bluuebunny/crossref_metadata_2025_split huggingface dataset:
Butyrated ManNAc analog improves protein expression in Chinese hamster ovary cells
Authors: Yin Bojiao , Wang Qiong , Chung Cheng‐Yu , Ren Xiaozhi , Bhattacharya Rahul , Yarema Kevin J. , Betenbaugh Michael J. 
Published: February 2018

AbstractThe chemical additive sodium butyrate (NaBu) has been applied in cell culture media as a direct and convenient method to increase the protein expression in Chinese hamster ovary (CHO) and other mammalian cells. In this study, we examined an alternative chemical additive, 1,3,4‐O‐Bu3ManNAc, for its effect on recombinant protein production in CHO. Supplementation with 1,3,4‐O‐Bu3ManNAc for two stable CHO cell lines, expressing human erythropoietin or IgG, enhanced protein expression for both products with negligible impact on cell growth, viability, glucose utilization, and lactate accumulation. In contrast, sodium butyrate treatment resulted in a ∼20% decrease in maximal viable cell density and ∼30% decrease in cell viability at the end of cell cultures compared to untreated or 1,3,4‐O‐Bu3ManNAc treated CHO cell lines for both products. While NaBu treatment enhanced product yields more than the 1,3,4‐O‐Bu3ManNAc treatment, the NaBu treated cells also exhibited higher levels of caspase 3 positive cells using microscopy analysis. Furthermore, the mRNA levels of four cell apoptosis genes (Cul2, BAK, BAX, and BCL2L11) were up‐regulated more in sodium butyrate treated wild‐type, erythropoietin, or IgG expressing CHO‐K1 cell lines while most of the mRNA levels of apoptosis genes in 1,3,4‐O‐Bu3ManNAc treated cell lines remained equal or increased only slightly compared to the levels in untreated CHO cell lines. Finally, lectin blot analysis revealed that the 1,3,4‐O‐Bu3ManNAc‐treated cells displayed higher relative sialylation levels on recombinant EPO, consistent with the effect of the ManNAc component of this additive, compared to control while NaBu treatment led to lower sialylation levels than control, or 1,3,4‐O‐Bu3ManNAc‐treatment. These findings demonstrate that 1,3,4‐O‐Bu3ManNAc has fewer negative effects on cell cytotoxicity and apoptosis, perhaps as a result of a more deliberate uptake and release of the butyrate compounds, while simultaneously increasing the expression of multiple recombinant proteins, and improving the glycosylation characteristics when applied at comparable molarity levels to NaBu. Thus, 1,3,4‐O‐Bu3ManNAc represents a highly promising media additive alternative in cell culture for improving protein yields without sacrificing cell mass and product quality in future bioproduction processes.
Highly sensitive detection of mutations in CHO cell recombinant DNA using multi‐parallel single molecule real‐time DNA sequencing
Authors: Cartwright Joseph F. , Anderson Karin , Longworth Joseph , Lobb Philip , James David C. 
Published: February 2018

AbstractHigh‐fidelity replication of biologic‐encoding recombinant DNA sequences by engineered mammalian cell cultures is an essential pre‐requisite for the development of stable cell lines for the production of biotherapeutics. However, immortalized mammalian cells characteristically exhibit an increased point mutation frequency compared to mammalian cells in vivo, both across their genomes and at specific loci (hotspots). Thus unforeseen mutations in recombinant DNA sequences can arise and be maintained within producer cell populations. These may affect both the stability of recombinant gene expression and give rise to protein sequence variants with variable bioactivity and immunogenicity. Rigorous quantitative assessment of recombinant DNA integrity should therefore form part of the cell line development process and be an essential quality assurance metric for instances where synthetic/multi‐component assemblies are utilized to engineer mammalian cells, such as the assessment of recombinant DNA fidelity or the mutability of single‐site integration target loci. Based on Pacific Biosciences (Menlo Park, CA) single molecule real‐time (SMRT™) circular consensus sequencing (CCS) technology we developed a rDNA sequence analysis tool to process the multi‐parallel sequencing of ∼40,000 single recombinant DNA molecules. After statistical filtering of raw sequencing data, we show that this analytical method is capable of detecting single point mutations in rDNA to a minimum single mutation frequency of 0.0042% (<1/24,000 bases). Using a stable CHO transfectant pool harboring a randomly integrated 5 kB plasmid construct encoding GFP we found that 28% of recombinant plasmid copies contained at least one low frequency (<0.3%) point mutation. These mutations were predominantly found in GC base pairs (85%) and that there was no positional bias in mutation across the plasmid sequence. There was no discernable difference between the mutation frequencies of coding and non‐coding DNA. The putative ratio of non‐synonymous and synonymous changes within the open reading frames (ORFs) in the plasmid sequence indicates that natural selection does not impact upon the prevalence of these mutations. Here we have demonstrated the abundance of mutations that fall outside of the reported range of detection of next generation sequencing (NGS) and second generation sequencing (SGS) platforms, providing a methodology capable of being utilized in cell line development platforms to identify the fidelity of recombinant genes throughout the production process.
Proteomics in biomanufacturing control: Protein dynamics of CHO‐K1 cells and conditioned media during apoptosis and necrosis
Authors: Albrecht Simone , Kaisermayer Christian , Gallagher Clair , Farrell Amy , Lindeberg Anna , Bones Jonathan 
Published: February 2018

AbstractCell viability has a critical impact on product quantity and quality during the biomanufacturing of therapeutic proteins. An advanced understanding of changes in the cellular and conditioned media proteomes upon cell stress and death is therefore needed for improved bioprocess control. Here, a high pH/low pH reversed phase data independent 2D‐LC‐MSE discovery proteomics platform was applied to study the cellular and conditioned media proteomes of CHO‐K1 apoptosis and necrosis models where cell death was induced by staurosporine exposure or aeration shear in a benchtop bioreactor, respectively. Functional classification of gene ontology terms related to molecular functions, biological processes, and cellular components revealed both cell death independent and specific features. In addition, label free quantitation using the Hi3 approach resulted in a comprehensive shortlist of 23 potential cell viability marker proteins with highest abundance and a significant increase in the conditioned media upon induction of cell death, including proteins related to cellular stress response, signal mediation, cytoskeletal organization, cell differentiation, cell interaction as well as metabolic and proteolytic enzymes which are interesting candidates for translating into targeted analysis platforms for monitoring bioprocessing response and increasing process control.
Chemical Composition and Antimicrobial Activity of Ageratina deltoidea
Authors: Arciniegas Amira , Pérez‐Castorena Ana L. , Meléndez‐Aguirre Mariana , Ávila José Guillermo , García‐Bores Ana María , Villaseñor José Luis , Romo de Vivar Alfonso 
Published: February 2018

The chemical study of Ageratina deltoidea afforded grandiflorenic acid (1), ent‐kaurenoic acid (2), and eight benzylbenzoates (3 – 10), two of them, 3,5‐dimethoxybenzyl 2,3,6‐trimethoxybenzoate (5) and 4‐(β‐d‐glucopyranosyloxy)‐3‐hydroxybenzyl 2,6‐dimethoxybenzoate (9), described for the first time. In addition, the new sesquiterpene lactone deltoidin C (13), together with the known 11 and 12, the phenolic compounds: ayanin, 2,6‐dimethoxybenzoic acid, methyl 3,4‐dihydroxycinnamate, chlorogenic acid, and 3,5‐dicaffeoylquinic acid were also isolated. The structures of these compounds were determined by spectroscopic methods and chemical reactions. The antibacterial and antifungal activities of compounds 1 – 12 were evaluated on Staphylococcus aureus, Escherichia coli, and Candida albicans. Deltoidin A (11) was the most active antibacterial agent (MIC 16.0 μg ml−1) against E. coli, and the ent‐kaurenoid derivatives (1 – 2) showed activity (MIC 31.0 μg ml−1) against S. aureus.
High‐Quality Platinum–Iron Nanodendrites with a Multibranched Architecture as Efficient Electrocatalysts for the Ethanol Oxidation Reaction
Authors: Xu Hui , Song Pingping , Wang Jin , Gao Fei , Zhang Yangping , Shiraishi Yukihide , Du Yukou 
Published: February 2018

AbstractAlthough great success has been made in the design of well‐defined nanocrystals (NCs) with various morphologies, a facile method to prepare desirable NCs with large active surface areas and unique facets remains an arduous challenge. Herein, we demonstrate a facile method for the successful synthesis of high‐quality PtFe nanodendrites with a multibranched architecture; these nanodendrites have an abundance of exposed surface active sites that are available for ethanol molecules. Detailed study of its electrocatalytic properties revealed that the resultant superbranched PtFe nanocatalysts displayed superior electrocatalytic activity towards ethanol oxidation with unprecedentedly high mass/specific activities of 3692.5 mA mg−1 and 7.02 mA cm−2; these values are 9.3 and 10.0‐fold higher than those of a commercial Pt/C catalyst, signifying that the these nanodendrites may serve as highly efficient catalysts for fuel cells and beyond.
Design Principles for the Atomic and Electronic Structure of Halide Perovskite Photovoltaic Materials: Insights from Computation
Authors: Berger Robert F. 
Published: February 2018

AbstractIn the current decade, perovskite solar cell research has emerged as a remarkably active, promising, and rapidly developing field. Alongside breakthroughs in synthesis and device engineering, halide perovskite photovoltaic materials have been the subject of predictive and explanatory computational work. In this Minireview, we focus on a subset of this computation: density functional theory (DFT)‐based work highlighting the ways in which the electronic structure and band gap of this class of materials can be tuned via changes in atomic structure. We distill this body of computational literature into a set of underlying design principles for the band gap engineering of these materials, and rationalize these principles from the viewpoint of band‐edge orbital character. We hope that this perspective provides guidance and insight toward the rational design and continued improvement of perovskite photovoltaics.
Anatomical characterization of PDF‐tri neurons and peptidergic neurons associated with eclosion behavior in Drosophila
Authors: Selcho Mareike , Mühlbauer Barbara , Hensgen Ronja , Shiga Sakiko , Wegener Christian , Yasuyama Kouji 
Published: February 2018

AbstractThe peptidergic Pigment‐dispersing factor (PDF)‐Tri neurons are a group of non‐clock neurons that appear transiently around the time of adult ecdysis (=eclosion) in the fruit fly Drosophila melanogaster. This specific developmental pattern points to a function of these neurons in eclosion or other processes that are active around pupal–adult transition. As a first step to understand the role of these neurons, we here characterize the anatomy of the PDF‐Tri neurons. In addition, we describe a further set of peptidergic neurons that have been associated with eclosion behavior, eclosion hormone (EH), and crustacean cardioactive peptide (CCAP) neurons, to single cell level in the pharate adult brain. PDF‐Tri neurons as well as CCAP neurons co‐express a classical transmitter indicated by the occurrence of small clear vesicles in addition to dense‐core vesicles containing the peptides. In the tritocerebrum, gnathal ganglion and the superior protocerebrum PDF‐Tri neurites contain peptidergic varicosities and both pre‐ and postsynaptic sites, suggesting that the PDF‐Tri neurons represent modulatory rather than pure interneurons that connect the subesophageal zone with the superior protocerebrum. The extensive overlap of PDF‐Tri arborizations with neurites of CCAP‐ and EH‐expressing neurons in distinct brain regions provides anatomical evidence for a possible function of the PDF‐Tri neurons in eclosion behavior.
Gradient‐based optimization with B‐splines on sparse grids for solving forward‐dynamics simulations of three‐dimensional, continuum‐mechanical musculoskeletal system models
Authors: Valentin J. , Sprenger M. , Pflüger D. , Röhrle O. 
Published: February 2018

AbstractInvestigating the interplay between muscular activity and motion is the basis to improve our understanding of healthy or diseased musculoskeletal systems. To be able to analyze the musculoskeletal systems, computational models are used. Albeit some severe modeling assumptions, almost all existing musculoskeletal system simulations appeal to multibody simulation frameworks. Although continuum‐mechanical musculoskeletal system models can compensate for some of these limitations, they are essentially not considered because of their computational complexity and cost. The proposed framework is the first activation‐driven musculoskeletal system model, in which the exerted skeletal muscle forces are computed using 3‐dimensional, continuum‐mechanical skeletal muscle models and in which muscle activations are determined based on a constraint optimization problem. Numerical feasibility is achieved by computing sparse grid surrogates with hierarchical B‐splines, and adaptive sparse grid refinement further reduces the computational effort. The choice of B‐splines allows the use of all existing gradient‐based optimization techniques without further numerical approximation. This paper demonstrates that the resulting surrogates have low relative errors (less than 0.76%) and can be used within forward simulations that are subject to constraint optimization. To demonstrate this, we set up several different test scenarios in which an upper limb model consisting of the elbow joint, the biceps and triceps brachii, and an external load is subjected to different optimization criteria. Even though this novel method has only been demonstrated for a 2‐muscle system, it can easily be extended to musculoskeletal systems with 3 or more muscles.
The influence of color on impulsiveness and arousal: Part 2 – Chroma
Authors: Duan Yiting , Rhodes Peter A. , Cheung Vien 
Published: February 2018

AbstractIn the preceding Part 1, the effect of hue on impulsiveness and arousal was studied. From those results, yellow, red and orange were selected for further investigation since participants' performance was consistent with a low arousal state (high error rate and long response time) for the yellow background and high arousal state (low error rate and short response time) for the red background, whereas orange tended to result in high impulsiveness. This article will mainly investigate the fundamental theory of how chroma influences people's impulsiveness and arousal state. As in the previous article, the two main factors used to measure impulsiveness and arousal are also response time and error rate for each colored background. In the psychophysical experiment, participants were looking separately at backgrounds consisting of three hues (red, yellow and orange) with different chroma levels on screen to complete a range of psychometric tests. During the experiment, participants gave their response to the psychometric test as quickly and accurately as possible. From the results it can be seen that chroma has a significant influence on participants' response time and error rate, and influences impulsiveness and arousal. Gender difference will also be discussed in this article.
Observer preference for perceived illumination chromaticity
Authors: Bodrogi Peter , Guo Xue , Stojanovic Dragana , Fischer Sebastian , Khanh Tran Quoc 
Published: February 2018

AbstractSubjects assessed white tone preference and tint percentage perception (e.g., a faint greenish tint perceived in the white tone) in a viewing booth containing small colored objects at the illuminance level of 1000 lx for cool white, neutral white and warm white spectra. White points with the lowest perceived tint percentage were most preferred. White tone preference was rated on interval scales labeled by semantic categories, for example, “very good,” “good,” and “moderate” The location of the white points of different preference levels (e.g., “good‐very good” level or “moderate‐good” level) was depicted in the u′‐v′ chromaticity diagram. The most preferred white points were located below the Planckian locus, inside the region of the white points required by CIE Publication 13.3 (1995) with the criterion of the chromaticity difference DC being <0.0054. The most preferred correlated color temperature (CCT) was at 3400, 4500, and 5800 K in the warm, neutral, and cool white CCT groups, respectively. Results were interpreted in terms of the Rea and Freyssinier (2014) model.
Computational color analysis of paintings for different artists of the XVI and XVII centuries
Authors: Romero Javier , Gómez‐Robledo Luis , Nieves Juan 
Published: February 2018

AbstractWe have performed a computational color analysis of images of paintings for six master painters: Titian, Rubens, El Greco, Velázquez, Rembrandt, and Vermeer. These painters show the evolution from the renaissance to the baroque style. Different first and second‐order statistical parameters have been obtained and analyzed in order to fix which of them can be common for the different artists and which of them can be representative of a certain period of time or the evolution of the art. The firsts include the orientation and semi‐axes ratio of the ellipses that define the gamut in the chromaticity diagram and the dependencies with the frequency of the power of the Fourier transforms. Most differences among artists can be found in the volume and area of the gamut, the number of discernible colors which is greater for Titian, El Greco and Rubens, compared to Velázquez, Rembrandt and Vermeer, the average value of L* and the number of dark pixels.
Transformation of Stored Energy into Light in the Chemiluminescence of 1,2‐Dioxetanes
Authors: Lu Gonghao , Oda Takahiro , Araki Hiroyuki , Iga Hiroshi , Matsumoto Masakatsu , Kimura Masaru , Hu Zhizhi , Zhang Zhiqiang 
Published: February 2018

AbstractChemiluminescence (CL) is a chemical phenomenon in which stored energy is transformed into light. The stored energy in a CL system must be sufficient to generate electronically excited carbonyl products. Rapid transfer of the heat of reaction is required to produce CL. However, this transformation of heat into light has not been demonstrated by correlating the reaction energies available with the light energies produced. We addressed this problem by re‐evaluating the reactions of a series of 1,2‐dioxetanes by making calorimetric measurements of heats of reaction and transformation efficiencies (ΦET), and compared the results with quantum yields (ΦCL) of CL reactions. Our results provide experimental support that the ΦET values of the 1,2‐dioxetanes were essentially the same as their ΦCL values. Additionally, we addressed the even−odd (meta–para) substitution issue through discussion of the heats of reaction of 1 m (3‐(2′‐spiroa‐damantane)‐4‐methoxy‐4‐(3“‐tert‐butyldimethylsilyloxy)phenyl‐1,2‐dioxetane) and 1 p (3‐(2′‐spiroadamantane)‐4‐methoxy‐4‐(4′′‐tert‐butyldimethyl‐silyloxy)‐phenyl‐1,2‐dioxetane) with the aid of empirical calculations and kinetic studies. We found that 1 m− provides sufficient stored energy to give the emitter 5 m−* while the energy level of emitter 5 p−* is higher than the stored energy of 1 p−. Thus, the transition energy of 1 m− is higher than that of 1 p−. The even−odd substitution effect therefore was manifested as different degrees of stored energy and transition‐state energy.
Circularly Polarized Luminescence and Circular Dichroisms in Small Organic Molecules: Correlation between Excitation and Emission Dissymmetry Factors
Authors: Tanaka Hiroki , Inoue Yoshihisa , Mori Tadashi 
Published: February 2018

AbstractPrompted by the recent rapid growth of interest in circularly polarized luminescence (CPL) of organic molecules, we have collected all the reliable CPL, as well as the corresponding circular dichroism (CD), data measured in fluid solutions. To analyze the correlation between CPL and CD, we employed the absorption and luminescence dissymmetry factors (gabs and glum) of the π–π* transition reported for chiral organic molecules of various categories, including planar chiral cyclophanes and helicenes, axially chiral biaryls and spiro compounds, and point‐ and axially chiral BODIPY derivatives. In rigid π‐systems, the absorption and fluorescence spectra are often mirror images of each other with a small Stokes shift, reflecting the minimal conformational relaxation in the emissive excited state, which should also affect the chiroptical properties in the excited state and be better sensed by CPL. However, no comprehensive efforts have hitherto been made to correlate the two relevant chiroptical properties, i. e. CPL versus CD, and also to quantitatively elucidate the effects of conformational relaxation in the excited state on the CPL behavior. The global linear regression analysis of all the reported gabs and glum values, though fairly scattered (see TOC), led us to a quantitative relationship: |glum|=0.81×|gabs| (r2=0.60), which demonstrates that the CPL dissymmetry factor is proportional to, and smaller than, the CD dissymmetry factor. A closer look revealed that the slope of the plot, or the proportional coefficient, is a critical function of the class of compounds, varying from 0.99 for cyclophanes to 0.93 for biaryls, to 0.77 for BODIPYs, and then to 0.61 for helicenes/helicenoids. The scattered glum–gabs plot and the general trend glum≤gabs appear to be inherent to the CPL of organic molecules in their isolated states, originating from the conformational flexibility, vibrational contribution, and Stokes shift that differ in each category.
The metabolism of flubendazole in human liver and cancer cell lines
Authors: Stuchlíková Lucie , Králová Věra , Lněničková Kateřina , Zárybnický Tomáš , Matoušková Petra , Hanušová Veronika , Ambrož Martin , Šubrt Zdeněk , Skálová Lenka 
Published: February 2018

AbstractFlubendazole (FLU), a benzimidazole anthelmintic drug widely used in veterinary medicine, has been approved for the treatment of gut‐residing nematodes in humans. In addition, FLU is now considered a promising anti‐cancer agent. Despite this, information about biotransformation of this compound in human is lacking. Moreover, there is no information regarding whether cancer cells are able to metabolize FLU in order to deactivate it. For these reasons, the present study was designed to identify all metabolites of Phase I and Phase II of FLU in human liver and in various cancer cells using ultra high‐performance liquid chromatography–tandem mass spectrometry (UHPLC–MS/MS) analysis. Precision‐cut human liver slices and 9 cell lines of different origin (breast, colon, oral cavity) were used as in vitro model systems. Our study showed that FLU with a reduced carbonyl group (FLUR) is the only FLU metabolite formed in the human liver. All human cancer cell lines were able to form FLUR. In addition, methylated FLUR was detected in breast cells MCF7 and intestinal SW480 cells. The accumulation of FLU and its reduction to FLUR markedly differed among cells. The extent of FLU reduction was in a good correlation with the detected expression level of carbonyl reductase 1. In most cases, FLU entered in a higher amount and was reduced to a lesser extent in proliferating (metastatic) cells than in differentiated (non‐cancerous, non‐metastatic) ones. These results support the promising potential of FLU in anti‐cancer therapy.