gebhart/patrepeval huggingface dataset:
Directed Assembly of One-Dimensional Nanostructures into Functional Networks (2001)

One-dimensional nanostructures, such as nanowires and nanotubes, represent the smallest dimension for efficient transport of electrons and excitons and thus are ideal building blocks for hierarchical assembly of functional nanoscale electronic and photonic structures. We report an approach for the hierarchical assembly of one-dimensional nanostructures into well-defined functional networks. We show that nanowires can be assembled into parallel arrays with control of the average separation and, by combining fluidic alignment with surface-patterning techniques, that it is also possible to control periodicity. In addition, complex crossed nanowire arrays can be prepared with layer-by-layer assembly with different flow directions for sequential steps. Transport studies show that the crossed nanowire arrays form electrically conducting networks, with individually addressable device function at each cross point.
Human bocavirus: Current knowledge and future challenges (2016)

Human bocavirus (HBoV) is a parvovirus isolated about a decade ago and found worldwide in both respiratory samples, mainly from early life and children of 6-24 mo of age with acute respiratory infection, and in stool samples, from patients with gastroenteritis. Since then, other viruses related to the first HBoV isolate (HBoV1), namely HBoV2, HBoV3 and HBoV4, have been detected principally in human faeces. HBoVs are small non-enveloped single-stranded DNA viruses of about 5300 nucleotides, consisting of three open reading frames encoding the first two the non-structural protein 1 (NS1) and nuclear phosphoprotein (NP1) and the third the viral capsid proteins 1 and 2 (VP1 and VP2). HBoV pathogenicity remains to be fully clarified mainly due to the lack of animal models for the difficulties in replicating the virus in <i>in vitro</i> cell cultures, and the fact that HBoV infection is frequently accompanied by at least another viral and/or bacterial respiratory and/or gastroenteric pathogen infection. Current diagnostic methods to support HBoV detection include polymerase chain reaction, real-time PCR, enzyme-linked immunosorbent assay and enzyme immunoassay using recombinant VP2 or virus-like particle capsid proteins, although sequence-independent amplification techniques combined with next-generation sequencing platforms promise rapid and simultaneous detection of the pathogens in the future. This review presents the current knowledge on HBoV genotypes with emphasis on taxonomy, phylogenetic relationship and genomic analysis, biology, epidemiology, pathogenesis and diagnostic methods. The emerging discussion on HBoVs as true pathogen or innocent bystander is also emphasized.
Single-Particle Detection System for Aβ Aggregates: Adaptation of Surface-Fluorescence Intensity Distribution Analysis to Laser Scanning Microscopy (2009)

Today, Alzheimer disease (AD) can be diagnosed with certainty only post mortem. A biomarker method for early diagnosis of AD is urgently needed. Abeta aggregates are directly involved in AD progression and therefore might be useful as biomarker in body fluids. We have developed an ultrasensitive assay system for the detection of Abeta aggregates in body fluids, called surface-fluorescence intensity distribution analysis (FIDA). Surface-FIDA in its first version was based on fluorescence correlation spectroscopy. Here we show that surface-FIDA can also be performed using a laser scanning microscope setup and is then nicely suitable for the characterization of Abeta aggregates.
Hexapeptide-11 is a novel modulator of the proteostasis network in human diploid fibroblasts (2015)

Despite the fact that several natural products (e.g. crude extracts or purified compounds) have been found to activate cell antioxidant responses and/or delay cellular senescence the effect(s) of small peptides on cell viability and/or modulation of protective mechanisms (e.g. the proteostasis network) remain largely elusive. We have thus studied a hexapeptide (Hexapeptide-11) of structure Phe-Val-Ala-Pro-Phe-Pro (FVAPFP) originally isolated from yeast extracts and later synthesized by solid state synthesis to high purity. We show herein that Hexapeptide-11 exhibits no significant toxicity in normal human diploid lung or skin fibroblasts. Exposure of fibroblasts to Hexapeptide-11 promoted dose and time-dependent activation of proteasome, autophagy, chaperones and antioxidant responses related genes. Moreover, it promoted increased nuclear accumulation of Nrf2; higher expression levels of proteasomal protein subunits and increased proteasome peptidase activities. In line with these findings we noted that Hexapeptide-11 conferred significant protection in fibroblasts against oxidative-stress-mediated premature cellular senescence, while at in vivo skin deformation assays in human subjects it improved skin elasticity. Finally, Hexapeptide-11 was found to induce the activity of extracellular MMPs and it also suppressed cell migration. Our presented findings indicate that Hexapeptide-11 is a promising anti-ageing agent.
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability (2013)

We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.
Selective protein and DNA adsorption on PLL-PEG films modulated by ionic strength (2008)

We describe a soft thin film which selectively adsorbs DNA but averts the non-specific binding of proteins. Indium tin oxide (ITO) substrates were surface-modified with a poly(L-lysine)-g-poly(ethylene glycol) (PLL-PEG) film which carries an outer protein-repelling PEG layer and an underlying positively charged PLL layer that attracts DNA. Binding of DNA could be tuned by a factor of over 90 by varying the salt concentration. The dependence of DNA binding on ionic strength was described with a physicochemical model which led to the conclusion of an unexpectedly high enrichment of salt inside the PEG layer. In addition, the model led to an expanded definition of the Debye–Hückel type effective screening length parameter z. Our new findings on a film with dual passivation/attraction properties can find applications in biopolymer-specific coatings useful in bioseparation and biosensing. In addition, the physicochemical characterisation provides new insight into the interactions between biopolymers and polymer-coated interfaces.
Mechanisms of Disease: The Blood-Brain Barrier (2004)

In health and disease and extending to old age, endothelial cells, neurons, and glia constitute a neurovascular unit that regulates the BBB. Advances toward penetrating the BBB must account for both normal and abnormal functions of the neurovascular unit.
Hypothesis: systemic lupus erythematosus as a disease secondary to polyclonal lymphocyte activation. (1991)

Systemic lupus erythematosus (SLE) is characterized by the concomitance of B cell polyclonal activation and the production of a wide spectrum of autoantibodies showing a marked preference for nuclear antigens. We propose the hypothesis that the production of the most pathogenic antinuclear antibodies with high affinity and IgG isotype is driven by antigens liberated by the death of rapidly proliferating lymphoid cells. The disease could evolve in three steps: (1) polyclonal B cell activation and proliferation caused by unknown etiologic factors (virus?, mitogen? ...); (2) primary activation of natural antibody-producing clones leading to the appearance in the serum of large amounts of natural autoantibodies with public idiotype; and (3) secondary immunization against molecules synthesized in large quantities during lymphocyte proliferation, released by dying cells and subsequently presented in an immunogenic form to T cells. These molecules include nucleic acids (DNA, RNA), nucleic acid-binding proteins (histones, Ro, La), and parts of the RNA splicing machinery (RNP). Other autoantibody activities could relate to cross-reactivities or the binding properties of DNA-anti-DNA immune complexes.
Codon 877 Mutation in the Androgen Receptor Gene in Advanced Prostate Cancer: Relation to Antiandrogen Withdrawal Syndrome (1996)

The growth of prostate cancer is androgen responsive, and androgen receptor (AR) is thought to play an important role in the development of this cancer. Recently, some reports demonstrated that AR gene mutations were detected in human prostate cancer tissues. We have previously reported that one of eight endocrine therapy-resistant prostate cancer cases showed AR gene mutation [Suzuki et al: J Steroid Biochem Mol Biol 46:759-765, 1993]. To further investigate structural abnormality of the AR in a large number of human prostate cancers, exons B-H encoding DNA-and hormone-binding domains were examined by single-strand conformation polymorphism analysis of polymerase chain reaction products and direct sequencing. Tissues surgically removed from 30 cases of stage B or C prostate cancer and from 22 cases of endocrine therapy-resistant cancers obtained at autopsy were used in the study. Three out of 22 cancer death cases (14%) revealed AR gene mutations, one of which contained two different mutations-exon D in cancerous prostate and exon H in metastatic tissues. In the other two cases, AR gene mutations in exon H were found in metastatic tissues. All three cases in metastatic tissues showed the same mutation at codon 877 (877Thr-->Ala). In stage B or C cancer tissues and the other cancer death samples, no AR mutation was detected. The mutation in exon H was identical to that reported in a human prostate cancer cell line, LNCaP. These results indicate that AR gene mutation scarcely occurs in the early stage of prostate cancer and that the mutation is found in relation to endocrine therapy resistance. Two patients with an AR gene mutation at codon 877 revealed a remarkable fall in prostate-specific antigen after withdrawal of antiandrogen. Data on the other case were not available. These results indicate that a codon 877 mutation in the AR gene in advanced prostate cancer evokes the antiandrogen withdrawal syndrome. To our knowledge, this report is the first description of relationship between an AR mutation at codon 877 and the antiandrogen withdrawal syndrome.
Electrogenerated Chemiluminescence. 55. Emission from Adsorbed Ru(bpy)32+ on Graphite, Platinum, and Gold (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectrogenerated Chemiluminescence. 55. Emission from Adsorbed Ru(bpy)32+ on Graphite, Platinum, and GoldXiao-Hong Xu and Allen J. BardCite this: Langmuir 1994, 10, 7, 2409–2414Publication Date (Print):July 1, 1994Publication History Published online1 May 2002Published inissue 1 July 1994https://pubs.acs.org/doi/10.1021/la00019a063https://doi.org/10.1021/la00019a063research-articleACS PublicationsRequest reuse permissionsArticle Views373Altmetric-Citations42LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Microscopy refocusing and dark-field imaging by using a simple LED array (2011)

The condenser is one of the main components in most transmitted light compound microscopes. In this Letter, we show that such a condenser can be replaced by a programmable LED array to achieve greater imaging flexibility and functionality. Without mechanically scanning the sample or changing the microscope setup, the proposed approach can be used for dark-field imaging, bright-field imaging, microscopy sectioning, and digital refocusing. Images of a starfish embryo were acquired by using such an approach for demonstration.
Oligosaccharides in the stem region maintain the influenza virus hemagglutinin in the metastable form required for fusion activity (1997)

The influenza A virus hemagglutinin (HA) has three conserved oligosaccharides located in the stem region at asparagine residues 12, 28, and 478. The biological role of these oligosaccharides has been investigated by mutational analysis of HA of fowl plague virus that was expressed from a simian virus 40 vector in the presence of ammonium chloride for protection from acid denaturation in the trans-Golgi network. Resistance to endoglycosidase H and cleavage of HA into the subunits HA1 and HA2 have been analyzed as markers for intracellular transport. Cell surface exposure has been determined by hemadsorption following neuraminidase treatment, by immunofluorescence staining, and by fluorescence-activated cell sorter analysis. When all three stem oligosaccharides were removed, transport was almost completely blocked. When two of the three stem oligosaccharides, particularly those at asparagine residues 12 and 28, were missing, HA was transported to the surface but showed extremely low fusion activity. With mutants lacking one stem oligosaccharide, fusion was reduced to a lesser extent. Removal of stem oligosaccharides resulted also in an increase in the pH optimum required for fusion. On the other hand, no reduction in fusion activity was observed when oligosaccharides in the head region of the HA spike were removed. These results indicate that the conserved oligosaccharides in the stem stabilize HA in the form susceptible to the conformational change necessary for fusion.
Production of β‐cells from human embryonic stem cells (2008)

The making of functional pancreatic islets in renewable numbers has been a goal of stem cell biologists since early 2000. Since that time, many studies have reported successful creation of glucose-responsive pancreatic beta-cells. Not until the more recent systematic application of developmental principles to stem cell biology systems were breakthroughs achieved on directed specification of the required early developmental intermediates. The most important first step is the formation of the definitive endoderm (DE) lineage which is compulsory for production of the epithelium of the pancreas and the other important endoderm-derived organs such as the liver, intestine and lung. The formation of DE from embryonic stem cells made possible additional experimentation aimed at directing the endoderm to further specified foregut and pancreatic endoderm lineages. With these discoveries came the first production of immature pancreatic endocrine cells. Most recently, the production in vivo of glucose-responsive insulin-producing cells with the capacity to correct Steptozotocin-induced hyperglycaemia in mice has been achieved. The work leading up to this achievement, in relation to the other principle human stem cell studies conducted in this area, will be briefly described. The necessary steps and ideal characteristics of embryonic stem cell-based differentiation to pancreatic beta-cells capable of glucose stimulated insulin secretion will be underscored.
The Challenge of Finding a Cure for HIV Infection (2009)

Although combination therapy for HIV infection represents a triumph for modern medicine, chronic suppressive therapy is required to contain persistent infection in reservoirs such as latently infected CD4+ lymphocytes and cells of the macrophage-monocyte lineage. Despite its success, chronic suppressive therapy is limited by its cost, the requirement of lifelong adherence, and the unknown effects of long-term treatment. This review discusses our current understanding of suppressive antiretroviral therapy, the latent viral reservoir, and the needs for and challenges of attacking this reservoir to achieve a cure.
Exploiting known sound source signals to improve ICA-based robot audition in speech separation and recognition (2007)

This paper describes a new semi-blind source separation (semi-BSS) technique with independent component analysis (ICA) for enhancing a target source of interest and for suppressing other known interference sources. The semi BSS technique is necessary for double-talk free robot audition systems in order to utilize known sound source signals such as self speech, music, or TV-sound, through a line-in or ubiquitous network. Unlike the conventional semi-BSS with ICA, we use the time-frequency domain convolution model to describe the reflection of the sound and a new mixing process of sounds for ICA. In other words, we consider that reflected sounds during some delay time are different from the original. ICA then separates the reflections as other interference sources. The model enables us to eliminate the frame size limitations of the frequency-domain ICA, and ICA can separate the known sources under a highly reverberative environment. Experimental results show that our method outperformed the conventional semi-BSS using ICA under simulated normal and highly reverberative environments.
Comparison of FcRn‐ and pIgR‐Mediated Transport in MDCK Cells by Fluorescence Confocal Microscopy (2010)

Protein delivery across polarized epithelia is controlled by receptor-mediated transcytosis. Many studies have examined basolateral-to-apical trafficking of polymeric IgA (pIgA) by the polymeric immunoglobulin receptor (pIgR). Less is known about apical-to-basolateral transcytosis, the direction the neonatal Fc receptor (FcRn) transports maternal IgGs across intestinal epithelia. To compare apical-to-basolateral and basolateral-to-apical transcytosis, we co-expressed FcRn and pIgR in Madin-Darby canine kidney (MDCK) cells and used pulse-chase experiments with confocal microscopy to examine transport of apically applied IgG Fcgamma and basolaterally applied pIgA. Fcgamma and pIgA trafficking routes were initially separate but intermixed at later chase times. Fcgamma was first localized near the apical surface, but became more equally distributed across the cell, consistent with concomitant transcytosis and recycling. By contrast, pIgA transport was strongly unidirectional: pIgA shifted from near the basolateral surface to an apical location with increasing time. Some Fcgamma and pIgA fluorescence colocalized in early (EEA1-positive), recycling (Rab11a-positive), and transferrin (Tf)-positive common/basolateral recycling endosomes. Fcgamma became more enriched in Tf-positive endosomes with time, whereas pIgA was sorted from these compartments. Live-cell imaging revealed that vesicles containing Fcgamma or pIgA shared similar mobility characteristics and were equivalently affected by depolymerizing microtubules, indicating that both trafficking routes depended to roughly the same extent on intact microtubules.
Optical Coherence Tomography: Advanced Technology for the Endoscopic Imaging of Barrett's Esophagus (2000)

OCT technology with compact fiberoptic imaging probes can be used as an adjunct to endoscopy for real-time image-guided evaluation of Barrett's esophagus. Linear and radial scan patterns have different advantages and limitations depending upon the application. Ultrahigh-resolution and spectroscopic OCT techniques improve structural tissue recognition and suggest future potential for resolution and contrast enhancements in clinical studies. A new balloon catheter-probe delivery device is proposed for systematic imaging and screening of the esophagus.
Oxidative stress generated by hemorrhagic shock recruits Toll-like receptor 4 to the plasma membrane in macrophages (2006)

Oxidative stress generated by ischemia/reperfusion is known to prime inflammatory cells for increased responsiveness to subsequent stimuli, such as lipopolysaccharide (LPS). The mechanism(s) underlying this effect remains poorly elucidated. These studies show that alveolar macrophages recovered from rodents subjected to hemorrhagic shock/resuscitation expressed increased surface levels of Toll-like receptor 4 (TLR4), an effect inhibited by adding the antioxidant N-acetylcysteine to the resuscitation fluid. Consistent with a role for oxidative stress in this effect, in vitro H2O2 treatment of RAW 264.7 macrophages similarly caused an increase in surface TLR4. The H2O2-induced increase in surface TLR4 was prevented by depleting intracellular calcium or disrupting the cytoskeleton, suggesting the involvement of receptor exocytosis. Further, fluorescent resonance energy transfer between TLR4 and the raft marker GM1 as well as biochemical analysis of the raft components demonstrated that oxidative stress redistributes TLR4 to lipid rafts in the plasma membrane. Preventing the oxidant-induced movement of TLR4 to lipid rafts using methyl-beta-cyclodextrin precluded the increased responsiveness of cells to LPS after H2O2 treatment. Collectively, these studies suggest a novel mechanism whereby oxidative stress might prime the responsiveness of cells of the innate immune system.
Projection display systems based on the Digital Micromirror Device (DMD) (1995)

The DMD is a semiconductor light switch which is making an impact in digital light processing<SUP>TM</SUP> (DLP) applications. It is the world's largest micro-electro-mechanical structures (MEMS) device with chips ranging from 442-thousand to 2.3 million moving mirrors. The DMD operates in a bistable (binary) mode and fully supports the movement to all-digital display systems. Currently, DMD devices are being used to develop a family of projection display products. An overview of digital light processing systems will be given with emphasis on the performance of the first prototypes using this technology, including their value propositions. Finally, the general markets served by this technology, along with the advantages DMD technology offers, will be discussed.
Extracellular Cyclophilin Levels Associate with Parameters of Asthma in Phenotypic Clusters (2011)

Cyps are present in nasal wash samples of asthma patients and may be a novel biomarker for clinical parameters of asthma severity.
Effects of Tumor Necrosis Factor Alpha Antagonist, Platelet Activating Factor Antagonist, and Nitric Oxide Synthase Inhibitor on Experimental Otitis Media with Effusion (2006)

We conclude that sTNFRI, A-85783, and L-NAME can be proposed as alternative future treatments for otitis media with effusion. However, L-NAME may be the least effective of these agents.