bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-range magnetic coupling across a polar insulating layer
Authors: Lü W. M. , Saha Surajit , Wang X. Renshaw , Liu Z. Q. , Gopinadhan K. , Annadi A. , Zeng S. W. , Huang Z. , Bao B. C. , Cong C. X. , Venkatesan M. , Yu T. , Coey J. M. D. , Ariando  , Venkatesan T. 
Published: March 2016

AbstractMagnetic interactions in solids are normally mediated by short-range exchange or weak dipole fields. Here we report a magnetic interaction that can propagate over long distances (∼10 nm) across a polar insulating oxide spacer. Evidence includes oscillations of magnetization, coercivity and field-cooled loop shift with the thickness of LaAlO3 in La0.67Sr0.33MnO3/LaAlO3/SrTiO3 heterostructures. Similar modifications of the hysteresis loop appear when two coupled films of La0.67Sr0.33MnO3 are separated by LaAlO3, or another polar insulator, but they are absent when the oxide spacer layer is nonpolar. The loop shift is attributed to strong spin–orbit coupling and Dzyaloshinskii–Moriya interaction at the interfaces. There is evidence from inelastic light scattering that the polar spacer mediates long-range transmission of orbital magnetization. This coupling mechanism is expected to apply for any conducting ferromagnetic oxide with mixed valence; in view of electron hopping frequency involved, it raises the prospect of terahertz tunability of magnetic coupling.
Cellular forces and matrix assembly coordinate fibrous tissue repair
Authors: Sakar Mahmut Selman , Eyckmans Jeroen , Pieters Roel , Eberli Daniel , Nelson Bradley J. , Chen Christopher S. 
Published: March 2016

AbstractPlanar in vitro models have been invaluable tools to identify the mechanical basis of wound closure. Although these models may recapitulate closure dynamics of epithelial cell sheets, they fail to capture how a wounded fibrous tissue rebuilds its 3D architecture. Here we develop a 3D biomimetic model for soft tissue repair and demonstrate that fibroblasts ensconced in a collagen matrix rapidly close microsurgically induced defects within 24 h. Traction force microscopy and time-lapse imaging reveal that closure of gaps begins with contractility-mediated whole-tissue deformations. Subsequently, tangentially migrating fibroblasts along the wound edge tow and assemble a progressively thickening fibronectin template inside the gap that provide the substrate for cells to complete closure. Unlike previously reported mechanisms based on lamellipodial protrusions and purse-string contraction, our data reveal a mode of stromal closure in which coordination of tissue-scale deformations, matrix assembly and cell migration act together to restore 3D tissue architecture.
Mechanistic signatures of HPV insertions in cervical carcinomas
Authors: Holmes Allyson , Lameiras Sonia , Jeannot Emmanuelle , Marie Yannick , Castera Laurent , Sastre-Garau Xavier , Nicolas Alain 
Published: March 2016

AbstractTo identify new personal biomarkers for the improved diagnosis, prognosis and biological follow-up of human papillomavirus (HPV)-associated carcinomas, we developed a generic and comprehensive Capture-HPV method followed by Next Generation Sequencing (NGS). Starting from biopsies or circulating DNA samples, this Capture-NGS approach rapidly identifies the HPV genotype, HPV status (integrated, episomal or absence), the viral-host DNA junctions and the associated genome rearrangements. This analysis of 72 cervical carcinomas identified five HPV signatures. The first two signatures contain two hybrid chromosomal–HPV junctions whose orientations are co-linear (2J-COL) or non-linear (2J-NL), revealing two modes of viral integration associated with chromosomal deletion or amplification events, respectively. The third and fourth signatures exhibit 3–12 hybrid junctions, either clustered in one locus (MJ-CL) or scattered at distinct loci (MJ-SC) while the fifth signature consists of episomal HPV genomes (EPI). Cross analyses between the HPV signatures and the clinical and virological data reveal unexpected biased representation with respect to the HPV genotype, patient age and disease outcome, suggesting functional relevance(s) of this new classification. Overall, our findings establish a facile and comprehensive rational approach for the molecular detection of any HPV-associated carcinoma and definitive personalised sequence information to develop sensitive and specific biomarkers for each patient.
Improving Low-dose Cardiac CT Images based on 3D Sparse Representation
Authors: Shi Luyao , Hu Yining , Chen Yang , Yin Xindao , Shu Huazhong , Luo Limin , Coatrieux Jean-Louis 
Published: March 2016

AbstractCardiac computed tomography (CCT) is a reliable and accurate tool for diagnosis of coronary artery diseases and is also frequently used in surgery guidance. Low-dose scans should be considered in order to alleviate the harm to patients caused by X-ray radiation. However, low dose CT (LDCT) images tend to be degraded by quantum noise and streak artifacts. In order to improve the cardiac LDCT image quality, a 3D sparse representation-based processing (3D SR) is proposed by exploiting the sparsity and regularity of 3D anatomical features in CCT. The proposed method was evaluated by a clinical study of 14 patients. The performance of the proposed method was compared to the 2D spares representation-based processing (2D SR) and the state-of-the-art noise reduction algorithm BM4D. The visual assessment, quantitative assessment and qualitative assessment results show that the proposed approach can lead to effective noise/artifact suppression and detail preservation. Compared to the other two tested methods, 3D SR method can obtain results with image quality most close to the reference standard dose CT (SDCT) images.
Angiogenic activity mediates bone repair from human pluripotent stem cell-derived osteogenic cells
Authors: Zou Li , Chen Qingshan , Quanbeck Zachary , Bechtold Joan E. , Kaufman Dan S. 
Published: March 2016

AbstractHuman pluripotent stem cells provide a standardized resource for bone repair. However, criteria to determine which exogenous cells best heal orthopedic injuries remain poorly defined. We evaluated osteogenic progenitor cells derived from both human embryonic stem cells (hESCs) and induced pluripotent stem cells (hiPSCs). Phenotypic and genotypic analyses demonstrated that these hESCs/hiPSCs are similar in their osteogenic differentiation efficiency and they generate osteogenic cells comparable to osteogenic cells derived from mesenchymal stromal cells (BM-MSCs). However, expression of angiogenic factors, such as vascular endothelial growth factor and basic fibroblast growth factor in these osteogenic progenitor cells are markedly different, suggesting distinct pro-angiogenic potential of these stem cell derivatives. Studies to repair a femur non-union fracture demonstrate only osteogenic progenitor cells with higher pro-angiogenic potential significantly enhance bone repair in vivo. Together, these studies highlight a key role of pro-angiogenic potential of transplanted osteogenic cells for effective cell-mediated bone repair.
RNA-dependent RNA polymerase 1 in potato (Solanum tuberosum) and its relationship to other plant RNA-dependent RNA polymerases
Authors: Hunter Lydia J. R. , Brockington Samuel F. , Murphy Alex M. , Pate Adrienne E. , Gruden Kristina , MacFarlane Stuart A. , Palukaitis Peter , Carr John P. 
Published: March 2016

AbstractCellular RNA-dependent RNA polymerases (RDRs) catalyze synthesis of double-stranded RNAs that can serve to initiate or amplify RNA silencing. Arabidopsis thaliana has six RDR genes; RDRs 1, 2 and 6 have roles in anti-viral RNA silencing. RDR6 is constitutively expressed but RDR1 expression is elevated following plant treatment with defensive phytohormones. RDR1 also contributes to basal virus resistance. RDR1 has been studied in several species including A. thaliana, tobacco (Nicotiana tabacum), N. benthamiana, N. attenuata and tomato (Solanum lycopersicum) but not to our knowledge in potato (S. tuberosum). StRDR1 was identified and shown to be salicylic acid-responsive. StRDR1 transcript accumulation decreased in transgenic potato plants constitutively expressing a hairpin construct and these plants were challenged with three viruses: potato virus Y, potato virus X, and tobacco mosaic virus. Suppression of StRDR1 gene expression did not increase the susceptibility of potato to these viruses. Phylogenetic analysis of RDR genes present in potato and in a range of other plant species identified a new RDR gene family, not present in potato and found only in Rosids (but apparently lost in the Rosid A. thaliana) for which we propose the name RDR7.
Mycobacterial escape from macrophage phagosomes to the cytoplasm represents an alternate adaptation mechanism
Authors: Jamwal Shilpa V. , Mehrotra Parul , Singh Archana , Siddiqui Zaved , Basu Atanu , Rao Kanury V.S. 
Published: March 2016

AbstractSurvival of Mycobacterium tuberculosis (Mtb) within the host macrophage is mediated through pathogen-dependent inhibition of phagosome-lysosome fusion, which enables bacteria to persist within the immature phagosomal compartment. By employing ultrastructural examination of different field isolates supported by biochemical analysis, we found that some of the Mtb strains were in fact poorly adapted for subsistence within endocytic vesicles of infected macrophages. Instead, through a mechanism involving activation of host cytosolic phospholipase A2, these bacteria rapidly escaped from phagosomes and established residence in the cytoplasm of the host cell. Interestingly, by facilitating an enhanced suppression of host cellular autophagy, this translocation served as an alternate virulence acquisition mechanism. Thus, our studies reveal plasticity in the adaptation strategies employed by Mtb, for survival in the host macrophage.
TLR3-/4-Priming Differentially Promotes Ca2+ Signaling and Cytokine Expression and Ca2+-Dependently Augments Cytokine Release in hMSCs
Authors: Park Kyoung Sun , Kim Sun Hwa , Das Amitabh , Yang Shao-Nian , Jung Kyoung Hwa , Kim Mi Kyung , Berggren Per-Olof , Lee YoungSeek , Chai Jin Choul , Kim Hyun Jin , Chai Young Gyu 
Published: March 2016

AbstractIn human mesenchymal stem cells (hMSCs), toll-like receptor 3 (TLR3) and TLR4 act as key players in the tissue repair process by recognizing their ligands and stimulating downstream processes including cytokine release. The mechanisms of TLR3- and TLR4-mediated cytokine releases from hMSCs remain uncertain. Here, we show that exposure to the TLR3 agonist polyinosinic-polycytidylic acid (poly(I:C)) or incubation with the TLR4 agonist lipopolysaccharide (LPS) increased the mRNA expression levels of TLR3, TLR4 and cytokines in hMSCs. Poly(I:C) exposure rather than LPS incubation not only elevated inositol 1,4,5-triphosphate receptor (IP3R) expression and IP3R-mediated Ca2+ release, but also promoted Orai and STIM expression as well as store-operated Ca2+ entry into hMSCs. In addition, we also observed that 21 Ca2+ signaling genes were significantly up-regulated in response to TLR3 priming of hMSCs by RNA sequencing analysis. Both poly(I:C) and LPS exposure enhanced cytokine release from hMSCs. The enhanced cytokine release vanished upon siRNA knockdown and chelation of intracellular Ca2+. These data demonstrate that TLR3- and TLR4-priming differentially enhance Ca2+ signaling and cytokine expression, and Ca2+ -dependently potentiates cytokine release in hMSCs.
Silencing of the olfactory co-receptor gene in Dendroctonus armandi leads to EAG response declining to major host volatiles
Authors: Zhang Ranran , Gao Guanqun , Chen Hui 
Published: March 2016

AbstractIn this study, a polymerase chain reaction (PCR) based on homology genes of Orco was utilized to identify DarmOrco, which is essential for olfaction in D. armandi. The results showed that DarmOrco shares significant sequence homology with Orco proteins had known in other insects. Quantitative real-time PCR (qRT-PCR) analysis suggested that DarmOrco was abundantly expressed in adult D. armandi; by contrast, DarmOrco showed trace amounts of expression level in other stages. Of different tissues, DarmOrco expression level was the highest in the antennae. In order to understand the functional significance of Orco, we injected siRNA of DarmOrco into the conjunctivum between the second and third abdominal segments and evaluated its expression after siRNA injected for 24 h, 48 h and 72 h. The results of qRT-PCR demonstrated that the reduction of mRNA expression level was significant (~80%) in DarmOrco siRNA-treated D. armandi than in water-injected and non-injected controls. The electroantennogram responses of females and males to 11 major volatiles of its host, were also reduced (30~68% for females; 16~70% for males) in siRNA-treated D. armandi compared with the controls. These results suggest that DarmOrco is crucial in mediating odorant perception.
Transcriptome analysis of different developmental stages of amphioxus reveals dynamic changes of distinct classes of genes during development
Authors: Yang Kevin Yi , Chen Yuan , Zhang Zuming , Ng Patrick Kwok-Shing , Zhou Wayne Junwei , Zhang Yinfeng , Liu Minghua , Chen Junyuan , Mao Bingyu , Tsui Stephen Kwok-Wing 
Published: March 2016

AbstractVertebrates diverged from other chordates approximately 500 million years ago and have adopted several modifications of developmental processes. Amphioxus is widely used in evolutionary developmental biology research, such as on the basic patterning mechanisms involved in the chordate body plan and the origin of vertebrates. The fast development of next-generation sequencing has advanced knowledge of the genomic organization of amphioxus; however, many aspects of gene regulation during amphioxus development have not been fully characterized. In this study, we applied high-throughput sequencing on the transcriptomes of 13 developmental stages of Chinese amphioxus to gain a comprehensive understanding of transcriptional processes occurring from the fertilized egg to the adult stage. The expression levels of 3,423 genes were significantly changed (FDR ≤ 0.01). All of these genes were included in a clustering analysis and enrichment of biological functions associated with these clusters was determined. Significant changes were observed in several important processes, including the down-regulation of the cell cycle and the up-regulation of translation. These results should build a foundation for identifying developmentally important genes, especially those regulatory factors involved in amphioxus development and advance understanding of the developmental dynamics in vertebrates.
Tracking neighbours promotes the coexistence of large carnivores
Authors: López-Bao José Vicente , Mattisson Jenny , Persson Jens , Aronsson Malin , Andrén Henrik 
Published: March 2016

AbstractThe study of competition and coexistence among similar interacting species has long been considered a cornerstone in evolutionary and community ecology. However, understanding coexistence remains a challenge. Using two similar and sympatric competing large carnivores, Eurasian lynx and wolverines, we tested the hypotheses that tracking among heterospecifics and reactive responses to potential risk decreases the probability of an agonistic encounter when predators access shared food resources, thus facilitating coexistence. Lynx and wolverines actively avoided each other, with the degree of avoidance being greater for simultaneous than time-delayed predator locations. Wolverines reacted to the presence of lynx at relatively short distances (mean: 383 m). In general, lynx stayed longer and were more stationary, around reindeer carcasses than wolverines. However, when both predators were present at the same time around a carcass, lynx shortened their visits, while wolverine behavior did not change. Our results support the idea that risk avoidance is a reactive, rather than a predictive, process. Since wolverines have adapted to coexist with lynx, exploiting lynx-killed reindeer carcasses while avoiding potential encounters, the combined presence of both predators may reduce wolverine kill rate and thus the total impact of these predators on semi-domestic reindeer in Scandinavia. Consequently, population management directed at lynx may affect wolverine populations and human-wolverine conflicts.
Chromatin interactions and candidate genes at ten prostate cancer risk loci
Authors: Du Meijun , Tillmans Lori , Gao Jianzhong , Gao Ping , Yuan Tiezheng , Dittmar Rachel L , Song Wei , Yang Yuehong , Sahr Natasha , Wang Tao , Wei Gong-Hong , Thibodeau Stephen N. , Wang Liang 
Published: March 2016

AbstractGenome-wide association studies have identified more than 100 common single nucleotide polymorphisms (SNPs) that are associated with prostate cancer risk. However, the vast majority of these SNPs lie in noncoding regions of the genome. To test whether these risk SNPs regulate their target genes through long-range chromatin interactions, we applied capture-based 3C sequencing technology to investigate possible cis-interactions at ten prostate cancer risk loci in six cell lines. We identified significant physical interactions between risk regions and their potential target genes including CAPG at 2p11.2, C2orf43 at 2p24.1, RFX6 at 6q22.1, NFASC at 1q32.1, MYC at 8q24.1 and AGAP7P at 10q11.23. Most of the interaction peaks were co-localized to regions of active histone modification and transcription factor binding sites. Expression quantitative trait locus (eQTL) analysis showed suggestive eQTL signals at rs1446669, rs699664 and rs1078004 for CAPG (p < 0.004), rs13394027 for C2orf43 (p = 2.25E-27), rs10993994 and rs4631830 for AGAP7P (p < 8.02E-5). Further analysis revealed an enhancer activity at genomic region surrounding rs4631830 which was expected to disrupt HOXB-like DNA binding affinity. This study identifies a set of candidate genes and their potential regulatory variants, and provides additional evidence showing the role of long-range chromatin interactions in prostate cancer etiology.
Effects of intervalley scattering on the transport properties in one−dimensional valleytronic devices
Authors: Zhou Jiaojiao , Cheng Shuguang , You Wen-Long , Jiang Hua 
Published: March 2016

AbstractBased on a one-dimensional valley junction model, the effects of intervalley scattering on the valley transport properties are studied. We analytically investigate the valley transport phenomena in three typical junctions with both intervalley and intravalley scattering included. For the tunneling between two gapless valley materials, different from conventional Klein tunneling theory, the transmission probability of the carrier is less than 100% while the pure valley polarization feature still holds. If the junction is composed of at least one gapped valley material, the valley polarization of the carrier is generally imperfect during the tunneling process. Interestingly, in such circumstance, we discover a resonance of valley polarization that can be tuned by the junction potential. The extension of our results to realistic valley materials are also discussed.
Distinct Biochemical Activities of Eyes absent During Drosophila Eye Development
Authors: Jin Meng , Mardon Graeme 
Published: March 2016

AbstractEyes absent (Eya) is a highly conserved transcriptional coactivator and protein phosphatase that plays vital roles in multiple developmental processes from Drosophila to humans. Eya proteins contain a PST (Proline-Serine-Threonine)-rich transactivation domain, a threonine phosphatase motif (TPM) and a tyrosine protein phosphatase domain. Using a genomic rescue system, we find that the PST domain is essential for Eya activity and Dac expression and the TPM is required for full Eya function. We also find that the threonine phosphatase activity plays only a minor role during Drosophila eye development and the primary function of the PST and TPM domains is transactivation that can be largely substituted by the heterologous activation domain VP16. Along with our previous results that the tyrosine phosphatase activity of Eya is dispensable for normal Eya function in eye formation, we demonstrate that a primary function of Eya during Drosophila eye development is as a transcriptional coactivator. Moreover, the PST/TPM and the threonine phosphatase activity are not required for in vitro interaction between retinal determination factors. Finally, this work is the first report of an Eya-Ey physical interaction. These findings are particularly important because they highlight the need for an in vivo approach that accurately dissects protein function.
Superhigh moduli and tension-induced phase transition of monolayer gamma-boron at finite temperatures
Authors: Zhao Junhua , Yang Zhaoyao , Wei Ning , Kou Liangzhi 
Published: March 2016

AbstractTwo dimensional (2D) gamma-boron (γ-B28) thin films have been firstly reported by the experiments of the chemical vapor deposition in the latest study. However, their mechanical properties are still not clear. Here we predict the superhigh moduli (785 ± 42 GPa at 300 K) and the tension-induced phase transition of monolayer γ-B28 along a zigzag direction for large deformations at finite temperatures using molecular dynamics (MD) simulations. The new phase can be kept stable after unloading process at these temperatures. The predicted mechanical properties are reasonable when compared with our results from density functional theory. This study provides physical insights into the origins of the new phase transition of monolayer γ-B28 at finite temperatures.
Step down Vascular Calcification Analysis using State-of-the-Art Nanoanalysis Techniques
Authors: Curtze Sven C. , Kratz Marita , Steinert Marian , Vogt Sebastian 
Published: March 2016

AbstractNew insights into the architecture and formation mechanisms of calcific lesions down to the nanoscale open a better understanding of atherosclerosis and its pathogenesis. Scanning electron – and atomic force microscope based nano-analytical characterization techniques were adapted to the assessment of an ex-vivo calcified coronary artery. Human atherosclerotic tissue and bone tissue reside a typical chemistry of Magnesium and Sodium rich Calcium phosphates, identified as whitlockite and Calcium apatite, respectively. Despite the obvious similarities in both chemistry and crystallography, there are also clear differences between calcified vascular tissue and bone such as the highly oriented growth in bone, revealing meso-crystal character, as opposed to the anisotropic character of calcified vascular lesions. While the grain size in vascular calcified plaques is in the range of nanometers, the grain size in bone appears larger. Spherical calcific particles present in both the coronary artery wall and embedded in plaques reveal concentric layers with variations in both organic content and degree of hydration.