bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic biochemical tissue analysis detects functional selectin ligands on human cancer tissues
Authors: Martin Eric W. , Malgor Ramiro , Resto Vicente A. , Goetz Douglas J. , Burdick Monica M. 
Published: June 2019

AbstractCell adhesion mediated by selectins (expressed by activated endothelium, activated platelets, and leukocytes) binding to their resepective selectin ligands (expressed by cancer cells) may be involved in metastasis. Therefore, methods of characterizing selectin ligands expressed on human tissue may serve as valuable assays. Presented herein is an innovative method for detecting functional selectin ligands expressed on human tissue that uses a dynamic approach, which allows for control over the force applied to the bonds between the probe and target molecules. This new method of tissue interrogation, known as dynamic biochemical tissue analysis (DBTA), involves the perfusion of molecular probe-coated microspheres over tissues. DBTA using selectin-coated probes is able to detect functional selectin ligands expressed on tissue from multiple cancer types at both primary and metastatic sites.
Cartography of odor chemicals in the dengue vector mosquito (Aedes aegypti L., Diptera/Culicidae)
Authors: Wang Fengen , Delannay Christelle , Goindin Daniella , Deng Ligang , Guan Shuai , Lu Xiao , Fouque Florence , Vega-Rúa Anubis , Picimbon Jean-François 
Published: June 2019

AbstractThis study was aimed to identify the chemical compounds ofAedes aegyptithat can be potentially used to develop pheromone-based vector control methods. In this study, we compared the chemical compounds collected from the organs of mosquitoes at different developmental stages in the life cycle. We also compared the composition and amount of extracts from the different tissues of male and female adult mosquito. Interestingly, we found large amount of C17-C20 ethyl and methyl esters in the wings of female and antennae of male mosquito. We also found that isopropyl esters, dodelactone, octadecenoic acid and medium-chain fatty acid increase drastically during the late larval stage (L4). Old adult mosquitoes showed remarkable increase in production of C16:1 and C18:1 methyl esters, as a first example of chemical signatures specifically associated with aging in the animals. This knowledge may open the ground to find new behaviorally-important molecules with the ability to controlAedesspecifically.
Endocrine aryl hydrocarbon receptor signaling is induced by moderate cutaneous exposure to ultraviolet light
Authors: Memari Babak , Nguyen-Yamamoto Loan , Salehi-Tabar Reyhaneh , Zago Michela , Fritz Jorg H. , Baglole Carolyn J. , Goltzman David , White John H. 
Published: June 2019

AbstractLinks between solar UV exposure and immunity date back to the ancient Greeks with the development of heliotherapy. Skin contains several UV-sensitive chromophores and exposure to sunlight can produce molecules, such as vitamin D3, that act in an endocrine manner. We investigated the role of the aryl hydrocarbon receptor (AHR), an environmental sensor and ligand-regulated transcription factor activated by numerous planar compounds of endogenous, dietary or environmental origin. 15- to 30-minute exposure of cells to a minimal erythemal dose of UVB irradiation in vitro induced translocation of the AHR to the nucleus, rapidly inducing site-specific DNA binding and target gene regulation. Importantly, ex vivo studies with Ahr wild-type or null fibroblasts showed that serum from mice whose skin was exposed to a 15 min UVB dose, but not control serum, contained agonist activity within 30 min of UV irradiation, inducing AHR-dependent gene expression. Moreover, a 15-min cutaneous UVB exposure induced AHR site-specific DNA binding and target gene regulation in vivo within 3–6 hr post-irradiation in blood and in peripheral tissues, including intestine. These results show that cutaneous exposure of mice to a single minimal erythemic dose of UVB induces rapid AHR signaling in multiple peripheral organs, providing compelling evidence that moderate sun exposure can exert endocrine control of immunity through the AHR.
Biotelemetry reveals migratory behaviour of large catfish in the Xingu River, Eastern Amazon
Authors: Hahn Lisiane , Martins Eduardo G. , Nunes Leonardo D. , da Câmara Luís Fernando , Machado Leonardo S. , Garrone-Neto Domingos 
Published: June 2019

AbstractWe used a combination of radio and acoustic telemetry to assess the movements of large catfish (Pimelodidae) in the Xingu River, a clearwater tributary of the Amazon River in Brazil. A total of 121 Phractocephalus hemioliopterus and 61 Pseudoplatystoma punctifer were tagged for monitoring within a 685 km segment, including the Belo Monte Hydroelectric Complex (BMHC), between February 2013 and July 2015. Long distance upstream movements were detected for P. hemioliopterus (up to 347 km) and for P. punctifer (up to 164 km) mainly during the transition between dry season and the rising water period. Both species moved through a long segment of rapids previously thought to function as barriers to migration. Several individuals exhibited long-distance bidirectional movements. Some tagged fish never left the release zone, indicating mortality, tag loss or resident individuals, which would characterize partial migration. The findings show evidence of migratory behaviour for large catfish within the Xingu River, emphasizing the influence of the hydrologic cycle on their movements. As part of the study area has become partially dewatered due to the BMHC, findings support the need of adequate management strategies to allow the movements of large catfish between spawning and feeding sites in the Xingu River.
Discovery of novel genic-SSR markers from transcriptome dataset of an important non-human primate, Macaca fascicularis
Authors: Chang Wendy , EE-ULI J. , NG W. L. , Rovie-Ryan Jeffrine J. , Tan S. G. , Yong Christina S. Y. 
Published: June 2019

AbstractMacaca fascicularis, also known as the cynomolgus macaque, is an important non-human primate animal model used in biomedical research. It is an Old-World primate widely distributed in Southeast Asia and is one of the most abundant macaque species in Malaysia. However, the genetic structure of wild cynomolgus macaque populations in Malaysia has not been thoroughly elucidated. In this study, we developed genic-simple sequence repeat (genic-SSR) markers from an in-house transcriptome dataset generated from the Malaysian cynomolgus macaque via RNA sequencing, and applied these markers on 26 cynomolgus macaque individuals. A collection of 14,751 genic-SSRs were identified, where 13,709 were perfect SSRs. Dinucleotide repeats were the most common repeat motifs with a frequency of 65.05%, followed by trinucleotide repeats (20.55%). Subsequently, we designed 300 pairs of primers based on perfect di- and trinucleotide SSRs, in which 105 SSRs were associated with functional genes. A subset of 30 SSR markers were randomly selected and validated, yielding 19 polymorphic markers with an average polymorphism information content value of 0.431. The development of genic-SSR markers in this study is indeed timely to provide useful markers for functional and population genetic studies of the cynomolgus macaque and other related non-human primate species.
A catalog of single nucleotide changes distinguishing modern humans from archaic hominins
Authors: Kuhlwilm Martin , Boeckx Cedric 
Published: June 2019

AbstractThroughout the past decade, studying ancient genomes has provided unique insights into human prehistory, and differences between modern humans and other branches like Neanderthals can enrich our understanding of the molecular basis of unique modern human traits. Modern human variation and the interactions between different hominin lineages are now well studied, making it reasonable to go beyond fixed genetic changes and explore changes that are observed at high frequency in present-day humans. Here, we identify 571 genes with non-synonymous changes at high frequency. We suggest that molecular mechanisms in cell division and networks affecting cellular features of neurons were prominently modified by these changes. Complex phenotypes in brain growth trajectory and cognitive traits are likely influenced by these networks and other non-coding changes presented here. We propose that at least some of these changes contributed to uniquely human traits, and should be prioritized for experimental validation.
Fibroblast growth factor 8b induces uncoupling protein 1 expression in epididymal white preadipocytes
Authors: Westphal Sören , Gantert Thomas , Kless Caroline , Hüttinger Kristina , Klingenspor Martin , Fromme Tobias 
Published: June 2019

AbstractThe number of brown adipocytes residing within murine white fat depots (brite adipocytes) varies a lot by depot, strain and physiological condition. Several endocrine fibroblast growth factors are implicated in the regulation of brite adipocyte abundance. The family of fibroblast growth factors can be categorized by their site of action into endocrine, paracrine and intracellular peptides. We here screened paracrine fibroblast growth factors for their potential to drive brite adipogenesis in differentiating epididymal white adipocytes and identified fibroblast growth factor 8b to induce uncoupling protein 1 expression, but at the same time to interfere in adipogenesis. In an in vivo trial, fibroblast growth factor 8b released into the epididymal fat depot failed to robustly increase the number of brite adipocytes. The specific action of fibroblast growth factor 8b on the uncoupling protein 1 promoter in cultured epididymal adipocytes provides a model system to dissect specific gene regulatory networks.
Effect of grinding, extraction time and type of coffee on the physicochemical and flavour characteristics of cold brew coffee
Authors: Cordoba Nancy , Pataquiva Laura , Osorio Coralia , Moreno Fabian Leonardo Moreno , Ruiz Ruth Yolanda 
Published: June 2019

AbstractThe effects of grinding (medium-coarse) and extraction time (14–22 h) on the physicochemical and sensorial properties of cold brew coffee produced using two types of Colombian specialty coffees (Huila and Nariño) were evaluated. Cold coffee brewed under coarse grinding and 22 h of extraction exhibited the highest values of total dissolved solids, extraction yield, pH, titratable acidity (TA), and total phenolic content. The type of coffee used mainly affected the TA and pH. All cold brew coffee samples had lower TA values than their hot counterparts. Nariño cold brew samples had higher TA values than those of Huila in all treatments evaluated. Higher scores were reported in the sensorial evaluation of cold brew coffee when prepared using the shortest time (14 h) and coarse grinding for both coffee types. These coffees were characterized by strong sweetness, fruity and floral flavours, medium bitterness and acidity, and a creamy body. Furans, pyrazines, ketones, aldehydes, pyrroles, esters, lactones, furanones, and phenols were detected as odour-active compounds. The findings of this study demonstrate that the particle size, contact time, and coffee type affect the physicochemical and sensorial characteristics of cold brew coffee, leading to cold brew coffees with different flavour profiles.
Analysis of Estonian surveillance in wild boar suggests a decline in the incidence of African swine fever
Authors: Schulz Katja , Staubach Christoph , Blome Sandra , Viltrop Arvo , Nurmoja Imbi , Conraths Franz Josef , Sauter-Louis Carola 
Published: June 2019

AbstractAfrican swine fever (ASF) in wild boar populations is difficult to control. In affected areas, samples from all wild boar shot and found dead are investigated. The use of laboratory tests allows estimating the duration of the infection in affected animals. The study aimed to test the hypothesis that the stage of the epidemic in different areas of Estonia can be assessed on the basis of prevalence estimates. ASF surveillance data of Estonian wild boar were used to estimate prevalences and compare them between the East and West of Estonia. The temporal trend of the estimated prevalence of ASF virus positive animals and of the estimated seroprevalence of wild boar showing antibodies against ASFV was analyzed. Due to the potential influence of population density on the course of ASF in wild boar, also population density data (number of wild boar/km2) were used to investigate the relationship with laboratory test results. In areas, where the epidemic had already lasted for a long time, a small number of new cases emerged recently. The prevalence of samples that were only seropositive was significantly higher in these regions as compared to areas, where the epidemic is in full progress. The observed course of the disease could be the beginning of an ASF endemicity in this region. However, the results may also indicate that ASF has started to subside in the areas that were first affected in Estonia.
Evaluation of ultra-low input RNA sequencing for the study of human T cell transcriptome
Authors: Wang Jingya , Rieder Sadiye Amcaoglu , Wu Jincheng , Hayes Susana , Halpin Rebecca A. , de los Reyes Melissa , Shrestha Yashaswi , Kolbeck Roland , Raja Rajiv 
Published: June 2019

AbstractDeeper understanding of T cell biology is crucial for the development of new therapeutics. Human naïve T cells have low RNA content and their numbers can be limiting; therefore we set out to determine the parameters for robust ultra-low input RNA sequencing. We performed transcriptome profiling at different cell inputs and compared three protocols: Switching Mechanism at 5′ End of RNA Template technology (SMART) with two different library preparation methods (Nextera and Clontech), and AmpliSeq technology. As the cell input decreased the number of detected coding genes decreased with SMART, while stayed constant with AmpliSeq. However, SMART enables detection of non-coding genes, which is not feasible for AmpliSeq. The detection is dependent on gene abundance, but not transcript length. The consistency between technical replicates and cell inputs was comparable across methods above 1 K but highly variable at 100 cell input. Sensitivity of detection for differentially expressed genes decreased dramatically with decreased cell inputs in all protocols, support that additional approaches, such as pathway enrichment, are important for data interpretation at ultra-low input. Finally, T cell activation signature was detected at 1 K cell input and above in all protocols, with AmpliSeq showing better detection at 100 cells.
Neutrophils mediate early cerebral cortical hypoperfusion in a murine model of subarachnoid haemorrhage
Authors: Neulen Axel , Pantel Tobias , Kosterhon Michael , Kramer Andreas , Kunath Sascha , Petermeyer Maximilian , Moosmann Bernd , Lotz Johannes , Kantelhardt Sven R. , Ringel Florian , Thal Serge C. 
Published: June 2019

AbstractCerebral hypoperfusion in the first hours after subarachnoid haemorrhage (SAH) is a major determinant of poor neurological outcome. However, the underlying pathophysiology is only partly understood. Here we induced neutropenia in C57BL/6N mice by anti-Ly6G antibody injection, induced SAH by endovascular filament perforation, and analysed cerebral cortical perfusion with laser SPECKLE contrast imaging to investigate the role of neutrophils in mediating cerebral hypoperfusion during the first 24 h post-SAH. SAH induction significantly increased the intracranial pressure (ICP), and significantly reduced the cerebral perfusion pressure (CPP). At 3 h after SAH, ICP had returned to baseline and CPP was similar between SAH and sham mice. However, in SAH mice with normal neutrophil counts cortical hypoperfusion persisted. Conversely, despite similar CPP, cortical perfusion was significantly higher at 3 h after SAH in mice with neutropenia. The levels of 8-iso-prostaglandin-F2α in the subarachnoid haematoma increased significantly at 3 h after SAH in animals with normal neutrophil counts indicating oxidative stress, which was not the case in neutropenic SAH animals. These results suggest that neutrophils are important mediators of cortical hypoperfusion and oxidative stress early after SAH. Targeting neutrophil function and neutrophil-induced oxidative stress could be a promising new approach to mitigate cerebral hypoperfusion early after SAH.
δ-MnO2 nanoflower/graphite cathode for rechargeable aqueous zinc ion batteries
Authors: Khamsanga Sonti , Pornprasertsuk Rojana , Yonezawa Tetsu , Mohamad Ahmad Azmin , Kheawhom Soorathep 
Published: June 2019

AbstractManganese oxide (MnO2) is one of the most promising intercalation cathode materials for zinc ion batteries (ZIBs). Specifically, a layered type delta manganese dioxide (δ-MnO2) allows reversible insertion/extraction of Zn2+ ions and exhibits high storage capacity of Zn2+ ions. However, a poor conductivity of δ-MnO2, as well as other crystallographic forms, limits its potential applications. This study focuses on δ-MnO2 with nanoflower structure supported on graphite flake, namely MNG, for use as an intercalation host material of rechargeable aqueous ZIBs. Pristine δ-MnO2 nanoflowers and MNG were synthesized and examined using X-ray diffraction, electron spectroscopy, and electrochemical techniques. Also, performances of the batteries with the pristine δ-MnO2 nanoflowers and MNG cathodes were studied in CR2032 coin cells. MNG exhibits a fast insertion/extraction of Zn2+ ions with diffusion scheme and pseudocapacitive behavior. The battery using MNG cathode exhibited a high initial discharge capacity of 235 mAh/g at 200 mA/g specific current density compared to 130 mAh/g which is displayed by the pristine δ-MnO2 cathode at the same specific current density. MNG demonstrated superior electrical conductivity compared to the pristine δ-MnO2. The results obtained pave the way for improving the electrical conductivity of MnO2 by using graphite flake support. The graphite flake support significantly improved performances of ZIBs and made them attractive for use in a wide variety of energy applications.
Single organelle analysis to characterize mitochondrial function and crosstalk during viral infection
Authors: Schneider Annika , Kurz Sandra , Manske Katrin , Janas Marianne , Heikenwälder Mathias , Misgeld Thomas , Aichler Michaela , Weissmann Sebastian Felix , Zischka Hans , Knolle Percy , Wohlleber Dirk 
Published: June 2019

AbstractMitochondria are key for cellular metabolism and signalling processes during viral infection. We report a methodology to analyse mitochondrial properties at the single-organelle level during viral infection using a recombinant adenovirus coding for a mitochondrial tracer protein for tagging and detection by multispectral flow cytometry. Resolution at the level of tagged individual mitochondria revealed changes in mitochondrial size, membrane potential and displayed a fragile phenotype during viral infection of cells. Thus, single-organelle and multi-parameter resolution allows to explore altered energy metabolism and antiviral defence by tagged mitochondria selectively in virus-infected cells and will be instrumental to identify viral immune escape and to develop and monitor novel mitochondrial-targeted therapies.
Mass spectra alignment using virtual lock-masses
Authors: Brochu Francis , Plante Pier-Luc , Drouin Alexandre , Gagnon Dominic , Richard Dave , Durocher Francine , Diorio Caroline , Marchand Mario , Corbeil Jacques , Laviolette François 
Published: June 2019

AbstractMass spectrometry is a valued method to evaluate the metabolomics content of a biological sample. The recent advent of rapid ionization technologies such as Laser Diode Thermal Desorption (LDTD) and Direct Analysis in Real Time (DART) has rendered high-throughput mass spectrometry possible. It is used for large-scale comparative analysis of populations of samples. In practice, many factors resulting from the environment, the protocol, and even the instrument itself, can lead to minor discrepancies between spectra, rendering automated comparative analysis difficult. In this work, a sequence/pipeline of algorithms to correct variations between spectra is proposed. The algorithms correct multiple spectra by identifying peaks that are common to all and, from those, computes a spectrum-specific correction. We show that these algorithms increase comparability within large datasets of spectra, facilitating comparative analysis, such as machine learning.
Auditory Steady State Response; nature and utility as a translational science tool
Authors: Kozono Naoki , Honda Sokichi , Tada Mariko , Kirihara Kenji , Zhao Zhilei , Jinde Seiichiro , Uka Takanori , Yamada Hiroshi , Matsumoto Mitsuyuki , Kasai Kiyoto , Mihara Takuma 
Published: June 2019

AbstractThe auditory steady-state response (ASSR) has been used to detect auditory processing deficits in patients with psychiatric disorders. However, the methodology of ASSR recording from the brain surface has not been standardized in preclinical studies, limiting its use as a translational biomarker. The sites of maximal ASSR in humans are the vertex and/or middle frontal area, although it has been suggested that the auditory cortex is the source of the ASSR. We constructed and validated novel methods for ASSR recording using a switchable pedestal which allows ASSR recording alternatively from temporal or parietal cortex with a wide range of frequencies in freely moving rats. We further evaluated ASSR as a translational tool by assessing the effect of ketamine. The ASSR measured at parietal cortex did not show clear event-related spectral perturbation (ERSP) or inter-trial coherence (ITC) in any frequency bands or a change with ketamine. In contrast, the ASSR at temporal cortex showed clear ERSP and ITC where 40 Hz was maximal in both gamma-band frequencies. Ketamine exerted a biphasic effect in ERSP at gamma bands. These findings suggest that temporal cortex recording with a wide frequency range is a robust methodology to detect ASSR, potentially enabling application as a translational biomarker in psychiatric and developmental disorders.
Toll-like Receptor-4 Activation Boosts the Immunosuppressive Properties of Tumor Cells-derived Exosomes
Authors: Domenis Rossana , Cifù Adriana , Marinò Daniele , Fabris Martina , Niazi Kayvan R. , Soon-Shiong Patrick , Curcio Francesco 
Published: June 2019

AbstractThe biology of tumor-derived exosomes (TEX) is only partially understood and much remains to be studied in order to define the effect that the tumor microenvironment or the activation of tumor cells exerts on their composition and functions. Increased expression and activity of toll-like receptor 4 (TLR4) in chronic infectious and inflammatory conditions is related with cancer progression: its activation induces an inflammatory signaling that increases the tumorigenic potential of cancer cells promoting their immune evasion. We investigated the immune modulatory properties of TEX released upon cell TLR4 activation, and we found that, although differences were observed depending on the type of the tumor, the treatment influences TEX composition and boosts their immunosuppressive ability. Our results suggest that the activation of TLR4 supports tumor progression by stimulating the release of more effective immunosuppressive exosomes, which allow tumor cells to escape immune surveillance and probably even play a role in the metastatic process.