gebhart/patrepeval huggingface dataset:
Targeting of renal cell carcinoma with iodine-131-labeled chimeric monoclonal antibody G250. (1997)

131I-cG250 tumor uptake is among the highest reported in clinical studies with antitumor antibodies in solid tumors. Since tumor-sterilizing levels may be guided to the tumor when high doses 131I-cG250 are administered (> 100 mCi) and cG250 appears to be immunosilent, cG250 is a promising vehicle for radioimmunotherapy in RCC.
Plasmonic Properties of Copper Nanoparticles Fabricated by Nanosphere Lithography (2007)

The localized surface plasmon resonance (LSPR) of oxide-free Cu nanoparticles fabricated by nanosphere lithography is examined by UV−vis extinction spectroscopy and electrodynamics theory. The LSPR of the Cu nanoparticles is significantly affected by the presence of copper oxides and the removal of the oxide species yields a dramatic difference in the observed LSPR. From a comparison of the LSPR of Cu, Ag, and Au nanoparticles of similar geometry, we conclude that Cu displays an intense and narrow LSPR peak that is comparable to Ag and Au.
Quantitative characterization of endoscopic imaging fibers (2017)

We describe a technique for the quantitative characterization of endoscopic imaging fibers using an interference pattern as the standard object to be imaged. The visibility of the pattern at the other end of the fiber is then analyzed as wavelength and fringe period are varied. We demonstrate the use of the technique by comparing three fibers: two fabricated in-house from the same preform, designed to minimize inter-core coupling at visible wavelengths less than 650 nm, and a commercial imaging fiber. The techniques discussed are currently being used to optimize fibers for fluorescence bronchoscopy to be used in intensive care clinics.
Formation of Silicon Nanoporous Structures Induced by Colloidal Gold Nanoparticles in HF/H2O2 Solutions (2009)

We developed an efficient method for the production of unique porous silicon structures, capable of achieving very small (less than 20 nm diameter) and uniform pore sizes, without the need for an external electrochemical cell or precoating of a discontinuous metal film. The method consists of the immersion of Si into a colloidal suspension of Au nanoparticles (NPs) containing a HF/H2O2 mixture. Gold colloids are known to be stable in neutral aqueous solutions, mainly because of the electrostatic repulsion between nanoparticles that carry the same negative surface charge. In acidic solutions obtained, for example, by addition of HF, however, conventional Au NPs colloids tend to lose their negative charge and to precipitate. A novel colloidal solution avoids NP precipitation upon acidification and thus enables Au NPs adsorption onto the Si surface, which triggers Si etching along definite crystallographic directions. The etching process occurs independently of the Si doping type or doping level. Because of its efficiency and simplicity, this method is of practical interest for the fabrication of submicrometer patterned silicon nanoporous structures. As a preliminary demonstration, the fabrication of Si membranes with nanosize pores is discussed.
Identification of a cell surface protein, p97, in human melanomas and certain other neoplasms. (1980)

BALB/c mice were immunized with a human melanoma cell line, SK-MEL 28, and their spleen cells were fused with mouse NS-1 myeloma cells. Hybrid cells were tested in an indirect 125I-labeled protein A assay for production of antibodies that bound to surface antigens of SK-MEL 28 melanoma cells but not to autologous skin fibroblasts. One hybridoma, designated 4.1, had the required specificity. It was cloned and grown in mice as an ascites tumor. The monoclonal IgG1 antibody produced by the hybridoma was purified from the ascites fluid and labeled with 125I. The labeled antibody bound, at significant levels, to approximately 90% of the melanomas tested and to approximately 55% of other tumor cells, but not to three B-lymphoblastoid cell lines or to cultivated fibroblasts from 15 donors. Immunoprecipitation and sodium dodecyl sulfate gel electrophoresis were used to detect the target antigen in 125I-labeled cell membranes of both cultivated cells and tumor biopsy samples. A protein with a molecular weight of 97,000 was identified. This protein, designated p97, was present in both cultured cells and biopsy material from melanomas and certain other tumors, but it was not detected in eight different samples of normal adult epithelial or mesenchymal tissues obtained from five donors.
cis and trans requirements for the selective packaging of adenovirus type 5 DNA (1992)

Polar packaging of adenovirus DNA into virions is dependent on the presence of cis-acting sequences at the left end of the viral genome. Our previous analyses demonstrated that the adenovirus type 5 (Ad5) packaging domain (nucleotides 194 to 358) is composed of at least five elements that are functionally redundant. A repeated sequence, termed the A repeat, was associated with packaging function. Here we report a more detailed analysis of the requirements for the selective packaging of Ad5 DNA. By introducing site-directed point mutations into specific A repeat sequences, we demonstrate that the A repeats represent cis-acting functional components of the packaging signal. Additional elements, located outside the originally defined packaging domain boundaries and that resemble the A repeat consensus sequence, also are capable of promoting the packaging of viral DNA. The cis-acting components of the packaging signal appear to be subject to certain spatial constraints for function, possibly reflecting a necessity for the coordinate binding of packaging proteins to these sites. In agreement with this idea, we present evidence that the interaction of a limiting trans-acting factor(s) with the packaging domain in vivo is required for efficient encapsidation of the Ad5 genome.
Expression of CEACAM6 in Resectable Colorectal Cancer: A Factor of Independent Prognostic Significance (2003)

Expression of the cell adhesion molecule CEACAM6 in CRC is an independent prognostic factor allowing subdivision of patients into low- and high-risk groups. Whether CEACAM6 or CEA and CEACAM1 might be useful as predictive markers of chemotherapy benefit remains unclear.
HPK1 positive expression associated with longer overall survival in patients with estrogen receptor-positive invasive ductal carcinoma-not otherwise specified (2017)

Hematopoietic progenitor kinase 1 (HPK1) belongs to the mitogen activated protein kinase kinase kinase kinase (MAP4K) family of serine/threonine kinases, which have been associated with the incidence and progression of a variety of gastrointestinal malignant tumors in humans. However, the potential association between HPK1 expression and breast cancer, particularly invasive ductal carcinoma‑not otherwise specified (IDC‑NOS) development, has not yet been examined. To address this gap, the present study aimed to evaluate HPK1 expression in IDC‑NOS samples and to determine a relationship with clinical prognostic indicators, such as the expression levels of estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2), as well as overall survival of the patients with IDC‑NOS. HPK1 mRNA and protein expression in samples from 148 patients with IDC‑NOS were detected using immunohistochemistry, western blotting and reverse transcription‑quantitative polymerase chain reaction. A total of 54 out of 148 (36.5%) samples were HPK1‑positive, and 100 out of 148 (67.6%) were ER‑positive. Of the latter, 28% (28/100) were HPK1‑positive, and a significant negative association of HPK1 expression with ER positivity was observed (P=0.002; r=‑0.254). In addition, 43.2% (64/148) and 32.4% (48/100) of IDC‑NOS tissues were PR‑ or HER2‑positive, respectively; however, neither indicator correlated with HPK1 (P=0.109 and P=0.558, respectively). HPK1 expression, axillary lymph node metastasis and tumor‑node‑metastasis (TNM) stage were identified as independent factors of overall survival (OS) in the ER‑positive group (P<0.05), and HPK1 positivity was associated with increased OS (P=0.048). HPK1 mRNA levels did not differ between IDC‑NOS and normal adjacent breast tissues, whereas HPK1 protein levels were lower in IDC‑NOS (P<0.05). These results suggested that HPK1 protein may be a potentially effective IDC-NOS therapeutic target.
Antigen-Specific Th9 Cells Exhibit Uniqueness in Their Kinetics of Cytokine Production and Short Retention at the Inflammatory Site (2010)

Recently reported lines of Th9 cells, producing IL-9 and IL-10, were generated by polarization with IL-4 and TGF-β and activation with Abs against CD3 and CD28. In this paper, we analyzed features of Th9 lines similarly polarized but activated by the "natural mode" (i.e., exposure of CD4 cells to their target Ag, hen egg lysozyme [HEL] and APCs). Main observations are the following: 1) both IL-9 and IL-10 were expressed by the line cells, but with strikingly different kinetics, with IL-9 being produced rapidly, reaching a peak on day 3 in culture and declining sharply thereafter, whereas IL-10 production increased gradually, resembling IL-4 and IL-17 production by their corresponding lineage cells; 2) reactivation of Th9, following expansion, triggered faster and higher production of both IL-9 and IL-10; 3) incubating Th9 cells in polarizing media specific for other phenotypes stimulated moderate levels of phenotype switching to Th1 or Th17 but a massive switching to Th2; 4) Th9 cells induced moderate inflammation in HEL-expressing recipient eyes but only when producing high levels of IL-9; and 5) IL-9-producing donor cells were detected in the blood of Th9 recipients but not in their inflamed eyes, suggesting that similar to findings in culture, exposure to HEL in these eyes arrested the IL-9 production in Th9 cells. Collectively, these data provide new information concerning Th9 cells and reveal their uniqueness, in particular with regard to the unusual production kinetics of IL-9 and the short retention of these cells in affected target tissues.
Response of Endophytic Bacterial Communities in Potato Plants to Infection with Erwinia carotovora subsp. atroseptica (2002)

The term endophyte refers to interior colonization of plants by microorganisms that do not have pathogenic effects on their hosts, and various endophytes have been found to play important roles in plant vitality. In this study, cultivation-independent terminal restriction fragment length polymorphism analysis of 16S ribosomal DNA directly amplified from plant tissue DNA was used in combination with molecular characterization of isolates to examine the influence of plant stress, achieved by infection with the blackleg pathogen Erwinia carotovora subsp. atroseptica, on the endophytic population in two different potato varieties. Community analysis clearly demonstrated increased bacterial diversity in infected plants compared to that in control plants. The results also indicated that the pathogen stress had a greater impact on the bacteria population than the plant genotype had. Partial sequencing of the 16S rRNA genes of isolated endophytes revealed a broad phylogenetic spectrum of bacteria, including members of the alpha, beta, and gamma subgroups of the Proteobacteria, high- and low-G+C-content gram-positive organisms, and microbes belonging to the Flexibacter-Cytophaga-Bacteroides group. Screening of the isolates for antagonistic activity against E. carotovora subsp. atroseptica revealed that 38% of the endophytes protected tissue culture plants from blackleg disease.
Applications of higher-order statistics to modelling, identification and cancellation of nonlinear distortion in high-speed samplers and analogue-to-digital converters using the Volterra and Wiener models (2002)

The authors demonstrate the use of the Volterra and Wiener models for the identification and removal of low order (soft) nonlinear distortion in high speed analogue-to-digital converters. In particular, they show that the Volterra and Wiener models may be used to identify and remove low order distortion in a typical high speed flash or two-stage subranging type analogue-to-digital converter, in which the input signal dependent timing jitter in its sample-and-hold circuit is the dominant source of distortion. A fifth order Volterra model is used to represent the sampler's timing jitter distortion. They obtain the Volterra model kernels using either the Lee-Schetzen (1976, 1989) method and the relationship between the Wiener and Volterra kernels, or by using an adaptive method to obtain the Volterra kernels directly. They then use a fifth order Volterra inverse to apply post-distortion to compensate for the sampler distortion.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Non-Conjugated Small Molecule FRET for Differentiating Monomers from Higher Molecular Weight Amyloid Beta Species (2011)

We believe that this FRET technique could potentially be used as a tool for screening for inhibitors of Aβ aggregation. We also suggest that this concept could be generalized to other misfolded proteins/peptides implicated in various pathologies including amyloid in diabetes, prion in bovine spongiform encephalopathy, tau protein in AD, and α-synuclein in Parkinson disease.
Direct Involvement of Yeast Type I Myosins in Cdc42-Dependent Actin Polymerization (2000)

The generation of cortical actin filaments is necessary for processes such as cell motility and cell polarization. Several recent studies have demonstrated that Wiskott-Aldrich syndrome protein (WASP) family proteins and the actin-related protein (Arp) 2/3 complex are key factors in the nucleation of actin filaments in diverse eukaryotic organisms. To identify other factors involved in this process, we have isolated proteins that bind to Bee1p/Las17p, the yeast WASP-like protein, by affinity chromatography and mass spectroscopic analysis. The yeast type I myosins, Myo3p and Myo5p, have both been identified as Bee1p-interacting proteins. Like Bee1p, these myosins are essential for cortical actin assembly as assayed by in vitro reconstitution of actin nucleation sites in permeabilized yeast cells. Analysis using this assay further demonstrated that the motor activity of these myosins is required for the polymerization step, and that actin polymerization depends on phosphorylation of myosin motor domain by p21-activated kinases (PAKs), downstream effectors of the small guanosine triphosphatase, Cdc42p. The type I myosins also interact with the Arp2/3 complex through a sequence at the end of the tail domain homologous to the Arp2/3-activating region of WASP-like proteins. Combined deletions of the Arp2/3-interacting domains of Bee1p and the type I myosins abolish actin nucleation sites at the cortex, suggesting that these proteins function redundantly in the activation of the Arp2/3 complex.
Anxiety Disorders and Risk for Suicidal Ideation and Suicide Attempts (2005)

This is the first study to demonstrate that a preexisting anxiety disorder is an independent risk factor for subsequent onset of suicidal ideation and attempts. Moreover, the data clearly demonstrate that comorbid anxiety disorders amplify the risk of suicide attempts in persons with mood disorders. Clinicians and policymakers need to be aware of these findings, and further research is required to delineate whether treatment of anxiety disorders reduces the risk of subsequent suicidal behavior.
Monoclonal antibody against the fusion junction of a deletion-mutant epidermal growth factor receptor (1996)

A mouse monoclonal antibody (IgG2b), 3C10, was produced against the truncated epidermal growth factor receptor (EGFR), encoded by the (type III) in-frame deletion mutation of 801 nucleotides of EGFR affecting the external domain, known to be expressed in some human glioblastoma. As this mutation newly generates a glycine residue at the fusion point, a 14 amino acid peptide around the fusion junction including this glycine was chemically synthesised and used for immunisation of (B6 x DBA/2) F1 mice. Flow cytometric analysis showed 3C10 antibody staining of a mouse NIH/3T3 transfectant (ERM5) with the type III EGFR deletion-mutant gene, but not one with wild-type EGFR. The antibody immunoprecipitated the truncated EGFR protein with a molecular mass of approximately 140 kDa from ERM5 cells. Immunostaining of glioblastomas revealed binding in the case with the type III EGFR mutation, the five other specimens without the mutation being negative despite overexpression of EGFR in some cases.
Electrical surface perturbation of a piezoelectric acoustic plate mode by a conductive liquid loading (1992)

Surface loading of a piezoelectric crystal supporting acoustic plate modes (APMs) by a dilute conductive liquid is analyzed using a perturbation theory. The formulation of the problem is such that only the electrical loading is relevant, and the mass loading and viscous entrainment caused by the solute are ignored. The perturbation in the propagation characteristics is then obtained relative to the solvent and is described in terms of the coupling coefficient, the capacitive loading, and the conductivity of the liquid. The results are compared to measurements made on Z-cut X-propagating LiNbO(3 ) APM device loaded with various conductive liquids of different concentrations. While an interpretation of the results can be given on the use of the APM device as a detector of the liquid properties, it is shown that a conductive liquid loading of the piezoelectric surface can be used as a means of assessing the electromechanical coupling coefficient of APMs.
Structural Changes in Silicon Anodes during Lithium Insertion/Extraction (2004)

The structural changes in silicon electrochemically lithiated and delithiated at room temperature were studied by X-ray powder diffraction. Crystalline silicon becomes amorphous during lithium insertion, confirming previous studies. Highly lithiated amorphous silicon suddenly crystallizes at 50 mV to form a new lithium-silicon phase, identified as This phase is the fully lithiated phase for silicon at room temperature, not as is widely believed. Delithiation of the phase results in the formation of amorphous silicon. Cycling silicon anodes above 50 mV avoids the formation of crystallized phases completely and results in better cycling performance. © 2004 The Electrochemical Society. All rights reserved.
Infrared-Mediated Thermocycling for Ultrafast Polymerase Chain Reaction Amplification of DNA (1998)

Interest in improving the speed of DNA analysis via capillary electrophoresis has led to efforts to integrate DNA amplification into microfabricated devices. This has been difficult to achieve since the thermocycling required for effective polymerase chain reaction (PCR) is dependent on an effective contact between the heating source and the PCR mixture vessel. We describe a noncontact method for rapid and effective thermocycling of PCR mixtures in electrophoretic chip-like glass chambers. The thermocycling is mediated through the use of a tungsten lamp as an inexpensive infrared radiation source, with cooling effected with a solenoid-gated compressed air source. With temperature ramping between 94 and 55 degrees C executed in glass microchambers as rapidly as 10 degrees C/s (heating) and 20 degrees C/s (cooling), cycle times as fast as 17 s could be achieved. Successful genomic DNA amplification was carried out with primers specific for the beta-chain of the T-cell receptor, and detectable product could be generated in a fraction of the time required with commercial PCR instrumentation. The noncontact-mediated thermocycling format was not found to be restricted to single DNA fragment amplification. Application of the thermocycling approach to both quantitative competitive PCR (simultaneous amplification of target and competitor DNA) and cycle sequencing reactions (simultaneous amplification of dideoxy terminated fragments) was successful. This sets the stage for implementing DNA thermocycling into a variety of microfabricated formats for rapid PCR fragment identification and DNA sequencing.
Progress Towards Validating the NMDA Receptor Hypofunction Hypothesis of Schizophrenia (2006)

This article describes recent progress towards validation of the N-methyl-D-aspartate (NMDA) receptor hypofunction hypothesis of schizophrenia in preclinical models. Schizophrenia, a complex disease characterized by positive, negative and cognitive symptoms, affects 1% of the world population and requires lifelong, daily maintenance therapy. For the last several decades, thinking in this field has been dominated by the hypothesis that hyperfunction of dopamine pathways played a key role in schizophrenia. However, the therapeutic agents developed from this hypothesis have a slow onset of action and tend to improve only the positive symptoms of the disease. The NMDA receptor antagonist PCP has been shown to induce the positive, negative and cognitive symptoms of schizophrenia in healthy patients and cause a resurgence of symptoms in stable patients. These observations led to the NMDA receptor hypofunction hypothesis as an alternative theory for the underlying cause of schizophrenia. According to this hypothesis, any agent that can potentiate NMDA receptor currents has the potential to ameliorate the symptoms of schizophrenia. To date, NMDA receptor currents can be modulated by either direct action on modulatory sites on the NMDA receptor (i.e., the glycine co-agonist binding site) or indirectly by activation of G-protein coupled receptors (GPCRs) known to potentiate NMDA receptor function (i.e., mGluR5). This review will discuss the NMDA receptor hypofunction hypothesis, the NMDA receptor as an emerging target for the development of novel antipsychotic agents and progress towards in vivo target validation with GlyT1 inhibitors and mGluR5 positive allosteric modulators. Other potential targets for modulating NMDA receptor currents (polyamine sites, muscarinic receptors, etc...) will also be addressed briefly.
A Frameshift Mutation inRPGRExon ORF15 Causes Photoreceptor Degeneration and Inner Retina Remodeling in a Model of X-Linked Retinitis Pigmentosa (2006)

XLPRA2 is an early-onset model of XLRP that is morphologically characterized by abnormal photoreceptor maturation followed by progressive rod-cone degeneration and early inner retina remodeling. The results suggest that therapeutic strategies for this retinal degeneration should target not solely photoreceptor cells but also inner retinal neurons.
Orchid: Integrating Schema Mapping and ETL (2008)

This paper describes Orchid, a system that converts declarative mapping specifications into data flow specifications (ETL jobs) and vice versa. Orchid provides an abstract operator model that serves as a common model for both transformation paradigms; both mappings and ETL jobs are transformed into instances of this common model. As an additional benefit, instances of this common model can be optimized and deployed into multiple target environments. Orchid is being deployed in <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">FastTrack</i> , a data transformation toolkit in IBM Information Server.
Targeting liposomes loaded with melphalan prodrug to tumour vasculature via the Sialyl Lewis X selectin ligand (2013)

SiaLe<sup>X</sup>-ligand provides targeting of cytotoxic liposomes to tumour endothelium and subsequent antivascular effect.