bluuebunny/crossref_metadata_2025_split huggingface dataset:
Two-dimensional multibit optoelectronic memory with broadband spectrum distinction
Authors: Xiang Du , Liu Tao , Xu Jilian , Tan Jun Y. , Hu Zehua , Lei Bo , Zheng Yue , Wu Jing , Neto A. H. Castro , Liu Lei , Chen Wei 
Published: July 2018

AbstractOptoelectronic memory plays a vital role in modern semiconductor industry. The fast emerging requirements for device miniaturization and structural flexibility have diverted research interest to two-dimensional thin layered materials. Here, we report a multibit nonvolatile optoelectronic memory based on a heterostructure of monolayer tungsten diselenide and few-layer hexagonal boron nitride. The tungsten diselenide/boron nitride memory exhibits a memory switching ratio approximately 1.1 × 106, which ensures over 128 (7 bit) distinct storage states. The memory demonstrates robustness with retention time over 4.5 × 104 s. Moreover, the ability of broadband spectrum distinction enables its application in filter-free color image sensor. This concept is further validated through the realization of integrated tungsten diselenide/boron nitride pixel matrix which captured a specific image recording the three primary colors (red, green, and blue). The heterostructure architecture is also applicable to other two-dimensional materials, which is confirmed by the realization of black phosphorus/boron nitride optoelectronic memory.
How do our cells build their protein interactome?
Authors: Coulombe Benoit , Cloutier Philippe , Gauthier Marie-Soleil 
Published: July 2018

AbstractChaperones are cellular factors that help in the folding of newly synthesized polypeptides (or clients) and, in some cases, ensure their integration within larger complexes. They often require non-client proteins, or co-chaperones, to help drive specificity to particular target polypeptides or facilitate the nucleotide hydrolysis cycle of some chaperones. The latest findings on the characterization of the PAQosome (Particle for Arrangement of Quaternary structure; formerly known as R2TP/PFDL complex) published recently in Nature Communications help to explain how this particular co-chaperone plays a central role in organizing our proteome into protein complexes and networks. The exploitation by the cell of alternative PAQosomes formed through the differential integration of homologous subunits, in conjunction with the use of several adaptors (specificity factors), provide the conceptual basis for interaction of multiple clients in a structure that is favorable to their simultaneous binding en route to protein complex and network assembly/maturation.
miRNAs regulate acute transcriptional changes in broiler embryos in response to modification of incubation temperature
Authors: Naraballobh Watcharapong , Trakooljul Nares , Murani Eduard , Krischek Carsten , Janisch Sabine , Wicke Michael , Ponsuksili Siriluck , Wimmers Klaus 
Published: July 2018

AbstractMicroRNAs are post-transcriptional regulators that play critical roles in diverse biological processes. We hypothesize that miRNAs may be involved in regulating transcriptome responses to changes in embryonic incubation temperature in chickens affecting differentiation and proliferation processes during tissue development. Therefore, we conducted comparative transcriptome profiling of miRNAs to examine altered expression in breast and hind muscle of embryos and day 35 chickens experiencing high (38.8 °C), control (37.8 °C), or low (36.8 °C) embryonic incubation temperature during embryonic day (ED) 7–10 or ED10–13. The results revealed differential expression of miRNAs due to modification of embryonic incubation temperature in a muscle type-specific and a developmental stage-specific manner. The immediate effects of thermal change observed in embryos were substantial compared to the subtle long-term effects in chickens at day 35 post-hatch. Upregulation of miR-133 in breast muscle and downregulation of miR-199a-5p, miR-1915, and miR-638 in hind muscle post ED7–10 high-temperature treatment are functionally associated with myogenesis and body size. ED10–13 low-temperature treatment led to downregulation of let-7, miR-93, and miR-130c that are related to proliferation and differentiation. The results provide insight into the dynamics of miRNA expression at variable embryonic incubation temperatures during developmental processes and indicate a major regulatory role of miRNAs in acute responses to modified environmental conditions that affect remodelling of cells and tissues.
Linking mixing processes and climate variability to the heat content distribution of the Eastern Mediterranean abyss
Authors: Artale Vincenzo , Falcini Federico , Marullo Salvatore , Bensi Manuel , Kokoszka Florian , Iudicone Daniele , Rubino Angelo 
Published: July 2018

AbstractThe heat contained in the ocean (OHC) dominates the Earth’s energy budget and hence represents a fundamental parameter for understanding climate changes. However, paucity of observational data hampers our knowledge on OHC variability, particularly in abyssal areas. Here, we analyze water characteristics, observed during the last three decades in the abyssal Ionian Sea (Eastern Mediterranean), where two competing convective sources of bottom water exist. We find a heat storage of ~1.6 W/m2 – twice that assessed globally in the same period – exceptionally well-spread throughout the local abyssal layers. Such an OHC accumulation stems from progressive warming and salinification of the Eastern Mediterranean, producing warmer near-bottom waters. We analyze a new process that involves convectively-generated waters reaching the abyss as well as the triggering of a diapycnal mixing due to rough bathymetry, which brings to a warming and thickening of the bottom layer, also influencing water-column potential vorticity. This may affect the prevailing circulation, altering the local cyclonic/anticyclonic long-term variability and hence precondition future water-masses formation and the redistribution of heat along the entire water-column.
Cotton rat lung transcriptome reveals host immune response to Respiratory Syncytial Virus infection
Authors: Rajagopala Seesandra V. , Singh Harinder , Patel Mira C. , Wang Wei , Tan Yi , Shilts Meghan H. , Hartert Tina V. , Boukhvalova Marina S. , Blanco Jorge C. G. , Das Suman R. 
Published: July 2018

AbstractAcute respiratory infection (ARI) with respiratory syncytial virus (RSV) is the most common cause of both hospitalizations and mortality in young infants worldwide. Repeat infections with RSV are common throughout life in both pediatric and elderly populations. Thus far, cotton rats (Sigmodon hispidus) are found to be the best animal model to study RSV infection. However, the lack of a cotton rat reference genome limits genome-wide host gene expression studies. We constructed the first lung tissue de novo transcriptome for the cotton rat. Cotton rat lung tissue transcripts were assigned to 12,211 unique UniProt genes, which were then utilized to profile the host immune response after RSV infection. Differential expression analysis showed up-regulation of host genes involved in cellular functions including defense responses to viral infection and immune system processes. A number of transcripts were downregulated during the later stage of infection. A set of transcripts unique to RSV-infected cotton rats was identified. To validate RNA-Seq data of three such transcripts (TR453762, TR529629, and TR5333), their expression was confirmed by quantitative real-time polymerase chain reaction.
Formation of unique nanocrystalline Cu-In-Se bulk pn homojunctions for opto-electronic devices
Authors: Menezes Shalini , Samantilleke Anura 
Published: July 2018

AbstractSemiconductor pn junctions, integrated in optoelectronic devices require high quality crystals, made by expensive, technically difficult processes. Bulk heterojunction (BHJ) structures offer practical alternatives to circumvent the cost, flexibility and scale-up challenges of crystalline planar pn junctions. Fabrication methods for the current organic or inorganic BHJ structures invariably create interface mismatch and low doping issues. To overcome such issues, we devised an innovative approach, founded on novel inorganic material system that ensued from single-step electrodeposited copper-indium-selenide compounds. Surface analytical microscopies and spectroscopies reveal unusual phenomena, electro-optical properties and quantum effects. They support the formation of highly-ordered, sharp, abrupt 3-dimensional nanoscale pn BHJs that facilitate efficient charge carrier separation and transport, and essentially perform the same functions as crystalline planar pn junctions. This approach offers a low-cost processing platform to create nanocrystalline films, with the attributes necessary for efficient BHJ operation. It allows roll-to-roll processing of flexible devices in simple thin-film form factor.
Histone deacetylase 8 protects human proximal tubular epithelial cells from hypoxia-mimetic cobalt- and hypoxia/reoxygenation-induced mitochondrial fission and cytotoxicity
Authors: Ha Soon-Duck , Solomon Ori , Akbari Masoud , Sener Alp , Kim Sung Ouk 
Published: July 2018

AbstractCell death by hypoxia followed by reoxygenation (H/R) is responsible for tissue injury in multiple pathological conditions. Recent studies found that epigenetic reprogramming mediated by histone deacetylases (HDACs) is implicated in H/R-induced cell death. However, among 18 different isoforms comprising 4 classes (I-IV), the role of each HDAC in cell death is largely unknown. This study examined the role of HDAC8, which is the most distinct isoform of class I, in the hypoxia mimetic cobalt- and H/R-induced cytotoxicity of human proximal tubular HK-2 cells. Using the HDAC8-specific activator TM-2-51 (TM) and inhibitor PCI34051, we found that HDAC8 played a protective role in cytotoxicity. TM or overexpression of wild-type HDAC8, but not a deacetylase-defective HDAC8 mutant, prevented mitochondrial fission, loss of mitochondrial transmembrane potential and release of cytochrome C into the cytoplasm. TM suppressed expression of dynamin-related protein 1 (DRP1) which is a key factor required for mitochondrial fission. Suppression of DRP1 by HDAC8 was likely mediated by decreasing the level of acetylated histone H3 lysine 27 (a hallmark of active promoters) at the DRP1 promoter. Collectively, this study shows that HDAC8 inhibits cytotoxicity induced by cobalt and H/R, in part, through suppressing DRP1 expression and mitochondrial fission.
Greater Microbial Translocation and Vulnerability to Metabolic Disease in Healthy Aged Female Monkeys
Authors: Wilson Quentin N. , Wells Magan , Davis Ashley T. , Sherrill Christina , Tsilimigras Matthew C. B. , Jones Roshonda B. , Fodor Anthony A. , Kavanagh Kylie 
Published: July 2018

AbstractMonkeys demonstrate gastrointestinal barrier dysfunction (leaky gut) as evidenced by higher biomarkers of microbial translocation (MT) and inflammation with ageing despite equivalent health status, and lifelong diet and environmental conditions. We evaluated colonic structural, microbiomic and functional changes in old female vervet monkeys (Chlorocebus aethiops sabeus) and how age-related leaky gut alters responses to Western diet. We additionally assessed serum bovine immunoglobulin therapy to lower MT burden. MT was increased in old monkeys despite comparable histological appearance of the ascending colon. Microbiome profiles from 16S sequencing did not show large differences by age grouping, but there was evidence for higher mucosal bacterial loads using qPCR. Innate immune responses were increased in old monkeys consistent with higher MT burdens. Western diet challenge led to elevations in glycemic and hepatic biochemistry values only in old monkeys, and immunoglobulin therapy was not effective in reducing MT markers or improving metabolic health. We interpret these findings to suggest that ageing may lead to lower control over colonization at the mucosal surface, and reduced clearance of pathogens resulting in MT and inflammation. Leaky gut in ageing, which is not readily rescued by innate immune support with immunoglobulin, primes the liver for negative consequences of high fat, high sugar diets.
Immunophenotyping and transcriptional profiling of in vitro cultured human adipose tissue derived stem cells
Authors: Mieczkowska Alina , Schumacher Adriana , Filipowicz Natalia , Wardowska Anna , Zieliński Maciej , Madanecki Piotr , Nowicka Ewa , Langa Paulina , Deptuła Milena , Zieliński Jacek , Kondej Karolina , Renkielska Alicja , Buckley Patrick G. , Crossman David K. , Crowley Michael R. , Czupryn Artur , Mucha Piotr , Sachadyn Paweł , Janus Łukasz , Skowron Piotr , Rodziewicz-Motowidło Sylwia , Cichorek Mirosława , Pikuła Michał , Piotrowski Arkadiusz 
Published: July 2018

AbstractAdipose-derived stem cells (ASCs) have become an important research model in regenerative medicine. However, there are controversies regarding the impact of prolonged cell culture on the ASCs phenotype and their differentiation potential. Hence, we studied 10 clinical ASCs replicates from plastic and oncological surgery patients, in six-passage FBS supplemented cultures. We quantified basic mesenchymal cell surface marker transcripts and the encoded proteins after each passage. In parallel, we investigated the differentiation potential of ASCs into chondrocytes, osteocytes and adipocytes. We further determined the effects of FBS supplementation and subsequent deprivation on the whole transcriptome by comprehensive mRNA and miRNA sequencing. Our results show that ASCs maintain differentiation potential and consistent profile of key mesenchymal markers, with apparent expression of distinct isoforms, in long-term cultures. No significant differences were observed between plastic and oncological surgery cohorts. ASCs in FBS supplemented primary cultures are almost committed to mesenchymal lineages as they express key epithelial-mesenchymal transition genes including early mesenchymal markers. Furthermore, combined mRNA/miRNA expression profiling strongly supports a modulatory role for the miR-30 family in the commitment process to mesenchymal lineages. Finally, we propose improvements to existing qPCR based assays that address alternative isoform expression of mesenchymal markers.
Analysis of naturally occurring mutations in the human uptake transporter NaCT important for bone and brain development and energy metabolism
Authors: Selch Stefan , Chafai Anja , Sticht Heinrich , Birkenfeld Andreas L. , Fromm Martin F. , König Jörg 
Published: July 2018

AbstractThe human uptake transporter NaCT is important for human brain development, brain function and energy metabolism and mediates the uptake of citrate and other intermediates of the tricarboxylic acid cycle from blood into neurons and hepatocytes. Mutations in the SLC13A5 gene encoding NaCT are associated with epileptic encephalopathy. To gain more insights into the transport mechanisms we analyzed the functional consequences of mutations in the SLC13A5 gene on NaCT-mediated transport function. Using HEK293 cells expressing wild-type and eight mutated NaCT proteins, we investigated the mRNA and protein amount as well as the protein localization of all NaCT variants. Furthermore, the impact on NaCT-mediated citrate uptake was measured. In addition, a structural model of the transport pore was generated to rationalize the consequences of the mutations on a structural basis. We demonstrated that all proteins were synthesized with an identical molecular weight as the wild-type transporter but several mutations (NaCTp.G219R, −p.G219E, −p.T227M, −p.L420P and −p.L488P) lead to a complete loss of NaCT-mediated citrate transport. This loss of transport activity can be explained on the basis of the developed structural model. This model may help in the further elucidation of the transport mechanism of this important uptake transporter.
Endoscopic Transplantation of Mesenchymal Stem Cell Sheets in Experimental Colitis in Rats
Authors: Pak Sehyung , Hwang Sung Wook , Shim In Kyong , Bae Sang Mun , Ryu Yeon- Mi , Kim Han-Byul , Do Eun-ju , Son Hye-Nam , Choi Eun-ji , Park Sun-ha , Kim Sang-Yeob , Park Sang Hyoung , Ye Byong Duk , Yang Suk-Kyun , Kanai Nobuo , Maeda Masanori , Okano Teruo , Yang Dong-Hoon , Byeon Jeong-Sik , Myung Seung-Jae 
Published: July 2018

AbstractOwing to the recent progress in regenerative medicine technology, clinical trials that harnessed the regeneration and immune modulation potentiality of stem cells for treating IBD have shown promising results. We investigated the feasibility and utility of intraluminal endoscopic transplantation of rat MSC sheets in murine models of experimental colitis for targeted delivery of stem cells to lesions. We isolated adipose-derived mesenchymal stem cells (AD-MSC) and bone marrow-derived mesenchymal stem cells (BM-MSC) from EGFP-transgenic rats and fabricated the cells in sheet forms using temperature-responsive culture dishes. The MSC sheets were endoscopically transplanted to the inflamed area in electrocoagulation and DNBS colitis model. The effect of the transplantation was verified using endoscopic scoring and histological analysis. In the electrocoagulation model, the AD-MSC group showed significantly decreased ulcer size in the transplanted regions. In the DNBS colitis model, the AD-MSC group showed decreased inflammation and colitis in the transplanted regions. Histologic analysis showed that the MSC sheets had successfully attached to the inflamed mucosa in both the electrocoagulation and DNBS colitis model. Our results show that endoscopic transplantation of MSC sheets could be a new effective mode of stem cell therapy for IBD treatment.
Influence of the long-range ordering of gold-coated Si nanowires on SERS
Authors: Cara Eleonora , Mandrile Luisa , Ferrarese Lupi Federico , Giovannozzi Andrea Mario , Dialameh Masoud , Portesi Chiara , Sparnacci Katia , De Leo Natascia , Rossi Andrea Mario , Boarino Luca 
Published: July 2018

AbstractControlling the location and the distribution of hot spots is a crucial aspect in the fabrication of surface-enhanced Raman spectroscopy (SERS) substrates for bio-analytical applications. The choice of a suitable method to tailor the dimensions and the position of plasmonic nanostructures becomes fundamental to provide SERS substrates with significant signal enhancement, homogeneity and reproducibility. In the present work, we studied the influence of the long-range ordering of different flexible gold-coated Si nanowires arrays on the SERS activity. The substrates are made by nanosphere lithography and metal-assisted chemical etching. The degree of order is quantitatively evaluated through the correlation length (ξ) as a function of the nanosphere spin-coating speed. Our findings showed a linear increase of the SERS signal for increasing values of ξ, coherently with a more ordered and dense distribution of hot spots on the surface. The substrate with the largest ξ of 1100 nm showed an enhancement factor of 2.6 · 103 and remarkable homogeneity over square-millimetres area. The variability of the signal across the substrate was also investigated by means of a 2D chemical imaging approach and a standard methodology for its practical calculation is proposed for a coherent comparison among the data reported in literature.
Transcriptional alterations during proliferation and lignification in Phyllostachys nigra cells
Authors: Ogita Shinjiro , Nomura Taiji , Kato Yasuo , Uehara-Yamaguchi Yukiko , Inoue Komaki , Yoshida Takuhiro , Sakurai Tetsuya , Shinozaki Kazuo , Mochida Keiichi 
Published: July 2018

AbstractHighly-lignified culms of bamboo show distinctive anatomical and mechanical properties compared with the culms of other grass species. A cell culture system for Phyllostachys nigra has enabled investigating the alterations in cellular states associated with secondary cell wall formation during its proliferation and lignification in woody bamboos. To reveal transcriptional changes related to lignification in bamboo, we analyzed transcriptome in P. nigra cells treated with the synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D) and the synthetic cytokinin benzylaminopurine (BA) by RNA-seq analysis. We found that some genes putatively involved in cell wall biogenesis and cell division were up-regulated in response to the 2,4-D treatment, and the induction of lignification by the BA treatment was correlated with up-regulation of genes involved in the shikimate pathway. We also found that genes encoding MYB transcription factors (TFs) show correlated expression patterns with those encoding cinnamyl alcohol dehydrogenase (CAD), suggesting that MYB TFs presumably regulate secondary cell wall formation in the bamboo cells. These findings suggest that cytokinin signaling may regulate lignification in P. nigra cells through coordinated transcriptional regulation and metabolic alterations. Our results have also produced a useful resource for better understanding of secondary cell wall formation in bamboo plants.
Effect of Thrombin-Induced MCP-1 and MMP-3 Production Via PAR1 Expression in Murine Intervertebral Discs
Authors: Takayama Yoshihiro , Ando Takashi , Ichikawa Jiro , Haro Hirotaka 
Published: July 2018

AbstractStructural changes in nucleus pulposus cells induce intervertebral disc (IVD) degeneration as a consequence of cytokine generation, biochemical products, and changes in the local environment. We have previously shown that inflammatory cytokines induce murine IVD (mIVD) angiogenesis and macrophage migration. Although the physiological roles of thrombin, a known proinflammatory factor, are documented, its relationship to IVD degeneration remains largely unexplored. Thrombin mediates cellular responses via the activation of protease-activated receptors such as PAR1 which has been studied in numerous cell types, but not extensively in IVD cells. This study was designed to investigate the endogenous expression of thrombin, tissue factor, and PAR1 in cultured coccygeal mIVDs. Thrombin exclusively induced MCP-1 via the MAPK-ERK and PI3K-AKT pathways. MCP-1 produced by mIVDs induced macrophage migration and thrombin treatment increased MMP-3 production to induce mIVD degeneration. These effects of thrombin on mIVDs were abrogated by a PAR1 inhibitor and suggest that thrombin may be a novel factor capable of stimulating cytokine activity implicated in the regulation several aspects of mIVDs. Mechanisms governing mIVDs, which are regulated by thrombin/PAR1 signaling, require elucidation if our understanding of IVD degenerative mechanisms is to advance.
Fields of a Bessel-Bessel light bullet of arbitrary order in an under-dense plasma
Authors: Salamin Yousef I. 
Published: July 2018

AbstractConsiderable theoretical and experimental work has lately been focused on waves localized in time and space. In optics, waves of that nature are often referred to as light bullets. The most fascinating feature of light bullets is their propagation without appreciable distortion by diffraction or dispersion. Here, analytic expressions for the fields of an ultra-short, tightly-focused and arbitrary-order Bessel pulse are derived and discussed. Propagation in an under-dense plasma, responding linearly to the fields of the pulse, is assumed throughout. The derivation stems from wave equations satisfied by the vector and scalar potentials, themselves following from the appropriate Maxwell equations and linked by the Lorentz gauge. It is demonstrated that the fields represent well a pulse of axial extension, L, and waist radius at focus, w0, both of the order of the central wavelength λ0. As an example, to lowest approximation, the pulse of order l = 2 is shown to propagate undistorted for many centimeters, in vacuum as well as in the plasma. As such, the pulse behaves like a “light bullet” and is termed a “Bessel-Bessel bullet of arbitrary order”. The field expressions will help to better understand light bullets and open up avenues for their utility in potential applications.