reporting (<IR>), and analyses the <IR> information using a specific qualitative SD technique, resource mapping, in order to visualize the key resources and their connections responsible for the performance of the organization. The study'; contribution is twofold. First, it provides insights on how to apply qualitative SD in the field of management accounting and corporate reporting. Second, it verifies the benefits of combining qualitative SD and corporate reporting tools to develop new knowledge useful to represent and face the dynamic complexity implicit in a business domain.
The size‐dependent genotoxic potentials of titanium dioxide nanoparticles to endothelial cells
Authors: Liao Fen , Chen Lingying , Liu Yuanfeng , Zhao Dongting , Peng Wenyi , Wang Wuxiang , Feng Shaolong 
Published: July 2019

AbstractDespite intensive research activities, there are still many major knowledge gaps over the potential adverse effects of titanium dioxide nanoparticles (TiO2‐NPs), one of the most widely produced and used nanoparticles, on human cardiovascular health and the underlying mechanisms. In the present study, alkaline comet assay and cytokinesis‐block micronucleus test were employed to determine the genotoxic potentials of four sizes (100, 50, 30, and 10 nm) of anatase TiO2‐NPs to human umbilical vein endothelial cells (HUVECs) in culture. Also, the intracellular redox statuses were explored through the measurement of the levels of reactive oxygen species (ROS) and reduced glutathione (GSH) with kits, respectively. Meanwhile, the protein levels of nuclear factor erythroid 2‐related factor 2 (Nrf2) were also detected by western blot. The results showed that at the exposed levels (1, 5, and 25 μg/mL), all the four sizes of TiO2‐NPs could elicit an increase of both DNA damage and MN frequency in HUVECs in culture, with a positive dose‐dependent and negative size‐dependent effect relationship (T100 < T50 < T30 < T10). Also, increased levels of intracellular ROS, but decreased levels of GSH, were found in all the TiO2‐NP‐treated groups. Intriguingly, a very similar manner of dose‐dependent and size‐dependent effect relationship was observed between the ROS test and both comet assay and MN test, but contrary to that of GSH assay. Correspondingly, the levels of Nrf2 protein were also elevated in the TiO2‐NP‐exposed HUVECs, with an inversely size‐dependent effect relationship. These findings indicated that induction of oxidative stress and subsequent genotoxicity might be an important biological mechanism by which TiO2‐NP exposure would cause detrimental effects to human cardiovascular health.
Sono‐photo‐assisted heterogeneous activation of peroxymonosulfate by Fe/CMK‐3 catalyst for the degradation of bisphenol A, optimization with response surface methodology
Authors: Rahimzadeh Hadi , Rahmani Alireza , Samadi Mohammad‐Taghi , Farmany Abbas , Asgari Ghorban 
Published: July 2019

AbstractThe present study examined the removal of bisphenol A (BPA) and total organic carbon (TOC) from aqueous solutions by the Fe/CMK‐3 as peroxymonosulfate activator used in the sono‐photo‐catalytic process. The synthesis of Fe/CMK‐3 was carried out using the co‐precipitation method, and it was characterized by FTIR, XRD, BET, EDX, and TEM. The results showed that the iron nanoparticles were uniformly embedded in the CMK‐3 pores. The effect of factors affecting on the removal of BPA and TOC was evaluated by response surface methodology (RSM) with center composite design (CCD). The analysis of variance of the quadratic model showed that the model is significant (p value < .0001 and R2 > 99.4%) and can be used to optimize the removal efficiency of BPA. Optimization results showed that the highest removal efficiency of BPA (100%) and TOC (80.6%) was achieved in optimum conditions of pH 7.8, catalyst dose 0.33 g/L, PMS dose 3.35 mmol/L, BPA concentration 39.3 mg/L, and 78.5 min. In addition, statistical analysis of the data showed that, in the studied range, the initial concentration of BPA was the most influential factor, followed by pH and PMS dose. Highest catalytic stability of Fe/CMK‐3 showed the potential applicability of catalyst in the treatment of BPA‐containing solutions. The quenching test showed that sulfate radical was the main responsible for the removal of BPA. The decrease in IOUR value after the 75‐min reaction time indicates that this process has a high ability for oxidation of the pollutant and its intermediates. Generally, the observed results suggest that the Fe‐CMK‐3/UV/US/PMS system can be a promising procedure for the removal of persistent pollutants such as BPA from aqueous media.Practitioner points

Fe/CMK‐3 exhibited prominent catalytic activity and high stability for peroxymonosulfate activation.

Effective degradation of bisphenol A was achieved in the Fe‐CMK‐3/UV/US/PMS system.

The effect of five factors at five levels and their interactions during the removal of BPA was evaluated by RSM method coupled with central composite design (CCD).

The analysis of variance of the quadratic model showed that the model is very significant (p value < .0001) and can be used to optimize the removal efficiency of BPA.

The quenching test showed that sulfate radical was the main responsible for the removal of BPA.

Reducing IOUR value after the 75‐min reaction time indicates that toxicity of the solution was significantly decreased in this system.
A review on sentiment discovery and analysis of educational big‐data
Authors: Han Zhongmei , Wu Jiyi , Huang Changqin , Huang Qionghao , Zhao Meihua 
Published: July 2019

AbstractSentiment discovery and analysis (SDA) aims to automatically identify the underlying attitudes, sentiments, and subjectivity towards a certain entity such as learners and learning resources. Due to its enormous potential for smart education, SDA has been deemed as a powerful technique for identifying and classifying sentiments from multimodal and multisource data over the whole process of education. For big educational data streams, SDA faces challenges in unimodal feature selection, sentiment classification, and multimodal fusion. As such, a large body of studies in the literature explores diverse approaches to SDA for educational applications. This paper provides a self‐contained, uniform overview of the SDA techniques for education. In particular, we focus on prominent studies in unimodal sentiment features and classifications (e.g., text, audio, and visual). In addition, we present a novel SDA framework of multimodal fusions, together with description of their crucial components. Based on this framework, we review different approaches to SDA on education from the perspectives of approaches and applications. After comprehensively reviewing the SDA techniques on education, we present the trends and prospectives of the future SDA research under ubiquitous education contexts.This article is categorized under:
Application Areas > Education and Learning
Size‐dependent free vibration of sandwich micro beam with porous core subjected to thermal load based on SSDBT
Authors: Amir Saeed , Soleimani‐Javid Zeinab , Arshid Ehsan 
Published: July 2019

AbstractIn this study, free vibration of the sandwich microbeam with porous core and FG carbon nanotubes reinforced composite face sheets which is rested on Winkler‐Pasternak substrate is investigated. It is assumed the beam is in thermal environment and is subjected to thermal load and the displacement components are described based on sinusoidal shear deformation beam theory. The small scale effects are taken into account according to the modified couple stress theory. The core and face sheets properties are diffused through the thickness. The motion equations are derived and solved using Hamilton's principle and Navier's method, respectively. Effect of different parameters such as porosity coefficient and distributions, different types of CNTs distribution, small scale and geometrical size of the beam is considered. The results show by enhancing the porosity, the frequency decreased. The findings of the current study can be used to design prominent role in modern engineering applications.
Vector SIMP dark matter with approximate custodial symmetry
Authors: Choi Soo-Min , Lee Hyun Min , Mambrini Yann , Pierre Mathias 
Published: July 2019

AbstractWe consider a novel scenario for Vector Strongly Interacting Massive Particle (VSIMP) dark matter with local SU(2)X× U(1)Z′symmetry in the dark sector. Similarly to the Standard Model (SM), after the dark symmetry is broken spontaneously by the VEVs of dark Higgs fields, the approximate custodial symmetry determines comparable but split masses for SU(2)Xgauge bosons. In this model, we show that the U(1)Z′-charged gauge boson of SU(2)X(X±) becomes a natural candidate for SIMP dark matter, annihilating through 3 → 2 or forbidden 2 → 2 annihilations due to gauge self-interactions. On the other hand, the U(1)Z′-neutral gauge boson of SU(2)Xachieves the kinetic equilibrium of dark matter through a gauge kinetic mixing between U(1)Z′and SM hypercharge. We present the parameter space for the correct relic density in our model and discuss in detail the current constraints and projections from colliders and direct detection experiments.
Unraveling the specific regulation of the shikimate pathway for tyrosine accumulation in Bacillus licheniformis
Authors: Xu Yinbiao , Li Youran , Zhang Liang , Ding Zhongyang , Gu Zhenghua , Shi Guiyang 
Published: July 2019

Abstract
l-Tyrosine serves as a common precursor for multiple valuable secondary metabolites. Synthesis of this aromatic amino acid in Bacillus licheniformis occurs via the shikimate pathway, but the underlying mechanisms involving metabolic regulation remain unclear. In this work, improved l-tyrosine accumulation was achieved in B. licheniformis via co-overexpression of aroGfbr and tyrAfbr from Escherichia coli to yield strain 45A12, and the l-tyrosine titer increased to 1005 mg/L with controlled glucose feeding. Quantitative RT-PCR results indicated that aroA, encoding DAHP synthase, and aroK, encoding shikimate kinase, were feedback-repressed by the end product l-tyrosine in the modified strain. Therefore, the native aroK was first expressed with multiple copies to yield strain 45A13, which could accumulate 1201 mg/L l-tyrosine. Compared with strain 45A12, the expression of aroB and aroF in strain 45A13 was upregulated by 21% and 27%, respectively, which may also have resulted in the improvement of l-tyrosine production. Furthermore, supplementation with 5 g/L shikimate enhanced the l-tyrosine titers of 45A12 and 45A13 by 29.1% and 24.0%, respectively. However, the yield of l-tyrosine per unit of shikimate decreased from 0.365 to 0.198 mol/mol after aroK overexpression in strain 45A12, which suggested that the gene product was also involved in uncharacterized pathways. This study provides a good starting point for further modification to achieve industrial-scale production of l-tyrosine using B. licheniformis, a generally recognized as safe workhorse.
Cystic Lesion in the Fetal Scalp: A Systematic Approach
Authors: Singh Divya , Kaur Ladbans 
Published: July 2019

AbstractDuring an anomaly scan, cystic lesion in the scalp may be encountered while examining the fetal head. Some of these originate from the scalp tissue and can be dealt with postnatally by simple excision. Others may be more than just scalp cysts and have an intracranial communication. The objective of this communication is to illustrate a few cystic lesions in the fetal scalp and suggest a systematic approach in arriving at a diagnosis.
Indications for Penile Prosthesis Revision: Lessons Learned to Limit Technical Causes of Reoperation
Authors: Chan Ernest Pang , Punjani Nahid , Campbell Jeffrey Douglas , Abed Haider , Brock Gerald 
Published: July 2019

ABSTRACT

Introduction
Reoperations are necessary in approximately 30% of penile prostheses over 15 years following original implantation.

Aim
To determine the most common indications for initial penile prosthesis reoperation at our institution and to describe technical alterations that have improved postoperative outcomes.

Methods
A retrospective review of all patients who underwent penile prosthesis reoperation surgery at a single, high-volume Canadian center between 2006 and 2018 was performed. Patient demographic information, prosthetic device factors, and surgical complications were analyzed.

Main Outcome Measure
The primary outcomes were the indications for and variables associated with initial penile prosthesis reoperation.

Results
During the study period, 99 first-time penile prosthesis reoperations were performed out of 1,161 penile prosthesis procedures (Figure 1). This included 14 (14.1%) explants, 32 (32.3%) revisions, and 53 (53.5%) explant and reimplants. Indications for reoperation included 49 (49.5%) mechanical failures, 28 (28.3%) technical causes (such as correction of malposition or device herniation), and 12 (12.1%) procedures to treat chronic postoperative pain. Median follow-up was 78.5 months, and median time to reoperation was 46 months. Mechanical failures commonly occurred in the tubing (n = 13, 26.5%) and cylinders (n = 13, 26.5%). The most frequently repositioned component was the valve pump (n = 11, 39.3%). Infection-related indications for reoperation were uncommon (n = 10, 10.1%).

Clinical Implications
More than a quarter of penile prosthesis reoperations may have been preventable with alterations in surgical technique, device positioning, and postoperative care.

Strengths and Limitations
This study evaluates a range of indications for initial penile prosthesis reoperation performed by a high-volume single surgeon over a 12-year period. Limitations include the retrospective nature of the study, loss of patients to follow-up, and lack of etiological determinants of prosthesis failure.

Conclusions
Reoperation for device repositioning and herniation was required for more than a quarter of the initial penile prosthesis implants. Modifications in surgical technique and perioperative care can help reduce the incidence of these technical causes for reoperation.