bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stability and function of adult vasculature is sustained by Akt/Jagged1 signalling axis in endothelium
Authors: Kerr Bethany A. , West Xiaoxia Z. , Kim Young-Woong , Zhao Yongzhong , Tischenko Miroslava , Cull Rebecca M. , Phares Timothy W. , Peng Xiao-Ding , Bernier-Latmani Jeremiah , Petrova Tatiana V. , Adams Ralf H. , Hay Nissim , Naga Prasad Sathyamangla V. , Byzova Tatiana V. 
Published: March 2016

AbstractThe signalling pathways operational in quiescent, post-development vasculature remain enigmatic. Here we show that unlike neovascularization, endothelial Akt signalling in established vasculature is crucial not for endothelial cell (EC) survival, but for sustained interactions with pericytes and vascular smooth muscle cells (VSMCs) regulating vascular stability and function. Inducible endothelial-specific Akt1 deletion in adult global Akt2KO mice triggers progressive VSMC apoptosis. In hearts, this causes a loss of arteries and arterioles and, despite a high capillary density, diminished vascular patency and severe cardiac dysfunction. Similarly, endothelial Akt deletion induces retinal VSMC loss and basement membrane deterioration resulting in vascular regression and retinal atrophy. Mechanistically, the Akt/mTOR axis controls endothelial Jagged1 expression and, thereby, Notch signalling regulating VSMC maintenance. Jagged1 peptide treatment of Akt1ΔEC;Akt2KO mice and Jagged1 re-expression in Akt-deficient endothelium restores VSMC coverage. Thus, sustained endothelial Akt1/2 signalling is critical in maintaining vascular stability and homeostasis, thereby preserving tissue and organ function.
Erratum: Multimodal stimulus coding by a gustatory sensory neuron in Drosophila larvae
Authors: van Giesen Lena , Hernandez-Nunez Luis , Delasoie-Baranek Sophie , Colombo Martino , Renaud Philippe , Bruggmann Rémy , Benton Richard , Samuel Aravinthan D. T. , Sprecher Simon G. 
Published: March 2016

Nature Communications 7: Article number: 10687 (2016); Published: 11 February 2016; Updated: 14 March 2016. The affiliation details for Martino Colombo, Rémy Bruggmann and Richard Benton are incorrect in this article. The correct affiliations for these authors are listed below. Martino Colombo, RémyBruggmann Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Berne, Berne 3012, Switzerland.
Microwave excitation of spin wave beams in thin ferromagnetic films
Authors: Gruszecki P. , Kasprzak M. , Serebryannikov A. E. , Krawczyk M. , Śmigaj W. 
Published: March 2016

AbstractAn inherent element of research and applications in photonics is a beam of light. In magnonics, which is the magnetic counterpart of photonics, where spin waves are used instead of electromagnetic waves to transmit and process information, the lack of a beam source limits exploration. Here, we present an approach enabling generation of narrow spin wave beams in thin homogeneous nanosized ferromagnetic films by microwave current. We show that the desired beam-type behavior can be achieved with the aid of a properly designed coplanar waveguide transducer generating a nonuniform microwave magnetic field. We test this idea using micromagnetic simulations, confirming numerically that the resulting spin wave beams propagate over distances of several micrometers. The proposed approach requires neither inhomogeneity of the ferromagnetic film nor nonuniformity of the biasing magnetic field. It can be generalized to different magnetization configurations and yield multiple spin wave beams of different width at the same frequency.
Guiding migration of transplanted glial progenitor cells in the injured spinal cord
Authors: Yuan Xiao-bing , Jin Ying , Haas Christopher , Yao Lihua , Hayakawa Kazuo , Wang Yue , Wang Chunlei , Fischer Itzhak 
Published: March 2016

AbstractTransplantation of glial-restricted progenitors (GRPs) is a promising strategy for generating a supportive environment for axon growth in the injured spinal cord. Here we explored the possibility of producing a migratory stream of GRPs via directional cues to create a supportive pathway for axon regeneration. We found that the axon growth inhibitor chondroitin sulfate proteoglycan (CSPG) strongly inhibited the adhesion and migration of GRPs, an effect that could be modulated by the adhesion molecule laminin. Digesting glycosaminoglycan side chains of CSPG with chondroitinase improved GRP migration on stripes of CSPG printed on cover glass, although GRPs were still responsive to the remaining repulsive signals of CSPG. Of all factors tested, the basic fibroblast growth factor (bFGF) had the most significant effect in promoting the migration of cultured GRPs. When GRPs were transplanted into either normal spinal cord of adult rats or the injury site in a dorsal column hemisection model of spinal cord injury, a population of transplanted cells migrated toward the region that was injected with the lentivirus expressing chondroitinase or bFGF. These findings suggest that removing CSPG-mediated inhibition, in combination with guidance by attractive factors, can be a promising strategy to produce a migratory stream of supportive GRPs.
Bacteriophage application to control the contaminated water with Shigella
Authors: Jun Jin Woo , Giri Sib Sankar , Kim Hyoun Joong , Yun Sae Kil , Chi Cheng , Chai Ji Young , Lee Byeong Chun , Park Se Chang 
Published: March 2016

AbstractShigella is one of the most important waterborne and foodborne pathogens around the world. Emergence of antibiotic-resistant Shigella has made the development of alternatives to conventional antibiotics necessary. In this study, a virulent Myoviridae bacteriophage, pSs-1 was isolated from environmental water in South Korea and showed infectivity to S. flexneri as well as S. sonnei strains. One-step growth analysis showed that pSs-1 has a short latent period (25 min) and a large burst size (97 PFU/cell). According to the genomic analysis, pSs-1 contains 164,999 bp of genome with a G + C content of 35.54% and it is considered as a member of the T4-like bacteriophage group. These results showed that pSs-1 may have potential as a biocontrol agent instead of conventional antibiotics for shigellosis.
Influence of cell physiological state on gene delivery to T lymphocytes by chimeric adenovirus Ad5F35
Authors: Zhang Wen-feng , Shao Hong-wei , Wu Feng-lin , Xie Xin , Li Zhu-Ming , Bo Hua-Ben , Shen Han , Wang Teng , Huang Shu-lin 
Published: March 2016

AbstractAdoptive transfer of genetically-modified T cells is a promising approach for treatment of both human malignancies and viral infections. Due to its ability to efficiently infect lymphocytes, the chimeric adenovirus Ad5F35 is potentially useful as an immunotherapeutic for the genetic modification of T cells. In previous studies, it was found that the infection efficiency of Ad5F35 was significantly increased without enhanced expression of the viral receptor after T cell stimulation; however, little is known about the underlying mechanism. Nonetheless, cell physiology has long been thought to affect viral infection. Therefore, we aimed to uncover the physiologic changes responsible for the increased infection efficiency of Ad5F35 following T cell stimulation. Given the complexity of intracellular transport we analyzed viral binding, entry and escape using a Jurkat T cell model and found that both cell membrane fluidity and endosomal escape of Ad5F35 were altered under different physiological states. This, in turn, resulted in differences in the amount of virus entering cells and reaching the cytoplasm. These results provide additional insight into the molecular mechanisms underlying Ad5F35 infection of T cells and consequently, will help further the clinical application of genetically-modified T cells for immunotherapy.
Classification of Valleytronics in Thermoelectricity
Authors: Norouzzadeh Payam , Vashaee Daryoosh 
Published: March 2016

AbstractThe theory of valleytronics as a material design tool for engineering both thermal and electrical transport properties is presented. It is shown that the interplay among the valleytronics parameters such as the degeneracy of the band, intervalley transitions, effective mass, scattering exponent, and the Fermi energy may deteriorate or ameliorate any or all of the main thermoelectric properties. A flowchart classifying the different paths through which the valleytronics can influence the thermoelectric figure-of-merit ZT is derived and discussed in detail. To exemplify the application of the flowchart, valleytronics in four different semiconductors, Mg2Si, Si0.8Ge0.2, AlxGa1−xAs and clathrate Si46-VIII were studied, which showed different trends. Therefore, a degenerate multivalley bandstructure, which is typically anticipated for a good thermoelectric material, cannot be a general design rule for ZT enhancement and a detailed transport study is required to engineer the optimum bandstructure.
Inverse regulation of two classic Hippo pathway target genes in Drosophila by the dimerization hub protein Ctp
Authors: Barron Daniel A. , Moberg Kenneth 
Published: March 2016

AbstractThe LC8 family of small ~8 kD proteins are highly conserved and interact with multiple protein partners in eukaryotic cells. LC8-binding modulates target protein activity, often through induced dimerization via LC8:LC8 homodimers. Although many LC8-interactors have roles in signaling cascades, LC8’s role in developing epithelia is poorly understood. Using the Drosophila wing as a developmental model, we find that the LC8 family member Cut up (Ctp) is primarily required to promote epithelial growth, which correlates with effects on the pro-growth factor dMyc and two genes, diap1 and bantam, that are classic targets of the Hippo pathway coactivator Yorkie. Genetic tests confirm that Ctp supports Yorkie-driven tissue overgrowth and indicate that Ctp acts through Yorkie to control bantam (ban) and diap1 transcription. Quite unexpectedly however, Ctp loss has inverse effects on ban and diap1: it elevates ban expression but reduces diap1 expression. In both cases these transcriptional changes map to small segments of these promoters that recruit Yorkie. Although LC8 complexes with Yap1, a Yorkie homolog, in human cells, an orthologous interaction was not detected in Drosophila cells. Collectively these findings reveal that that Drosophila Ctp is a required regulator of Yorkie-target genes in vivo and suggest that Ctp may interact with a Hippo pathway protein(s) to exert inverse transcriptional effects on Yorkie-target genes.
The role of ion exchange in the passivation of In(Zn)P nanocrystals with ZnS
Authors: Cho Deok-Yong , Xi Lifei , Boothroyd Chris , Kardynal Beata , Lam Yeng Ming 
Published: March 2016

AbstractWe have investigated the chemical state of In(Zn)P/ZnS core/shell nanocrystals (NCs) for color conversion applications using hard X-ray absorption spectroscopy (XAS) and photoluminescence excitation (PLE). Analyses of the edge energies as well as the X-ray absorption fine structure (XAFS) reveal that the Zn2+ ions from ZnS remain in the shell while the S2− ions penetrate into the core at an early stage of the ZnS deposition. It is further demonstrated that for short growth times, the ZnS shell coverage on the core was incomplete, whereas the coverage improved gradually as the shell deposition time increased. Together with evidence from PLE spectra, where there is a strong indication of the presence of P vacancies, this suggests that the core-shell interface in the In(Zn)P/ZnS NCs are subject to substantial atomic exchanges and detailed models for the shell structure beyond simple layer coverage are needed. This substantial atomic exchange is very likely to be the reason for the improved photoluminescence behavior of the core-shell particles compare to In(Zn)P-only NCs as S can passivate the NCs surfaces.
Inhibition of pancreatic oxidative damage by stilbene derivative dihydro-resveratrol: implication for treatment of acute pancreatitis
Authors: Tsang Siu Wai , Guan Yi-Fu , Wang Juan , Bian Zhao-Xiang , Zhang Hong-Jie 
Published: March 2016

AbstractTrans-resveratrol is a natural stilbenoid possessing multifarious pharmacological benefits; however, when orally consumed, it is rapidly metabolised by colonic microflora and converted to dihydro-resveratrol. Thus, this microbial metabolite is of great therapeutic relevance. In the present study, upon the oral administration of dihydro-resveratrol (10–50 mg/kg), the severity of acute pancreatitis in the cerulein-treated rats was significantly ameliorated as evidenced by decreased α-amylase activities in the plasma and lessened oedema formation in the pancreatic parenchyma. In addition, the generation of intracellular reactive oxidative products, including malondialdehyde and protein carbonyls, was accordingly reduced, so as the production of pro-inflammatory cytokines. While inhibiting the activities of NADPH oxidase and myeloperoxidase, the depletion of glutathione was considerably restored. Importantly, the attenuation of pancreatic oxidative damage by dihydro-resveratrol was associated with a down-regulation of the nuclear factor-kappaB and phosphatidylinositol 3′-kinase-serine/threonine kinase signalling pathways. Furthermore, we demonstrated that the solubility of dihydro-resveratrol was at least 5 times higher than trans-resveratrol whilst exhibiting a much lower cytotoxicity. Collectively, the current findings accentuate new mechanistic insight of dihydro-resveratrol in pancreatic oxidative damage and advocate its therapeutic potential for the management of acute pancreatitis, particularly for patients unresponsive to trans-resveratrol due to the lack of proper microbial strains.
Structure of the fimbrial protein Mfa4 from Porphyromonas gingivalis in its precursor form: implications for a donor-strand complementation mechanism
Authors: Kloppsteck Patrik , Hall Michael , Hasegawa Yoshiaki , Persson Karina 
Published: March 2016

AbstractGingivitis and periodontitis are chronic inflammatory diseases that can lead to tooth loss. One of the causes of these diseases is the Gram-negative Porphyromonas gingivalis. This periodontal pathogen is dependent on two fimbriae, FimA and Mfa1, for binding to dental biofilm, salivary proteins, and host cells. These fimbriae are composed of five proteins each, but the fimbriae assembly mechanism and ligands are unknown. Here we reveal the crystal structure of the precursor form of Mfa4, one of the accessory proteins of the Mfa1 fimbria. Mfa4 consists of two β-sandwich domains and the first part of the structure forms two well-defined β-strands that run over both domains. This N-terminal region is cleaved by gingipains, a family of proteolytic enzymes that encompass arginine- and lysine-specific proteases. Cleavage of the N-terminal region generates the mature form of the protein. Our structural data allow us to propose that the new N-terminus of the mature protein may function as a donor strand in the polymerization of P. gingivalis fimbriae.
Rationalising the role of Keratin 9 as a biomarker for Alzheimer’s disease
Authors: Richens Joanna L. , Spencer Hannah L. , Butler Molly , Cantlay Fiona , Vere Kelly-Ann , Bajaj Nin , Morgan Kevin , O’Shea Paul 
Published: March 2016

AbstractKeratin 9 was recently identified as an important component of a biomarker panel which demonstrated a high diagnostic accuracy (87%) for Alzheimer’s disease (AD). Understanding how a protein which is predominantly expressed in palmoplantar epidermis is implicated in AD may shed new light on the mechanisms underlying the disease. Here we use immunoassays to examine blood plasma expression patterns of Keratin 9 and its relationship to other AD-associated proteins. We correlate this with the use of anin silicoanalysis tool VisANT to elucidate possible pathways through which the involvement of Keratin 9 may take place. We identify possible links with Dickkopf-1, a negative regulator of the wnt pathway, and propose that the abnormal expression of Keratin 9 in AD blood and cerebrospinal fluid may be a result of blood brain barrier dysregulation and disruption of the ubiquitin proteasome system. Our findings suggest that dysregulated Keratin 9 expression is a consequence of AD pathology but, as it interacts with a broad range of proteins, it may have other, as yet uncharacterized, downstream effects which could contribute to AD onset and progression.
Metagenomic and functional analyses of the consequences of reduction of bacterial diversity on soil functions and bioremediation in diesel-contaminated microcosms
Authors: Jung Jaejoon , Philippot Laurent , Park Woojun 
Published: March 2016

AbstractThe relationship between microbial biodiversity and soil function is an important issue in ecology, yet most studies have been performed in pristine ecosystems. Here, we assess the role of microbial diversity in ecological function and remediation strategies in diesel-contaminated soils. Soil microbial diversity was manipulated using a removal by dilution approach and microbial functions were determined using both metagenomic analyses and enzymatic assays. A shift from Proteobacteria- to Actinobacteria-dominant communities was observed when species diversity was reduced. Metagenomic analysis showed that a large proportion of functional gene categories were significantly altered by the reduction in biodiversity. The abundance of genes related to the nitrogen cycle was significantly reduced in the low-diversity community, impairing denitrification. In contrast, the efficiency of diesel biodegradation was increased in the low-diversity community and was further enhanced by addition of red clay as a stimulating agent. Our results suggest that the relationship between microbial diversity and ecological function involves trade-offs among ecological processes, and should not be generalized as a positive, neutral, or negative relationship.
Polymorphisms of the IL27 gene in a Chinese Han population complicated with pre-eclampsia
Authors: Liu Bin , Li Yuan , Yao Yuan , Li Hua , Liang Hongda , Xin Miaomiao , Wang Liqin , Zhao Lei , Lin Jizheng , Liu Shiguo 
Published: March 2016

AbstractIL-27 could inhibit the development of Th17 cells, and the Th17/regulatory T-cell imbalance may reverse maternal tolerance in pre-eclampsia (PE). The aim of this study was to investigate the association between genetic polymorphisms in IL27 with PE. Three SNPs in IL27 (rs153109, rs17855750, and rs181206) were genotyped in a Chinese Han cohort of 1040 PE patients and 1247 normal pregnant women using the TaqMan allelic discrimination real-time PCR method. The CC genotypic distribution of rs153109 was significantly higher among cases than controls (19.1% versus 13.3%, odds ratio [OR]: 1.54, 95% confidence interval [CI]: 1.23–1.93, p < 0.001), and the CT genotype was found to be significantly lower in cases than controls (41.7% versus 49.0%, OR: 0.74, 95% CI: 0.63–0.88, p < 0.001), disputing existing reports indicating the allele frequency of rs153109 is not significantly different between PE patients and controls. Additionally, the CC genotype of rs153109 was significantly more prevalent in PE cases than controls using a recessive model (p < 0.001). The allelic and genotypic frequencies of rs17855750 and rs181206 were not significantly different between two groups. Our results reveal that IL27 polymorphisms may be involved in the development of PE in Chinese Han population.
Sustained PI3K Activation exacerbates BLM-induced Lung Fibrosis via activation of pro-inflammatory and pro-fibrotic pathways
Authors: Kral Julia Barbara , Kuttke Mario , Schrottmaier Waltraud Cornelia , Birnecker Birgit , Warszawska Joanna , Wernig Christina , Paar Hannah , Salzmann Manuel , Sahin Emine , Brunner Julia Stefanie , Österreicher Christoph , Knapp Sylvia , Assinger Alice , Schabbauer Gernot 
Published: March 2016

AbstractIdiopathic pulmonary fibrosis (IPF) is a life-threatening disease with limited treatment options. Additionally, the lack of a complete understanding of underlying immunological mechanisms underscores the importance of discovering novel options for therapeutic intervention. Since the PI3K/PTEN pathway in myeloid cells influences their effector functions, we wanted to elucidate how sustained PI3K activity induced by cell-type specific genetic deficiency of its antagonist PTEN modulates IPF, in a murine model of bleomycin-induced pulmonary fibrosis (BIPF). We found that myeloid PTEN deficient mice (PTENMyKO), after induction of BIPF, exhibit increased TGF-β1 activation, mRNA expression of pro-collagens and lysyl oxidase as well as augmented collagen deposition compared to wild-type littermates, leading to enhanced morbidity and decreased survival. Analysis of alveolar lavage and lung cell composition revealed that PTENMyKO mice exhibit reduced numbers of macrophages and T-cells in response to bleomycin, indicating an impaired recruitment function. Interestingly, we found dysregulated macrophage polarization as well as elevated expression and release of the pro-fibrotic cytokines IL-6 and TNF-α in PTENMyKO mice during BIPF. This might point to an uncontrolled wound healing response in which the inflammatory as well as tissue repair mechanisms proceed in parallel, thereby preventing resolution and at the same time promoting extensive fibrosis.
Differential network analysis reveals the genome-wide landscape of estrogen receptor modulation in hormonal cancers
Authors: Hsiao Tzu-Hung , Chiu Yu-Chiao , Hsu Pei-Yin , Lu Tzu-Pin , Lai Liang-Chuan , Tsai Mong-Hsun , Huang Tim H.-M. , Chuang Eric Y. , Chen Yidong 
Published: March 2016

AbstractSeveral mutual information (MI)-based algorithms have been developed to identify dynamic gene-gene and function-function interactions governed by key modulators (genes, proteins, etc.). Due to intensive computation, however, these methods rely heavily on prior knowledge and are limited in genome-wide analysis. We present the modulated gene/gene set interaction (MAGIC) analysis to systematically identify genome-wide modulation of interaction networks. Based on a novel statistical test employing conjugate Fisher transformations of correlation coefficients, MAGIC features fast computation and adaption to variations of clinical cohorts. In simulated datasets MAGIC achieved greatly improved computation efficiency and overall superior performance than the MI-based method. We applied MAGIC to construct the estrogen receptor (ER) modulated gene and gene set (representing biological function) interaction networks in breast cancer. Several novel interaction hubs and functional interactions were discovered. ER+ dependent interaction between TGFβ and NFκB was further shown to be associated with patient survival. The findings were verified in independent datasets. Using MAGIC, we also assessed the essential roles of ER modulation in another hormonal cancer, ovarian cancer. Overall, MAGIC is a systematic framework for comprehensively identifying and constructing the modulated interaction networks in a whole-genome landscape. MATLAB implementation of MAGIC is available for academic uses at https://github.com/chiuyc/MAGIC.