gebhart/patrepeval huggingface dataset:
Near-field imaging of optical field and plasmon wavefunctions in metal nanoparticles (2006)

Scanning near-field optical microscopes enable optical measurements and observations with a spatial resolution far beyond the diffraction limit of light. This allows us to spatially resolve the positions in nanoparticles and at the same time to investigate spectroscopic characteristics point by point. In this feature article, we focus on near-field microscopic studies on surface plasmons in anisotropic gold nanoparticles and aggregates (nanorods, triangular nanoplates, and aggregated nanospheres). We have utilized linear transmission/scattering as well as nonlinear two-photon excitation measurements in the near field, to observe the local electric field or electromagnetic local density of states. We show that the wavefunction of the plasmon excitation in the nanoparticle resonant with the incident radiation field is visualized by the near-field methods. In the aggregated nanoparticles, strong electric-field enhancement localized in the interstitial sites, which was theoretically predicted previously, is clearly imaged, and its major contribution to surface enhanced Raman scattering is also shown by the near-field images.
Transcriptional Repression of Catalase in Mouse Skin Tumor Progression (2004)

Previous studies in our laboratory have shown that the elevation of reactive oxygen species levels and the repression of the antioxidant enzyme, catalase, played a critical role in the in vitro progression of benign papilloma cells to malignant carcinoma cells. Catalase message, protein levels, and activity levels were found to be downregulated in the malignantly progressed cells. The goal of this study is to further characterize the repression of catalase in malignant progression of mouse skin tumors. To validate the in vitro observations, we examined catalase expression in tumor samples generated by the multistep chemical carcinogenesis protocol. Higher levels of catalase mRNA and protein were observed in benign papillomas versus malignant carcinomas. Nuclear run-on analysis showed that catalase repression in the cultured malignant cells was transcription-dependent. Results from luciferase reporter assays indicated that malignant cells have lower catalase promoter activities than benign papilloma cells, in part through the Wilm's tumor suppressor 1 (WT1) binding site within the proximal promoter region. The WT1 protein levels were found to be inversely correlated with the observed catalase promoter activities, with higher levels observed in the malignant cells versus the benign cells. These results led us to conclude that WT1 is acting as a transcription repressor in catalase gene regulation during tumor progression.
Salt Effects on the Phase Behavior, Structure, and Rheology of Chromonic Liquid Crystals (2005)

Chromonic liquid crystals are formed by the addition of aromatic molecules such as disodium chromoglycate (cromolyn) to water. In this study, we investigate the addition of salts to the lyotropic nematic phase of cromolyn aqueous solutions. The addition of sodium and potassium salts shifts the isotropic-nematic phase boundary upward by more than 10 degrees C, so that samples that were isotropic at room temperature are transformed into nematic phases. Salt effects are predominantly dictated by the cation, not the anion, and appear to differ based on cation size. In contrast to small, hydrated cations like sodium, large, weakly hydrated cations such as tetraethylammonium and tetrabutylammonium shift the phase boundary downward, thus stabilizing the isotropic phase at the expense of the nematic one. The phase behavior results are highly correlated with viscosity measurements, with an upward shift in the phase boundary correlating with an increase in solution viscosity and vice versa. We also probe the microstructure in cromolyn-salt solutions, both indirectly by small-angle neutron scattering (SANS) and directly by cryo-transmission electron microscopy (cryo-TEM). The cryo-TEM images show the presence of rodlike aggregates that possibly undergo a higher order aggregation into bundles in the presence of salt.
Structure of the T cell antigen receptor (TCR): two CD3 epsilon subunits in a functional TCR/CD3 complex. (1991)

Transgenic mice carrying and expressing the human CD3 epsilon gene incorporate the corresponding protein product into T cell receptor (TCR)/CD3 complexes on thymocyte and T cell surfaces. The chimeric antigen receptors allow normal T cell development and selection of repertoires in vivo and are able to transduce activation signals in vitro. We have exploited the ability to distinguish mouse (m) and human (h)CD3 epsilon chains to analyze the stoichiometry of CD3 epsilon in transgenic mouse TCRs. Immunoprecipitation and fluorescence resonance energy transfer experiments demonstrate that such TCRs can contain both h- and mCD3 epsilon chains, implying that more than one CD3 epsilon subunit occurs per TCR. Antigen comodulation studies are consistent with a stochastic use of h- or mCD3 epsilon during receptor assembly, and further suggest a structure for the TCR/CD3 complex with two CD3 epsilon chains. The determination of CD3 epsilon subunit stoichiometry, together with existing biochemical data, allows the generation of a minimal model for the structure of the TCR and illustrates the potential value of the transgenic approach to the analysis of complex receptors.
Integrin-mediated Activation of Focal Adhesion Kinase Is Required for Signaling to Jun NH2-terminal Kinase and Progression through the G1 Phase of the Cell Cycle (1999)

The extracellular matrix exerts a stringent control on the proliferation of normal cells, suggesting the existence of a mitogenic signaling pathway activated by integrins, but not significantly by growth factor receptors. Herein, we provide evidence that integrins cause a significant and protracted activation of Jun NH2-terminal kinase (JNK), while several growth factors cause more modest or no activation of this enzyme. Integrin-mediated stimulation of JNK required the association of focal adhesion kinase (FAK) with a Src kinase and p130(CAS), the phosphorylation of p130(CAS), and subsequently, the recruitment of Crk. Ras and PI-3K were not required. FAK-JNK signaling was necessary for proper progression through the G1 phase of the cell cycle. These findings establish a role for FAK in both the activation of JNK and the control of the cell cycle, and identify a physiological stimulus for JNK signaling that is consistent with the role of Jun in both proliferation and transformation.
IgE-Mediated Allergic Reactions to Potatoes (1990)

We investigated sera of 12 patients with IgE-mediated hypersensitivity reactions to potato, using different in vitro methods. Radioallergosorbent test classes 2-4 (7.6-46.5% binding) were measured with potato allergen disks. Immunoblot detected allergen bands with an isoelectric point range of approximately 4.5-5.2 and mainly in a molecular weight range between 16.00 and 30.00 kD. But also at molecular weights of 43.00 and 65.00 kD allergen bands (IgE specificities) could be detected. Histamine release assay performed with isolated fractions of the potato extract showed a great individual variation and positive results of fractions of molecular weights between 10.00 and 80.00 kD. From our data we conclude that raw potato is a 'multiallergenic' vegetable.
Antibody recognition of a unique tumor-specific glycopeptide antigen (2010)

Aberrant glycosylation and the overexpression of certain carbohydrate moieties is a consistent feature of cancers, and tumor-associated oligosaccharides are actively investigated as targets for immunotherapy. One of the most common aberrations in glycosylation patterns is the presentation of a single O-linked N-acetylgalactosamine on a threonine or serine residue known as the "Tn antigen." Whereas the ubiquitous nature of Tn antigens on cancers has made them a natural focus of vaccine research, such carbohydrate moieties are not always tumor-specific and have been observed on embryonic and nonmalignant adult tissue. Here we report the structural basis of binding of a complex of a monoclonal antibody (237mAb) with a truly tumor-specific glycopeptide containing the Tn antigen. In contrast to glycopeptide-specific antibodies in complex with simple peptides, 237mAb does not recognize a conformational epitope induced in the peptide by sugar substitution. Instead, 237mAb uses a pocket coded by germ-line genes to completely envelope the carbohydrate moiety itself while interacting with the peptide moiety in a shallow groove. Thus, 237mAb achieves its striking tumor specificity, with no observed physiological cross-reactivity to the unglycosylated peptide or the free glycan, by a combination of multiple weak but specific interactions to both the peptide and to the glycan portions of the antigen.
Impact of a novel, antimicrobial dressing on in vivo, Pseudomonas aeruginosa wound biofilm: Quantitative comparative analysis using a rabbit ear model (2014)

The importance of bacterial biofilms to chronic wound pathogenesis is well established. Different treatment modalities, including topical dressings, have yet to show consistent efficacy against wound biofilm. This study evaluates the impact of a novel, antimicrobial Test Dressing on Pseudomonas aeruginosa biofilm-infected wounds. Six-mm dermal punch wounds in rabbit ears were inoculated with 10(6) colony-forming units of P. aeruginosa. Biofilm was established in vivo using our published model. Dressing changes were performed every other day with either Active Control or Test Dressings. Treated and untreated wounds were harvested for several quantitative endpoints. Confirmatory studies were performed to measure treatment impact on in vitro P. aeruginosa and in vivo polybacterial wounds containing P. aeruginosa and Staphylococcus aureus. The Test Dressing consistently decreased P. aeruginosa bacterial counts, and improved wound healing relative to Inactive Vehicle and Active Control wounds (p < 0.05). In vitro bacterial counts were also significantly reduced following Test Dressing therapy (p < 0.05). Similarly, improvements in bacterial burden and wound healing were also achieved in polybacterial wounds (p < 0.05). This study represents the first quantifiable and consistent in vivo evidence of a topical antimicrobial dressing's impact against established wound biofilm. The development of clinically applicable therapies against biofilm such as this is critical to improving chronic wound care.
RayCore (2014)

We present RayCore, a mobile ray-tracing hardware architecture. RayCore facilitates high-quality rendering effects, such as reflection, refraction, and shadows, on mobile devices by performing real-time Whitted ray tracing. RayCore consists of two major components: ray-tracing units (RTUs) based on a unified traversal and intersection pipeline and a tree-building unit (TBU) for dynamic scenes. The overall RayCore architecture offers considerable benefits in terms of die area, memory access, and power consumption. We have evaluated our architecture based on FPGA and ASIC evaluations and demonstrate its performance on different benchmarks. According to the results, our architecture demonstrates high performance per unit area and unit energy, making it highly suitable for use in mobile devices.
Theoretical studies of surface enhanced Raman scattering (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleTheoretical studies of surface enhanced Raman scatteringGeorge C. SchatzCite this: Acc. Chem. Res. 1984, 17, 10, 370–376Publication Date (Print):October 1, 1984Publication History Published online1 May 2002Published inissue 1 October 1984https://pubs.acs.org/doi/10.1021/ar00106a005https://doi.org/10.1021/ar00106a005research-articleACS PublicationsRequest reuse permissionsArticle Views2496Altmetric-Citations408LEARN 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
Molecular and cellular heterogeneity: the hallmark of glioblastoma (2014)

There has been increasing awareness that glioblastoma, which may seem histopathologically similar across many tumors, actually represents a group of molecularly distinct tumors. Emerging evidence suggests that cells even within the same tumor exhibit wide-ranging molecular diversity. Parallel to the discoveries of molecular heterogeneity among tumors and their individual cells, intense investigation of the cellular biology of glioblastoma has revealed that not all cancer cells within a given tumor behave the same. The identification of a subpopulation of brain tumor cells termed "glioblastoma cancer stem cells" or "tumor-initiating cells" has implications for the management of glioblastoma. This focused review will therefore summarize emerging concepts on the molecular and cellular heterogeneity of glioblastoma and emphasize that we should begin to consider each individual glioblastoma to be an ensemble of molecularly distinct subclones that reflect a spectrum of dynamic cell states.
Genetic network inference: from co-expression clustering to reverse engineering (2000)

Advances in molecular biological, analytical and computational technologies are enabling us to systematically investigate the complex molecular processes underlying biological systems. In particular, using high-throughput gene expression assays, we are able to measure the output of the gene regulatory network. We aim here to review datamining and modeling approaches for conceptualizing and unraveling the functional relationships implicit in these datasets. Clustering of co-expression profiles allows us to infer shared regulatory inputs and functional pathways. We discuss various aspects of clustering, ranging from distance measures to clustering algorithms and multiple-cluster memberships. More advanced analysis aims to infer causal connections between genes directly, i.e. who is regulating whom and how. We discuss several approaches to the problem of reverse engineering of genetic networks, from discrete Boolean networks, to continuous linear and non-linear models. We conclude that the combination of predictive modeling with systematic experimental verification will be required to gain a deeper insight into living organisms, therapeutic targeting and bioengineering.
Cytoplasmic control of nuclear behavior during meiotic maturation of frog oocytes (1971)

Abstract Fully grown oocytes of the frog ( Rana pipiens ) undergo cytoplasmic and nuclear maturation when treated with progesterone after the follicular envelopes have been removed. The mechanism of this maturation was investigated by injection of cytoplasm from progesterone‐treated oocytes at various stages of maturation into fully grown but immature oocytes. The injected cytoplasm becomes effective in inducing maturation by 12 hours after progesterone administration, reaches a maximum effectiveness around 20 hours, and then declines after the donor oocytes complete maturation. However, even cytoplasm from early embryos retains some capacity to induce oocyte maturation. The frequency with which maturation is induced is proportional to the volume of the injected cytoplasm. Progesterone itself is not directly responsible for the maturation‐producing effect of injected cytoplasm since injected progesterone does not promote maturation. However, externally applied progesterone does induce the completion of the first meiotic division, presumably by releasing a cytoplasmic “maturation promoting factor.” The production of this cytoplasmic factor was not affected by removal of the nucleus. After completion of the first meiotic division, oocytes cease further development at the metaphase of the second meiotic division, where they remain until fertilized or activated to develop. Cytoplasm from such secondary oocytes when injected into one of the blastomeres at the two‐cell stage of development suppresses mitosis as well as cleavage. Mitosis is usually arrested at metaphase. No such inhibition was brought about by injection of cytoplasm from cleaving blastomeres. Thus, the arrest of mitosis and cleavage can be attributed to a specific “cytostatic factor” in the cytoplasm of the secondary oocyte. Activation of donor secondary oocytes by insemination or pricking with a glass needle soon destroys the cytostatic factor. Likewise, addition of cortical cytoplasm to endoplasm from the secondary oocyte rapidly destroys the cytostatic capacity. This result implies that cortical material is involved in the process of removing the cytostatic factor at the time of normal activation or fertilization. Enucleation of oocytes demonstrated that production and removal of the cytostatic factor is independent of the nucleus.
Preventing Thiol-Yne Addition Improves the Specificity of Strain-Promoted Azide–Alkyne Cycloaddition (2012)

The 1,3-dipolar cycloaddition of azides with ring-strained alkynes is one of the few bioorthogonal reactions suitable for specific biomolecule labeling in complex biological systems. Nevertheless, azide-independent labeling of proteins by strained alkynes can occur to a varying extent, thereby limiting the sensitivity of assays based on strain-promoted azide–alkyne cycloaddition (SPAAC). In this study, a subset of three cyclooctynes, dibenzocyclooctyne (DIBO), azadibenzocyclooctyne (DIBAC), and bicyclo[6.1.0]nonyne (BCN), was used to evaluate the azide-independent labeling of proteins in vitro. For all three cyclooctynes, we show that thiol-yne addition with reduced peptidylcysteines is responsible for most of the azide-independent polypeptide labeling. The identity of the reaction product was confirmed by LC-MS and NMR analysis. Moreover, we show that undesired thiol-yne reactions can be prevented by alkylating peptidylcysteine thiols with iodoacetamide (IAM). Since IAM is compatible with SPAAC, a more specific azide-dependent labeling is achieved by preincubating proteins containing reduced cysteines with IAM.
Human Factor H-related Protein 5 (FHR-5) (2001)

A novel human plasma protein has been identified as a universal component of complement deposits, when complement is detected immunohistochemically in vivo. The protein is homologous to complement factor H and related proteins and has been designated factor H-related protein 5 (FHR-5). FHR-5 was identified by a monoclonal antibody raised using pathologic human glomerular preparations as the immunogen. FHR-5 was purified by affinity chromatography from complement-lysed erythrocytes, and the peptide sequence was obtained. The cDNA was cloned from a human liver library, and FHR-5 was deduced to be a protein containing 551 amino acids organized into nine short consensus repeat motifs. The short consensus repeats of FHR-5 show homology to Factor H and to other Factor H-related proteins, with some unique features demonstrated. Recombinant FHR-5, expressed in insect cells, was shown to bind C3b in vitro. The strong association of FHR-5 with tissue complement deposits in vivo suggests that this additional member of the Factor H family of proteins has a function in complement regulation.
CONTROL OF THE FABRICATION STEPS OF InP MIS TRANSISTORS BY MEANS OF SCANNING PHOTOLUMINESCENCE MEASUREMENTS (1988)

We show the efficiency of scanning photoluminescence measurements for monitoring the quality, homogeneity and reproducibility of the starting wafers and processed substrates after each technological step during the realization of InP MIS transistors. Owing to this new technique, which is noninvasive, contactless and fast, we have obtained a considerable improvement of the fabricated devices.
Fast and robust hand tracking using detection-guided optimization (2015)

Markerless tracking of hands and fingers is a promising enabler for human-computer interaction. However, adoption has been limited because of tracking inaccuracies, incomplete coverage of motions, low framerate, complex camera setups, and high computational requirements. In this paper, we present a fast method for accurately tracking rapid and complex articulations of the hand using a single depth camera. Our algorithm uses a novel detectionguided optimization strategy that increases the robustness and speed of pose estimation. In the detection step, a randomized decision forest classifies pixels into parts of the hand. In the optimization step, a novel objective function combines the detected part labels and a Gaussian mixture representation of the depth to estimate a pose that best fits the depth. Our approach needs comparably less computational resources which makes it extremely fast (50 fps without GPU support). The approach also supports varying static, or moving, camera-to-scene arrangements. We show the benefits of our method by evaluating on public datasets and comparing against previous work.
Auto-Assembling of Ditopic Macrocyclic Lanthanide Chelates with Transition-Metal Ions. Rigid Multimetallic High Relaxivity Contrast Agents for Magnetic Resonance Imaging (2006)

PhenHDO3A is a ditopic ligand featuring a tetraazacyclododecane unit substituted by three acetate arms and one 6-hydroxy-5,6-dihydro-1,10-phenanthroline group (PhenHDO3A = rel-10-[(5R,6R)-5,6-dihydro-6-hydroxy-1,10-phenantholin-5-yl)-1,4,7,10-tetraazacyclododecane-1,4,7-triacetic acid). This ligand was specially designed so as to obtain highly stable heteropolymetallic assemblies. PhenHDO3A has been prepared starting from phenanthroline epoxide and either a triprotected tetraazacyclododecane or tert-butyl triester of N,N‘,N‘ ‘-tetraazacyclododecane-triacetic acid. The latter yields PhenHDO3A in a single step. PhenHDO3A forms kinetically stable lanthanide complexes (acid-catalyzed kinetic constant kH = (1.2 ± 0.2) × 10-3 s-1 M-1) whose solution structure has been deduced from a quantitative analysis of the paramagnetic shifts and the longitudinal relaxation times of the proton nuclei of YbPhenHDO3A. The alcohol group of the dihydro-phenanthroline unit remains coordinated to the encapsulated metal ion despite the steric crowding brought about by this group. Furthermore, the complexes are monohydrated, as shown by luminescence lifetime measurements on EuPhenHDO3A solutions. Relaxivity titrations at 20 MHz clearly indicate that the phenanthroline unit of GdPhenHDO3A is available for the spontaneous formation of highly stable tris complexes with the Fe2+ and Ni2+ ions. The water-exchange times and the rotational correlation times of GdPhenHDO3A and Fe(GdPhenHDO3A)32+ have been deduced from variable temperature 17O NMR studies and from nuclear relaxation dispersion curves. Despite rather slow water-exchange rates (τm0 = 1.0−1.2 × 10-6 s), relaxivity gains of 90% have been observed upon the formation of the heterometallic tris complexes. The latter rotate about four times more slowly (τr0 = 398 ps) than the monomeric unit (τr0 = 105 ps) and their relaxivity is, accordingly, twice as high. The relaxivity of the tris complexes between 10 and 50 MHz is comparable to relaxivities reported for Gd3+-containing dendrimers of much higher molecular weights. The high relaxivity of the tris-PhenHDO3A lanthanide complexes is attributed to their internal rigidity.