bluuebunny/crossref_metadata_2025 huggingface dataset:
APRENDIZAGEM COOPERATIVA NO ENSINO CONTÁBIL
Authors: Benevides Victória , Lima Filho Raimundo Nonato
Published: June 2020

As atividades praticadas pelos estudantes no ensino tradicional usualmente não permitem vivenciar experiências de trabalho de cooperação, de partilha de responsabilidades e não possibilita também a construção de relações positivas entre os integrantes dos grupos, enquanto que a aprendizagem cooperativa tem sido descrita pela literatura especializada como uma forma eficaz de praticar de modo concreto a diferenciação em sala de aula. Esta pesquisa teve como objetivo verificar as contribuições advindas de um método ativo de ensino. Neste estudo, foi realizado um experimento, adotando a Taxonomia de Bloom, no qual o grupo que obteve o ensino de forma ativa teve um desempenho superior ao grupo cujo ensino foi de forma tradicional. Além disso, também foram verificadas relações com a nota, com a idade, sexo e tipo de escola estudada durante o ensino médio, para assim identificar a influência desses fatores na nota final. Com base nos resultados obtidos, constatou-se que esse estudo contribuiu de forma positiva para o ensino/aprendizado, pois com ela há um estímulo cognitivo desencadeando a percepção do aluno sobre o conteúdo ministrado, e assim tornando o aprendizado mais estimulante.
A Model Research Curriculum for Emergency Medicine Residency: A Modified Delphi Consensus
Authors: Hartman Nicholas , Jordan Jaime , Gottlieb Michael , Mahler Simon A. , Cline David ,   For the CORD Academy for Scholarship
Published: June 2020

Background

Research training is important for all resident physicians to be able to interpret and critically appraise scientific literature. It is particularly important for those desiring future careers in academics or research. However, there is limited literature on research training in residency. The ideal scope and content of a model curriculum for research in emergency medicine (EM) residency programs has not been recently defined.

Methods

We used a modified Delphi method to achieve expert consensus as to what content should be included in a model research curriculum for EM residents as well as for those who choose to undertake an elective in EM research.

Results

Eight experts in EM clinical and education research participated in the modified Delphi process with two rounds of responses. Cronbach's alpha was 0.82 for round 1 and 0.95 for round 2. A curricular outline of 44 items was produced by this consensus process.

Conclusions

A model curriculum for EM research is proposed here, along with references to assist residencies in building curricular components.
A case report of Noonan syndrome‐like disorder with loose anagen hair 2 treated with recombinant human growth hormone
Authors: Zhou Ping , Zhu Lin , Fan Qiongli , Liu Yongfang , Zhang Tianxiu , Yang Ting , Chen Jie , Cheng Qian , Li Tingyu , Chen Li
Published: June 2020

Protein phosphatase 1 catalytic subunit beta (PPP1CB) is a disease‐causing gene of Noonan‐like syndrome, which acts via the RAS/MAPK pathway. To date, only 17 patients diagnosed with PPP1CB‐related Noonan‐like syndrome have been reported around the world, with few reports in Asia. Twelve reported patients are of short stature and only one patient was treated with growth hormone (GH); however, follow‐up data is lacking. To the best of our knowledge, this is the first reported patient with complete recombinant human growth hormone (rhGH) treatment follow‐up data; the patient has a de novo c.146C>G (p.Pro49Arg) mutation in the PPP1CB gene. The hair pattern of the patient (coarse, curly, slow growing, and fragile) combined with Noonan dysmorphic features, developmental delay, and congenital heart disease, are highly consistent with the typical features observed in Noonan syndrome‐like disorder with loose anagen hair 2 (NSLH2). rhGH treatment, administered for 3 years and 8 months, promoted the patient's linear growth. Our findings expand the data regarding the treatment of short stature in patients with NSLH2 caused by PPP1CB mutation. Clinical manifestation, growth and development process, and rhGH therapy effect data will aid in future revision of the relevant diagnosis and treatment guidelines.
Confirmatory testing illustrates additional risks for structural sex chromosome abnormalities in fetuses with a non‐invasive prenatal screen positive for monosomy X
Authors: Sund Kristen L. , Khattar Divya , Boomer Theresa , Caldwell Samantha , Dyer Lisa , Hopkin Robert J. , Smolarek Teresa A.
Published: June 2020

More and more women rely on non‐invasive prenatal screening (NIPS) to detect fetal sex and risk for aneuploidy. The testing applies massively parallel sequencing or single nucleotide polymorphism (SNP) microarray to circulating cell‐free DNA to determine relative copy number. In addition to trisomies 13, 18, and 21, some labs offer screening for sex chromosome abnormalities as part of their test. In this study, an index neonate screened positive for monosomy X and had discordant postnatal chromosomes indicating an X;autosome translocation. This patient prompted a retrospective chart review for similar cases at a large NIPS testing center. The review found 28 patients with an abnormal NIPS for monosomy X who were eventually diagnosed with additional discrepant structural sex chromosome abnormalities including translocations, isochromosomes, deletions, rings, markers, and uniparental disomy. The majority of these were mosaic with monosomy X, but in seven cases, there was no evidence of mosaicism on confirmatory testing. The identification of multiple sex chromosome aneuploidies in these cases supports the need for additional genetic counseling prior to NIPS testing and following abnormal NIPS results that are positive for monosomy X. This finding broadens our knowledge about the variable outcomes of positive monosomy X NIPS results and emphasizes the importance of confirmatory testing and clinical follow up for these patients.
Effects of povidone‐iodine composite on the elimination of bacterial biofilm
Authors: Jeronimo Leonita Pinto , Choi Mi‐Ra , Yeon Sun Hee , Park Soo Kyoung , Yoon Young Hoon , Choi Seung Hyeon , Kim Hwa‐Jung , Jang In‐Taek , Park Jeong‐Kyu , Rha Ki‐sang , Kim Yong Min
Published: June 2020

Background

Povidone‐iodine (PVP‐I) is well known as an antiseptic and exhibits extensive activity against various pathogens. However, due to its uniquely unpleasant nature, it cannot be used locally to deactivate various sinonasal pathogens. Therefore, we developed a PVP‐I composite that blocks the unpleasant odor of PVP‐I for use as a local antiseptic in the sinonasal cavity and evaluated its effect on bacterial biofilm's formation and elimination in in vivo and in vitro models.

Methods

MTT, lactate dehydrogenase, and live/dead staining assay were performed to examine the cellular toxicity of PVP‐I composites on the primary human nasal epithelial and RPMI 2650 cells. Crystal violet assay was performed to quantify bacterial biofilm after treating with various agents, including PVP‐I and antibiotics. Hematoxylin‐and‐eosin staining, live/dead staining assay, and scanning electron microscopy were conducted to evaluate the effect of PVP‐I on biofilm formation in a mice biofilm model.

Results

It was observed that the PVP‐I composite did not have any significant toxic effect on the nasal epithelial cells. Furthermore, the PVP‐I composite effectively inhibited the formation of bacterial biomass within a dose‐dependent manner after 48 hours of incubation with Pseudomonas aeruginosa and Staphylococcus aureus. In mice, it effectively eliminated biofilm from the mucosa of the nasal cavity and maxillary sinus at the tested concentrations.

Conclusion

The results of this study indicate that the PVP‐I composite is a promising compound that could be used locally to prevent the formation of biofilms and to eliminate them from the sinonasal cavity.
Fluorescence microscopy‐based analysis of apoptosis induced by platinum nanoparticles against breast cancer cells
Authors: Puja Patel , Vinita Nadar Manimaran , Devan Umapathy , Velangani Antony Joseph , Srinivasan Pappu , Yuvakkumar Rathinam , Arul Prakash Pitchan , Kumar Ponnuchamy
Published: June 2020

In recent years, capping molecules onto the surface of nanomaterials has become an interesting field of research. This idea facilitates the biological applications of nanomaterials with a modified surface. Keeping this in mind, the present study addresses the development of polymeric platinum nanoparticles using polyvinyl pyrrolidone (PVP). High‐throughput characterization indicates that polymeric platinum nanoparticles have an excellent surface morphology and good dispersity in aqueous solution. More specifically, high resolution‐transmission electron microscopy studies showed that the polymeric platinum nanoparticles were spherical and measured 2–10 nm. Furthermore, the polymeric platinum nanoparticles were evaluated for anticancer properties against human MCF‐7 breast cancer cell lines. The results show that polymeric platinum nanoparticles inhibited the growth of cancer cells in a dose‐dependent manner with a half‐maximum inhibitory concentration of 96.36 μg ml−1. In addition, fluorescence‐based staining methods confirmed an inquest in the pattern of cell death inferring late apoptotic bodies, nuclear fragmentation, mitochondrial membrane potential and generation of reactive oxygen species. The overall findings suggest that the polymeric platinum nanoparticles confer anticancer activity and may be suitable chemotherapeutic agents in the future. Finally, the results from this study can be extended to other types of cancer as well.
Synthesis, spectral, DFT calculations and biological studies of solvatochromic copper(II)‐ONS hydrazone derived from 2‐aminochromone‐3‐carboxaldehyde
Authors: Adly Omima M.I. , Taha Ali , Ibrahim Magdy A. , Fahmy Shery A.
Published: June 2020

New ONS hydrazone ligand, 2‐[(2‐aminochromon‐3‐yl)methylidene]‐N‐phenylhydrazinecarbothioamide, HL, was synthesized and reacted with different salts of Cu (II) ion (OAc−, NO3−, SO42− and Cl−) in absence and presence of secondary ligands (L′); 8‐hydroxyquinoline, 1,10‐phenanthroline or SCN−; to form binary and ternary Cu(II)‐chelates. The ligand and its Cu(II)‐complexes were fully characterized by analytical, spectral, thermal, conductivity and magnetic susceptibility measurements. The metal chelates showed octahedral, square planar and /or distorted tetraherdal arrangements. Coats–Redfern equations used to calculate the kinetic parameters of the thermal decomposition stages (Ea, A, ΔH, ΔS and ΔG). The compounds exhibit luminescence property; promising interesting potential applications as photoactive materials. Lippert–Mataga, Bakhshiev, Kawski–Chamma–Viallet and microscopic solvent polarity parameter and ETN correlation methods were applied on the solvatochromic shifts of emission spectra to evaluate the ground (μg) and excited (μe) states dipole moments. Excited state dipole moment is larger than the ground state which may be attributed to π‐π* transition. The coordinating anions play an important role on the position and intensity of emission band. The ligand and its metal complexes showed antimicrobial activity towards Gram–positive bacteria, Gram–negative bacteria, yeast and fungus. The molecular structural parameters of HL and its Cu(II)‐ complexes have been calculated on the basis of DFT engaged in the Gaussian 09 program at the B3LYP/6‐31G(d,p) level; the theoretical data are correlated with the experimental data.
Construction of biocompatible bilayered light‐driven actuator composed of rGO/PNIPAM and PEGDA hydrogel
Authors: Yang Liai , Zhang Ting , Sun Wei
Published: June 2020

To construct an actuator with biocompatibility and potential use in biomedicine field, a light‐driven actuator composed of reduced graphene oxide (rGO)/poly (N‐isopropyl acrylamide) (PNIPAM) and poly (ethylene glycol) diacrylate (PEGDA) hydrogel is constructed. First, rGO/PNIPAM hydrogel is prepared by free radical polymerization and l‐ascorbic acid reduction, of which the surface temperature increases quickly under near‐infrared (NIR) laser indicating the efficient photothermal conversion of rGO. The results of cytotoxicity tests demonstrate that rGO/PNIPAM is biocompatible and has no obvious toxicity to myoblast line C2C12 cells. Second, bilayer hydrogel composed of rGO/PNIPAM and PEGDA is prepared using a similar method layer‐by‐layer. The bilayer strip bends towards rGO/PNIPAM under NIR laser. The bending is improved after reduction. The laser power density has a strong impact on the bending rate and degree. The reversible bending deformation indicates the structural stability. All the above results approve that the bilayer actuator has great potential to be applied in biomedicine fields such as organ‐on‐chip, drug‐carrier, or surgical aid.
Preparation and investigation of acid–base composite membranes with modified graphitic carbon nanosheets for direct methanol fuel cells
Authors: Dong Cuicui , Shi Zhentang , Zhou Qiong
Published: June 2020

The ethylenediamine‐modified graphite oxide (EGO)‐doped sulfonated poly (arylene ether ketone) (SPEEK) composite membranes have been prepared and developed for fuel cell applications in the present work. The base‐modified EGO improves the dispersion of inorganic nanosheet in the polymer matrix and enhances proton conductivity by creating continuous conduction pathways. Furthermore, the methanol barrier property also be enhanced due to the nanosheet block the methanol‐transport channels. EGO‐filled membranes display improved dimensional stability, proton conductivity, and ethanol permeability than those using SPEEK control and graphite oxide (GO)‐filled membranes. In the direct methanol fuel cells (DMFCs), the SPEEK/EGO‐1.5 membrane displays the highest current density of 395.9 mA/cm2at 60°C, which is 1.6‐ and 1.4‐fold higher than that of SPEEK (254.0 mA/cm2) and SPEEK/GO membrane (292.6 mA/cm2).
Vapor treatment, liquid crystal formation, magnetic orientation, and crystallization (VLMC) to form helical polyisocyanides with oriented crystal‐like structure
Authors: Yonehara Takuya , Hayashi Hiroki , Nimori Shigeki , Goto Hiromasa
Published: June 2020

We describe a four‐step process [solvent vapor treatment, liquid crystal formation, magnetic orientation, and crystallization (VLMC)] for producing oriented helical polyisocyanides with crystal‐like structure. We synthesized a series of ortho‐alkyl groups substituted with poly(phenyl isocyanide), and characterized the polymer structure using polarizing optical microscopy, scanning electron microscopy, and X‐ray diffraction. The results demonstrated that the polymer has a crystal‐like structure and the sample forms cholesteric liquid crystal phase. Vapor treatment of polymer films under a magnetic field produced an aligned fiber structure at the submicron level and demonstrated magnetic alignment and formation of a solvent vapor‐induced polymer crystal. These results demonstrated formation of a polymer with a one‐handed helical structure, formation of a liquid crystal and polymer crystal via solvent vapor treatment, and magnetic alignment of a textile‐like polymer crystal domain.
Ultra‐flexiblePLA‐based blends for the manufacturing of biodegradable tamper‐evident screw caps by injection molding
Authors: Barletta Massimiliano , Aversa Clizia , Puopolo Michela , Vesco Silvia
Published: June 2020

Mono‐material in the manufacturing of oil‐based plastic bottles has been so far not considered because of the poor flexibility of polyethylene terephthalate (PET). The undercuts of PET caps (i.e., the threads of the screw caps) would be torn‐off during the ejection step of the injection/compression molding processes that are commonly used to fabricate them. In this respect, the present work deals with the design and development of innovative biodegradable polyester‐based blends with high flexibility, intended for the manufacturing of screw‐cap, being this element the most critical in the implementation of the complete bottle. The blend is based on polylactic acid and it is tailored for injection molding of tamper‐evident screw plastic caps by the addition of another biodegradable polyester, that is, polybutylene adipate‐co‐terephthalate. The effect of the addition of a barrier agent, polyvinyl alcohol, on the overall behavior of the blends was also studied in the perspective of the implementation of caps featuring barrier properties against water vapor and oxygen. The same material could be, however, easily tailored for the fabrication of the bottle body and printed label to get to the mono‐material bottle. Twin‐screw corotating extrusion of the compound, injection molding of the plastic material for the fabrication of the screw caps, and evaluation of the thermophysical and mechanical properties of the screw caps are hereinafter discussed. The biodegradable polyester‐based blends are found to be suitable for injection molding of the tamper‐evident screw caps, exhibiting adequate flexibility during ejection from the mold. The screw caps can also boast appreciable mechanical strength and impact resistance as well as good thermal stability.
Improved dimensional stability of water‐blown polyurethane foam with aluminum hydroxide and magnesium hydroxide
Authors: Yi Sujin , Cho Young‐Jun , Roh Jung‐Sim
Published: June 2020

Water is eco‐friendly and safe; thus, it used as a blowing agent in the fabrication of water‐blown polyurethane (PU) foam. However, water‐blown PU foam may experience dimensional instability due to shrinkage of the cells inside the foam. In order to reduce cell shrinkage due to the loss of CO2 gas, vacuum formation is prevented in the closed‐cell foam and the maximum reaction temperature must be raised to increase the degree of curing of the PU foam. In this study, two flame retardants, aluminum trihydrate (ATH) and magnesium dihydrate (MDH), were selected as additives to partially open the cells and increase the maximum reaction temperature. ATH and MDH were both effective for increasing the maximum foam reaction temperature and decreasing dimensional change. Notably, PU foams with 7.5 wt% ATH were the most dimensionally stable at both room temperature and high temperature. Moreover, the compressive strength and flexural strength of such foams were also improved compared to those of the foams without any additive.
Application of high‐throughput single nucleotide polymorphism genotyping for assessing the origin of Engraulis encrasicolus eggs
Authors: Catanese Gaetano , Di Capua Iole , Iriondo Mikel , Bonanno Angelo , Estonba Andone , Procaccini Gabriele
Published: June 2020

Single nucleotide polymorphism (SNP) markers in anchovy (Engraulis encrasicolus) egg samples were analysed to detect their origin on a small spatial scale (200 km) by assigning genotypes to adult anchovy stocks. The novelty of this work is the application of a rapid high‐throughput method for genotyping each single anchovy egg, in a single execution, using a set of 96 genome‐wide SNPs in a dynamic array system with microfluidic technology (Fluidigm 96.96).

The existence of two ecotypes in E. encrasicolus had already been identified based on SNP polymorphism in the Atlantic Ocean and in the Mediterranean Sea, showing that habitat type (offshore versus coastal/estuarine) is the most important component of genetic differentiation among populations of anchovy.

In this work, anchovy egg genotypes from areas of the Western Mediterranean were assigned to adult populations. Only two localities in which adult anchovies were sampled represented donor populations for the coastal/estuarine egg genotypes. Although some degree of mixing among the hauls could exist, the assignment of egg groups to adult populations led to distinguishing the contributions of distinct ecotypes to new wild generations. We can conclude that the high rate of egg dispersion caused by marine currents and the different degrees of local retention could explain the genetic heterogeneity observed in the adult populations, where eggs from neighbouring spawning sites tend to mix.

The results highlight that this technique represents a new and useful tool for addressing evolutionary questions, breed recognition, assignment, and connectivity assessment of individual eggs, and anchovy population dynamics, for the management of stocks.
Computed tomographic analysis of internal structures within the nasal cavities of green, loggerhead and leatherback sea turtles
Authors: Yamaguchi Yohei , Kitayama Chiyo , Tanaka Shinichi , Kondo Satomi , Miyazaki Ayano , Okamoto Kei , Yanagawa Masashi , Kondoh Daisuke
Published: June 2020

The morphology of the tetrapod nasal cavity has adapted to the environment in terms of olfaction and respiration. Reports indicate that the internal structure of the nasal cavity of green sea turtles is more complex than that of turtles in general, but whether or not it is similar among sea turtle species remains unknown. The present study aimed to define the internal structures of the nasal cavity of green (Chelonian mydas), loggerhead (Caretta caretta) and leatherback (Dermochelys coriacea) sea turtles using computed tomography. The nasal cavity of green and loggerhead sea turtles contained anterodorsal, anteroventral, posterodorsal diverticula and a posteroventral excavation in the middle. In contrast, the nasal cavity of leatherback sea turtles had more complicated dorsal region comprising anterodorsal and posterodorsal diverticula, and two excavations between the nostril and anterodorsal diverticulum, but no distinct structures at the ventral region. The airway in the nasal cavity was shorter and thicker in the leatherback, than in the green and loggerhead turtles. These species differences might reflect ecological variety and different evolutionary strategies.
Non‐destructive approach for studying medieval settlements destroyed by ploughing: combining aerial photography, geophysical and soil surveys
Authors: Zhurbin Igor V. , Borisov Alexander V.
Published: June 2020

The procedure for studying medieval settlements destroyed by ploughing is applied to one of the largest Finno‐Ugric ancient settlement sites of western Urals, Guryakar (ninth–thirteenth centuries ad). The approach implies the consistent use of a number of mutually confirming non‐destructive methods of survey: aerial photography using unmanned aerial vehicles followed by geophysical and soil surveying. Aerial photography in the visible spectrum enables the evaluation of possible settlement boundaries. The wavelet transmission of multispectral aerial photography data makes it possible to disclose the areas of the preserved cultural layer. A set of geophysical methods (resistivity survey, magnetic survey and electrical resistivity tomography) is used to verify and analyse these data. Additionally, geophysics makes it possible to identify fortifications and diverse layout objects that are not expressed by the surface topography. Follow‐up soil drilling is a way to verify the proposed reconstruction of the layout, and the study of the chemical properties of soil cores makes it possible to justify the boundaries of the residential and industrial areas of the settlement. For this purpose, in the final stage, statistical processing of the chemical properties of soil materials is carried out (principal component analysis and the k‐means algorithm classification). This approach complements the comparative analysis of diverse data and significantly increases the reliability of historical reconstruction.

Interdisciplinary studies conducted at the medieval Finno‐Ugric settlement of ancient Guryakar allowed fundamentally new information to be obtained for use in historical reconstructions: this work revealed a previously unknown line of the layered fortification system, reconstructed the layout of all four structural parts of the settlement and justified diverse building areas.
The Mechanism of the Intramolecular Hydrocarbyl Metathesis within a Planar Triruthenium Cluster: Combining Core Flexibility with Hydride Mobility
Authors: Castillo Carmen E. , Algarra Andrés G.
Published: June 2020

The transition metal catalysed formation and cleavage of C−C bonds is of utmost importance in synthetic chemistry. While most of the existing homogeneous catalysts are mononuclear, knowledge of the behaviour of polynuclear species is much more limited. By using computational methods, here we shed light into the mechanistic details of the thermally‐induced isomerization of Cp*3Ru3(μ‐H)2(μ3‐η2‐pentyne)(μ3‐pentylidyne) (2) into Cp*3Ru3(μ‐H)2(μ3‐η2‐octyne)(μ3‐ethylidyne) (3), a process that involves the migration of a C3 fragment between the hydrocarbyl ligands and across the plane formed by the three Ru centres. Our results show this to be a complex transformation that comprises of five individual rearrangements in an A→B→A→B→A order. Each so‐called rearrangement A consists of the CH migration from the μ3‐η2‐alkyne into the μ3‐alkylidine ligand in the other side of the Ru3 plane. This process is facilitated by the cluster's ability to adopt open‐core structures in which one Ru−Ru bond is broken and a new C−C bond is formed. In contrast, rearrangements B do not involve the formation or cleavage of C−C bonds, nor do they require the opening of the cluster core. Instead, they consist of the isomerization of the μ3‐η2‐alkyne and μ3‐alkylidyne ligands on each side of the triruthenium plane into μ3‐alkylidyne and μ3‐η2‐alkyne, respectively. Such transformation implies the migration of three H atoms within the hydrocarbyl ligands, and in this case, it is aided by the cluster's ability to behave as a H reservoir. All in all, this study highlights the plasticity of these Ru3 clusters, whereby Ru−Ru, Ru−C, Ru−H, C−C, and C−H bonds are formed and broken with surprising ease.
Aqueous Flow Reactor and Vapour‐Assisted Synthesis of Aluminium Dicarboxylate Metal–Organic Frameworks with Tuneable Water Sorption Properties
Authors: Stassin Timothée , Waitschat Steve , Heidenreich Niclas , Reinsch Helge , Pluschkell Finn , Kravchenko Dmitry , Marreiros João , Stassen Ivo , van Dinter Jonas , Verbeke Rhea , Dickmann Marcel , Egger Werner , Vankelecom Ivo , De Vos Dirk , Ameloot Rob , Stock Norbert
Published: June 2020

Energy‐efficient indoors temperature and humidity control can be realised by using the reversible adsorption and desorption of water in porous materials. Stable microporous aluminium‐based metal–organic frameworks (MOFs) present promising water sorption properties for this goal. The development of synthesis routes that make use of available and affordable building blocks and avoid the use of organic solvents is crucial to advance this field. In this work, two scalable synthesis routes under mild reaction conditions were developed for aluminium‐based MOFs: (1) in aqueous solutions using a continuous‐flow reactor and (2) through the vapour‐assisted conversion of solid precursors. Fumaric acid, its methylated analogue mesaconic acid, as well as mixtures of the two were used as linkers to obtain polymorph materials with tuneable water sorption properties. The synthesis conditions determine the crystal structure and either the MIL‐53 or MIL‐68 type structure with square‐grid or kagome‐grid topology, respectively, is formed. Fine‐tuning resulted in new MOF materials thus far inaccessible through conventional synthesis routes. Furthermore, by varying the linker ratio, the water sorption properties can be continuously adjusted while retaining the sigmoidal isotherm shape advantageous for heat transformation and room climatisation applications.
iSwathX 2.0 for Processing DDA Spectral Libraries for DIA Data Analysis
Authors: Noor Zainab , Mohamedali Abidali , Ranganathan Shoba
Published: June 2020

The iSwathX web application processes and normalizes mass spectrometry−based proteomics spectral libraries generated in the data‐dependent acquisition (DDA) approach. These libraries are stored in various proteomics repositories such as PeptideAtlas and NIST, or are user‐generated and provide reference data for data‐independent acquisition (DIA) targeted data extraction and analysis. iSwathX 2.0 can efficiently normalize DDA data from different instruments, gathered at different instances, and make it compatible with specific DIA experiments. Novel functions for parallel processing of DDA libraries and DIA report files, along with various data visualizations, are available in iSwathX 2.0. The step‐by‐step protocols provided here describe how the libraries are uploaded, processed, visualized, and downloaded using various modules of the application. They also provide detailed guidelines on the use of DIA report files for data analysis and visualization. © 2020 Wiley Periodicals LLC.

Basic Protocol 1: Processing, combining, and visualizing two DDA libraries

Basic Protocol 2: Parallel processing and combination of multiple DDA libraries

Basic Protocol 3: Downstream processing, comparison, and visualization of DIA report files
Pruning SMAC search space based on key hyperparameters
Authors: Li Hui , Liang Qingqing , Chen Mei , Dai Zhenyu , Li Huanjun , Zhu Ming
Published: June 2020

Machine learning (ML) has been widely applied in many areas in recent decades. However, because of its inherent complexity and characteristics, the efficiency and effectiveness of ML algorithm often to be heavily relies on the technical experts' experience and expertise which play a crucial role to optimize hyperparameters of algorithms. Generally, the procedure tuning the exposed hyperparameters of ML algorithm to achieve better performance is called Hyperparameters Optimization. Traditional hyperparameters optimization methods are manually exhaustive search, which is unavailable for high dimensional search spaces and large datasets. Recent automated sequential model‐based optimization led to substantial improvements for this problem, whose core idea is fitting a regression model to describe the importance and dependence of algorithm's performance on certain given hyperparameter setting. Sequential model‐based algorithm configuration (SMAC) is a the‐state‐of‐art approach, which is specified by four components, Initialize, FitModel, SelectConfigurations, and Intensify. In this article, we propose to add a pruning procedure into SMAC approach, it quantifies the importance of hyperparameters by analyzing the performance of a list of promising configurations and reduces search space by discarding noncritical and bad key hyperparameters. To investigate the impact of pruning for model's performance, we conducted experiments on the configuration space constructed by Auto‐Sklearn and compared the effect of run time and pruning ratio with our algorithm. The experiments results verified that, our method made the configuration selected by SMAC more stable and achieved better performance.
Urchin‐Like Cobalt‐Copper (Hydr)oxides as an Efficient Water Oxidation Electrocatalyst
Authors: Ye Qilun , Hou Xiyan , Lee Husileng , Liu Hongzhen , Lu Liangjie , Wu Xiujuan , Sun Licheng
Published: June 2020

The development of eﬃcient and low‐cost oxygen evolution reaction (OER) catalysts is essential for the generation of clean hydrogen energy from water splitting. Herein, a novel hierarchical urchin‐like cobalt‐copper (hydr)oxide in situ grown on copper foam (CoCuOxHy(S)/CF) was synthesized through the electrochemical transformation of cobalt‐copper sulfides (Co9S8‐Cu1.81S) via anodization process. This CoCuOxHy(S)/CF anode exhibited a low overpotential (η) of 274 mV at a current density of 100 mA cm−2 with a robust durability over a period of 40 h when operated at 10 mA cm−2. Further investigations imply that the unique nanowires aggregated urchin‐like structure of CoCuOxHy(S) derived from the in situ anion exchange process could facilitate the exposure of active sites and accelerate electron transfer. More importantly, the incorporation of copper resulted in an electronic delocalization around the cobalt species, which contributed to reach a high‐valent catalytically active cobalt species and further improved the OER performance.
Occurrence of 2nmicrospore production in diploid interspecific hybrids between the wild parental species of peanut (Arachis hypogaeaL., Leguminosae) and its relevance in the genetic origin of the cultigen
Authors: García A. V. , Ortiz A. M. , Silvestri M. C. , Custodio A. R. , Moretzsohn M. C. , Lavia G. I.
Published: June 2020

Unreduced (2n) gametes are the driving force that leads to polyploidization of plants in nature and an important tool for ploidy breeding. Peanut (Arachis hypogaeaL., Leguminosae) seems most likely to have originated by sexual polyploidization through interspecific hybridization between the wild diploid relatives—A. duranensisKrapov. & W.C. Greg. andA. ipaënsisKrapov. & W.C. Greg—and subsequent binding of the unreduced gametes in the hybrid. Therefore, aiming to contribute to understanding the event of polyploid origin of this important crop, we made diploid hybrids betweenA. duranensisandA. ipaënsisand then investigated the production of unreduced gametes in the hybrids by analyzing the size range of pollen, the constitution of the sporads, and the microsporogenesis process. The meiotic abnormalities found, such as persistent bridges, tripolar spindles, and cytomixis processes, would lead to the formation of restitution nuclei in both the first and second meiotic division. These failures in the regularity of meiosis lead to the formation of dyads and triads, and consequently to 2npollen grains. These findings constitute the first evidence of the formation of unreduced gametes in intergenomic hybrids obtained between the wild progenitors ofA. hypogaeaand enable us to propose a model of origin of the crop through sexual polyploidization.
Fluorescence and Light Scatter Calibration Allow Comparisons of Small Particle Data in Standard Units across Different Flow Cytometry Platforms and Detector Settings
Authors: Welsh Joshua A. , Jones Jennifer C. , Tang Vera A.
Published: June 2020

Flow cytometers have been utilized for the analysis of submicron‐sized particles since the late 1970s. Initially, virus analyses preceded extracellular vesicle (EV), which began in the 1990s. Despite decades of documented use, the lack of standardization in data reporting has resulted in a growing body of literature that cannot be easily interpreted, validated, or reproduced. This has made it difficult for objective assessments of both assays and instruments, in‐turn leading to significant hindrances in scientific progress, specifically in the study of EVs, where the phenotypic analysis of these submicron‐sized vesicles is becoming common‐place in every biomedical field. Methods for fluorescence and light scatter standardization are well established and the reagents to perform these analyses are commercially available. However, fluorescence and light scatter calibration are not widely adopted by the small particle community as methods to standardize flow cytometry (FCM) data. In this proof‐of‐concept study carried out as a resource for use at the CYTO2019 workshop, we demonstrate for the first‐time simultaneous fluorescence and light scatter calibration of small particle data to show the ease and feasibility of this method for standardized FCM data reporting. This data was acquired using standard configuration commercial flow cytometers, with commercially available materials, published methods, and freely available software tools. We show that application of light scatter, fluorescence, and concentration calibration can result in highly concordant data between FCM platforms independent of instrument collection angle, gain/voltage settings, and flow rate; thus, providing a means of cross comparison in standard units. © 2020 International Society for Advancement of Cytometry
Qualitative threshold method validation and uncertainty evaluation: A theoretical framework and application to a 40 analytes liquid chromatography–tandem mass spectrometry method
Authors: Camirand Lemyre Félix , Desharnais Brigitte , Laquerre Julie , Morel Marc‐André , Côté Cynthia , Mireault Pascal , Skinner Cameron D.
Published: June 2020

Qualitative methods hold an important place in drug testing, filling central needs in screening and analyses, among others, linked to per se legislation. Nevertheless, the bioanalytical method validation guidelines do not discuss this type of method or describe method validation procedures ill‐adapted to qualitative methods. The output of qualitative methods are typically categorical, binary results, such as presence/absence or above cut‐off/below cut‐off. As the goal of any method validation is to demonstrate fitness for use under production conditions, qualitative validation guidelines should evaluate performance based on discrete, binary results instead of the continuous measurements obtained from the instrument (e.g. area).

A tentative validation guideline for threshold qualitative methods was developed by in silico modelling of measurements and derived binary results. This preliminary guideline was applied to a liquid chromatography–tandem mass spectrometry method for 40 analytes, each with a defined threshold concentration. Validation parameters calculated from the analysis of 30 samples spiked above and below the threshold concentration (false negative rate, false positive rate, selectivity rate, sensitivity rate and reliability rate) showed a surprisingly high failure rate. Overall, 13 out of the 40 analytes were not considered validated. A subsequent examination found that this was attributable to an appreciable shift in the standard deviation of the area ratio on a day‐to‐day basis, a previously undescribed and unaccounted‐for behaviour in the qualitative threshold method validation literature. Consequently, the developed guideline was modified and used to validate a qualitative threshold method, based on the binary results for performance evaluation and incorporating measurement uncertainty.
No evidence of sickness behavior in immune‐challenged field crickets
Authors: Kelly Clint D. , Mc Cabe Leroux Jules
Published: June 2020

Sickness behavior is a taxonomically widespread coordinated set of behavioral changes that increases shelter‐seeking while reducing levels of general activity, as well as food (anorexia) and water (adipsia) consumption, when fighting infection by pathogens and disease. The leading hypothesis explaining such sickness‐related shifts in behavior is the energy conservation hypothesis. This hypothesis argues that sick (i.e., immune‐challenged) animals reduce energetic expenditure in order have more energy to fuel an immune response, which in some vertebrates, also includes producing an energetically expensive physiological fever. We experimentally tested the hypothesis that an immune challenge with lipopolysaccharide (LPS) will cause Gryllus firmus field crickets to reduce their activity, increase shelter use and avoid foods that interfere with an immune response (i.e., fat) while preferring a diet that fuels an immune response (i.e., protein). We found little evidence of sickness behavior in Gryllus firmus as immune‐challenged individuals did not reduce their activity or increase their shelter‐seeking. Neither did we observe changes in feeding or drinking behavior nor a preference for protein or avoidance of lipids. Males tended to use shelters less than females but no other behaviors differed between the sexes. The lack of sickness behavior in our study might reflect the fact that invertebrates do not possess energetically expensive physiological fever as part of their immune response. Therefore, there is little reason to conserve energy via reduced activity or increased shelter use when immune‐challenged.
Robbery in progress: Historical museum collections bring to light a mitochondrial capture within a bird species widespread across southern Australia, the Copperback Quail‐thrush Cinclosoma clarum
Authors: McElroy Kerensa , Black Andrew , Dolman Gaynor , Horton Philippa , Pedler Lynn , Campbell Catriona D. , Drew Alex , Joseph Leo
Published: June 2020

We surveyed mitochondrial, autosomal, and Z chromosome diversity within and between the Copperback Quail‐thrush Cinclosoma clarum and Chestnut Quail‐thrush C. castanotum, which together span the arid and semi‐arid zones of southern Australia, and primarily from specimens held in museum collections. We affirm the recent taxonomic separation of the two species and then focus on diversity within the more widespread of the two species, C. clarum. To guide further study of the system and what it offers to understanding the genomics of the differentiation and speciation processes, we develop and present a hypothesis to explain mitonuclear discordance that emerged in ourdata. Following a period of historical allopatry, secondary contact has resulted in an eastern mitochondrial genome replacing the western mitochondrial genome in western populations. This is predicted under a population‐level invasion in the opposite direction, that of the western population invading the range of the eastern one. Mitochondrial captures can be driven by neutral, demographic processes, or adaptive mechanisms, and we favor the hypothesized capture being driven by neutral means. We cannot fully reject the adaptive process but suggest how these alternatives may be further tested. We acknowledge an alternative hypothesis, which finds some support in phenotypic data published elsewhere, namely that outcomes of secondary contact have been more complex than our current genomic data suggest. Discriminating and reconciling these two alternative hypotheses, which may not be mutually exclusive, could be tested with closer sampling at levels of population, individual, and nucleotide than has so far been possible. This would be further aided by knowledge of the genetic basis to phenotypic variation described elsewhere.
Metal–Organic Frameworks‐Derived Porous Yolk–Shell MoP/Cu3P@carbon Microcages as High‐Performance Anodes for Sodium‐Ion Batteries
Authors: Yin Yanyou , Zhang Yu , Liu Nannan , Fan Lishuang , Zhang Naiqing
Published: June 2020

Transitional metal phosphides (TMPs) anode materials usually have large volume change and weak diffusion kinetics, leading to poor cycle stability. Combining TMPs with conductive carbon matrix has been widely used to boost sodium storage. However, it still needs to make efforts in the rational and facile design of nano/micro‐structural TMPs/carbon hybrid anode material. Herein, a MOFs‐derived strategy is developed to synthesize porous yolk–shell MoP/Cu3P@carbon microcages (MoP/Cu3P@C) through in situ and confined phosphidation reaction as a high‐performance sodium‐ion batteries anode. This yolk–shell structure can offer adequate internal space to buffer the large volume expansion, shorten diffusion distance, and create more active sites of Na+. Especially, the Cu nanoparticles generated from Cu3P have remarkable electronic conductivity of 5.7 × 107 S m−1 (the second most conductive metal) to benefit transporting electrons. And the introduction of Mo (MoP has high theoretical capacity of 633 mA h g−1) can enhance the reversible capacity of the whole anode material. Therefore, these porous yolk–shell MoP/Cu3P@carbon microcages possess excellent reversible capacity of 307.8 mA h g−1 at 1.0 A g−1 and extraordinary cycle stability of 132.1 mA h g−1 at 5.0 A g−1 even after 6000 cycles.
Polynomial edge reconstruction sensitivity, subpixel Sobel gradient kernel analysis
Authors: Wells Nicholas , See Chung W.
Published: June 2020

In digital image processing the accuracy and precision of edge detectors within noisy temporal environments can be imperative. In this article, a report on the polynomial reconstruction of 22.5° Sobel kernels using additional points through imaging system noise are analyzed. In comparison to the accuracy of first‐order interval kernel masks, the first‐order 45° kernel approximation using 5‐points provides consistent stability in accuracy and precision across pixel and subpixel gradients. For a 22.5° sampling interval, a 3‐point polynomial evaluation minimizes the error of the subpixel orientation of the gradient. These characteristics are derived from the retention of kernel symmetry using noninteger coefficients. Critical to gradient precision is the distortion of the evaluated points due to system noise or their value away from second‐order symmetry. For a refined measurement estimate, sensitivity up to 10−5 is demonstrated.
Evaluating the OECD’s main economic indicators at anticipating recessions*
Authors: Camacho Máximo , Palmieri Gonzalo
Published: June 2020

Using receiver operating characteristic (ROC) techniques, we evaluate the predictive content of the monthly main economic indicators (MEI) of the Organization for Economic Co‐operation and Development (OECD) for predicting both growth cycle and business cycle recessions at different horizons. From a sample that covers 123 indicators for 32 OECD countries as well as for Brazil, China, India, Indonesia, the Russian Federation, and South Africa, our results suggest that the OECD's MEI show a high overall performance in providing early signals of economic downturns worldwide, albeit they perform a bit better at anticipating business cycles than growth cycles. Although the performance for OECD and non‐OECD members is similar in terms of timeliness, the indicators are more accurate at anticipating recessions for OECD members. Finally, we find that some single indicators, such as interest rates, spreads, and credit indicators, perform even better than the composite leading indicators.
Enhanced oral bioavailability of oligomeric proanthocyanidins by a self‐double‐emulsifying drug delivery system
Authors: Tian Yuan , Mao Xinyu , Sun Rui , Zhang Ming , Xia Qiang
Published: June 2020

The present study aims at the formulation and evaluation of solid self‐double‐emulsifying drug delivery system (SDEDDS) to increase the bioavailability of oligomeric proanthocyanidin (OPC). The formulation is prepared through two‐step method and is able to form water‐in‐oil‐in‐water (W/O/W) double emulsions after diluted with aqueous medium while keeping the drug in inner water phase. Solid‐state characterization is performed by DSC and X‐ray powder diffraction. Furthermore, antioxidant capacity shows that OPC is preserved by the solid SDEDDS. OPC‐SDEDDS exhibit sustained release of OPC under the conditions mimicking gastrointestinal tract. The result shows that bioaccessibility of OPC is improved after incorporating into SDEDDS formulation compared to pure drug. The proposed SDEDDS is a promising carrier strategy for delivering the hydrophilic compounds with low‐oral bioavailability.
Miocene age of the Huanan basalt lava flow (NEChina) inferred by reset of zircon (U–Th)/He thermochronometer in the underlying sand
Authors: Zhou Jianping , Dunkl István , Liu Yongjiang , Li Weimin , Wolf Anna , von Eynatten Hilmar
Published: June 2020

Mafic lavas of Cenozoic age are widely distributed in northeast China and received much attention as an important part of the Circum‐Pacific volcanic belt. The age constraints for the volcanic activity were determined mostly by K/Ar and40Ar/39Ar methods. We present zircon (U–Th)/He ages obtained on the thermally overprinted sands directly underlying a basaltic lava. This thermochronometer is insensitive to weathering and not biased by excess argon, thus it can express accurately the age of thermal effect of the lava flow. As a regional cooling age reference, three granite samples were dated from basement units that have not been thermally influenced by the basalt eruptions. The reference granite samples revealed well‐defined Cretaceous (U–Th)/He‐ages, while 20 zircon crystals from the sand below the basalt lava revealed a prominent Miocene (U–Th)/He age component of 9.33 ± 0.24 Ma. Raman spectroscopy of these zircon crystals supports their thermally overprinted character. We infer that the sand sample has experienced significant thermal overprint by the overlying basalt lava leading to thermal reset of the majority of the detrital zircon crystals. The obtained age is thus interpreted as the eruption age of the basalt lava. The Huanan basalt flow thus belongs to volcanics of the Laoyeling episode in NE China.