gebhart/patrepeval huggingface dataset:
Major histocompatibility complex class I presentation of exogenous soluble tumor antigen fused to the B-fragment of Shiga toxin (1998)

Targeting exogenous antigen into the MHC class I-restricted presentation pathway is a prerequisite for the induction of cytotoxic T lymphocytes (CTL) which have been shown to represent an important component of the protective and therapeutic immune response to viral infections and tumors. In this study, we produced recombinant proteins composed of the receptor-binding non-toxic B-fragment of bacterial Shiga toxin derived from Shigella dysenteriae associated with an epitope from a model tumor antigen, Mage 1. We show that Shiga B-Mage 1 fusion proteins carrying an active or inactive endoplasmic reticulum retrieval signal (the C-terminal peptides KDEL or KDELGL, respectively) could be presented by peripheral blood mononuclear cells in an MHC class I-restricted manner to Mage 1-specific CTL. After pulsing B lymphoblastoid cells or dendritic cells with Shiga B-Mage 1 fusion protein, activation of the MHC class I-restricted Mage 1-specific CTL was also demonstrated. In further analysis, we showed that treatment with brefeldin A or paraformaldehyde fixation of Epstein-Barr virus-transformed B cells prevented the presentation of the Mage 1 T cell epitope, which excluded extracellular processing of the antigen. Immunofluorescence analysis also revealed that the Shiga B-Mage 1 fusion protein was largely excluded from Lamp-2-positive lysosomal structures. Therefore, the ability of Shiga toxin B-fragment to target dendritic cells and B cells and to direct antigen into the exogenous class I-restricted pathway makes it an attractive non-living and non-toxic vaccine vector.
Current methods for the prediction of T‐cell epitopes (2018)

Abstract T‐cell epitopes are specific peptide sequences derived from foreign or own proteins that can initiate an immune response and which are recognized by specific T‐cells when displayed on the surface of other cells. The prediction of T‐cell epitopes is of particular interest in vaccine design, disease prevention and the development of immunotherapeutics. There are two principal categories of predictive methods: peptide‐sequence based and peptide‐structure‐based. Sequence‐based methods make use of various approaches to identify likely immunogenic amino acid sequences, such as sequence motifs, decision trees, partial least squares (PLS), quantitative matrices (QM), artificial neural networks (ANN), hidden Markov models (HMM), and support vector machines (SVM). Structure‐based methods are more diverse in nature and involve approaches such as quantitative structure‐activity relationships (QSAR), molecular modelling, molecular docking and molecular dynamics simulations (MD). This review highlights the key features of all of these approaches, provides some key examples of their application, and compares and contrasts the most important methods currently in use.
Biased utilization of DHQ52 and JH4 gene segments in a human Ig transgenic minilocus is independent of antigenic selection. (1994)

We have assessed the effect of antigenic selection on human Ig heavy chain D and JH gene segment utilization in mice that contain transgenes composed of 2 VH (psi VH3-105 and VH5-251), 10 D, 6 JH, C mu, and C gamma 1 human gene segments. Human heavy chains using the functional VH5-251 gene segment are expressed in the serum and on the surface of murine B cells. The second VH gene segment (psi VH3-105) is not expressed as a protein but is rearranged and transcribed into mRNA. We previously reported that the functional VH5-251 mu transcripts preferentially used the DHQ52 and JH4 gene segments similar to their use in the human repertoire. Here, we demonstrate that the nonfunctional (psi VH3-105) gene segment shows the same bias in D and JH gene segment utilization. Because transcripts using the pseudo-VH gene segment cannot be subjected to antigenic selection, we conclude that the restricted repertoire observed is Ag independent. Analysis of pseudo VH gene segment recombination products reveals no bias in D gene segment reading frame utilization. Finally, we demonstrate that in the human transgene coding sequence complementarities can affect the recombination site and that D inversion is common.
Direct Observation of Size-Dependent Optical Enhancement in Single Metal Nanoparticles (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationDirect Observation of Size-Dependent Optical Enhancement in Single Metal NanoparticlesSteven R. Emory, William E. Haskins, and Shuming NieView Author Information Department of Chemistry, Indiana University Bloomington, Indiana 47405 Cite this: J. Am. Chem. Soc. 1998, 120, 31, 8009–8010Publication Date (Web):July 24, 1998Publication History Received5 May 1998Published online24 July 1998Published inissue 1 August 1998https://pubs.acs.org/doi/10.1021/ja9815677https://doi.org/10.1021/ja9815677rapid-communicationACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views2876Altmetric-Citations304LEARN 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 SUBJECTS:Colloidal particles,Metal nanoparticles,Nanoparticles,Quantum mechanics,Raman spectroscopy Get e-Alerts
컴퓨터 매개통신 ( CMC ) 학습을 위한 구성주의 교수 설계자 (1999)

오늘날의 원격 교육은 급격하게 변하는 새로운 테크놀로지를 교육에 적용하는데 많은 관심이 집중되어 발전되고 있으나 테크놀로지 활용에 따르는 효율성에 대한 연구나 적절한 교수설계에 대한 연구가 미흡하다. 특히 컴퓨터매개통신(Computer Mediated Communication: 이후로는 CMC)을 활용한 원격교육에서의 교육적 활용과 교수설계에 대한 연구가 절실히 필요하다. 과거의 전통적인 교수설계이론과 객관주의적 교육관을 갖고 있는 교사나 교수설계자는 새로운 테크놀로지인 CMC를 통한 효과적인 학습과 교수설계를 지원하지 못하고 있다고 지적되었다. 그러므로 객관주의적 전통적 교육관 중심의 교수 설계에서 훈련된 교육자들은 CMC 교육환경에서 자신들의 교수설계와 교수 방법적인 측면에서 구성주의적 입장으로 재평가할 필요가 있다. 본 논문에서는 효율적인 CMC 학습활동을 교수설계하기 위한 교수설계와 전이의 유동성(feasibility of the transition)에 역점을 둔 교수설계자에 대해 살펴보았고, 원격교육이론에 입각한 구성주의적 요소와 교수설계시 고려되어야할 심리적 사항들을 검토하였다.
‘‘Self-thickness-limited’’ plasma polymerization of an ultrathin antiadhesive film (1996)

Ultrathin (&amp;lt;5 nm) fluorinated polymer films of homogeneous thicknesses have been deposited from a CF4/H2 microwave discharge. The films have an extremely low surface energy of 4.2 mJ/m2, which is more than four times lower than that for polytetrafluoroethylene. The deposition was carried out in a type of ‘‘self-thickness-limited’’ mode, in which the thickness of the deposited polymer film is limited by the plasma parameters. The deposition can be separated into two phases, a growth and a treatment phase. During the treatment phase, the deposited film is fluorinated, which results in a dramatic decrease of the surface energy. The thickness limiting behavior of the plasma is explained by the dualism of etching and polymerization occurring in fluorocarbon discharges. The film was tested as antiadhesion film for the replication of micro-optical structures, using a Ni shim with a very fine surface relief grating (400 nm periodicity) to hot emboss (at 180 °C) polycarbonate sheed. The tests demonstrate the excellent antiadhesive property of the film with the polycarbonate and reveal a good adhesion of the film with the Ni substrate.
Nucleoporins as Components of the Nuclear Pore Complex Core Structure and Tpr as the Architectural Element of the Nuclear Basket (2004)

The vertebrate nuclear pore complex (NPC) is a macromolecular assembly of protein subcomplexes forming a structure of eightfold radial symmetry. The NPC core consists of globular subunits sandwiched between two coaxial ring-like structures of which the ring facing the nuclear interior is capped by a fibrous structure called the nuclear basket. By postembedding immunoelectron microscopy, we have mapped the positions of several human NPC proteins relative to the NPC core and its associated basket, including Nup93, Nup96, Nup98, Nup107, Nup153, Nup205, and the coiled coil-dominated 267-kDa protein Tpr. To further assess their contributions to NPC and basket architecture, the genes encoding Nup93, Nup96, Nup107, and Nup205 were posttranscriptionally silenced by RNA interference (RNAi) in HeLa cells, complementing recent RNAi experiments on Nup153 and Tpr. We show that Nup96 and Nup107 are core elements of the NPC proper that are essential for NPC assembly and docking of Nup153 and Tpr to the NPC. Nup93 and Nup205 are other NPC core elements that are important for long-term maintenance of NPCs but initially dispensable for the anchoring of Nup153 and Tpr. Immunogold-labeling for Nup98 also results in preferential labeling of NPC core regions, whereas Nup153 is shown to bind via its amino-terminal domain to the nuclear coaxial ring linking the NPC core structures and Tpr. The position of Tpr in turn is shown to coincide with that of the nuclear basket, with different Tpr protein domains corresponding to distinct basket segments. We propose a model in which Tpr constitutes the central architectural element that forms the scaffold of the nuclear basket.
Diffraction Gratings (1976)

Most modern diffraction gratings are metal coated plastic film replicas, on rigid substrates, that were taken from a master. Master gratings are made either by mechanical ruling, where uniformly spaced grooves are burnished in soft metal films by a diamond tool, or by exposing a photoresist coated blank to an interference fringe field generated with the aid of high powered lasers. Basic techniques are described for plane and concave gratings. Performance tests are concerned primarily with diffraction efficiency and with perfection of the diffracted wavefront. Imaging defects show up in reduced resolution. Groove spacing effects show up as ghosts, stray light and satellites. These will be reviewed.
The challenge of cross-trial comparisons using limited data (2014)

The manuscript by Dr David Siegel and colleagues,[1][1] “Integrated safety profile of single-agent carfilzomib: experience from 526 patients enrolled in 4 phase 2 clinical studies”, provides a comprehensive assessment of the available safety data associated with the new proteasome inhibitor
Prevalence and molecular analysis of Anaplasma platys in dogs in Lara, Venezuela (2005)

Blood specimens from clinically normal military dogs and their trainers, in Lara, Venezuela were screened for Anaplasma platys, A. phagocytophilum, or Ehrlichia ewingii using 16S rRNA PCR tests. Sixteen percent (7/43) of dog specimens were positive by A. platys PCR test followed by sequencing of the PCR products, and all human blood specimens [25] were negative. All specimens from these dogs and humans were PCR negative for E. ewingii or A. phagocytophilum. Twelve Rhipicephalus sanguineus ticks removed from these dogs were negative for A. platys by reverse transcription PCR test. Almost the entire 16S rRNA gene (1,364 bp) and groESL operon (1,646 bp) sequences of A. platys isolated from a dog were determined, revealing that both sequences were closely related to the sequences of an A. platys strain detected in R. sanguineus ticks from the Democratic Republic of Congo.
Quantifying Common Drilling Problems With Mechanical Specific Energy and a Bit-Specific Coefficient of Sliding Friction (1992)

ABSTRACT The conventional way to assess drilling performance in the oil field is to compare actual performance to statistical standards derived from offset records. By their nature, these standards are subjective and variable. While they are ideal to monitor short-range performance and trends in well- known, older fields, they lack the power of physical models to establish absolute, technical performance standards. Several authors have proposed models in which the drilling process is treated as a mechanical, energy-balanced system. Mechanical specific energy input, drilling efficiency, and a minimum specific energy equal to the rock strength are the three key elements of these systems. Full-scale simulator tests were conducted under controlled laboratory conditions to develop and validate an energy- balanced model for drilling under hydrostatic pressure. In these tests, wide variations in drilling efficiency from a few percent to three and four times were observed in the spectrum of common drilling practices. They provided new insights into the drilling process and the nature of common drilling problems. Analysis of field data revealed good correlation between simulator and field results. Using mechanical efficiency, specific energy input, and a bit-specific coefficient of sliding friction as key indexes of drilling performance makes bit selection and the diagnosis of failures and drilling practices more accurate and less ambiguous.
The NOTCH Ligand JAGGED2 Promotes Pancreatic Cancer Metastasis Independent of NOTCH Signaling Activation (2014)

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive and lethal disease with a high rate of metastasis. Numerous signaling events have been implicated in the molecular pathogenesis of this neoplasm. Aberrantly high expression of JAGGED2, one of the NOTCH ligands, often occurs in human PDAC. However, what role JAGGED2 plays in the disease development and whether JAGGED2 executes its function through activating NOTCH signaling remain to be determined. We report here that JAGGED2 plays a critical role in promoting PDAC metastasis in vitro and in vivo. Depletion of JAGGED2, but not its homolog JAGGED1, profoundly inhibited both migration and invasion without influencing cell proliferation. Furthermore, reconstitution of JAGGED2 expression rescued the migratory defect. Surprisingly, neither pharmacologic nor genetic inhibition of NOTCH downstream signaling resulted in obvious defect in metastasis. Instead, depletion of NOTCH1 expression per se gave rise to migratory defects similar to JAGGED2 ablation. Moreover, blockade of ligand-receptor interaction by a specific JAGGED2-Fc fusion protein dramatically inhibited PDAC cell migration, suggesting that tumor metastasis relies on physical interactions of JAGGED2-NOTCH1 but not Notch downstream signaling activation. Taken together, our data reveal a novel role of NOTCH in regulation of PDAC metastasis, and identify JAGGED2 as a critical mediator in this event. These findings also provide rationale for developing small molecules or biologic agents targeting JAGGED2 for therapeutic intervention.
A 100 MHz output rate analog-to-digital interface for PRML magnetic-disk read channels in 1.2 μm CMOS (2002)

A key element in the signal path of magnetic-disk read channels employing digital implementations of PRML and other discrete-time signalling approaches is the analog-to-digital (A/D) interface containing a pre-filter, sampler, and analog-to-digital converter (ADC). The pre-filter performs noise filtering, anti-aliasing, and pre-equalization prior to sampling and conversion to the digital domain. At symbol rates of 100 MHz and above, envisioned in the future, implementation of the required filtering is difficult using conventional approaches. This paper describes a filter/ADC combination that uses a switched-capacitor FIR passive sampling approach.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Random Mutagenesis of theAspergillus oryzaeGenome Results in Fungal Antibacterial Activity (2013)

Multidrug-resistant bacteria cause severe infections in hospitals and communities. Development of new drugs to combat resistant microorganisms is needed. Natural products of microbial origin are the source of most currently available antibiotics. We hypothesized that random mutagenesis of Aspergillus oryzae would result in secretion of antibacterial compounds. To address this hypothesis, we developed a screen to identify individual A. oryzae mutants that inhibit the growth of Methicillin-resistant Staphylococcus aureus (MRSA) in vitro. To randomly generate A. oryzae mutant strains, spores were treated with ethyl methanesulfonate (EMS). Over 3000 EMS-treated A. oryzae cultures were tested in the screen, and one isolate, CAL220, exhibited altered morphology and antibacterial activity. Culture supernatant from this isolate showed antibacterial activity against Methicillin-sensitive Staphylococcus aureus, MRSA, and Pseudomonas aeruginosa, but not Klebsiella pneumonia or Proteus vulgaris. The results of this study support our hypothesis and suggest that the screen used is sufficient and appropriate to detect secreted antibacterial fungal compounds resulting from mutagenesis of A. oryzae. Because the genome of A. oryzae has been sequenced and systems are available for genetic transformation of this organism, targeted as well as random mutations may be introduced to facilitate the discovery of novel antibacterial compounds using this system.
Effect of Chronic Electrical Stimulation of Laryngeal Muscle on Voice (2002)

Conventional surgical therapies for bilateral laryngeal paralysis sacrifice voice to enlarge the airway. Electrical pacing of the posterior cricoarytenoid (PCA) muscle to restore glottal opening and allow ventilation offers a new treatment approach. The purpose of this investigation was to determine whether long-term stimulation of the PCA muscle altered perceptual, acoustic, and aerodynamic parameters of voice. Two patients underwent implantation of a Medtronic Itrel II laryngeal pacemaker. Voice evaluation was performed before surgery and at monthly postoperative sessions with the pacemaker off. Months of PCA stimulation did not change perceptual descriptors of voice quality. Measures of fundamental frequency and intensity, upper and lower limits of the dynamic frequency and intensity range, and phonatory flow rates were largely unaltered. The results indicated that there was no effect of laryngeal pacing on voice.
Age‐ and gender‐related changes in the cellularity of human bone marrow and the prevalence of osteoblastic progenitors (2001)

Bone marrow harvested by aspiration contains connective tissue progenitor cells which can be induced to express a bone phenotype in vitro. The number of osteoblastic progenitors can be estimated by counting the colony-forming units which express alkaline phosphatase (CFU-APs). This study was undertaken to test the hypothesis that human aging is associated with a significant change in the number or prevalence of osteoblastic progenitors in the bone marrow. Four 2-ml bone marrow aspirates were harvested bilaterally from the anterior iliac crest of 57 patients, 31 men (age 15-83) and 26 women (age 13-79). A mean of 64 million nucleated cells was harvested per aspirate. The mean prevalence of CFU-APs was found to be 55 per million nucleated cells. These data revealed a significant age-related decline in the number of nucleated cells harvested per aspirate for both men and women (P = 0.002). The number of CFU-APs harvested per aspirate also decreased significantly with age for women (P = 0.02), but not for men (P = 0.3). These findings are relevant to the harvest of bone marrow derived connective tissue progenitors for bone grafting and other tissue engineering applications, and may also be relevant to the pathophysiology of age-related bone loss and post-menopausal osteoporosis.
A new method to measure nitrate/nitrite with a NO-sensitive electrode (2001)

There are different methods to measure the unstable molecule nitric oxide (NO). We will describe a new sensitive method to measure NO by reconversion of nitrate/nitrite to NO, which will be determined with an amperometric Clark-type electrode. Nitrate and nitrite are the degradation products of NO. First, nitrate is enzymatically converted to nitrite with the use of the nitrate reductase. Second, nitrite is reduced to equimolar NO concentrations by an acidic iodide solution. The detection limit of the electrode in an aqueous solution was 2 nmol/l NO (meaning the threshold was depending on the volume added: 500 microl of a 0.2 micromol/l nitrite solution added to a 10-ml bath). This method provides the ability to assess basal and agonist-stimulated NO releases of different biological models. We measured basal and carbachol-stimulated NO release of native endothelial cells from porcine coronary arteries and porcine aortic endothelial cell cultures. Moreover, it was possible to measure the nitrate/nitrite concentration in the coronary effluent of a guinea pig heart. In conclusion, we present a valid, highly sensitive new method of measuring nitrite/NO in biological systems with a commercially available electrode.
Nerve growth factor‐immobilized polypyrrole: Bioactive electrically conducting polymer for enhanced neurite extension (2006)

Biomaterials that present multiple stimuli are attractive for a number of biomedical applications. In particular, electrical and biological cues are important factors to include in interfaces with neurons for applications such as nerve conduits and neural probes. Here, we report the combination of these two stimuli, by immobilizing nerve growth factor (NGF) on the surface of the electrically conducting polymer polypyrrole (PPy). NGF was immobilized using an intermediate linker provided by a layer of polyallylamine conjugated to an arylazido functional group. Upon exposure to UV light and activation of the azido groups, NGF was fixed to the substrate. Three different surface concentrations were obtained (0.21-0.98 ng/mm(2)) and similar levels of neurite extension were observed on immobilized NGF as with soluble NGF. Additionally, electrical stimulation experiments were conducted with the modified polymer and revealed a 50% increase in neurite outgrowth in PC12 cells compared to experiments without electrical stimulation. This novel modification of PPy provides both electrical and biological stimulation, by presenting tethered growth factors and only producing a small decrease in the material's properties (conductivity approximately 10 S cm(-1)) when compared to other modification techniques (conductivity approximately 10(-3)-10(-6) S cm(-1)).
Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome (2017)

Independent of IBS, ME/CFS is associated with dysbiosis and distinct bacterial metabolic disturbances that may influence disease severity. However, our findings indicate that dysbiotic features that are uniquely ME/CFS-associated may be masked by disturbances arising from the high prevalence of IBS co-morbidity in ME/CFS. These insights may enable more accurate diagnosis and lead to insights that inform the development of specific therapeutic strategies in ME/CFS subgroups.