bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of hematopoietic cells
Authors: Hardison Ross C. , Zhang Yu , Keller Cheryl A. , Xiang Guanjue , Heuston Elisabeth F. , An Lin , Lichtenberg Jens , Giardine Belinda M. , Bodine David , Mahony Shaun , Li Qunhua , Yue Feng , Weiss Mitchell J. , Blobel Gerd A. , Taylor James , Hughes Jim , Higgs Douglas R. , Göttgens Berthold 
Published: November 2019

AbstractMembers of the GATA family of transcription factors play key roles in the differentiation of specific cell lineages by regulating the expression of target genes. Three GATA factors play distinct roles in hematopoietic differentiation. In order to better understand how these GATA factors function to regulate genes throughout the genome, we are studying the epigenomic and transcriptional landscapes of hematopoietic cells in a model‐driven, integrative fashion. We have formed the collaborative multi‐lab VISION project to conduct ValIdated Systematic IntegratiON of epigenomic data in mouse and human hematopoiesis. The epigenomic data included nuclease accessibility in chromatin, CTCF occupancy, and histone H3 modifications for 20 cell types covering hematopoietic stem cells, multilineage progenitor cells, and mature cells across the blood cell lineages of mouse. The analysis used the Integrative and Discriminative Epigenome Annotation System (IDEAS), which learns all common combinations of features (epigenetic states) simultaneously in two dimensions—along chromosomes and across cell types. The result is a segmentation that effectively paints the regulatory landscape in readily interpretable views, revealing constitutively active or silent loci as well as the loci specifically induced or repressed in each stage and lineage. Nuclease accessible DNA segments in active chromatin states were designated candidate cis‐regulatory elements in each cell type, providing one of the most comprehensive registries of candidate hematopoietic regulatory elements to date. Applications of VISION resources are illustrated for the regulation of genes encoding GATA1, GATA2, GATA3, and Ikaros. VISION resources are freely available from our website http://usevision.org.
Evidence of structural cavities in 3D printed acetabular cups for total hip arthroplasty
Authors: Hothi Harry , Dall'Ava Lorenzo , Henckel Johann , Di Laura Anna , Iacoviello Francesco , Shearing Paul , Hart Alister 
Published: November 2019

AbstractThe use of three‐dimensional (3D) printing to manufacture off‐the‐shelf titanium acetabular cups for hip arthroplasty has increased; however, the impact of this manufacturing technology is yet not fully understood. Although several studies have described the presence of structural cavities in 3D printed parts, there has been no analysis of full postproduction acetabular components. The aim of this study was to investigate the effect of 3D printing on the material structure of acetabular implants, first comparing different designs of 3D printed cups, second comparing 3D printed with conventionally manufactured cups. Two of the 3D printed cups were produced using electron beam melting (EBM), one using laser rapid manufacturing (LRM). The investigation was performed using X‐ray microcomputed tomography, imaging both the entire cups and samples sectioned from different regions of each cup. All 3D printed cups showed evidence of structural cavities; these were uniformly distributed in the volume of the samples and exhibited a prevalent spherical shape. The LRM‐manufactured cup had significantly higher cavity density (p = .0286), with a median of 21 cavities/mm3 compared to 3.5 cavities/mm3 for EBM cups. However, the cavity size was similar, with a median of 20 μm (p = .7385). The conventional cups showed a complete absence of distinguishable cavities. The presence of cavities is a known limitation of the 3D printing technology; however, it is noteworthy that we found them in orthopedic implants used in patients. Although this may impact their mechanical properties, to date, 3D printed cups have not been reported to encounter such failures.
Green synthesis of pyrido[2,1‐a]isoquinolines and pyrido[1,2‐a]quinolins using Fe3O4‐MNPs as efficient nanocatalyst: Study of antioxidant activity
Authors: Faal Hamedani Naghmeh , Ghazvini Maryam , Azad Leila , Noushin Annataj 
Published: November 2019

AbstractIn this work, synthesis of pyrido[2,1‐a]isoquinolines and pyrido[1,2‐a]quinolins in excellent yield using multicomponent reaction of phthalaldehyde, methyl amine, methyl malonyl chloride, alkyl bromides, and triphenylphosphine in the presence of catalytic amount of Fe3O4‐MNPs with aqueous sodium hydroxide at 80°C was investigated. The reduction of ferric chloride solution with Clover Leaf water extract caused to synthesis of magnetic iron oxide nanoparticles (Fe3O4‐MNPs) as a green method. As well, antioxidant activity was studied for the some newly synthesized compounds such as 6a, 6c, 9b, and 9c using the DPPH radical trapping and reducing of ferric ion experiments and comparing results with synthetic antioxidants (TBHQ and BHT). As a result, compounds 6a, 6c, 9b, and 9c show good DPPH radical trapping and excellent reducing strength of ferric ion.
Automatic identification and classification of the northern part of the Red Sea trough and its application for climatological analysis
Authors: Saaroni Hadas , Harpaz Tzvi , Alpert Pinhas , Ziv Baruch 
Published: November 2019

AbstractThe Red Sea trough (RST) is a low‐pressure trough extending from south towards the Levant. Unlike previous synoptic classifications covering all systems that affect the region, our algorithm focuses on the RST alone. It uses sea‐level pressure (SLP) and relative geostrophic vorticity for identifying the existence of an RST and classifying it to one of three types, according to the location of the trough axis with respect to 35°E longitude. The following conditions were imposed to assure the existence of an RST: (a) north to south SLP drop across the Levant, (b) average positive sea‐level relative vorticity over the region of interest, (c) existence of a distinct and continuous trough axis from the south towards the region of interest and (d) absence of any pronounced closed cyclone near the Levant. The algorithm was applied on the NCEP/NCAR reanalysis, 2.5° × 2.5° resolution and the ERA‐Interim, 2.5° × 2.5° and 0.75° × 0.75° resolutions. An evaluation of the algorithm against subjective identification, based on the NCEP reanalysis, showed an agreement of 93% for RST identification and 79% for correct classification. The use of fine resolution data may insert noise that reduce the identification rate of RSTs but improves the axis locating. The autumn is the main season of RST, with a maximum in November and a consistent decrease towards the July minimum. The annual frequency varies among the data sources between 17.6 and 24.6%. The trough axis is shown to have a diurnal oscillation; towards the eastern coast of the Mediterranean at nighttime and eastward, inland, at noontime. No consistent long‐term trend was found for the period 1979–2016, during which the global warming was persistent. This automated algorithm is flexible in the sense that it is not confined to any predetermined spatial resolution and is applicable to operational forecast model as well as to climate model outputs.
Transesterification of Palm‐based Methyl Palmitate into Esteramine Catalyzed by Calcium Oxide Catalyst
Authors: Aziz Haliza Abdul , Abas Noor Azeerah , Ping Bonnie Tay Yen , Idris Zainab 
Published: November 2019

AbstractThe technology for transesterification reactions between methyl esters and alcohols is well established by using classical homogeneous alkaline catalysts, which provide high conversion of methyl esters to specialty or nonindigenous esters. However, in certain products where the purity of the esters is of concern, the removal of homogeneous catalysts after the completion of the reaction is a challenge in terms of production cost and water footprint. Therefore, a study to investigate the potential of heterogeneous catalysts was conducted on reactions between methyl palmitate and triethanolamine. The degree of basicity and active surface area of calcium oxide (CaO), zinc oxide (ZnO), and magnesium oxide (MgO) were first characterized by using temperature‐programmed desorption (TPD‐CO2) and Brunauere–Emmett–Teller (BET), respectively. Among the metal oxides investigated, the CaO catalyst showed the best catalytic activity toward the transesterification process as it gave the highest conversion of methyl palmitate and yielded fatty esteramine compositions similar to the conventional homogeneous catalyst. The optimum transesterification condition by using the CaO catalyst utilized a lower vacuum system of approximately 200 mbar, which could minimize a considerable amount of energy consumption. Furthermore, low CaO dosage of 0.1% was able to give a conversion of 94.5% methyl ester and formed esteramine at 170 °C for 2 h. Therefore, the production of esterquats from esteramine may become more economically feasible through the methyl ester route by using the CaO catalyst, which can be recycled three times.
Changes in vineyard productive attributes and phytochemical composition of sauvignon blanc grape and wine induced by the application of silicon and calcium
Authors: Gomes Trilícia Margarida , Mazon Luiza Freitas , Panceri Carolina Pretto , Machado Bruno Dalazen , Brighenti Alberto , Burin Vívian Maria , Bordignon‐Luiz Marilde T 
Published: November 2019

AbstractBACKGROUNDIt is important to increase productivity and improve plant quality at the same time as preserving the principles of safety and productivity. The present study aimed to evaluate the effects of different concentrations of sodium metasilicate and calcium chloride, applied as fertilizers, on the productivity and phytochemical characteristics of Sauvignon Blanc grapes and their respective wines.RESULTSThe experiments were conducted using 2017 and 2018 vintages of commercial Sauvignon Blanc grapes. The treatments consisted of applying separately different concentrations of sodium metasilicate (0, 4, 8 and 12 g L−1) or calcium chloride (0, 5, 10 and 15 g L−1). The treatments were carried out during four phenological phases. The grapes were harvested at technical maturity and white wines were elaborated. The application of inorganic salts, silicon and calcium to the grapes had a significant effect on the vineyard productivity. The best results were obtained with 4 and 8 g L−1 silicon and 15 g L−1 calcium. An increase in the concentration of phenolics in the grapes was noted. These compounds have antioxidant capacity, which is one of the factors responsible for the resistance of the grapes to pathogens.CONCLUSIONThe application of 4 and 8 g L−1 silicon and 15 g L−1 calcium to the grapes represents a potential alternative fertilizing strategy, which could increase the plant yield without damaging the phytochemical characteristics of the fruit and its derivatives. © 2020 Society of Chemical Industry
Combining ability and heterosis for grain iron biofortification in bread wheat
Authors: Younas Abia , Sadaqat Hafeez Ahmad , Kashif Muhammad , Ahmed Nisar , Farooq Muhammad 
Published: November 2019

AbstractBACKGROUNDIron is one of the nutrients that is essential for the human body. Despite the abundance of iron on earth, about two billion people worldwide are affected by iron deficiency. Iron biofortification of wheat, instead of supplementation and food fortification, provides a pragmatic approach to solve the problem of iron deficiency. In this study, 144 diverse wheat genotypes were evaluated for grain iron and yield potential, to estimate the potential for the iron biofortification of high‐yielding wheat varieties.RESULTSGenotypes did not differ significantly across the species, but within species the differences were significant for grain iron content and the phytate:iron molar ratio. Triticum aestivum (bread wheat) had the highest yield potential with more diversity than other Triticum species. Genotypes with high iron contents were crossed with high‐yielding genotypes in line × tester fashion to check the gene action controlling these traits. The combining ability analysis showed non‐additive gene action controlling grain iron, grain phytate, and grain yield. Heterosis manifestation also indicated some transgressive segregates with high specific combining ability effects.CONCLUSIONThere was considerable genetic potential for improving the grain iron content in the germplasm to provide an economical and long‐lasting solution to benefit an iron‐deficient population. Triticum aestivum had the highest variation and potential for iron biofortification. This study indicated the possibility of simultaneous improvement in grain iron and grain yield by producing a new variety through continuous selective breeding. © 2019 Society of Chemical Industry
Efficiency of two arbuscular mycorrhizal fungal inocula to improve saline stress tolerance in lettuce plants by changes of antioxidant defense mechanisms
Authors: Santander Christian , Ruiz Antonieta , García Susana , Aroca Ricardo , Cumming Jonathan , Cornejo Pablo 
Published: November 2019

AbstractBACKGROUNDArbuscular mycorrhizal (AM) fungi establish symbioses with most agricultural plants and improves growth under soil stress conditions. The present study aimed to evaluate the functional contribution of 2 AM fungal inocula (a native consortium isolated from saline soils of the Atacama Desert, ‘HMC’, and a reference inoculum Claroideoglomus claroideum, ‘Cc’) on the growth and antioxidant compounds of two cultivars of lettuce (Lactuca sativa cvs. ‘Grand Rapids’ and ‘Lollo Bionda’) at increasing salt stress conditions (0, 40, and 80 mmol L–1 NaCl). At 60 days of plant growth, the symbiotic development, biomass production, lipid peroxidation, proline content, antioxidant enzymes, phenolic compound profiles and antioxidant activity were evaluated.RESULTSThe 2 AM inocula differentially colonized the roots of Grand Rapids and Lollo Bionda lettuce plants. The AM symbioses increased proline synthesis and superoxide dismutase, catalase and ascorbate peroxidase activities and diminished phenolic compound synthesis and oxidative damage in lettuce, which was related positively to a higher growth of inoculated plants under salt exposure. The higher concentration of phenolic compounds induced by salinity in non‐inoculated plants was associated with high oxidative stress and low fresh biomass production.CONCLUSIONModulation of salinity stress in lettuce by AM root colonization is a result of changes of antioxidant enzymatic systems that reduce oxidative damage and sustain growth. The application of AM fungi to improve crop production by means of directed inoculation with efficient AM fungal strains may enhance lettuce production on soils plagued with salinity worldwide. © 2019 Society of Chemical Industry
Rapid Bending Origami in Micro/Nanoscale toward a Versatile 3D Metasurface
Authors: Pan Ruhao , Li Zhancheng , Liu Zhe , Zhu Wei , Zhu Liang , Li Yunlong , Chen Shuqi , Gu Changzhi , Li Junjie 
Published: November 2019

AbstractDevices consisting of 3D components are always desired for their far more controllable degrees of freedom compared with their planar counterparts; however, the limitations on the fabrication of 3D nanostructures have severely restricted their applications. Here, a focused ion beam (FIB) defined rapid bending origami method is reported to fabricate 3D micro/nanoscale architectures, by relying on ion irradiation induced 2D structure bending mechanism based on the residual stress formation in metal/dielectric film. Regulated by ions irradiation dose and energy, a large‐scale programmable 2D patterns can be controllably bended to configure versatile 3D micro/nanostructures with scalable bending capacity and feature sizes down to 175 nm. The benefit of this method is, a 3D bended metasurface is designed and fabricated as an asymmetric mirror, showing a very simple strategy to realize high‐efficiency unidirectional reflectionless effect. This FIB‐defined bending origami proves to be a rapid fabrication approach of varied 3D configuration in micro/nanoscale with extremely flexible controllability of spatial orientation, providing more opportunities and options for various functional devices based on 3D configurations, especially for 3D metasurfaces.
Rational Design of 2D p–π Conjugated Polysquaraines for Both Fullerene and Nonfullerene Polymer Solar Cells
Authors: Xiao Qi , Li Yanxun , Han Mengmeng , Wu Fei , Leng Xuanye , Zhang Dongyang , Zhang Xuning , Yang Shuo , Zhang Yuan , Li Zhen , Zhou Huiqiong , Li Zhong'an 
Published: November 2019

AbstractSo far, squaraine‐based polymer donors have been less explored for the bulk heterojunction (BHJ) polymer solar cells. In this work, two new p–π conjugated polysquaraines (PASQ‐BDT1 and PASQ‐BDT2) with different electron‐rich subunits on the squaraine skeleton are rationally developed as new polymer donors based on the 2D structure design concept. PASQ‐BDT2 with N,N‐diisobutylaniline subunits shows superior device performances in both fullerene and nonfullerene PSCs compared to PASQ‐BDT1 containing triphenylamine subunits, with power conversion efficiencies (PCEs) of 4.34% and 3.72%, respectively, owing to increased light‐harvesting ability and more favorable nanoscale morphology in the BHJ films. Moreover, its demonstrated that solvent effects can play an effective role in elevating the device performance. For the PASQ‐BDT2/PC71BM blend, the PCE is improved from 3.19% to 4.34% after solvent vapor annealing treatment, mainly attributed to the optimized film morphology and increased hole mobility. More interestingly, when the processing solvent for nonfullerene devices is changed from chlorobenzene to chloroform, a significant enhancement on PCE from 1.96% to 3.72% is yielded for the PASQ‐BDT2/ITIC blend, due to suppressed charge recombination and enhanced crystallinity in the chloroform‐processed BHJ films.
Nonpharmacological, Nonsurgical Treatments for Freezing of Gait in Parkinson's Disease: A Systematic Review
Authors: Delgado‐Alvarado Manuel , Marano Massimo , Santurtún Ana , Urtiaga‐Gallano Ainhoa , Tordesillas‐Gutierrez Diana , Infante Jon 
Published: November 2019

AbstractFreezing of gait is a disabling phenomenon that appears in a substantial number of Parkinson's disease (PD) patients as the disease evolves. It is considered to be one of the most relevant contributing factors to worsening of quality of life. Current pharmacological or surgical treatment options have limited efficacy. Thus, alternative nonpharmacological/nonsurgical approaches have emerged in recent years in an attempt to improve quality of life in PD. This systematic review summarizes studies of such therapies over the past 5 years. Thirty‐five studies were evaluated by use of a qualitative evaluation, while the methodological quality was assessed using validated tools. According to our results, there appear to be two broad categories of nonpharmacological therapies: those that seek a long‐lasting benefit and those that aim to achieve a transient effect to overcome the freezing of gait episode. Among the former, it is possible to differentiate between “passive” therapies, which include transcranial magnetic stimulation or transcranial direct current stimulation, and “active” therapies, which are based on different cognitive or physical training programs. Finally, “transient effect” therapies use different types of cues, such as visual, auditory, or proprioceptive stimuli, to attempt to shift the patient's habitual motor control to a goal‐directed one. In conclusion, a broad spectrum of nonpharmacological/nonsurgical approaches for freezing of gait has emerged in recent years with promising results. © 2019 International Parkinson and Movement Disorder Society
Numerical modeling of strongly coupled microscale multiphase flow and solid deformation
Authors: Fagbemi Samuel , Tahmasebi Pejman , Piri Mohammad 
Published: November 2019

SummaryWhen fluid flows in porous media under subsurface conditions, significant deformation can occur. Such deformation is dependent on structural and phase characteristics. In this paper, we investigate the effect of multiphase flow on the deformation of porous media at the pore scale by implementing a strongly coupled partitioned solver discretized with finite volume (FV) technique. Specifically, the role of capillary forces on grain deformation in porous media is investigated. The fluid and solid subdomains are meshed using unstructured independent grids. The model is applied for solving multiphase coupled equations and is capable of capturing pore scale physics during primary drainage by solving the Navier‐Stokes equation and advecting fluid indicator function using volume of fluid (VOF) while the fluid is interacting with a nonlinear elastic solid matrix. The convergence of the coupled solver is accelerated by Aitken underrelaxation. We also reproduce geomechanical stress conditions, at the pore scale, by applying uniaxial stress on the solid while simultaneously solving the multiphase fluid‐solid interaction problem to investigate the effect of external stress on fluid occupancy, velocity‐field distribution, and relative permeability. We observe that the solid matrix exhibits elasto‐capillary behavior during the drainage sequence. Relative permeability endpoints are shifted on the basis of the external stress exerted.
The image‐source method: a tool for geoacoustic inversion
Authors: Pinson Samuel , Guillon Laurent , Holland Charles W. 
Published: November 2019

ABSTRACTThe image source method is a fast tool to perform sound‐speed profile estimations for sediment tomography. It uses a broadband source and an array of receivers and is based on the representation of the reflected wave from sediment interfaces by image sources and on array processing techniques. Image sources are automatically detected by the array and the sound‐speed profile is deduced directly from their locations. Thus, the method has a low computational cost and can be applied to large data sets. The image source method has been under development during the last decade and has proven its efficiency on simulated data and at‐sea experiment data. The objective of this paper is to review these advances of the image source method.
Weak Galerkin finite element methods for electric interface model with nonhomogeneous jump conditions
Authors: Deka Bhupen , Roy Papri 
Published: November 2019

AbstractIn this paper, the weak Galerkin finite element method (WG‐FEM) is applied to a pulsed electric model arising in biological tissue when a biological cell is exposed to an electric field. A fitted WG‐FEM is proposed to approximate the voltage of the pulsed electric model across the physical media involving an electric interface (surface membrane), and heterogeneous permittivity and a heterogeneous conductivity. This method uses totally discontinuous functions in approximation space and allows the usage of finite element partitions consisting of general polygonal meshes. Optimal pointwise‐in‐time error estimates in L2‐norm and H1‐norm are shown to hold for the semidiscrete scheme even if the regularity of the solution is low on the whole domain. Furthermore, a fully discrete approximation based on backward Euler scheme is analyzed and related optimal error estimates are derived.