bluuebunny/crossref_metadata_2025_split huggingface dataset:
Growth, productivity and relative extinction risk of a data-sparse devil ray
Authors: Pardo Sebastián A. , Kindsvater Holly K. , Cuevas-Zimbrón Elizabeth , Sosa-Nishizaki Oscar , Pérez-Jiménez Juan Carlos , Dulvy Nicholas K. 
Published: September 2016

AbstractDevil rays (Mobula spp.) face intensifying fishing pressure to meet the ongoing international demand for gill plates. The paucity of information on growth, mortality and fishing effort for devil rays make quantifying population growth rates and extinction risk challenging. Furthermore, unlike manta rays (Manta spp.), devil rays have not been listed on CITES. Here, we use a published size-at-age dataset for the Spinetail Devil Ray (Mobula japanica), to estimate somatic growth rates, age at maturity, maximum age and natural and fishing mortality. We then estimate a plausible distribution of the maximum intrinsic population growth rate (rmax) and compare it to 95 other chondrichthyans. We find evidence that larger devil ray species have low somatic growth rate, low annual reproductive output and low maximum population growth rates, suggesting they have low productivity. Fishing rates of a small-scale artisanal Mexican fishery were comparable to our estimate of rmax and therefore probably unsustainable. Devil ray rmax is very similar to that of manta rays, indicating devil rays can potentially be driven to local extinction at low levels of fishing mortality and that a similar degree of protection for both groups is warranted.
Bioelectronic interfaces by spontaneously organized peptides on 2D atomic single layer materials
Authors: Hayamizu Yuhei , So Christopher R. , Dag Sefa , Page Tamon S. , Starkebaum David , Sarikaya Mehmet 
Published: September 2016

AbstractSelf-assembly of biological molecules on solid materials is central to the “bottom-up” approach to directly integrate biology with electronics. Inspired by biology, exquisite biomolecular nanoarchitectures have been formed on solid surfaces. We demonstrate that a combinatorially-selected dodecapeptide and its variants self-assemble into peptide nanowires on two-dimensional nanosheets, single-layer graphene and MoS2. The abrupt boundaries of nanowires create electronic junctions via spatial biomolecular doping of graphene and manifest themselves as a self-assembled electronic network. Furthermore, designed peptides form nanowires on single-layer MoS2 modifying both its electric conductivity and photoluminescence. The biomolecular doping of nanosheets defined by peptide nanostructures may represent the crucial first step in integrating biology with nano-electronics towards realizing fully self-assembled bionanoelectronic devices.
Quantifying overlap between the Deepwater Horizon oil spill and predicted bluefin tuna spawning habitat in the Gulf of Mexico
Authors: Hazen Elliott L. , Carlisle Aaron B. , Wilson Steven G. , Ganong James E. , Castleton Michael R. , Schallert Robert J. , Stokesbury Michael J. W. , Bograd Steven J. , Block Barbara A. 
Published: September 2016

AbstractAtlantic bluefin tuna (Thunnus thynnus) are distributed throughout the North Atlantic and are both economically valuable and heavily exploited. The fishery is currently managed as two spawning populations, with the GOM population being severely depleted for over 20 years. In April-August of 2010, the Deepwater Horizon oil spill released approximately 4 million barrels of oil into the GOM, with severe ecosystem and economic impacts. Acute oil exposure results in mortality of bluefin eggs and larvae, while chronic effects on spawning adults are less well understood. Here we used 16 years of electronic tagging data for 66 bluefin tuna to identify spawning events, to quantify habitat preferences, and to predict habitat use and oil exposure within Gulf of Mexico spawning grounds. More than 13,600 km2 (5%) of predicted spawning habitat within the US EEZ was oiled during the week of peak oil dispersal, with potentially lethal effects on eggs and larvae. Although the oil spill overlapped with a relatively small portion of predicted spawning habitat, the cumulative impact from oil, ocean warming and bycatch mortality on GOM spawning grounds may result in significant effects for a population that shows little evidence of rebuilding.
Mesenchymal Stem/Stromal Cells seeded on cartilaginous endplates promote Intervertebral Disc Regeneration through Extracellular Matrix Remodeling
Authors: Pereira Catarina Leite , Teixeira Graciosa Q. , Ribeiro-Machado Cláudia , Caldeira Joana , Costa Madalena , Figueiredo Francisco , Fernandes Rui , Aguiar Paulo , Grad Sibylle , Barbosa Mário A. , Gonçalves Raquel M. 
Published: September 2016

AbstractIntervertebral disc (IVD) degeneration is characterized by significant biochemical and histomorphological alterations, such as loss of extracellular matrix (ECM) integrity, by abnormal synthesis of ECM main components, resultant from altered anabolic/catabolic cell activities and cell death. Mesenchymal Stem/Stromal Cell (MSC) migration towards degenerated IVD may represent a viable strategy to promote tissue repair/regeneration. Here, human MSCs (hMSCs) were seeded on top of cartilaginous endplates (CEP) of nucleotomized IVDs of bovine origin and cultured ex vivo up to 3 weeks. hMSCs migrated from CEP towards the lesion area and significantly increased expression of collagen type II and aggrecan in IVD, namely in the nucleus pulposus. Concomitantly, hMSCs stimulated the production of growth factors, promoters of ECM synthesis, such as fibroblast growth factor 6 (FGF-6) and 7 (FGF-7), platelet-derived growth factor receptor (PDGF-R), granulocyte-macrophage colony-stimulating factor (GM-CSF) and insulin-like growth factor 1 receptor (IGF-1sR). Overall, our results demonstrate that CEP can be an alternative route to MSC-based therapies for IVD regeneration through ECM remodeling, thus opening new perspectives on endogenous repair capacity through MSC recruitment.
Systematic analysis of genetic variants in Han Chinese patients with sporadic Parkinson’s disease
Authors: Yuan Lamei , Song Zhi , Deng Xiong , Zheng Wen , Guo Yi , Yang Zhijian , Deng Hao 
Published: September 2016

AbstractParkinson’s disease (PD) is one of the most common neurodegenerative disorders. Accumulated evidence confirms that genetic factors play a considerable role in PD pathogenesis. To examine whether point variants or haplotypes are associated with PD development, genotyping of 35 variants in 22 PD-related genes was performed in a well-characterized cohort of 512 Han Chinese PD patients and 512 normal controls. Both Pearson’s χ2 test and haplotype analysis were used to evaluate whether variants or their haplotypes were associated with PD in this cohort. The only statistically significant differences in genotypic and allelic frequencies between the patients and the controls were in the DnaJ heat shock protein family (Hsp40) member C10 gene (DNAJC10) variant rs13414223 (P = 0.004 and 0.002, respectively; odds ratio = 0.652, 95% confidence interval: 0.496–0.857). No other variants or haplotypes exhibited any significant differences between these two groups (all corrected P > 0.05). Our findings indicate that the variant rs13414223 in the DNAJC10 gene, a paralog of PD-related genes DNAJC6 and DNAJC13, may play a protective role in PD. This suggests it may be a PD-associated gene.
Roll-to-Roll sputtered ITO/Cu/ITO multilayer electrode for flexible, transparent thin film heaters and electrochromic applications
Authors: Park Sung-Hyun , Lee Sang-Mok , Ko Eun-Hye , Kim Tae-Ho , Nah Yoon-Chae , Lee Sang-Jin , Lee Jae Heung , Kim Han-Ki 
Published: September 2016

AbstractWe fabricate high-performance, flexible, transparent electrochromic (EC) films and thin film heaters (TFHs) on an ITO/Cu/ITO (ICI) multilayer electrode prepared by continuous roll-to-roll (RTR) sputtering of ITO and Cu targets. The RTR-sputtered ICI multilayer on a 700 mm wide PET substrate at room temperature exhibits a sheet resistance of 11.8 Ω/square and optical transmittance of 73.9%, which are acceptable for the fabrication of flexible and transparent EC films and TFHs. The effect of the Cu interlayer thickness on the electrical and optical properties of the ICI multilayer was investigated in detail. The bending and cycling fatigue tests demonstrate that the RTR-sputtered ICI multilayer was more flexible than a single ITO film because of high strain failure of the Cu interlayer. The flexible and transparent EC films and TFHs fabricated on the ICI electrode show better performances than reference EC films and TFHs with a single ITO electrode. Therefore, the RTR-sputtered ICI multilayer is the best substitute for the conventional ITO film electrode in order to realize flexible, transparent, cost-effective and large-area EC devices and TFHs that can be used as flexible and smart windows.
Prevention of allograft rejection in heart transplantation through concurrent gene silencing of TLR and Kinase signaling pathways
Authors: Wang Hongmei , Zhang Xusheng , Zheng Xiufen , Lan Zhu , Shi Jun , Jiang Jifu , Zwiep Terry , Li Qing , Quan Douglas , Zhang Zhu-Xu , Min Weiping 
Published: September 2016

AbstractToll-like receptors (TLRs) act as initiators and conductors responsible for both innate and adaptive immune responses in organ transplantation. The mammalian target of rapamycin (mTOR) is one of the most critical signaling kinases that affects broad aspects of cellular functions including metabolism, growth and survival. Recipients (BALB/c) were treated with MyD88, TRIF and mTOR siRNA vectors, 3 and 7 days prior to heart transplantation and 7, 14 and 21 days after transplantation. After siRNA treatment, recipients received a fully MHC-mismatched C57BL/6 heart. Treatment with mTOR siRNA significantly prolonged allograft survival in heart transplantation. Moreover, the combination of mTOR siRNA with MyD88 and TRIF siRNA further extended the allograft survival; Flow cytometric analysis showed an upregulation of FoxP3 expression in spleen lymphocytes and a concurrent downregulation of CD40, CD86 expression, upregulation of PD-L1 expression in splenic dendritic cells in MyD88, TRIF and mTOR treated mice. There is significantly upregulated T cell exhaustion in T cells isolated from tolerant recipients. This study is the first demonstration of preventing immune rejection of allogeneic heart grafts through concurrent gene silencing of TLR and kinase signaling pathways, highlighting the therapeutic potential of siRNA in clinical transplantation.
24(S)-Hydroxycholesterol protects the ex vivo rat retina from injury by elevated hydrostatic pressure
Authors: Ishikawa Makoto , Yoshitomi Takeshi , Zorumski Charles F. , Izumi Yukitoshi 
Published: September 2016

AbstractIn the central nervous system, 24(S)-hydroxycholesterol (24(S)-HC) is an oxysterol synthesized from cholesterol by cholesterol 24-hydroxylase (CYP46A1) encoded by the cyp46a1 gene. In the present study using a rat ex vivo glaucoma model, we found that retinal 24(S)-HC synthesis is facilitated by pressure elevation. Moreover, we found that 24(S)-HC is neuroprotective against pressure mediated retinal degeneration. Quantitative real-time RT-PCR, ELISA and immunohistochemistry revealed that elevated pressure facilitated the expression of cyp46a1 and CYP46A1. Immunohistochemically, the enhanced expression of CYP46A1 was mainly observed in retinal ganglion cells (RGC). LC-MS/MS revealed that 24(S)-HC levels increased in a pressure-dependent manner. Axonal injury and apoptotic RGC death induced by 75 mmHg high pressure was ameliorated by exogenously administered 1 μM 24(S)-HC. In contrast, voriconazole, a CYP46A1 inhibitor, was severely toxic even at normobaric pressure. Under normobaric conditions, 30 μM 24(S)-HC was required to prevent the voriconazole-mediated retinal damage. Taken together, our findings indicate that 24(S)-HC is facilitated by elevated pressure and plays a neuroprotective role under glaucomatous conditions, while voriconazole, an antifungal drug, is retinotoxic. 24(S)-HC and related compounds may serve as potential therapeutic targets for protecting glaucomatous eyes from pressure-induced injuries.
Pharmacological LRRK2 kinase inhibition induces LRRK2 protein destabilization and proteasomal degradation
Authors: Lobbestael E. , Civiero L. , De Wit T. , Taymans J.-M. , Greggio E. , Baekelandt V. 
Published: September 2016

AbstractLeucine-rich repeat kinase 2 (LRRK2) kinase activity is increased in several pathogenic mutations, including the most common mutation, G2019S and is known to play a role in Parkinson’s disease (PD) pathobiology. This has stimulated the development of potent, selective LRRK2 kinase inhibitors as one of the most prevailing disease-modifying therapeutic PD strategies. Although several lines of evidence support beneficial effects of LRRK2 kinase inhibitors, many questions need to be answered before clinical applications can be envisaged. Using six different LRRK2 kinase inhibitors, we show that LRRK2 kinase inhibition induces LRRK2 dephosphorylation and can reduce LRRK2 protein levels of overexpressed wild type and G2019S, but not A2016T or K1906M, LRRK2 as well as endogenous LRRK2 in mouse brain, lung and kidney. The inhibitor-induced reduction in LRRK2 levels could be reversed by proteasomal inhibition, but not by lysosomal inhibition, while mRNA levels remained unaffected. In addition, using LRRK2 S910A and S935A phosphorylation mutants, we show that dephosphorylation of these sites is not required for LRRK2 degradation. Increasing our insight in the molecular and cellular consequences of LRRK2 kinase inhibition will be crucial in the further development of LRRK2-based PD therapies.
Curli mediate bacterial adhesion to fibronectin via tensile multiple bonds
Authors: Oh Yoo Jin , Hubauer-Brenner Michael , Gruber Hermann J. , Cui Yidan , Traxler Lukas , Siligan Christine , Park Sungsu , Hinterdorfer Peter 
Published: September 2016

AbstractMany enteric bacteria including pathogenic Escherichia coli and Salmonella strains produce curli fibers that bind to host surfaces, leading to bacterial internalization into host cells. By using a nanomechanical force-sensing approach, we obtained real-time information about the distribution of molecular bonds involved in the adhesion of curliated bacteria to fibronectin. We found that curliated E. coli and fibronectin formed dense quantized and multiple specific bonds with high tensile strength, resulting in tight bacterial binding. Nanomechanical recognition measurements revealed that approximately 10 bonds were disrupted either sequentially or simultaneously under force load. Thus the curli formation of bacterial surfaces leads to multi-bond structural components of fibrous nature, which may explain the strong mechanical binding of curliated bacteria to host cells and unveil the functions of these proteins in bacterial internalization and invasion.
Direct synthesis of nanodiamonds by femtosecond laser irradiation of ethanol
Authors: Nee Chen-Hon , Yap Seong-Ling , Tou Teck-Yong , Chang Huan-Cheng , Yap Seong- Shan 
Published: September 2016

AbstractCarbon nanomaterials exhibit novel characteristics including enhanced thermal, electrical, mechanical and biological properties. Nanodiamonds; first discovered in meteorites are found to be biocompatible, non-toxic and have distinct optical properties. Here we show that nanodiamonds with the size of <5 nm are formed directly from ethanol via 1025 nm femtosecond laser irradiation. The absorption of laser energy by ethanol increased non-linearly above 100 μJ accompanied by a white light continuum arises from fs laser filamentation. At laser energy higher than 300 μJ, emission spectra of C, O and H in the plasma were detected, indicating the dissociation of C2H5OH. Nucleation of the carbon species in the confined plasma within the laser filaments leads to the formation of nanodiamonds. The energy dependence and the roles of the nonlinear phenomenon to the formation of homogeneous nanodiamonds are discussed. This work brings new possibility for bottom-up nanomaterials synthesis based on nano and ultrafast laser physics.
Full-Color Biomimetic Photonic Materials with Iridescent and Non-Iridescent Structural Colors
Authors: Kawamura Ayaka , Kohri Michinari , Morimoto Gen , Nannichi Yuri , Taniguchi Tatsuo , Kishikawa Keiki 
Published: September 2016

AbstractThe beautiful structural colors in bird feathers are some of the brightest colors in nature and some of these colors are created by arrays of melanin granules that act as both structural colors and scattering absorbers. Inspired by the color of bird feathers, high-visibility structural colors have been created by altering four variables: size, blackness, refractive index and arrangement of the nano-elements. To control these four variables, we developed a facile method for the preparation of biomimetic core-shell particles with melanin-like polydopamine (PDA) shell layers. The size of the core-shell particles was controlled by adjusting the core polystyrene (PSt) particles’ diameter and the PDA shell thicknesses. The blackness and refractive index of the colloidal particles could be adjusted by controlling the thickness of the PDA shell. The arrangement of the particles was controlled by adjusting the surface roughness of the core-shell particles. This method enabled the production of both iridescent and non-iridescent structural colors from only one component. This simple and novel process of using core-shell particles containing PDA shell layers can be used in basic research on structural colors in nature and their practical applications.
A 2D virtual reality system for visual goal-driven navigation in zebrafish larvae
Authors: Jouary Adrien , Haudrechy Mathieu , Candelier Raphaël , Sumbre German 
Published: September 2016

AbstractAnimals continuously rely on sensory feedback to adjust motor commands. In order to study the role of visual feedback in goal-driven navigation, we developed a 2D visual virtual reality system for zebrafish larvae. The visual feedback can be set to be similar to what the animal experiences in natural conditions. Alternatively, modification of the visual feedback can be used to study how the brain adapts to perturbations. For this purpose, we first generated a library of free-swimming behaviors from which we learned the relationship between the trajectory of the larva and the shape of its tail. Then, we used this technique to infer the intended displacements of head-fixed larvae, and updated the visual environment accordingly. Under these conditions, larvae were capable of aligning and swimming in the direction of a whole-field moving stimulus and produced the fine changes in orientation and position required to capture virtual prey. We demonstrate the sensitivity of larvae to visual feedback by updating the visual world in real-time or only at the end of the discrete swimming episodes. This visual feedback perturbation caused impaired performance of prey-capture behavior, suggesting that larvae rely on continuous visual feedback during swimming.
Systematical Evaluation of Mechanically Strong 3D Printed Diluted magnesium Doping Wollastonite Scaffolds on Osteogenic Capacity in Rabbit Calvarial Defects
Authors: Sun Miao , Liu An , Shao Huifeng , Yang Xianyan , Ma Chiyuan , Yan Shigui , Liu Yanming , He Yong , Gou Zhongru 
Published: September 2016

AbstractWollastonite (CaSiO3; CSi) ceramic is a promising bioactive material for bone defect repair due to slightly fast degradation of its porous constructs in vivo. In our previous strategy some key features of CSi ceramic have been significantly improved by dilute magnesium doping for regulating mechanical properties and biodegradation. Here we demonstrate that 6 ~ 14% of Ca substituted by Mg in CSi (CSi-Mgx, x = 6, 10, 14) can enhance the mechanical strength (>40 MPa) but not compromise biological performances of the 3D printed porous scaffolds with open porosity of 60‒63%. The in vitro cell culture tests in vitro indicated that the dilute Mg doping into CSi was beneficial for ALP activity and high expression of osteogenic marker genes of MC3T3-E1 cells in the scaffolds. A good bone tissue regeneration response and elastoplastic response in mechanical strength in vivo were determined after implantation in rabbit calvarial defects for 6‒12 weeks. Particularly, the CSi-Mg10 and CSi-Mg14 scaffolds could enhance new bone regeneration with a significant increase of newly formed bone tissue (18 ~ 22%) compared to the pure CSi (~14%) at 12 weeks post-implantation. It is reasonable to consider that, therefore, such CSi-Mgx scaffolds possessing excellent strength and reasonable degradability are promising for bone reconstruction in thin-wall bone defects.
Sweeter and stronger: enhancing sweetness and stability of the single chain monellin MNEI through molecular design
Authors: Leone Serena , Pica Andrea , Merlino Antonello , Sannino Filomena , Temussi Piero Andrea , Picone Delia 
Published: September 2016

AbstractSweet proteins are a family of proteins with no structure or sequence homology, able to elicit a sweet sensation in humans through their interaction with the dimeric T1R2-T1R3 sweet receptor. In particular, monellin and its single chain derivative (MNEI) are among the sweetest proteins known to men. Starting from a careful analysis of the surface electrostatic potentials, we have designed new mutants of MNEI with enhanced sweetness. Then, we have included in the most promising variant the stabilising mutation E23Q, obtaining a construct with enhanced performances, which combines extreme sweetness to high, pH-independent, thermal stability. The resulting mutant, with a sweetness threshold of only 0.28 mg/L (25 nM) is the strongest sweetener known to date. All the new proteins have been produced and purified and the structures of the most powerful mutants have been solved by X-ray crystallography. Docking studies have then confirmed the rationale of their interaction with the human sweet receptor, hinting at a previously unpredicted role of plasticity in said interaction.
Characterization and Comparative Genomic Analyses of Pseudomonas aeruginosa Phage PaoP5: New Members Assigned to PAK_P1-like Viruses
Authors: Shen Mengyu , Le Shuai , Jin Xiaolin , Li Gang , Tan Yinling , Li Ming , Zhao Xia , Shen Wei , Yang Yuhui , Wang Jing , Zhu Hongbin , Li Shu , Rao Xiancai , Hu Fuquan , Lu Shuguang 
Published: September 2016

AbstractAs a potential alternative to antibiotics, phages can be used to treat multi-drug resistant bacteria. As such, the biological characteristics of phages should be investigated to utilize them as effective antimicrobial agents. In this study, phage PaoP5, a lytic virus that infects Pseudomonas aeruginosa PAO1, was isolated and genomically characterized. PaoP5 comprises an icosahedral head with an apex diameter of 69 nm and a contractile tail with a length of 120 nm. The PaoP5 genome is a linear dsDNA molecule containing 93,464 base pairs (bp) with 49.51% G + C content of 11 tRNA genes and a 1,200 bp terminal redundancy. A total of 176 protein-coding genes were predicted in the PaoP5 genome. Nine PaoP5 structural proteins were identified. Three hypothetical proteins were determined as structural. Comparative genomic analyses revealed that seven new Pseudomonas phages, namely, PaoP5, K8, C11, vB_PaeM_C2-10_Ab02, vB_PaeM_C2-10_Ab08, vB_PaeM_C2-10_Ab10 and vB_PaeM_C2-10_Ab15, were similar to PAK_P1-like viruses. Phylogenetic and pan-genome analyses suggested that the new phages should be assigned to PAK_P1-like viruses, which possess approximately 100 core genes and 150 accessory genes. This work presents a detailed and comparative analysis of PaoP5 to enhance our understanding of phage biology.