bluuebunny/crossref_metadata_2025_split huggingface dataset:
Murine xenograft bioreactors for human immunopeptidome discovery
Authors: Heather James M. , Myers Paisley T. , Shi Feng , Aziz-Zanjani Mohammad Ovais , Mahoney Keira E. , Perez Matthew , Morin Benjamin , Brittsan Christine , Shabanowitz Jeffrey , Hunt Donald F. , Cobbold Mark 
Published: December 2019

AbstractThe study of peptides presented by MHC class I and class II molecules is limited by the need for relatively large cell numbers, especially when studying post-translationally modified or otherwise rare peptide species. To overcome this problem, we pose the hypothesis that human cells grown as xenografts in immunodeficient mice should produce equivalent immunopeptidomes as cultured cells. Comparing human cell lines grown eitherin vitroor as murine xenografts, we show that the immunopeptidome is substantially preserved. Numerous features are shared across both sample types, including peptides and proteins featured, length distributions, and HLA-binding motifs. Peptides well-represented in both groups were from more abundant proteins, or those with stronger predicted HLA binding affinities. Samples grownin vivoalso recapitulated a similar phospho-immunopeptidome, with common sequences being those found at high copy number on the cell surface. These data indicate that xenografts are indeed a viable methodology for the production of cells for immunopeptidomic discovery.
Investigating the energy crisis in Alzheimer disease using transcriptome study
Authors: Dharshini S. Akila Parvathy , Taguchi Y.-h. , Gromiha M. Michael 
Published: December 2019

AbstractAlzheimer disease (AD) is a devastating neurological disorder, which initiates from hippocampus and proliferates to cortical regions. The neurons of hippocampus require higher energy to preserve the firing pattern. In AD, aberrant energy metabolism is the critical factor for neurodegeneration. However, the reason for the energy crisis in hippocampus neurons is still unresolved. Transcriptome analysis enables us in understanding the underlying mechanism of energy crisis. In this study, we identified variants/differential gene/transcript expression profiles from hippocampus RNA-seq data. We predicted the effect of variants in transcription factor (TF) binding using in silico tools. Further, a hippocampus-specific co-expression and functional interaction network were designed to decipher the relationships between TF and differentially expressed genes (DG). Identified variants predominantly influence TF binding, which subsequently regulates the DG. From the results, we hypothesize that the loss of vascular integrity is the fundamental attribute for the energy crisis, which leads to neurodegeneration.
In Vitro Expansion of Keratinocytes on Human Dermal Fibroblast-Derived Matrix Retains Their Stem-Like Characteristics
Authors: Wong Chee-Wai , LeGrand Catherine F. , Kinnear Beverley F. , Sobota Radoslaw M. , Ramalingam Rajkumar , Dye Danielle E. , Raghunath Michael , Lane E. Birgitte , Coombe Deirdre R. 
Published: December 2019

AbstractThe long-term expansion of keratinocytes under conditions that avoid xenogeneic components (i.e. animal serum- and feeder cell-free) generally causes diminished proliferation and increased terminal differentiation. Here we present a culture system free of xenogeneic components that retains the self-renewal capacity of primary human keratinocytes. In vivo the extracellular matrix (ECM) of the tissue microenvironment has a major influence on a cell’s fate. We used ECM from human dermal fibroblasts, cultured under macromolecular crowding conditions to facilitate matrix deposition and organisation, in a xenogeneic-free keratinocyte expansion protocol. Phospholipase A2 decellularisation produced ECM whose components resembled the core matrix composition of natural dermis by proteome analyses. Keratinocytes proliferated rapidly on these matrices, retained their small size, expressed p63, lacked keratin 10 and rarely expressed keratin 16. The colony forming efficiency of these keratinocytes was enhanced over that of keratinocytes grown on collagen I, indicating that dermal fibroblast-derived matrices maintain the in vitro expansion of keratinocytes in a stem-like state. Keratinocyte sheets formed on such matrices were multi-layered with superior strength and stability compared to the single-layered sheets formed on collagen I. Thus, keratinocytes expanded using our xenogeneic-free protocol retained a stem-like state, but when triggered by confluence and calcium concentration, they stratified to produce epidermal sheets with a potential clinical use.
Tracing the mass flow from glucose and phenylalanine to pinoresinol and its glycosides in Phomopsis sp. XP-8 using stable isotope assisted TOF-MS
Authors: Zhang Yan , Shi Junling , Ni Yongqing , Liu Yanlin , Zhao Zhixia , Zhao Xixi , Gao Zhenhong 
Published: December 2019

AbstractPhomopsis sp. XP-8, an endophytic fungus from the bark of Tu-Chung (Eucommia ulmoides Oliv) showed capability to biosynthesize pinoresinol (Pin) and pinoresinol diglucoside (PDG) from glucose (glu) and phenylalanine (Phe). To verify the mass flow in the biosynthesis pathway, [13C6]-labeled glu and [13C6]-labeled Phe were separately fed to the strain as sole substrates and [13C6]-labeled products were detected by ultra-high-performance liquid chromatography-quadrupole time of flight mass spectrometry. As results, [13C6]-labeled Phe was incorporated into [13C6]-cinnamylic acid (Ca) and p-coumaric acid (p-Co), and [13C12]-labeled Pin, which revealed that the Pin benzene ring came from Phe via the phenylpropane pathway. [13C6]-Labeled Ca and p-Co, [13C12]-labeled Pin, [13C18]-labeled pinoresinol monoglucoside (PMG), and [13C18]-labeled PDG products were found when [13C6]-labeled glu was used, demonstrating that the benzene ring and glucoside of PDG originated from glu. It was also determined that PMG was not the direct precursor of PDG in the biosynthetic pathway. The study identified the occurrence of phenylalanine- lignan biosynthesis pathway in fungi at the level of mass flow.
Simulated CO2-induced ocean acidification for ocean in the East China: historical conditions since preindustrial time and future scenarios
Authors: Zhang Han , Wang Kuo 
Published: December 2019

AbstractSince preindustrial times, as atmospheric CO2 concentration increases, the ocean continuously absorbs anthropogenic CO2, reducing seawater pH and $$[{{\rm{C}}{\rm{O}}}_{3}^{2-}]$$
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, which is termed ocean acidification. We perform Earth system model simulations to assess CO2-induced acidification for ocean in the East China, one of the most vulnerable areas to ocean acidification. By year 2017, ocean surface pH in the East China drops from the preindustrial level of 8.20 to 8.06, corresponding to a 35% rise in [H+], and reduction rate of pH becomes faster in the last two decades. Changes in surface seawater acidity largely result from CO2-induced changes in surface dissolved inorganic carbon (DIC), alkalinity (ALK), salinity and temperature, among which DIC plays the most important role. By year 2300, simulated reduction in sea surface $$[{{\rm{C}}{\rm{O}}}_{3}^{2-}]$$
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is 13% under RCP2.6, contrasted to 72% under RCP8.5. Furthermore, simulated results show that CO2-induced warming acts to mitigate reductions in $$[{{\rm{C}}{\rm{O}}}_{3}^{2-}]$$
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, but the individual effect of oceanic CO2 uptake is much greater than the effect of CO2-induced warming on ocean acidification. Our study quantifies ocean acidification induced by anthropogenic CO2, and indicates the potentially important role of accelerated CO2 emissions in projections of future changes in biogeochemistry and ecosystem of ocean in the East China.
RAG-2 deficiency results in fewer phosphorylated histone H2AX foci, but increased retinal ganglion cell death and altered axonal growth
Authors: Álvarez-Lindo Noemí , Baleriola Jimena , de los Ríos Vivian , Suárez Teresa , de la Rosa Enrique J. 
Published: December 2019

AbstractDNA double-strand breaks (DSBs), selectively visualized as γ-H2AX+ foci, occur during the development of the central nervous system, including the retina, although their origin and biological significance are poorly understood. Mutant mice with DSB repair mechanism defects exhibit increased numbers of γ-H2AX+ foci, increased cell death during neural development, and alterations in axonogenesis in the embryonic retina. The aim of this study was to identify putative sources of DSBs. One of the identified DSBs sources is LINE-1 retrotransposition. While we did not detect changes in LINE-1 DNA content during the early period of cell death associated with retinal neurogenesis, retinal development was altered in mice lacking RAG-2, a component of the RAG-1,2-complex responsible for initiating somatic recombination in lymphocytes. Although γ-H2AX+ foci were less abundant in the rag2−/− mouse retina, retinal ganglion cell death was increased and axonal growth and navigation were impaired in the RAG-2 deficient mice, a phenotype shared with mutant mice with defective DNA repair mechanisms. These findings demonstrate that RAG-2 is necessary for proper retinal development, and suggest that both DSB generation and repair are genuine processes intrinsic to neural development.
Emotion-related impulsivity moderates the cognitive interference effect of smartphone availability on working memory
Authors: Canale Natale , Vieno Alessio , Doro Mattia , Rosa Mineo Erika , Marino Claudia , Billieux Joël 
Published: December 2019

AbstractAlthough recent studies suggest that the mere presence of a smartphone might negatively impact on working memory capacity, fluid intelligence, and attentional processes, less is known about the individual differences that are liable to moderate this cognitive interference effect. This study tested whether individual differences in emotion-related impulsivity traits (positive urgency and negative urgency) moderate the effect of smartphone availability on cognitive performance. We designed an experiment in which 132 college students (age 18–25 years) completed a laboratory task that assessed visual working memory capacity in three different conditions: two conditions differing in terms of smartphone availability (smartphone turned off and visible, smartphone in silent mode and visible) and a condition in which the smartphone was not available and was replaced by a calculator (control condition). Participants also completed self-reports that assessed their thoughts after the task performance, positive/negative urgency, and problematic smartphone use. The results showed that participants with higher positive urgency presented increased cognitive interference (reflected by poorer task performance) in the “silent-mode smartphone” condition compared with participants in the “turned-off smartphone” condition. The present study provides new insights into the psychological factors that explain how smartphone availability is liable to interfere with high-level cognitive processes.
Double-parabolic-reflectors acoustic waveguides for high-power medical ultrasound
Authors: Chen Kang , Irie Takasuke , Iijima Takashi , Morita Takeshi 
Published: December 2019

AbstractHigh intensity focused ultrasound therapeutics are widely used to noninvasively treat various types of primary tumors and metastasis. However, ultrasound penetration depth is shallowed with increasing frequency which limits the therapeutic accuracy for deep tissues. Although acoustic waveguides are commonly inserted into tissue for localized therapy, powerful ultrasound delivery is difficult. Here, we invent double-parabolic-reflectors acoustic waveguides, where high-power ultrasound emission and large mechanical vibration enhance the therapeutic efficiency. High-energy-density ultrasound with around 20 times amplification by two parabolic reflectors propagates through the thin waveguide between 1 to 2 MHz, and wideband large mechanical vibration at the waveguide tip from 1 kHz to 2.5 MHz accelerates the therapeutics. This fundamental work serves as a milestone for future biomedical applications, from therapeutics to diagnostics. Since the high-power ability at high frequencies, our waveguide will also open up new research fields in medical, bio, physics and so on.
Cryo-Electron Microscopy Reveals That Sperm Modification Coincides with Female Fertility in the Mosquito Aedes aegypti
Authors: Noble Jade M. , Degner Ethan C. , Harrington Laura C. , Kourkoutis Lena F. 
Published: December 2019

AbstractManipulating mosquito reproduction is a promising approach to reducing mosquito populations and the burden of diseases they carry. A thorough understanding of reproductive processes is necessary to develop such strategies, but little is known about how sperm are processed and prepared for fertilization within female mosquitoes. By employing cryo-electron microscopy for the first time to study sperm of the mosquito Aedes aegypti, we reveal that sperm shed their entire outer coat, the glycocalyx, within 24 hours of being stored in the female. Motility assays demonstrate that as their glycocalyx is shed in the female’s sperm storage organs, sperm transition from a period of dormancy to rapid motility—a critical prerequisite for sperm to reach the egg. We also show that females gradually become fertile as sperm become motile, and that oviposition behavior increases sharply after females reach peak fertility. Together, these experiments demonstrate a striking coincidence of the timelines of several reproductive events in Ae. aegypti, suggesting a direct relationship between sperm modification and female reproductive capacity.
Vibrational communication between a myrmecophilous butterfly Spindasis lohita (Lepidoptera: Lycaenidae) and its host ant Crematogaster rogenhoferi (Hymenoptera: Formicidae)
Authors: Lin Yueh-Hsien , Liao Yi-Chang , Yang Chin-Cheng Scotty , Billen Johan , Yang Man-Miao , Hsu Yu-Feng 
Published: December 2019

AbstractAnts are a dominant insect group in terrestrial ecosystems and many myrmecophilous species evolve to associate with ants to gain benefits. One iconic example is myrmecophilous butterflies that often produce ant-mimicking vibrational calls to modulate ant behaviors. Despite its popularity, empirical exploration of how butterflies utilize vibrational signals to communicate with ants is scarce. In this study, we reported that the myrmecophilous butterflySpindasis lohitaproduce three types of larval calls and one type of pupal call, while its tending ant,Crematogaster rogenhoferiemit a single type of call. The results of discriminant analysis revealed that calls of the two species are quantitatively similar in their signal attributes; the potential role of butterfly calls are further confirmed by the playback experiments in which certain ant behaviors including antennation, aggregation, and guarding were induced when one of the butterfly calls was played toC.rogenhoferiworkers. The findings in the current study represent the very first evidence on vibrational communication betweenSpindasisandCrematogasterand also imply thatS.lohitamay have been benefited from ant attendance due to the ability to produce similar calls of the antC.rogenhoferi.
General scaling in bidirectional flows of self-avoiding agents
Authors: Cristín Javier , Méndez Vicenç , Campos Daniel 
Published: December 2019

AbstractThe analysis of the classical radial distribution function of a system provides a possible procedure for uncovering interaction rules between individuals out of collective movement patterns. A formal extension of this approach has revealed recently the existence of a universal scaling in the collective spatial patterns of pedestrians, characterized by an effective potential of interaction $$V(\tau )$$V(τ) conveniently defined in the space of the times-to-collision $${\boldsymbol{\tau }}$$τ between the individuals. Here we significantly extend and clarify this idea by exploring numerically the emergence of that scaling for different scenarios. In particular, we compare the results of bidirectional flows when completely different rules of self-avoidance between individuals are assumed (from physical-like repulsive potentials to standard heuristic rules commonly used to reproduce pedestrians dynamics). We prove that all the situations lead to a common scaling in the t-space both in the disordered phase ($$V(\tau ) \sim {\tau }^{-2}$$V(τ)~τ−2) and in the lane-formation regime ($$V(\tau ) \sim {\tau }^{-1}$$V(τ)~τ−1), independent of the nature of the interactions considered. Our results thus suggest that these scalings cannot be interpreted as a proxy for how interactions between pedestrians actually occur, but they rather represent a common feature for bidirectional flows of self-avoiding agents.
A stochastic generative model of the World Trade Network
Authors: García-Algarra Javier , Mouronte-López Mary Luz , Galeano Javier 
Published: December 2019

AbstractThe World Trade Network (WTN) is a network of exchange flows among countries whose topological and statistical properties are a valuable source of information. Degree and strength (weighted degree) are key magnitudes to understand its structure and generative mechanisms. In this work, we describe a stochastic model that yields synthetic networks that closely mimic the properties of annual empirical data. The model combines two popular mechanisms of network generation: preferential attachment and multiplicative process. Agreement between empirical and synthetic networks is checked using the available series from 1962 to 2017.
Future large hydropower dams impact global freshwater megafauna
Authors: Zarfl Christiane , Berlekamp Jürgen , He Fengzhi , Jähnig Sonja C. , Darwall William , Tockner Klement 
Published: December 2019

AbstractDam construction comes with severe social, economic and ecological impacts. From an ecological point of view, habitat types are altered and biodiversity is lost. Thus, to identify areas that deserve major attention for conservation, existing and planned locations for (hydropower) dams were overlapped, at global extent, with the contemporary distribution of freshwater megafauna species with consideration of their respective threat status. Hydropower development will disproportionately impact areas of high freshwater megafauna richness in South America, South and East Asia, and the Balkan region. Sub-catchments with a high share of threatened species are considered to be most vulnerable; these are located in Central America, Southeast Asia and in the regions of the Black and Caspian Sea. Based on this approach, planned dam locations are classified according to their potential impact on freshwater megafauna species at different spatial scales, attention to potential conflicts between climate mitigation and biodiversity conservation are highlighted, and priorities for freshwater management are recommended.
Morpho-physiological and proteomic responses to water stress in two contrasting tobacco varieties
Authors: Chen Zheng , Xu Jiayang , Wang Fazhan , Wang Lin , Xu Zicheng 
Published: December 2019

AbstractTo gain insight into the molecular mechanisms underpinning tobacco (Nicotiana tabacum) tolerance to drought stress, we integrated anatomical, physiological, and proteomic analyses of drought-tolerant (Yuyan6, [Y6]) and -sensitive (Yunyan87 [Y87]) varieties. In comparison to Y87, Y6 exhibited higher water retention capability, improved photosynthetic performance, delayed leaf-senescence, stable leaf ultrastructure, a stronger antioxidant defense, and lesser ROS accumulation when subjected to water stress. Using an iTRAQ-based proteomics approach, 405 and 1,560 differentially accumulated proteins (DAPs) were identified from Y6 and Y87 plants, respectively, of which 114 were found to be present in both cultivars. A subsequent functional characterization analysis revealed that these DAPs were significantly enriched in eight biological processes, six molecular functions, and six cellular components and displayed differential expression patterns in Y6 and Y87 plants, suggesting that the response to water stress between both varieties differed at the proteomic level. Furthermore, we constructed protein coexpression networks and identified hub proteins regulating tobacco defenses to water stress. Additionally, qPCR analysis indicated that the majority of genes encoding selected proteins showed consistency between mRNA levels and their corresponding protein expression levels. Our results provide new insights into the genetic regulatory mechanisms associated with drought response in tobacco plants.
Dose-response of different dietary leucine levels on growth performance and amino acid metabolism in piglets differing for aminoadipate-semialdehyde synthase genotypes
Authors: Bertocchi Micol , Bosi Paolo , Luise Diana , Motta Vincenzo , Salvarani Chiara , Ribani Anisa , Bovo Samuele , Simongiovanni Aude , Matsunaga Keiko , Takimoto Tetsuya , Bannai Makoto , Corrent Etienne , Fontanesi Luca , Chalvon-Demersay Tristan , Trevisi Paolo 
Published: December 2019

AbstractDose-response studies of dietary leucine (Leu) in weaners are needed for a proper diet formulation. Dietary Leu effect was assessed in a 3-weeks dose-response trial with a 2 (genotype) x 5 (diets) factorial arrangement on one-hundred weaned pigs (9 to 20 kg body weight (BW)). Pigs differed for a polymorphism at the aminoadipate-semialdehyde synthase (AASS) gene, involved in lysine (Lys) metabolism. Pigs received experimental diets (d7 to d28) differing for the standardized ileal digestible (SID) Leu:Lys: 70%, 85%, 100%, 115%, 130%. Daily feed intake (ADFI), daily gain (ADG) and feed:gain (F:G) in all pigs and ADG and F:G in two classes of BW were analyzed using regression analysis with curvilinear-plateau (CLP) and linear quadratic function (LQ) models. Amino acid (AA) concentrations in plasma, liver, muscle and urine were determined. AASS genotype did not affect the parameters. Dietary Leu affected performance parameters, with a maximum response for ADG and F:G between 100.5% and 110.7% SID Leu:Lys, higher than the usually recommended one, and between 110.5% and 115.4% and between 94.9% and 110.2% SID Leu:Lys for ADG for light and heavy pigs respectively. AA variations in tissues highlighted Leu role in protein synthesis and its influence on the other branched chain AAs.