bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of the novel role of butyrate as AhR ligand in human intestinal epithelial cells
Authors: Marinelli Ludovica , Martin-Gallausiaux Camille , Bourhis Jean-Marie , Béguet-Crespel Fabienne , Blottière Hervé M. , Lapaque Nicolas 
Published: January 2019

AbstractThe ligand activated transcription factor, aryl hydrocarbon receptor (AhR) emerged as a critical regulator of immune and metabolic processes in the gastrointestinal tract. In the gut, a main source of AhR ligands derives from commensal bacteria. However, many of the reported microbiota-derived ligands have been restricted to indolyl metabolites. Here, by screening commensal bacteria supernatants on an AhR reporter system expressed in human intestinal epithelial cell line (IEC), we found that the short chain fatty acid (SCFA) butyrate induced AhR activity and the transcription of AhR-dependent genes in IECs. We showed that AhR ligand antagonists reduced the effects of butyrate on IEC suggesting that butyrate could act as a ligand of AhR, which was supported by the nuclear translocation of AhR induced by butyrate and in silico structural modelling. In conclusion, our findings suggest that (i) butyrate activates AhR pathway and AhR-dependent genes in human intestinal epithelial cell-lines (ii) butyrate is a potential ligand for AhR which is an original mechanism of gene regulation by SCFA.
Mammalian plasma fetuin-B is a selective inhibitor of ovastacin and meprin metalloproteinases
Authors: Karmilin Konstantin , Schmitz Carlo , Kuske Michael , Körschgen Hagen , Olf Mario , Meyer Katharina , Hildebrand André , Felten Matthias , Fridrich Sven , Yiallouros Irene , Becker-Pauly Christoph , Weiskirchen Ralf , Jahnen-Dechent Willi , Floehr Julia , Stöcker Walter 
Published: January 2019

AbstractVertebrate fetuins are multi-domain plasma-proteins of the cystatin-superfamily. Human fetuin-A is also known as AHSG, α2-Heremans-Schmid-glycoprotein. Gene-knockout in mice identified fetuin-A as essential for calcified-matrix-metabolism and bone-mineralization. Fetuin-B deficient mice, on the other hand, are female infertile due to zona pellucida ‘hardening’ caused by the metalloproteinase ovastacin in unfertilized oocytes. In wildtype mice fetuin-B inhibits the activity of ovastacin thus maintaining oocytes fertilizable. Here we asked, if fetuins affect further proteases as might be expected from their evolutionary relation to single-domain-cystatins, known as proteinase-inhibitors. We show that fetuin-A is not an inhibitor of any tested protease. In stark contrast, the closely related fetuin-B selectively inhibits astacin-metalloproteinases such as meprins and ovastacin, but not astacins of the tolloid-subfamily, nor any other proteinase. The analysis of fetuin-B expressed in various mammalian cell types, insect cells, and truncated fish-fetuin expressed in bacteria, showed that the cystatin-like domains alone are necessary and sufficient for inhibition. This report highlights fetuin-B as a specific antagonist of ovastacin and meprin-metalloproteinases. Control of ovastacin was shown to be indispensable for female fertility. Meprin inhibition, on the other hand, renders fetuin-B a potential key-player in proteolytic networks controlling angiogenesis, immune-defense, extracellular-matrix-assembly and general cell-signaling, with implications for inflammation, fibrosis, neurodegenerative disorders and cancer.
Adipose fin development and its relation to the evolutionary origins of median fins
Authors: Stewart Thomas A. , Bonilla Melvin M. , Ho Robert K. , Hale Melina E. 
Published: January 2019

AbstractThe dorsal, anal and caudal fins of vertebrates are proposed to have originated by the partitioning and transformation of the continuous median fin fold that is plesiomorphic to chordates. Evaluating this hypothesis has been challenging, because it is unclear how the median fin fold relates to the adult median fins of vertebrates. To understand how new median fins originate, here we study the development and diversity of adipose fins. Phylogenetic mapping shows that in all lineages except Characoidei (Characiformes) adipose fins develop from a domain of the larval median fin fold. To inform how the larva’s median fin fold contributes to the adipose fin, we studyCorydoras aeneus(Siluriformes). As the fin fold reduces around the prospective site of the adipose fin, a fin spine develops in the fold, growing both proximally and distally, and sensory innervation, which appears to originate from the recurrent ramus of the facial nerve and from dorsal rami of the spinal cord, develops in the adipose fin membrane. Collectively, these data show how a plesiomorphic median fin fold can serve as scaffolding for the evolution and development of novel, individuated median fins, consistent with the median fin fold hypothesis.
Dynamics of the gut microbiota in developmental stages of Litopenaeus vannamei reveal its association with body weight
Authors: Fan Jiqiang , Chen Limei , Mai Guoqin , Zhang Haoran , Yang Jinfang , Deng Deng , Ma Yingfei 
Published: January 2019

AbstractIncreasing evidences have revealed a close interaction between the intestinal microbes and host growth performance. The shrimp (Litopenaeus vannamei) gut harbors a diverse microbial community, yet its associations with dietary, body weight and weaning age remain a matter of debate. In this study, we analyzed the effects of different dietary (fishmeal group (NC), krill meal group (KM)) and different growth stages (age from 42 day-old to 98 day-old) of the shrimp on the intestinal microbiota. High throughput sequencing of the 16S rRNA genes of shrimp intestinal microbes determined the novelty of bacteria in the shrimp gut microbiota and a core of 58 Operation Taxonomic Units (OTUs) was present among the shrimp gut samples. Analysis results indicated that the development of the shrimp gut microbiota is a dynamic process with three stages across the age according to the gut microbiota compositions. Furthermore, the dietary of KM group did not significantly change the intestinal microbiota of the shrimps compared with NC group. Intriguingly, compared to NC group, we observed in KM group that a fluctuation of the shrimp gut microbiota coincided with the shrimp body weight gain between weeks 6–7. Six OTUs associated with the microbiota change in KM group were identified. This finding strongly suggests that the shrimp gut microbiota may be correlated with the shrimp body weight likely by influencing nutrient uptake in the gut. The results obtained from this study potentially will be guidelines for manipulation to provide novel shrimp feed management approaches.
Organic-Inorganic Solid-State Hybridization with High-Strength and Anti-Hydrolysis Interface
Authors: Yang Tilo H. , Kao C. Robert , Shigetou Akitsu 
Published: January 2019

AbstractOrganic-inorganic material hybridization at the solid-state level is indispensable for the integration of IoT applications, but still remains a challenging issue. Existing bonding strategies in the field of electronic packaging tend to employ vacuum or ultrahigh temperature; however, these can cause process complications and material deterioration. Here we report an easy-to-tune method to achieve hybrid bonding at the solid-state level and under the ambient atmosphere. Vacuum-ultraviolet (VUV)-induced reorganization with ethanol was used to develop hydroxyl-carrying alkyl chains through coordinatively-bonded carboxylate onto aluminum, whereas numerous hydroxyl-carrying alkyls were created on polyimide. The triggering of dehydration through these hydroxyls by merely heating at 150 °C for a few minutes produced robust organic-inorganic reticulated complexes within the aluminum/polyimide interface. The as-bonded aluminum/polyimide interface possessed an superior fracture energy of (2.40 ± 0.36) × 103 (J/m2) compared with aluminum and polyimide matrices themselves, which was mainly attributed to crack deflection due to the nano-grains of inorganic-organic reticulated complexes. The interfacial adhesion was successfully kept after humidity test, which was contributed by those anti-hydrolytic carboxylates. To the best of our knowledge, for the first time organic-inorganic bonding at the solid-state level was achieved using the ethanol-assisted VUV (E-VUV) process, a strategy which should be applicable to a diversity of plastics and metals with native oxides.
Ionization injection of highly-charged copper ions for laser driven acceleration from ultra-thin foils
Authors: Li Jun , Arefiev Alexey V. , Bulanov Stepan S. , Kawahito Daiki , Bailly-Grandvaux Mathieu , Petrov George M. , McGuffey Christopher , Beg Farhat N. 
Published: January 2019

AbstractLaser-driven ion acceleration is often analyzed assuming that ionization reaches a steady state early in the interaction of the laser pulse with the target. This assumption breaks down for materials of high atomic number for which the ionization occurs concurrently with the acceleration process. Using particle-in-cell simulations, we have examined acceleration and simultaneous field ionization of copper ions in ultra-thin targets (20–150 nm thick) irradiated by a laser pulse with intensity 1 × 1021 W/cm2. At this intensity, the laser pulse drives strong electric fields at the rear side of the target that can ionize Cu to charge states with valence L-shell or full K-shell. The highly-charged ions are produced only in a very localized region due to a significant gap between the M- and L-shells’ ionization potentials and can be accelerated by strong, forward-directed sections of the field. Such an “ionization injection” leads to well-pronounced bunches of energetic, highly-charged ions. We also find that for the thinnest target (20 nm) a push by the laser further increases the ion energy gain. Thus, the field ionization, concurrent with the acceleration, offers a promising mechanism for the production of energetic, high-charge ion bunches.
Neutron visualization of inhomogeneous buried interfaces in thin films
Authors: Sakurai Kenji , Jiang Jinxing , Mizusawa Mari , Ito Takayoshi , Akutsu Kazuhiro , Miyata Noboru 
Published: January 2019

AbstractWhen designing some functions in thin film systems, one of the key concepts is the structure of the constituent layers and interfaces. In an actual system, the layers and interfaces are often inhomogeneous in different scales, from hundreds of microns to several nanometers, causing differences in properties, despite very similar average structures. In this case, the choice of the observation point is critical to clarify the problem. Another critical aspect is the identification of these points by surveying the entire inhomogeneous thin film system. This article presents a description of a novel promising solution that is suitable for nondestructive visualization of inhomogeneous buried layers and interfaces in thin films. Such observations have been impossible until now. In this investigation, a unique extension of neutron reflectometry is proposed. While conventional neutron reflectivity just gives average depth-profiling of the scattering length density of layered thin films, the present method provides full picture of the inhomogeneity. In general, achieving a high spatial-resolving power for neutron scattering is not straightforward because the neutron counts become fairly limited at the sample or the detector position when the beam size is reduced. As a result, XY scanning of a sample with a small neutron beam is fairly difficult because of the required long measurement time. To address these issues, new concepts have been introduced for neutron reflectivity. The proposed method uses a wide beam instead of reducing the beam size. In addition, it measures the projection reflection profile instead of the total integrated intensity. These profiles are collected at a set of different in-plane angles. Similar to computed tomography, it is possible to obtain the specimen’s two-dimensional (2D) neutron reflectivity distribution as one image. Because the spatial resolution is limited by the detection method, a Hadamard coded mask is employed to measure the reflection projection with only 50% loss of the primary neutron intensity. When the time-of-flight (ToF) mode is used for the neutron experiment, one can obtain many images as a function of ToF, i.e., the wavevector transfer. Such series of images can be displayed as a video. This indicates that the neutron reflectivity profiles of local points can be retrieved from the above video images. This paper presents the first report on the development of neutron reflectivity with imaging capability, and the analysis of local points in inhomogeneous layered thin-films without utilizing a small neutron beam. In the present work, the feasibility of the proposed method with approximately 1 mm spatial resolution was examined. In addition, further improvements of the approach are discussed. It is anticipated that this technique will facilitate new opportunities in the study of buried function interfaces.
The antiquity of Nullarbor speleothems and implications for karst palaeoclimate archives
Authors: Woodhead Jon D. , Sniderman J. M. Kale , Hellstrom John , Drysdale Russell N. , Maas Roland , White Nicholas , White Susan , Devine Paul 
Published: January 2019

AbstractSpeleothems represent important archives of terrestrial climate variation that host a variety of proxy signals and are also highly amenable to radiometric age determination. Although speleothems have been forming on Earth for at least 400 million years, most studies rely upon the U-Th chronometer which extends only to the mid Pleistocene, leaving important questions over their longer-term preservation potential. To date, older records, exploiting the advantages of the U-Pb chronometer, remain fragmentary ‘snapshots in time’. Here we demonstrate the viability of speleothems as deep time climate archives by showing that a vast system of shallow caves beneath the arid Nullarbor plain of southern Australia, the world’s largest exposed karst terrain, formed largely within the Pliocene epoch, with a median age of 4.2 Ma, and that, in these caves, even the most delicate formations date from this time. The long-term preservation of regional-scale cave networks such as this demonstrates that abundant speleothem archives do survive to permit the reconstruction of climates and environments for much older parts of Earth history than the ~600 ka period to which most previous studies have been limited.
Comparison between dopaminergic and non-dopaminergic neurons in the VTA following chronic nicotine exposure during pregnancy
Authors: Keller Renee F. , Kazemi Tina , Dragomir Andrei , Akay Yasemin M. , Akay Metin 
Published: January 2019

AbstractExposure to nicotine during pregnancy through maternal smoking or nicotine replacement therapy is associated with adverse birth outcomes as well as several cognitive and neurobehavioral deficits. Several studies have shown that nicotine produces long-lasting effects on gene expression within many brain regions, including the ventral tegmental area (VTA), which is the origin of dopaminergic neurons and the dopamine reward pathway. Using a well-established rat model for perinatal nicotine exposure, we sought to investigate altered biological pathways using mRNA and miRNA expression profiles of dopaminergic (DA) and non-dopaminergic (non-DA) neurons in this highly-valuable area. Putative miRNA-gene target interactions were assessed as well as miRNA-pathway interactions. Our results indicate that extracellular matrix (ECM) receptor interactions were significantly altered in DA and non-DA neurons due to chronic nicotine exposure during pregnancy. They also show that the PI3K/AKT signaling pathway was enriched in DA neurons with multiple significant miRNA-gene targets, but the same changes were not seen in non-DA neurons. We speculate that nicotine exposure during pregnancy could differentially affect the gene expression of DA and non-DA neurons in the VTA.
Phosphatidylinositol 4-kinase IIIβ (PI4KB) forms highly flexible heterocomplexes that include ACBD3, 14-3-3, and Rab11 proteins
Authors: Chalupska Dominika , Różycki Bartosz , Humpolickova Jana , Faltova Lenka , Klima Martin , Boura Evzen 
Published: January 2019

AbstractPhosphatidylinositol 4-kinase IIIβ (PI4KB) is a key enzyme of the Golgi system because it produces its lipid hallmark - the phosphatidylinositol 4-phosphate (PI4P). It is recruited to Golgi by the Golgi resident ACBD3 protein, regulated by 14-3-3 proteins and it also serves as an adaptor because it recruits the small GTPase Rab11. Here, we analyzed the protein complexes formed by PI4KB in vitro using small angle x-ray scattering (SAXS) and we discovered that these protein complexes are highly flexible. The 14-3-3:PI4KB:Rab11 protein complex has 2:1:1 stoichiometry and its different conformations are rather compact, however, the ACBD3:PI4KB protein complex has both, very compact and very extended conformations. Furthermore, in vitro reconstitution revealed that the membrane is necessary for the formation of ACBD3:PI4KB:Rab11 protein complex at physiological (nanomolar) concentrations.
Physical plasma-treated saline promotes an immunogenic phenotype in CT26 colon cancer cells in vitro and in vivo
Authors: Freund Eric , Liedtke Kim Rouven , van der Linde Julia , Metelmann Hans-Robert , Heidecke Claus-Dieter , Partecke Lars-Ivo , Bekeschus Sander 
Published: January 2019

AbstractMetastatic colorectal cancer is the fourth most common cause of cancer death. Current options in palliation such as hyperthermic intraperitoneal chemotherapy (HIPEC) present severe side effects. Recent research efforts suggested the therapeutic use of oxidant-enriched liquid using cold physical plasma. To investigate a clinically accepted treatment regimen, we assessed the antitumor capacity of plasma-treated saline solution. In response to such liquid, CT26 murine colon cancer cells were readily oxidized and showed cell growth with subsequent apoptosis, cell cycle arrest, and upregulation of immunogenic cell death (ICD) markersin vitro. This was accompanied by marked morphological changes with re-arrangement of actin fibers and reduced motility. Induction of an epithelial-to-mesenchymal transition phenotype was not observed. Key results were confirmed in MC38 colon and PDA6606 pancreatic cancer cells. Compared to plasma-treated saline, hydrogen peroxide was inferiorly toxic in 3D tumor spheroids but of similar efficacy in 2D models.In vivo, plasma-treated saline decreased tumor burden in Balb/C mice. This was concomitant with elevated numbers of intratumoral macrophages and increased T cell activation following incubation with CT26 cellsex vivo. Being a potential adjuvant for HIPEC therapy, our results suggest oxidizing saline solutions to inactivate colon cancer cells while potentially stimulating antitumor immune responses.
Acetaldehyde forms covalent GG intrastrand crosslinks in DNA
Authors: Sonohara Yuina , Yamamoto Junpei , Tohashi Kosuke , Takatsuka Reine , Matsuda Tomonari , Iwai Shigenori , Kuraoka Isao 
Published: January 2019

AbstractCarcinogens often generate mutable DNA lesions that contribute to cancer and aging. However, the chemical structure of tumorigenic DNA lesions formed by acetaldehyde remains unknown, although it has long been considered an environmental mutagen in alcohol, tobacco, and food. Here, we identify an aldehyde-induced DNA lesion, forming an intrastrand crosslink between adjacent guanine bases, but not in single guanine bases or in other combinations of nucleotides. The GG intrastrand crosslink exists in equilibrium in the presence of aldehyde, and therefore it has not been detected or analyzed in the previous investigations. The newly identified GG intrastrand crosslinks might explain the toxicity and mutagenicity of acetaldehyde in DNA metabolism.
Label-free classification of neurons and glia in neural stem cell cultures using a hyperspectral imaging microscopy combined with machine learning
Authors: Ogi Hiroshi , Moriwaki Sanzo , Kokubo Masahiko , Hikida Yuichiro , Itoh Kyoko 
Published: January 2019

AbstractDue to a growing demand for a viable label-free observation method in the biomedical field, many techniques, such as quantitative phase imaging and Raman spectroscopy, have been studied, and a complementary approach, hyperspectral imaging, has also been introduced. We developed a high-speed hyperspectral imaging microscopy imaging method with commercially available apparatus, employing a liquid crystal tunable bandpass filter combined with a pixel-wise machine learning classification. Next, we evaluated the feasibility of the application of this method for stem cell research utilizing neural stem cells. Employing this microscopy method, with a 562 × 562 μm2 field of view, 2048 × 2048 pixel resolution images containing 63 wavelength pixel-wise spectra could be obtained in 30 seconds. The neural stem cells were differentiated into neurons and astroglia (glia), and a four-class cell classification evaluation (including neuronal cell body, glial cell body, process and extracellular region) was conducted under co-cultured conditions. As a result, an average of 88% of the objects of interest were correctly classified, with an average precision of 94%, and more than 99% of the extracellular pixels were correctly segregated. These results indicated that the proposed hyperspectral imaging microscopy is feasible as a label-free observation method for stem cell research.
Tumor resection ameliorates tumor-induced suppression of neuroinflammatory and behavioral responses to an immune challenge in a cancer survivor model
Authors: Santos Jessica C. , Bever Savannah R. , Pereira-da-Silva Gabriela , Pyter Leah M. 
Published: January 2019

AbstractBreast cancer survivors display altered inflammatory responses to immune challenges relative to cancer-naive controls likely due to previous cancer treatments, stress associated with cancer, and/or tumor physiology. Proper inflammatory responses are necessary for adaptive sickness behaviors (e.g., fatigue, anorexia, and fever) and neuroinflammatory pathways are also implicated in mental health disturbances (e.g., cognitive impairment, depression) suffered by cancer patients and survivors. Rodent cancer models indicate that tumors are sufficient to exacerbate neuroinflammatory responses after an immune challenge, however primary tumors are not usually present in cancer survivors, and the behavioral consequences of these brain changes remain understudied. Therefore, we tested the extent to which mammary tumor resection attenuates tumor-induced neuroinflammation and sickness behavior following an immune challenge (i.p. lipopolysaccharide [LPS] injection) in mice. Tnf-α, Il-1β, and Il-6 mRNA decreased in multiple brain regions of LPS-treated tumor-bearing mice relative to LPS-treated controls; tumor resection attenuated these effects in some cases (but not Tnf-α). Tumors also attenuated sickness behaviors (hypothermia and lethargy) compared to LPS-treated controls. Tumor resection reversed these behavioral consequences, although basal body temperature remained elevated, comparable to tumor-bearing mice. Thus, tumors significantly modulate neuroinflammatory pathways with functional consequences and tumor resection mitigates most, but not all, of these changes.