bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nucleus Morphometry in Cultured Epithelial Cells Correlates with Phenotype
Authors: Khan Ayyad Z. , Utheim Tor P. , Jackson Catherine J. , Reppe Sjur , Lyberg Torstein , Eidet Jon R. 
Published: June 2016

AbstractPhenotype of cultured ocular epithelial transplants has been shown to affect clinical success rates following transplantation to the cornea. The purpose of this study was to evaluate the relationship between cell nucleus morphometry and phenotype in three types of cultured epithelial cells. This study provides knowledge for the development of a non-invasive method of determining the phenotype of cultured epithelium before transplantation. Cultured human conjunctival epithelial cells (HCjE), human epidermal keratinocytes (HEK), and human retinal pigment epithelial cells (HRPE) were analyzed by quantitative immunofluorescence. Assessments of nucleus morphometry and nucleus-to-cytoplasm ratio (N/C ratio) were performed using ImageJ. Spearman’s correlation coefficient was employed for statistical analysis. Levels of the proliferation marker PCNA in HCjE, HEK, and HRPE correlated positively with nuclear area. Nuclear area correlated significantly with levels of the undifferentiated cell marker ABCG2 in HCjE. Bmi1 levels, but not p63αlevels, correlated significantly with nuclear area in HEK. The N/C ratio did not correlate significantly with any of the immunomarkers in HCjE (ABCG2, CK7, and PCNA) and HRPE (PCNA). In HEK, however, the N/C ratio was negatively correlated with levels of the undifferentiated cell marker CK14 and positively correlated with Bmi1 expression. The size of the nuclear area correlated positively with proliferation markers in all three epithelia. Morphometric indicators of phenotype in cultured epithelia can be identified using ImageJ. Conversely, the N/C ratio did not show a uniform relationship with phenotype in HCjE, HEK, or HRPE. N/C ratio therefore, may not be a useful morphometric marker forin vitroassessment of phenotype in these three epithelia.
(Second) Harmonic Disharmony: Nonlinear Microscopy Shines New Light on the Pathology of Atherosclerosis
Authors: Watson Shana R. , Lessner Susan M. 
Published: June 2016

AbstractThere has been increasing interest in second harmonic generation (SHG) imaging approaches for the investigation of atherosclerosis due to the deep penetration and three-dimensional sectioning capabilities of the nonlinear optical microscope. Atherosclerosis involves remodeling or alteration of the collagenous framework in affected vessels. The disease is often characterized by excessive collagen deposition and altered collagen organization. SHG has the capability to accurately characterize collagen structure, which is an essential component in understanding atherosclerotic lesion development and progression. As a structure-based imaging modality, SHG is most impactful in atherosclerosis evaluation in conjunction with other, chemically specific nonlinear optics (NLO) techniques to identify additional components of the lesion. These include the use of coherent anti-Stokes Raman scattering and two-photon excitation fluorescence for studying atherosclerosis burden, and application of stimulated Raman scattering to image cholesterol crystals. However, very few NLO studies have attempted to quantitate differences in control versus atherosclerotic states or to correlate the application to clinical situations. This review highlights the potential of SHG imaging to directly and indirectly describe atherosclerosis as a pathological condition.
Thrombin-Mediated Platelet Activation of Lysed Whole Blood and Platelet-Rich Plasma: A Comparison Between Platelet Activation Markers and Ultrastructural Alterations
Authors: Augustine Tanya N. , van der Spuy Wendy J. , Kaberry Lindsay L. , Shayi Millicent 
Published: June 2016

AbstractPlatelet ultrastructural alterations representing spurious activation have been identified in pathological conditions. A limitation of platelet studies is that sample preparation may lead to artifactual activation processes which may confound results, impacting the use of scanning electron microscopy as a supplemental diagnostic tool. We used scanning electron microscopy and flow cytometry to analyze platelet activation in platelet-rich plasma (PRP) and whole blood (WB) samples. PRP generated using a single high g force centrifugation, and WB samples treated with a red blood cell lysis buffer, were exposed to increasing concentrations of the agonist thrombin. Platelets in lysed WB samples responded to thrombin by elevating the activation marker CD62p definitively, with corresponding ultrastructural changes indicating activation. Conversely, CD62p expression in PRP preparations remained static. Ultrastructural analysis revealed fully activated platelets even under low concentration thrombin stimulation, with considerable fibrin deposition. It is proposed that the method for PRP production induced premature platelet activation, preventable by using an inhibitor of platelet aggregation and fibrin polymerization. Nevertheless, our results show a definitive correspondence between flow cytometry and scanning electron microscopy in platelet activation studies, highlighting the potential of the latter technique as a supplemental diagnostic tool.
The New Space Age in the making: Emergence of exo-mining, exo-burials and exo-marketing
Authors: Capova Klara Anna 
Published: June 2016

AbstractAt the beginning of the 21st century we witness considerable global developments in space exploration and a new era has begun: the New Space Age. The principal symbols of that age are firstly internationalization of space activities, secondly commercial utilization of space technologies, and lastly emergence of outer space economy. This paper presents selected signposts of the New Space Age. Three cases of recent outer space enterprises: recovery of asteroid resources (exo-mining), post-cremation memorial spaceflight (exo-burials) and first extraterrestrial advert (exo-marketing), are introduced in order to emphasize the monetary and social dimension of commercial application of space technologies. To give an illustration of these trends, this paper provides a brief socioculturally minded account of three outer space undertakings that are interpreted as signposts of the new era.
Experimental demonstration of the microscopic origin of circular dichroism in two-dimensional metamaterials
Authors: Khanikaev A. B. , Arju N. , Fan Z. , Purtseladze D. , Lu F. , Lee J. , Sarriugarte P. , Schnell M. , Hillenbrand R. , Belkin M. A. , Shvets G. 
Published: June 2016

AbstractOptical activity and circular dichroism are fascinating physical phenomena originating from the interaction of light with chiral molecules or other nano objects lacking mirror symmetries in three-dimensional (3D) space. While chiral optical properties are weak in most of naturally occurring materials, they can be engineered and significantly enhanced in synthetic optical media known as chiral metamaterials, where the spatial symmetry of their building blocks is broken on a nanoscale. Although originally discovered in 3D structures, circular dichroism can also emerge in a two-dimensional (2D) metasurface. The origin of the resulting circular dichroism is rather subtle, and is related to non-radiative (Ohmic) dissipation of the constituent metamolecules. Because such dissipation occurs on a nanoscale, this effect has never been experimentally probed and visualized. Using a suite of recently developed nanoscale-measurement tools, we establish that the circular dichroism in a nanostructured metasurface occurs due to handedness-dependent Ohmic heating.
Programming a topologically constrained DNA nanostructure into a sensor
Authors: Liu Meng , Zhang Qiang , Li Zhongping , Gu Jimmy , Brennan John D. , Li Yingfu 
Published: June 2016

AbstractMany rationally engineered DNA nanostructures use mechanically interlocked topologies to connect individual DNA components, and their physical connectivity is achieved through the formation of a strong linking duplex. The existence of such a structural element also poses a significant topological constraint on functions of component rings. Herein, we hypothesize and confirm that DNA catenanes with a strong linking duplex prevent component rings from acting as the template for rolling circle amplification (RCA). However, by using an RNA-containing DNA [2] catenane with a strong linking duplex, we show that a stimuli-responsive RNA-cleaving DNAzyme can linearize one component ring, and thus enable RCA, producing an ultra-sensitive biosensing system. As an example, a DNA catenane biosensor is engineered to detect the model bacterial pathogen Escherichia coli through binding of a secreted protein, with a detection limit of 10 cells ml−1, thus establishing a new platform for further applications of mechanically interlocked DNA nanostructures.
Intrinsic hepatocyte dedifferentiation is accompanied by upregulation of mesenchymal markers, protein sialylation and core alpha 1,6 linked fucosylation
Authors: Mehta Anand , Comunale Mary Ann , Rawat Siddhartha , Casciano Jessica C. , Lamontagne Jason , Herrera Harmin , Ramanathan Aarti , Betesh Lucy , Wang Mengjun , Norton Pamela , Steel Laura F. , Bouchard Michael J. 
Published: June 2016

AbstractAlterations in N-linked glycosylation have long been associated with cancer but for the most part, the reasons why have remained poorly understood. Here we show that increased core fucosylation is associated with de-differentiation of primary hepatocytes and with the appearance of markers indicative of a transition of cells from an epithelial to a mesenchymal state. This increase in core fucosylation was associated with increased levels of two enzymes involved in α-1,6 linked fucosylation, GDP-mannose 4, 6-dehydratase (Gmds) and to a lesser extent fucosyltransferase 8 (Fut8). In addition, the activation of cancer-associated cellular signaling pathways in primary rat hepatocytes can increase core fucosylation and induce additional glycoform alterations on hepatocyte proteins. Specifically, we show that increased levels of protein sialylation and α-1,6-linked core fucosylation are observed following activation of the β-catenin pathway. Activation of the Akt signaling pathway or induction of hypoxia also results in increased levels of fucosylation and sialylation. We believe that this knowledge will help in the better understanding of the genetic factors associated with altered glycosylation and may allow for the development of more clinically relevant biomarkers.
Foetal hepatic progenitor cells assume a cholangiocytic cell phenotype during two-dimensional pre-culture
Authors: Anzai Kazuya , Chikada Hiromi , Tsuruya Kota , Ida Kinuyo , Kagawa Tatehiro , Inagaki Yutaka , Mine Tesuya , Kamiya Akihide 
Published: June 2016

AbstractLiver consists of parenchymal hepatocytes and other cells. Liver progenitor cell (LPC) is the origin of both hepatocytes and cholangiocytic cells. The analyses of mechanism regulating differentiation of LPCs into these functional cells are important for liver regenerative therapy using progenitor cells. LPCs in adult livers were found to form cysts with cholangiocytic characteristics in 3D culture. In contrast, foetal LPCs cannot form these cholangiocytic cysts in the same culture. Thus, the transition of foetal LPCs into cholangiocytic progenitor cells might occur during liver development. Primary CD45−Ter119−Dlk1+ LPCs derived from murine foetal livers formed ALBUMIN (ALB)+CYTOKERATIN (CK)19− non-cholangiocytic cysts within 3D culture. In contrast, when foetal LPCs were pre-cultured on gelatine-coated dishes, they formed ALB−CK19+ cholangiocytic cysts. When hepatocyte growth factor or oncostatin M, which are inducers of hepatocytic differentiation, was added to pre-culture, LPCs did not form cholangiocytic cysts. These results suggest that the pre-culture on gelatine-coated dishes changed the characteristics of foetal LPCs into cholangiocytic cells. Furthermore, neonatal liver progenitor cells were able to form cholangiocytic cysts in 3D culture without pre-culture. It is therefore possible that the pre-culture of mid-foetal LPCs in vitro functioned as a substitute for the late-foetal maturation step in vivo.
Sorghum Dw1, an agronomically important gene for lodging resistance, encodes a novel protein involved in cell proliferation
Authors: Yamaguchi Miki , Fujimoto Haruka , Hirano Ko , Araki-Nakamura Satoko , Ohmae-Shinohara Kozue , Fujii Akihiro , Tsunashima Masako , Song Xian Jun , Ito Yusuke , Nagae Rie , Wu Jianzhong , Mizuno Hiroshi , Yonemaru Jun-ichi , Matsumoto Takashi , Kitano Hidemi , Matsuoka Makoto , Kasuga Shigemitsu , Sazuka Takashi 
Published: June 2016

AbstractSemi-dwarfing genes have contributed to enhanced lodging resistance, resulting in increased crop productivity. In the history of grain sorghum breeding, the spontaneous mutation, dw1found in Memphis in 1905, was the first widely used semi-dwarfing gene. Here, we report the identification and characterization ofDw1. We performed quantitative trait locus (QTL) analysis and cloning, and revealed thatDw1encodes a novel uncharacterized protein. Knockdown or T-DNA insertion lines of orthologous genes in rice and Arabidopsis also showed semi-dwarfism similar to that of a nearly isogenic line (NIL) carryingdw1(NIL-dw1) of sorghum. A histological analysis of the NIL-dw1revealed that the longitudinal parenchymal cell lengths of the internode were almost the same between NIL-dw1and wildtype, while the number of cells per internode was significantly reduced in NIL-dw1.NIL-dw1dw3, carrying bothdw1anddw3(involved in auxin transport), showed a synergistic phenotype. These observations demonstrate that thedw1reduced the cell proliferation activity in the internodes, and the synergistic effect ofdw1anddw3contributes to improved lodging resistance and mechanical harvesting.
Flexible decision-making relative to reward quality and tool functionality in Goffin cockatoos (Cacatua goffiniana)
Authors: Laumer I. B. , Bugnyar T. , Auersperg A. M. I. 
Published: June 2016

AbstractDecisions involving the use of tools may require an agent to consider more levels of relational complexity than merely deciding between an immediate and a delayed option. Using a new experimental approach featuring two different types of tools, two apparatuses as well as two different types of reward, we investigated the Goffin cockatoos’ ability to make flexible and profitable decisions within five different setups. Paralleling previous results in primates, most birds overcame immediate drives in favor of future gains; some did so even if tool use involved additional work effort. Furthermore, at the group level subjects maximized their profit by simultaneously considering both the quality of an immediate versus a delayed food reward (accessible with a tool) and the functionality of the available tool. As their performance levels remained stable across trials in all testing setups, this was unlikely the result of a learning effect. The Goffin cockatoos’ ability to focus on relevant information was constrained when all task components (both food qualities, both apparatuses and both tools) were presented at the same time.
Genome-wide identification of microRNA-related variants associated with risk of Alzheimer’s disease
Authors: Ghanbari Mohsen , Ikram M. Arfan , de Looper Hans W. J. , Hofman Albert , Erkeland Stefan J. , Franco Oscar H. , Dehghan Abbas 
Published: June 2016

AbstractMicroRNAs (miRNAs) serve as key post-transcriptional regulators of gene expression. Genetic variation in miRNAs and miRNA-binding sites may affect miRNA function and contribute to disease risk. Here, we investigated the extent to which variants within miRNA-related sequences could constitute a part of the functional variants involved in developing Alzheimer’s disease (AD), using the largest available genome-wide association study of AD. First, among 237 variants in miRNAs, we found rs2291418 in the miR-1229 precursor to be significantly associated with AD (p-value = 6.8 × 10−5, OR = 1.2). Our in-silico analysis and in-vitro miRNA expression experiments demonstrated that the variant’s mutant allele enhances the production of miR-1229-3p. Next, we found miR-1229-3p target genes that are associated with AD and might mediate the miRNA function. We demonstrated that miR-1229-3p directly controls the expression of its top AD-associated target gene (SORL1) using luciferase reporter assays. Additionally, we showed that miR-1229-3p and SORL1 are both expressed in the human brain. Second, among 42,855 variants in miRNA-binding sites, we identified 10 variants (in the 3′ UTR of 9 genes) that are significantly associated with AD, including rs6857 that increases the miR-320e-mediated regulation of PVRL2. Collectively, this study shows that miRNA-related variants are associated with AD and suggests miRNA-dependent regulation of several AD genes.
Identification of Tissue-Specific Protein-Coding and Noncoding Transcripts across 14 Human Tissues Using RNA-seq
Authors: Zhu Jinhang , Chen Geng , Zhu Sibo , Li Suqing , Wen Zhuo , Bin Li  , Zheng Yuanting , Shi Leming 
Published: June 2016

AbstractMany diseases and adverse drug reactions exhibit tissue specificity. To better understand the tissue-specific expression characteristics of transcripts in different human tissues, we deeply sequenced RNA samples from 14 different human tissues. After filtering many lowly expressed transcripts, 24,729 protein-coding transcripts and 1,653 noncoding transcripts were identified. By analyzing highly expressed tissue-specific protein-coding transcripts (TSCTs) and noncoding transcripts (TSNTs), we found that testis expressed the highest numbers of TSCTs and TSNTs. Brain, monocytes, ovary, and heart expressed more TSCTs than the rest tissues, whereas brain, placenta, heart, and monocytes expressed more TSNTs than other tissues. Co-expression network constructed based on the TSCTs and TSNTs showed that each hub TSNT was co-expressed with several TSCTs, allowing functional annotation of TSNTs. Important biological processes and KEGG pathways highly related to the specific functions or diseases of each tissue were enriched with the corresponding TSCTs. These TSCTs and TSNTs may participate in the tissue-specific physiological or pathological processes. Our study provided a unique data set and systematic analysis of expression characteristics and functions of both TSCTs and TSNTs based on 14 distinct human tissues, and could facilitate future investigation of the mechanisms behind tissue-specific diseases and adverse drug reactions.
Dioscin strengthens the efficiency of adriamycin in MCF-7 and MCF-7/ADR cells through autophagy induction: More than just down-regulation of MDR1
Authors: Wang Changyuan , Huo Xiaokui , Wang Lijuan , Meng Qiang , Liu Zhihao , Liu Qi , Sun Huijun , Sun Pengyuan , Peng Jinyong , Liu Kexin 
Published: June 2016

AbstractThe purpose of present study was to investigate the effect of dioscin on activity of adriamycin (ADR) in ADR-sensitive (MCF-7) and ADR-resistant (MCF-7/ADR) human breast cancer cells and to clarify the molecular mechanisms involved. Antiproliferation effect of ADR was enhanced by dioscin in MCF-7 and MCF-7/ADR cells. Dioscin significantly inhibited MDR1 mRNA and protein expression and MDR1 promoter and nuclear factor κ-B (NF-κB) activity in MCF-7/ADR cells. Additionally, inhibitor κB-α (IκB-α) degradation was inhibited by dioscin. Moreover, dioscin induced the formation of vacuoles in the cytoplasm and protein level of LC3-II in MCF-7 and MCF-7/ADR cells. Autophagy inhibitor 3-MA abolished the effect of dioscin on ADR cytotoxicity. Dioscin inhibited phosphorylation of PI3K and Akt, resulting in upregulation of LC3-II expression. In conclusion, dioscin increased ADR chemosensitivity by down-regulating MDR1 expression through NF-κB signaling inhibition in MCF-7/ADR cells. Autophagy was induced by dioscin to ameliorate the cytotoxicity of ADR via inhibition of the PI3K/AKT pathways in MCF-7 and MCF-7/ADR cells. These findings provide evidence in support of further investigation into the clinical application of dioscin as a chemotherapy adjuvant.
On the importance of full-dimensionality in low-energy molecular scattering calculations
Authors: Faure Alexandre , Jankowski Piotr , Stoecklin Thierry , Szalewicz Krzysztof 
Published: June 2016

AbstractScattering of H2 on CO is of great importance in astrophysics and also is a benchmark system for comparing theory to experiment. We present here a new 6-dimensional potential energy surface for the ground electronic state of H2-CO with an estimated uncertainty of about 0.6 cm−1 in the global minimum region, several times smaller than achieved earlier. This potential has been used in nearly exact 6-dimensional quantum scattering calculations to compute state-to-state cross-sections measured in low-energy crossed-beam experiments. Excellent agreement between theory and experiment has been achieved in all cases. We also show that the fully 6-dimensional approach is not needed with the current accuracy of experimental data since an equally good agreement with experiment was obtained using only a 4-dimensional treatment, which validates the rigid-rotor approach widely used in scattering calculations. This finding, which disagrees with some literature statements, is important since for larger systems full-dimensional scattering calculations are currently not possible.