bluuebunny/crossref_metadata_2025_split huggingface dataset:
A unique biofilm in human deep mycoses: fungal amyloid is bound by host serum amyloid P component
Authors: Garcia-Sherman Melissa C , Lundberg Tracy , Sobonya Richard E , Lipke Peter N , Klotz Stephen A 
Published: July 2015

Abstract
Background/objectives:
We have demonstrated the presence of Candida cell surface amyloids that are important in aggregation of fungi and adherence to tissue. Fungal amyloid was present in invasive human candidal infections and host serum amyloid P component (SAP) bound to the fungal amyloid. SAP is a protease-resistant glycoprotein that binds avidly to amyloid and interferes with host defence, especially against bacterial pathogens for which neutrophils are important. In this study, we investigated whether biofilm of fungal amyloid and SAP was a feature of other disseminated fungal infections.

Methods:
Tissue specimens from 15 autopsies were systematically evaluated with multiple histochemical stains including thioflavin T and Congo red (dyes that stain amyloid), as well as antibody to SAP. We studied specimens with disseminated aspergillosis, mucormycosis and coccidioidomycosis. The structure of the lesions, host inflammatory cells and the presence of fungal amyloid and SAP were determined.

Results:
The structure of the lesions was characteristic in aspergillosis (‘starburst’) and mucormycosis (closely apposed bundles of hyphae). Host inflammatory cells were absent or few in number within these lesions. In Coccidioides lesions, host inflammation was sparse as well. Fungal amyloid was a prominent feature of all lesions along with abundant SAP bound to hyphae and spherules. Fungal amyloid and SAP perhaps contributed to persistence in caseous necrosis lesions. SAP also bound to Aspergillus and Mucorales amyloid in vitro.

Conclusions:
A biofilm including amyloid and SAP is present in invasive fungal infections. This biofilm may dampen host defence leading to the characteristic sparse inflammatory reaction found in these infections.
A versatile snap chip for high-density sub-nanoliter chip-to-chip reagent transfer
Authors: Li Huiyan , Munzar Jeffrey D. , Ng Andy , Juncker David 
Published: July 2015

AbstractThe coordinated delivery of minute amounts of different reagents is important for microfluidics and microarrays, but is dependent on advanced equipment such as microarrayers. Previously, we developed the snap chip for the direct transfer of reagents, thus realizing fluidic operations by only manipulating microscope slides. However, owing to the misalignment between arrays spotted on different slides, millimeter spacing was needed between spots and the array density was limited. In this work, we have developed a novel double transfer method and have transferred 625 spots cm−2, corresponding to >10000 spots for a standard microscope slide. A user-friendly snapping system was manufactured to make liquid handling straightforward. Misalignment, which for direct transfer ranged from 150–250 μm, was reduced to <40 μm for double transfer. The snap chip was used to quantify 50 proteins in 16 samples simultaneously, yielding limits of detection in the pg/mL range for 35 proteins. The versatility of the snap chip is illustrated with a 4-plex homogenous enzyme inhibition assay analyzing 128 conditions with precise timing. The versatility and high density of the snap chip with double transfer allows for the development of high throughput reagent transfer protocols compatible with a variety of applications.
Synthesis of diamond-like phase from graphite by ultrafast laser driven dynamical compression
Authors: Maia Francisco C. B. , Samad Ricardo E. , Bettini Jefferson , Freitas Raul O. , Vieira Junior Nilson D. , Souza-Neto Narcizo M. 
Published: July 2015

AbstractRapid variations of the environmental energy caused by ultrashort laser pulses have induced phase transitions in carbon allotropes, therefore bringing the promise of revealing new carbon phases. Here, by exposing polycrystalline graphite to 25 fs laser pulses at 4 J/cm2 fluence under standard air atmosphere, we demonstrated the synthesis of translucent micrometer-sized structures carrying diamond-like and onion-like carbon phases. Texturized domains of the diamond phase were also identified. Concerning different synthesized carbon forms, pulse superposition and singularities of the thermodynamical process, we pinpoint the synthesis mechanism by the laser-induced subsequent products energetically evolving to attain the diamond-like phase.
Strategy to enhance efficacy of doxorubicin in solid tumor cells by methyl-β-cyclodextrin: Involvement of p53 and Fas receptor ligand complex
Authors: Mohammad Naoshad , Vikram Singh Shivendra , Malvi Parmanand , Chaube Balkrishna , Athavale Dipti , Vanuopadath Muralidharan , Nair Sudarslal Sadasivan , Nair Bipin , Bhat Manoj Kumar 
Published: July 2015

AbstractDoxorubicin (DOX) is one of the preferred drugs for treating breast and liver cancers. However, its clinical application is limited due to severe side effects and the accompanying drug resistance. In this context, we investigated the effect on therapeutic efficacy of DOX by cholesterol depleting agent methyl-β-cyclodextrin (MCD) and explored the involvement of p53. MCD sensitizes MCF-7 and Hepa1–6 cells to DOX, Combination of MCD and marginal dose of DOX reduces the cell viability and promoted apoptosis through induction of pro-apoptotic protein, Bax, activation of caspase-8 and caspase-7, down regulation of anti-apoptotic protein Bcl-2 and finally promoting PARP cleavage. Mechanistically, sensitization to DOX by MCD was due to the induction of FasR/FasL pathway through p53 activation. Furthermore, inhibition of p53 by pharmacological inhibitor pifithrin-α (PFT-α) or its specific siRNA attenuated p53 function and down-regulated FasR/FasL, thereby preventing cell death. Animal experiments were performed using C57BL/6J mouse isografted with Hepa1–6 cells. Tumor growth was retarded and survival increased in mice administered MCD together with DOX to as compared to either agent alone. Collectively, these results suggest that MCD enhances the sensitivity to DOX for which wild type p53 is an important determinant.
Incorporation of a GPI-anchored engineered cytokine as a molecular adjuvant enhances the immunogenicity of HIV VLPs
Authors: Feng Hao , Zhang Han , Deng Jiusheng , Wang Li , He Yuan , Wang Shelly , Seyedtabaei Roheila , Wang Qing , Liu Laiting , Galipeau Jacques , Compans Richard W. , Wang Bao-Zhong 
Published: July 2015

AbstractHIV vaccines should elicit immune responses at both the mucosal portals of entry to block transmission and systemic compartments to clear disseminated viruses. Co-delivery of mucosal adjuvants has been shown to be essential to induce effective mucosal immunity by non-replicating vaccines. A novel cytokine, GIFT4, engineered by fusing GM-CSF and interleukin-4, was previously found to simulate B cell proliferation and effector function. Herein a membrane-anchored form of GIFT4 was constructed by fusing a glycolipid (GPI)-anchoring sequence and incorporated into Env-enriched HIV virus-like particles (VLPs) as a molecular adjuvant. Guinea pigs were immunized with the resulting HIV VLPs through an intramuscular priming-intranasal boosting immunization route. The GIFT4-containing VLPs induced higher levels of systemic antibody responses with significantly increased binding avidity and improved neutralizing breadth and potency to a panel of selected strains, as well as higher levels of IgG and IgA at several mucosal sites. Thus, the novel GPI-GIFT4-containging VLPs have the potential to be developed into a prophylactic HIV vaccine. Incorporation of GPI-anchored GIFT4 into VLPs as a molecular adjuvant represents a novel approach to increase their immunogenicity.
Who started first? Bird species visiting novel birdfeeders
Authors: Tryjanowski Piotr , Morelli Federico , Skórka Piotr , Goławski Artur , Indykiewicz Piotr , Pape Møller Anders , Mitrus Cezary , Wysocki Dariusz , Zduniak Piotr 
Published: July 2015

AbstractAdapting to exploit new food sources may be essential, particularly in winter, when the impact of food limitation on survival of individuals is critical. One of the most important additional sources of food for birds in human settlements is birdfeeders. At a large spatial scale, we experimentally provided birdfeeders with four different kinds of food to analyze exploitation and use of a novel food supply provided by humans. Nine species started foraging at the new birdfeeders. The species that exploited the new feeders the fastest was the great tit. Use of novel food sources was faster in urban habitats and the presence of other feeders reduced the time until a new feeder was located. Urbanization may be associated with behavioural skills, technical innovations and neophilia resulting in faster discovery of new food sources. This process is accelerated by the experience of feeder use in the vicinity, with a strong modifying effect of the number of domestic cats.
Electrically induced ambipolar spin vanishments in carbon nanotubes
Authors: Matsumoto D. , Yanagi K. , Takenobu T. , Okada S. , Marumoto K. 
Published: July 2015

AbstractCarbon nanotubes (CNTs) exhibit various excellent properties, such as ballistic transport. However, their electrically induced charge carriers and the relation between their spin states and the ballistic transport have not yet been microscopically investigated because of experimental difficulties. Here we show an electron spin resonance (ESR) study of semiconducting single-walled CNT thin films to investigate their spin states and electrically induced charge carriers using transistor structures under device operation. The field-induced ESR technique is suitable for microscopic investigation because it can directly observe spins in the CNTs. We observed a clear correlation between the ESR decrease and the current increase under high charge density conditions, which directly demonstrated electrically induced ambipolar spin vanishments in the CNTs. The result provides a first clear evidence of antimagnetic interactions between spins of electrically induced charge carriers and vacancies in the CNTs. The ambipolar spin vanishments would contribute the improvement of transport properties of CNTs because of greatly reduced carrier scatterings.
Mechanistic studies of a novel C-S lyase in ergothioneine biosynthesis: the involvement of a sulfenic acid intermediate
Authors: Song Heng , Hu Wen , Naowarojna Nathchar , Her Ampon Sae , Wang Shu , Desai Rushil , Qin Li , Chen Xiaoping , Liu Pinghua 
Published: July 2015

AbstractErgothioneine is a histidine thio-derivative isolated in 1909. In ergothioneine biosynthesis, the combination of a mononuclear non-heme iron enzyme catalyzed oxidative C-S bond formation reaction and a PLP-mediated C-S lyase (EgtE) reaction results in a net sulfur transfer from cysteine to histidine side-chain. This demonstrates a new sulfur transfer strategy in the biosynthesis of sulfur-containing natural products. Due to difficulties associated with the overexpression of Mycobacterium smegmatis EgtE protein, the proposed EgtE functionality remained to be verified biochemically. In this study, we have successfully overexpressed and purified M. smegmatis EgtE enzyme and evaluated its activities under different in vitro conditions: C-S lyase reaction using either thioether or sulfoxide as a substrate in the presence or absence of reductants. Results from our biochemical characterizations support the assignment of sulfoxide 4 as the native EgtE substrate and the involvement of a sulfenic acid intermediate in the ergothioneine C-S lyase reaction.
Intravitreal TSG-6 suppresses laser-induced choroidal neovascularization by inhibiting CCR2+ monocyte recruitment
Authors: Jin Kim Sang , Ju Lee Hyun , Yun Ji-Hyun , Hwa Ko Jung , Choi Da Ye , Youn Oh Joo 
Published: July 2015

AbstractChoroidal neovascularization (CNV) is the hallmark of wet age-related macular degeneration (AMD), one of the leading causes of blindness in the elderly. Although the pathogenesis of CNV is not clear, a number of studies show that ocular-infiltrating macrophages and inflammation play a critical role in the development of CNV. TNFα-stimulated gene/protein (TSG)-6 is a multifunctional endogenous protein that has anti-inflammatory activities partly by regulating macrophage activation. Therefore, we here investigated the therapeutic potential of TSG-6 in a rat model of CNV induced by laser photocoagulation. Time course analysis showed that the expression of VEGF and pro-inflammatory cytokines in the choroid was up-regulated early after laser injury and gradually decreased to baseline over 14 days. An intravitreal injection of TSG-6 suppressed the expression of VEGF and pro-inflammatory cytokines including CCL2 and reduced the size of CNV. Also, the number of Iba+ and CCR2+ cells including infiltrating macrophages was markedly lower in the CNV lesion of TSG-6-treated eyes. Further analysis identified CCR2+ CD11b+ CD11c+ cells and CCR2+ CD11b-CD11c+ cells as the cell populations that were increased by laser injury and reduced by TSG-6 treatment. Together, the results demonstrate that TSG-6 inhibits inflammation and CCR2+ monocyte recruitment into the choroid and suppresses the development of CNV.
Quantitative constraint-based computational model of tumor-to-stroma coupling via lactate shuttle
Authors: Capuani Fabrizio , De Martino Daniele , Marinari Enzo , De Martino Andrea 
Published: July 2015

AbstractCancer cells utilize large amounts of ATP to sustain growth, relying primarily on non-oxidative, fermentative pathways for its production. In many types of cancers this leads, even in the presence of oxygen, to the secretion of carbon equivalents (usually in the form of lactate) in the cell’s surroundings, a feature known as the Warburg effect. While the molecular basis of this phenomenon are still to be elucidated, it is clear that the spilling of energy resources contributes to creating a peculiar microenvironment for tumors, possibly characterized by a degree of toxicity. This suggests that mechanisms for recycling the fermentation products (e.g. a lactate shuttle) may be active, effectively inducing a mutually beneficial metabolic coupling between aberrant and non-aberrant cells. Here we analyze this scenario through a large-scale in silico metabolic model of interacting human cells. By going beyond the cell-autonomous description, we show that elementary physico-chemical constraints indeed favor the establishment of such a coupling under very broad conditions. The characterization we obtained by tuning the aberrant cell’s demand for ATP, amino-acids and fatty acids and/or the imbalance in nutrient partitioning provides quantitative support to the idea that synergistic multi-cell effects play a central role in cancer sustainment.
Trapped lipopolysaccharide and LptD intermediates reveal lipopolysaccharide translocation steps across the Escherichia coli outer membrane
Authors: Li Xuejun , Gu Yinghong , Dong Haohao , Wang Wenjian , Dong Changjiang 
Published: July 2015

AbstractLipopolysaccharide (LPS) is a main component of the outer membrane of Gram-negative bacteria, which is essential for the vitality of most Gram-negative bacteria and plays a critical role for drug resistance. LptD/E complex forms a N-terminal LPS transport slide, a hydrophobic intramembrane hole and the hydrophilic channel of the barrel, for LPS transport, lipid A insertion and core oligosaccharide and O-antigen polysaccharide translocation, respectively. However, there is no direct evidence to confirm that LptD/E transports LPS from the periplasm to the external leaflet of the outer membrane. By replacing LptD residues with an unnatural amino acid p-benzoyl-L-phenyalanine (pBPA) and UV-photo-cross-linking in E.coli, the translocon and LPS intermediates were obtained at the N-terminal domain, the intramembrane hole, the lumenal gate, the lumen of LptD channel and the extracellular loop 1 and 4, providing the first direct evidence and “snapshots” to reveal LPS translocation steps across the outer membrane.
Dielectric Optical-Controllable Magnifying Lens by Nonlinear Negative Refraction
Authors: Cao Jianjun , Shang Ce , Zheng Yuanlin , Feng Yaming , Chen Xianfeng , Liang Xiaogan , Wan Wenjie 
Published: July 2015

AbstractA simple optical lens plays an important role for exploring the microscopic world in science and technology by refracting light with tailored spatially varying refractive indices. Recent advancements in nanotechnology enable novel lenses, such as, superlens and hyperlens, with sub-wavelength resolution capabilities by specially designed materials’ refractive indices with meta-materials and transformation optics. However, these artificially nano- or micro-engineered lenses usually suffer high losses from metals and are highly demanding in fabrication. Here, we experimentally demonstrate, for the first time, a nonlinear dielectric magnifying lens using negative refraction by degenerate four-wave mixing in a plano-concave glass slide, obtaining magnified images. Moreover, we transform a nonlinear flat lens into a magnifying lens by introducing transformation optics into the nonlinear regime, achieving an all-optical controllable lensing effect through nonlinear wave mixing, which may have many potential applications in microscopy and imaging science.
Protein alterations in women with chronic widespread pain – An explorative proteomic study of the trapezius muscle
Authors: Olausson Patrik , Gerdle Björn , Ghafouri Nazdar , Sjöström Dick , Blixt Emelie , Ghafouri Bijar 
Published: July 2015

AbstractChronic widespread pain (CWP) has a high prevalence in the population and is associated with prominent negative individual and societal consequences. There is no clear consensus concerning the etiology behind CWP although alterations in the central processing of nociception maintained by peripheral nociceptive input has been suggested. Here, we use proteomics to study protein changes in trapezius muscle from 18 female patients diagnosed with CWP compared to 19 healthy female subjects. The 2-dimensional gel electrophoresis (2-DE) in combination with multivariate statistical analyses revealed 17 proteins to be differently expressed between the two groups. Proteins were identified by mass spectrometry. Many of the proteins are important enzymes in metabolic pathways like the glycolysis and gluconeogenesis. Other proteins are associated with muscle damage, muscle recovery, stress and inflammation. The altered expressed levels of these proteins suggest abnormalities and metabolic changes in the myalgic trapezius muscle in CWP. Taken together, this study gives further support that peripheral factors may be of importance in maintaining CWP.
Survival in patchy landscapes: the interplay between dispersal, habitat loss and fragmentation
Authors: Niebuhr Bernardo B. S. , Wosniack Marina E. , Santos Marcos C. , Raposo Ernesto P. , Viswanathan Gandhimohan M. , da Luz Marcos G. E. , Pie Marcio R. 
Published: July 2015

AbstractHabitat loss and fragmentation are important factors determining animal population dynamics and spatial distribution. Such landscape changes can lead to the deleterious impact of a significant drop in the number of species, caused by critically reduced survival rates for organisms. In order to obtain a deeper understanding of the threeway interplay between habitat loss, fragmentation and survival rates, we propose here a spatially explicit multi-scaled movement model of individuals that search for habitat. By considering basic ecological processes, such as predation, starvation (outside the habitat area) and competition, together with dispersal movement as a link among habitat areas, we show that a higher survival rate is achieved in instances with a lower number of patches of larger areas. Our results demonstrate how movement may counterbalance the effects of habitat loss and fragmentation in altered landscapes. In particular, they have important implications for conservation planning and ecosystem management, including the design of specific features of conservation areas in order to enhance landscape connectivity and population viability.
Two Types of Discontinuous Percolation Transitions in Cluster Merging Processes
Authors: Cho Y. S. , Kahng B. 
Published: July 2015

AbstractPercolation is a paradigmatic model in disordered systems and has been applied to various natural phenomena. The percolation transition is known as one of the most robust continuous transitions. However, recent extensive studies have revealed that a few models exhibit a discontinuous percolation transition (DPT) in cluster merging processes. Unlike the case of continuous transitions, understanding the nature of discontinuous phase transitions requires a detailed study of the system at hand, which has not been undertaken yet for DPTs. Here we examine the cluster size distribution immediately before an abrupt increase in the order parameter of DPT models and find that DPTs induced by cluster merging kinetics can be classified into two types. Moreover, the type of DPT can be determined by the key characteristic of whether the cluster kinetic rule is homogeneous with respect to the cluster sizes. We also establish the necessary conditions for each type of DPT, which can be used effectively when the discontinuity of the order parameter is ambiguous, as in the explosive percolation model.
Quantitative and qualitative analysis of the novel antitumor 1,3,4-oxadiazole derivative (GLB) and its metabolites using HPLC-UV and UPLC-QTOF-MS
Authors: Li Pu , Wang Xin , Li Jian , Meng Zhi-Yun , Li Shu-Chun , Li Zhong-Jun , Lu Ying-Yuan , Ren Hong , Lou Ya-Qing , Lu Chuang , Dou Gui-Fang , Zhang Guo-Liang 
Published: July 2015

AbstractFructose-based 3-acetyl-2,3-dihydro-1,3,4-oxadiazole (GLB) is a novel antitumor agent and belongs to glycosylated spiro-heterocyclic oxadiazole scaffold derivative. This research first reported a simple, specific, sensitive and stable high performance liquid chromatography -ultraviolet detector (HPLC-UV) method for the quantitative determination of GLB in plasma. In this method, the chromatographic separation was achieved with a reversed phase C18 column. The calibration curve for GLB was linear at 300 nm. The lower limit of quantification was 10 ng/mL. The precision, accuracy and stability of the method were validated adequately. This method was successfully applied to the pharmacokinetic study in rats for detection of GLB after oral administration. Moreover, the structures of parent compound GLB and its two major metabolites M1 and M2 were identified in plasma using an ultra performance liquid chromatography- electrospray ionization-quadrupole-time of flight- mass spectrometry (UPLC-ESI-QTOF-MS) method. Our results indicated that the di-hydroxylation (M1) and hydroxylation (M2) of GLB are the major metabolites. In conclusion, the present study provided valuable information on an analytical method for the determination of GLB and its metabolites in rats, can be used to support further developing of this antitumor agent.