bluuebunny/crossref_metadata_2025_split huggingface dataset:
A High-Throughput, Multi-Cell Phenotype Assay for the Identification of Novel Inhibitors of Chemotaxis/Migration
Authors: Liao Xin-Hua , Meena Netra Pal , Southall Noel , Liu Lunhua , Swaroop Manju , Zhang Arina Li , Xiang Jan Jian , Parent Carole A. , Zheng Wei , Kimmel Alan R. 
Published: March 2016

AbstractChemotaxis and cell migration are fundamental, universal eukaryotic processes essential for biological functions such as embryogenesis, immunity, cell renewal and wound healing, as well as for pathogenesis of many diseases including cancer metastasis and chronic inflammation. To identify novel chemotaxis inhibitors as probes for mechanistic studies and leads for development of new therapeutics, we developed a unique, unbiased phenotypic chemotaxis-dependent Dictyostelium aggregation assay for high-throughput screening using rapid, laser-scanning cytometry. Under defined conditions, individual Dictyostelium secrete chemoattractants, migrate and aggregate. Chemotaxis is quantified by laser-scanning cytometry with a GFP marker expressed only in cells after chemotaxis/multi-cell aggregation. We applied the assay to screen 1,280 known compounds in a 1536-well plate format and identified two chemotaxis inhibitors. The chemotaxis inhibitory activities of both compounds were confirmed in both Dictyostelium and in human neutrophils in a directed EZ-TAXIscan chemotaxis assay. The compounds were also shown to inhibit migration of two human cancer cell lines in monolayer scratch assays. This test screen demonstrated that the miniaturized assay is extremely suited for high-throughput screening of very large libraries of small molecules to identify novel classes of chemotaxis/migratory inhibitors for drug development and research tools for targeting chemotactic pathways universal to humans and other systems.
Novel EGFR-targeted strategy with hybrid peptide against oesophageal squamous cell carcinoma
Authors: Kikuchi Osamu , Ohashi Shinya , Horibe Tomohisa , Kohno Masayuki , Nakai Yukie , Miyamoto Shin’ichi , Chiba Tsutomu , Muto Manabu , Kawakami Koji 
Published: March 2016

AbstractEpidermal growth factor receptor (EGFR) is a key molecule in the pathophysiology of oesophageal squamous cell carcinoma (OSCC). However, EGFR-targeted agents such as anti-EGFR antibody or tyrosine kinase inhibitors for OSCC have not demonstrated any clinical benefits. Recently, a novel chemotherapeutic agent, EGFR(2R)-lytic hybrid peptide, a composite of EGFR-binding peptide and lytic peptide fragments, has been shown to exhibit a potent anti-tumour effect against cancers that express high EGFR levels. In this study, we investigated the validity of employing EGFR(2R)-lytic hybrid peptide against OSCC cells both in vitro and in vivo. Additionally, the toxicity of this peptide was assessed in mice. We found high EGFR expression levels on the cell surface of OSCC cells and the EGFR-binding peptide fragment showed high affinity for OSCC cells. A potent cytotoxic effect was induced within 30 minutes by the exposure of OSCC cells to EGFR(2R)-lytic hybrid peptide. Furthermore, EGFR(2R)-lytic hybrid peptide markedly suppressed the tumour growth of OSCC cells in a xenograft model. Moreover, it did not cause any identifiable adverse effects in mice. Taken together, EGFR(2R)-lytic hybrid peptide was shown to be a valid therapeutic agent against OSCC, providing a crucial rationale regarding novel EGFR-targeted therapies against OSCC.
Controlled Electromagnetically Induced Transparency and Fano Resonances in Hybrid BEC-Optomechanics
Authors: Yasir Kashif Ammar , Liu Wu-Ming 
Published: March 2016

AbstractCavity-optomechanics, a tool to manipulate mechanical effects of light to couple optical field with other physical objects, is the subject of increasing investigations, especially with regards to electromagnetically induced transparency (EIT). EIT, a result of Fano interference among different atomic transition levels, has acquired a significant importance in many areas of physics, such as atomic physics and quantum optics. However, controllability of such multi-dimensional systems has remained a crucial issue. In this report, we investigate the controllability of EIT and Fano resonances in hybrid optomechanical system composed of cigar-shaped Bose-Einstein condensate (BEC), trapped inside high-finesse Fabry-Pérot cavity with one vibrational mirror, driven by a single mode optical field and a transverse pump field. The transverse field is used to control the phenomenon of EIT. It is detected that the strength of transverse field is not only efficiently amplifying or attenuating out-going optical mode but also providing an opportunity to enhance the strength of Fano-interactions which leads to the amplification of EIT-window. To observe these phenomena in laboratory, we suggest a certain set of experimental parameters. The results provide a route for tunable manipulation of optical phenomena, like EIT, which could be a significant step in quantum engineering.
Model of THz Magnetization Dynamics
Authors: Bocklage Lars 
Published: March 2016

AbstractMagnetization dynamics can be coherently controlled by THz laser excitation, which can be applied in ultrafast magnetization control and switching. Here, transient magnetization dynamics are calculated for excitation with THz magnetic field pulses. We use the ansatz of Smit and Beljers, to formulate dynamic properties of the magnetization via partial derivatives of the samples free energy density and extend it to solve the Landau-Lifshitz-equation to obtain the THz transients of the magnetization. The model is used to determine the magnetization response to ultrafast multi- and single-cycle THz pulses. Control of the magnetization trajectory by utilizing the THz pulse shape and polarization is demonstrated.
Experiments testing macroscopic quantum superpositions must be slow
Authors: Mari Andrea , De Palma Giacomo , Giovannetti Vittorio 
Published: March 2016

AbstractWe consider a thought experiment where the preparation of a macroscopically massive or charged particle in a quantum superposition and the associated dynamics of a distant test particle apparently allow for superluminal communication. We give a solution to the paradox which is based on the following fundamental principle: any local experiment, discriminating a coherent superposition from an incoherent statistical mixture, necessarily requires a minimum time proportional to the mass (or charge) of the system. For a charged particle, we consider two examples of such experiments and show that they are both consistent with the previous limitation. In the first, the measurement requires to accelerate the charge, that can entangle with the emitted photons. In the second, the limitation can be ascribed to the quantum vacuum fluctuations of the electromagnetic field. On the other hand, when applied to massive particles our result provides an indirect evidence for the existence of gravitational vacuum fluctuations and for the possibility of entangling a particle with quantum gravitational radiation.
Atomic-Scale Engineering of Abrupt Interface for Direct Spin Contact of Ferromagnetic Semiconductor with Silicon
Authors: Averyanov Dmitry V. , Karateeva Christina G. , Karateev Igor A. , Tokmachev Andrey M. , Vasiliev Alexander L. , Zolotarev Sergey I. , Likhachev Igor A. , Storchak Vyacheslav G. 
Published: March 2016

AbstractControl and manipulation of the spin of conduction electrons in industrial semiconductors such as silicon are suggested as an operating principle for a new generation of spintronic devices. Coherent injection of spin-polarized carriers into Si is a key to this novel technology. It is contingent on our ability to engineer flawless interfaces of Si with a spin injector to prevent spin-flip scattering. The unique properties of the ferromagnetic semiconductor EuO make it a prospective spin injector into silicon. Recent advances in the epitaxial integration of EuO with Si bring the manufacturing of a direct spin contact within reach. Here we employ transmission electron microscopy to study the interface EuO/Si with atomic-scale resolution. We report techniques for interface control on a submonolayer scale through surface reconstruction. Thus we prevent formation of alien phases and imperfections detrimental to spin injection. This development opens a new avenue for semiconductor spintronics.
Silver nanoparticle-enriched diamond-like carbon implant modification as a mammalian cell compatible surface with antimicrobial properties
Authors: Gorzelanny Christian , Kmeth Ralf , Obermeier Andreas , Bauer Alexander T. , Halter Natalia , Kümpel Katharina , Schneider Matthias F. , Wixforth Achim , Gollwitzer Hans , Burgkart Rainer , Stritzker Bernd , Schneider Stefan W. 
Published: March 2016

AbstractThe implant-bone interface is the scene of competition between microorganisms and distinct types of tissue cells. In the past, various strategies have been followed to support bony integration and to prevent bacterial implant-associated infections. In the present study we investigated the biological properties of diamond-like carbon (DLC) surfaces containing silver nanoparticles. DLC is a promising material for the modification of medical implants providing high mechanical and chemical stability and a high degree of biocompatibility. DLC surface modifications with varying silver concentrations were generated on medical-grade titanium discs, using plasma immersion ion implantation-induced densification of silver nanoparticle-containing polyvinylpyrrolidone polymer solutions. Immersion of implants in aqueous liquids resulted in a rapid silver release reducing the growth of surface-bound and planktonicStaphylococcus aureusandStaphylococcus epidermidis. Due to the fast and transient release of silver ions from the modified implants, the surfaces became biocompatible, ensuring growth of mammalian cells. Human endothelial cells retained their cellular differentiation as indicated by the intracellular formation of Weibel-Palade bodies and a high responsiveness towards histamine. Our findings indicate that the integration of silver nanoparticles into DLC prevents bacterial colonization due to a fast initial release of silver ions, facilitating the growth of silver susceptible mammalian cells subsequently.
Oxidation Effects in Rare Earth Doped Topological Insulator Thin Films
Authors: Figueroa A. I. , van der Laan G. , Harrison S. E. , Cibin G. , Hesjedal T. 
Published: March 2016

AbstractThe breaking of time-reversal symmetry (TRS) in topological insulators is a prerequisite for unlocking their exotic properties and for observing the quantum anomalous Hall effect (QAHE). The incorporation of dopants which exhibit magnetic long-range order is the most promising approach for TRS-breaking. REBiTe3, wherein 50% of the Bi is substitutionally replaced by a RE atom (RE = Gd, Dy, and Ho), is a predicted QAHE system. Despite the low solubility of REs in bulk crystals of a few %, highly doped thin films have been demonstrated, which are free of secondary phases and of high crystalline quality. Here we study the effects of exposure to atmosphere of rare earth-doped Bi2(Se, Te)3 thin films using x-ray absorption spectroscopy. We demonstrate that these RE dopants are all trivalent and effectively substitute for Bi3+ in the Bi2(Se, Te)3 matrix. We find an unexpected high degree of sample oxidation for the most highly doped samples, which is not restricted to the surface of the films. In the low-doping limit, the RE-doped films mostly show surface oxidation, which can be prevented by surface passivation, encapsulation, or in-situ cleaving to recover the topological surface state.
Dislocation “Bubble-Like-Effect” and the Ambient Temperature Super-plastic Elongation of Body-centred Cubic Single Crystalline Molybdenum
Authors: Lu Yan , Xiang Sisi , Xiao Lirong , Wang Lihua , Deng Qingsong , Zhang Ze , Han Xiaodong 
Published: March 2016

AbstractWith our recently developed deformation device, the in situ tensile tests of single crystal molybdenum nanowires with various size and aspect ratio were conducted inside a transmission electron microscope (TEM). We report an unusual ambient temperature (close to room temperature) super-plastic elongation above 127% on single crystal body-centred cubic (bcc) molybdenum nanowires with an optimized aspect ratio and size. A novel dislocation “bubble-like-effect” was uncovered for leading to the homogeneous, large and super-plastic elongation strain in the bcc Mo nanowires. The dislocation bubble-like-effect refers to the process of dislocation nucleation and annihilation, which likes the nucleation and annihilation process of the water bubbles. A significant plastic deformation dependence on the sample’s aspect ratio and size was revealed. The atomic scale TEM observations also demonstrated that a single crystal to poly-crystal transition and a bcc to face-centred cubic phase transformation took place, which assisted the plastic deformation of Mo in small scale.
Behaviour of one-step spray-coated carbon nanotube supercapacitor in ambient light harvester circuit with printed organic solar cell and electrochromic display
Authors: Tuukkanen Sampo , Välimäki Marja , Lehtimäki Suvi , Vuorinen Tiina , Lupo Donald 
Published: March 2016

AbstractA printed energy harvesting and storage circuit powered by ambient office lighting and its use to power a printed display is reported. The autonomous device is composed of three printed electronic components: an organic photovoltaic module, a carbon-nanotubes-only supercapacitor and an electrochromic display element. Components are fabricated from safe and environmentally friendly materials and have been fabricated using solution processing methods, which translate into low-cost and high-throughput manufacturing. A supercapacitor made of spray-coated carbon nanotube based ink and aqueous NaCl electrolyte was charged using a printed organic photovoltaic module exposed to office lighting conditions. The supercapacitor charging rate, self-discharge rate and display operation were studied in detail. The supercapacitor self-discharge rate was found to depend on the charging rate. The fully charged supercapacitor was used as a power source to run the electrochromic display over 50 times.
Ultra–sensitive droplet digital PCR for detecting a low–prevalence somatic GNAQ mutation in Sturge–Weber syndrome
Authors: Uchiyama Yuri , Nakashima Mitsuko , Watanabe Satoshi , Miyajima Masakazu , Taguri Masataka , Miyatake Satoko , Miyake Noriko , Saitsu Hirotomo , Mishima Hiroyuki , Kinoshita Akira , Arai Hajime , Yoshiura Ko–ichiro , Matsumoto Naomichi 
Published: March 2016

AbstractDroplet digital PCR (ddPCR), a method for measuring target nucleic acid sequence quantity, is useful for determining somatic mutation rates using TaqMan probes. In this study, the detection limit of copy numbers of test DNA by ddPCR was determined based on Poisson distribution. Peptide nucleic acid (PNA), which strongly hybridises to target lesions, can inhibit target amplification by PCR. Therefore, by combination of PCR with PNA and ddPCR (PNA–ddPCR), the detection limit could be lowered. We reanalysed a somatic GNAQ mutation (c.548G > A) in patients with Sturge–Weber syndrome (SWS) using ddPCR and PNA–ddPCR. Importantly, among three patients previously found to be mutation negative by next–generation sequencing, two patients had the GNAQ mutation with a mutant allele frequency of less than 1%. Furthermore, we were able to find the same mutation in blood leukocyte or saliva DNA derived from four out of 40 SWS patients. Vascular anomalies and blood leukocytes originate from endothelial cells and haemangioblasts, respectively, which are both of mesodermal origin. Therefore, blood leukocytes may harbour the GNAQ mutation, depending on the time when the somatic mutation is acquired. These data suggest the possibility of diagnosis using blood DNA in some patients with SWS.
Chronic Kidney Disease Impairs Bone Defect Healing in Rats
Authors: Liu Weiqing , Kang Ning , Seriwatanachai Dutmanee , Dong Yuliang , Zhou Liyan , Lin Yunfeng , Ye Ling , Liang Xing , Yuan Quan 
Published: March 2016

AbstractChronic kidney disease (CKD) has been regarded as a risk for bone health. The aim of this study was to evaluate the effect of CKD on bone defect repair in rats. Uremia was induced by subtotal renal ablation and serum levels of BUN and PTH were significantly elevated four weeks after the second renal surgery. Calvarial defects of 5-mm diameter were created and implanted with or without deproteinized bovine bone mineral (DBBM). Micro-CT and histological analyses consistently revealed a decreased newly regenerated bone volume for CKD rats after 4 and 8 weeks. In addition, 1.4-mm-diameter cortical bone defects were established in the distal end of femora and filled with gelatin sponge. CKD rats exhibited significantly lower values of regenerated bone and bone mineral density (BMD) within the cortical gap after 2 and 4 weeks. Moreover, histomorphometric analysis showed an increase in both osteoblast number (N.Ob/B.Pm) and osteoclast number (N.Oc/B.Pm) in CKD groups due to hyperparathyroidism. Notably, collagen maturation was delayed in CKD rats as verified by Masson’s Trichrome staining. These data indicate that declined renal function negatively affects bone regeneration in both calvarial and femoral defects.
Topologically associated domains enriched for lineage-specific genes reveal expression-dependent nuclear topologies during myogenesis
Authors: Neems Daniel S. , Garza-Gongora Arturo G. , Smith Erica D. , Kosak Steven T. 
Published: March 2016

Significance
Genome biology aims to gain insight into nuclear function through the study of genome architecture. Analysis of the completed sequences of various eukaryotic genomes indicates that genes are nonrandomly distributed along chromosomes. Recent molecular approaches based on chromosome confirmation capture have identified topologically associated domains (TADs) as a unifying structural model for chromatin organization; however, whether linear gene order and TADs intersect to affect nuclear organization remains to be resolved. Using human myogenesis as a model, we found that a population of TADs have significant enrichment for myogenic-specific genes that results in changes in their subnuclear and intrachromosomal territory structure. We found that these changes in organization impact biallelic transcription and require cell division to be established.
Perceptual learning of degraded speech by minimizing prediction error
Authors: Sohoglu Ediz , Davis Matthew H. 
Published: March 2016

Significance
Experience-dependent changes in sensory processing are critical for successful perception in dynamic and noisy environments. However, the neural and computational mechanisms supporting such changes have remained elusive. Using electrical and magnetic recordings of human brain activity, we demonstrate that two different sources of experience-dependent improvement in perception of degraded speech—the immediate effects of prior knowledge and longer-term changes resulting from perceptual learning—arise from common neural machinery in the sensory cortex although they operate over dramatically different behavioral timescales. Our findings support a specific neuro-computational account of perception in which a single mechanism, minimization of prediction error, drives both the immediate perceptual effects of prior knowledge and longer-term perceptual learning.
Rapid expansion of the protein disulfide isomerase gene family facilitates the folding of venom peptides
Authors: Safavi-Hemami Helena , Li Qing , Jackson Ronneshia L. , Song Albert S. , Boomsma Wouter , Bandyopadhyay Pradip K. , Gruber Christian W. , Purcell Anthony W. , Yandell Mark , Olivera Baldomero M. , Ellgaard Lars 
Published: March 2016

Significance
The majority of secreted proteins contain disulfide bonds that provide structural stability in the extracellular environment. The formation of correct disulfide bonds is assisted by the enzyme protein disulfide isomerase (PDI). Most secreted structural domains are ancient and widely distributed in all metazoans; in contrast, diverse sets of unique disulfide-rich structural domains have more recently evolved in venomous marine snails (superfamily Conoidea comprising >10,000 species). We have discovered a previously undescribed gene family encoding PDIs of unprecedented diversity. We suggest that these enzymes constitute an important part of the supporting molecular infrastructure required for properly folding the plethora of structural domains expressed in the venoms of snails in different conoidean lineages.
Forkhead box A3 mediates glucocorticoid receptor function in adipose tissue
Authors: Ma Xinran , Xu Lingyan , Mueller Elisabetta 
Published: March 2016

SignificanceThis paper shows a previously unidentifed relationship between the transcription factor forkhead box a3 (Foxa3) and the glucocorticoid receptor (GR) by demonstrating, for the first time to our knowledge, that Foxa3 is a target of GR and that it is required for GR transcriptional function in fat depots. Via animal studies we show that the absence of the Foxa3 gene protects the fat depot from the expansion associated with chronic exposure to glucocorticoids, drugs widely used in medical practice to treat inflammatory disease and autoimmune disorders. Overall our findings suggest that Foxa3 can be a potential target for the prevention of glucocorticoid-induced pathological side effects in adipose tissues.
Pathway analysis by randomization incorporating structure—PARIS: an update
Authors: Butkiewicz Mariusz , Cooke Bailey Jessica N. , Frase Alex , Dudek Scott , Yaspan Brian L. , Ritchie Marylyn D. , Pendergrass Sarah A. , Haines Jonathan L. 
Published: March 2016

Abstract
Motivation: We present an update to the pathway enrichment analysis tool ‘Pathway Analysis by Randomization Incorporating Structure (PARIS)’ that determines aggregated association signals generated from genome-wide association study results. Pathway-based analyses highlight biological pathways associated with phenotypes. PARIS uses a unique permutation strategy to evaluate the genomic structure of interrogated pathways, through permutation testing of genomic features, thus eliminating many of the over-testing concerns arising with other pathway analysis approaches.
Results: We have updated PARIS to incorporate expanded pathway definitions through the incorporation of new expert knowledge from multiple database sources, through customized user provided pathways, and other improvements in user flexibility and functionality.
Availability and implementation: PARIS is freely available to all users at https://ritchielab.psu.edu/software/paris-download.
Contact: jnc43@case.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Relationship Between Upper Respiratory Tract Influenza Test Result and Clinical Outcomes Among Critically Ill Influenza Patients
Authors: Reddy Krishna P. , Bajwa Ednan K. , Parker Robert A. , Onderdonk Andrew B. , Walensky Rochelle P. 
Published: March 2016

Abstract
Among critically ill patients with lower respiratory tract (LRT)-confirmed influenza, we retrospectively observed worse 28-day clinical outcomes in upper respiratory tract (URT)-negative versus URT-positive subjects. This finding may reflect disease progression and highlights the need for influenza testing of both URT and LRT specimens to improve diagnostic yield and possibly inform prognosis.