gebhart/patrepeval huggingface dataset:
In vitroevolution of a T cell receptor with high affinity for peptide/MHC (2000)

T cell receptors (TCRs) exhibit genetic and structural diversity similar to antibodies, but they have binding affinities that are several orders of magnitude lower. It has been suggested that TCRs undergo selection in vivo to maintain lower affinities. Here, we show that there is not an inherent genetic or structural limitation on higher affinity. Higher-affinity TCR variants were generated in the absence of in vivo selective pressures by using yeast display and selection from a library of Valpha CDR3 mutants. Selected mutants had greater than 100-fold higher affinity (K(D) approximately 9 nM) for the peptide/MHC ligand while retaining a high degree of peptide specificity. Among the high-affinity TCR mutants, a strong preference was found for CDR3alpha that contained Pro or Gly residues. Finally, unlike the wild-type TCR, a soluble monomeric form of a high-affinity TCR was capable of directly detecting peptide/MHC complexes on antigen-presenting cells. These findings prove that affinity maturation of TCRs is possible and suggest a strategy for engineering TCRs that can be used in targeting specific peptide/MHC complexes for diagnostic and therapeutic purposes.
Linear spatial pyramid matching using sparse coding for image classification (2009)

Recently SVMs using spatial pyramid matching (SPM) kernel have been highly successful in image classification. Despite its popularity, these nonlinear SVMs have a complexity O(n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ∼ n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> ) in training and O(n) in testing, where n is the training size, implying that it is nontrivial to scaleup the algorithms to handlemore than thousands of training images. In this paper we develop an extension of the SPM method, by generalizing vector quantization to sparse coding followed by multi-scale spatial max pooling, and propose a linear SPM kernel based on SIFT sparse codes. This new approach remarkably reduces the complexity of SVMs to O(n) in training and a constant in testing. In a number of image categorization experiments, we find that, in terms of classification accuracy, the suggested linear SPM based on sparse coding of SIFT descriptors always significantly outperforms the linear SPM kernel on histograms, and is even better than the nonlinear SPM kernels, leading to state-of-the-art performance on several benchmarks by using a single type of descriptors.
Data Warehousing (1996)

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Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers (2014)

The transcription activator-like effectors (TALEs) and the RNA-guided clustered regularly interspaced short palindromic repeat (CRISPR) associated protein (Cas9) utlilize distinct molecular mechanisms in targeting site recognition. The two proteins can be modified to carry additional functional domains to regulate expression of genomic loci in mammalian cells. In this study, we have compared the two systems in activation and suppression of the Oct4 and Nanog loci by targeting their enhancers. Although both are able to efficiently activate the luciferase reporters, the CRISPR/dCas9 system is much less potent in activating the endogenous loci and in the application of reprogramming somatic cells to iPS cells. Nevertheless, repression by CRISPR/dCas9 is comparable to or even better than TALE repressors. We demonstrated that dCas9 protein binding results in significant physical interference to binding of native transcription factors at enhancer, less efficient active histone markers induction or recruitment of activating complexes in gene activation. This study thus highlighted the merits and drawbacks of transcription regulation by each system. A combined approach of TALEs and CRISPR/dCas9 should provide an optimized solution to regulate genomic loci and to study genetic elements such as enhancers in biological processes including somatic cell reprogramming and guided differentiation.
HER2 and EGFR Overexpression Support Metastatic Progression of Prostate Cancer to Bone (2016)

Activation of the EGF receptors EGFR (ErbB1) and HER2 (ErbB2) drives the progression of multiple cancer types through complex mechanisms that are still not fully understood. In this study, we report that HER2 expression is elevated in bone metastases of prostate cancer independently of gene amplification. An examination of HER2 and NF-κB receptor (RANK) coexpression revealed increased levels of both proteins in aggressive prostate tumors and metastatic deposits. Inhibiting HER2 expression in bone tumor xenografts reduced proliferation and RANK expression while maintaining EGFR expression. In examining the role of EGFR in tumor-initiating cells (TIC), we found that EGFR expression was required for primary and secondary sphere formation of prostate cancer cells. EGFR expression was also observed in circulating tumor cells (CTC) during prostate cancer metastasis. Dual inhibition of HER2 and EGFR resulted in significant inhibition of tumor xenograft growth, further supporting the significance of these receptors in prostate cancer progression. Overall, our results indicate that EGFR promotes survival of prostate TIC and CTC that metastasize to bone, whereas HER2 supports the growth of prostate cancer cells once they are established at metastatic sites. Cancer Res; 77(1); 74-85. ©2016 AACR.
Efferent sympathetic and vagal innervation of the canine right ventricle. (1994)

Efferent vagal and sympathetic innervation of the right ventricle resembles that of the left ventricle. A major difference is that efferent sympathetic fibers to the right ventricular outflow tract are located not only in the subepicardium but in the subendocardium as well.
Iron(III)-Based Metal–Organic Frameworks As Visible Light Photocatalysts (2013)

Herein, a new group of visible light photocatalysts is described. Iron(III) oxides could be promising visible light photocatalysts because of their small band gap enabling visible light excitation. However, the high electron-hole recombination rate limits the yield of highly oxidizing species. This can be overcome by reducing the particle dimensions. In this study, metal-organic frameworks (MOFs), containing Fe3-μ3-oxo clusters, are proposed as visible light photocatalysts. Their photocatalytic performance is tested and proven via the degradation of Rhodamine 6G in aqueous solution. For the first time, the remarkable photocatalytic efficiency of such Fe(III)-based MOFs under visible light illumination (350 up to 850 nm) is shown.
Chemical and Functional Analysis of MHC Class II-Restricted T Cell Epitopes (1991)

Various aspects of antigen degradation and presentation are reviewed, in particular with respect to fragmentation of native vs. denatured proteins, different enzymatic machinery present in different cells and individuals, characterization of epitopes and their persistence on antigen-presenting cells as well as their capacity to interact with different MHC class II molecules. Finally, the structure of antigenic peptides is discussed.
Hemocompatibility, biocompatibility, inflammatory and in vivo studies of primary reference materials low‐density polyethylene and polydimethylsiloxane: A review (2001)

In 1984, low-density polyethylene (LDPE) and polymethylsiloxane (PDMS), two primary reference materials (PRM), were made available by the National Heart, Lung, and Blood Institute (NHLBI) as discriminatory tools for the validation of standardized and novel in vitro and in vivo tests in the evaluation of biomaterials. This article reviews the results and conclusions obtained by several studies investigating the hemocompatibility, in vitro biocompatibility, inflammatory response, and in vivo tissue reactions of these two reference materials. Variable results obtained with LDPE and PDMS in ex vivo hemocompatibility studies were attributed to the type of animal model used, the flow velocity of the circulating blood, the time of exposure, and the methodology used to measure blood cell adhesion or activation at the surface of the materials. In contrast, both the LDPE and PDMS appeared to be suitable reference materials when used in in vitro biocompatibility, inflammatory response, and in vivo studies. However, caution must be taken when interpreting the results, because gamma sterilization of these two materials as well as their origin (for example PDMS) are two critically important factors. In conclusion, we see a definite need for standardized hemocompatible parameters and better high-quality hemocompatibility studies on PRM. This review also suggests other materials as potential PRM candidates, namely, Biomer and Intramedic polyethylene.
Nano-Pulse Stimulation induces immunogenic cell death in human papillomavirus-transformed tumors and initiates an adaptive immune response (2018)

Nano-Pulse Stimulation (NPS) is a non-thermal pulsed electric field modality that has been shown to have cancer therapeutic effects. Here we applied NPS treatment to the human papillomavirus type 16 (HPV 16)-transformed C3.43 mouse tumor cell model and showed that it is effective at eliminating primary tumors through the induction of immunogenic cell death while subsequently increasing the number of tumor-infiltrating lymphocytes within the tumor microenvironment. In vitro NPS treatment of C3.43 cells resulted in a doubling of activated caspase 3/7 along with the translocation of phosphatidylserine (PS) to the outer leaflet of the plasma membrane, indicating programmed cell death activity. Tumor-bearing mice receiving standard NPS treatment showed an initial decrease in tumor volume followed by clearing of tumors in most mice, and a significant increase in overall survival. Intra-tumor analysis of mice that were unable to clear tumors showed an inverse correlation between the number of tumor infiltrating lymphocytes and the size of the tumor. Approximately half of the mice that cleared established tumors were protected against tumor re-challenge on the opposite flank. Selective depletion of CD8+ T cells eliminated this protection, suggesting that NPS treatment induces an adaptive immune response generating CD8+ T cells that recognize tumor antigen(s) associated with the C3.43 tumor model. This method may be utilized in the future to not only ablate primary tumors, but also to induce an anti-tumor response driven by effector CD8+ T cells capable of protecting individuals from disease recurrence.
Nanofabricated and self-assembled magnetic structures as data storage media (2005)

Nanofabrication of magnetic storage media, where servo marks, discrete tracks or individual islands are defined, offer the prospect for improved performance and increased areal density. However, this increase in performance will require that new and additional processes be introduced into disk manufacturing. We review here the fundamental patterning and fabrication processes that have been proposed, along with their respective strengths and weaknesses and the potential advantages they may offer for magnetic recording. The increase in data density afforded by nanofabrication may have added significance as more conventional approaches to ever increasing density will encounter physical limitations set by the thermal stability of the recorded bits. © 2005 IOP Publishing Ltd.
Health aspects of wireless communication (2001)

article Share on Health aspects of wireless communication: the risk of human exposure to cellular mobile communication radiation Author: James C. Lin University of Illinois at Chicago, Chicago, IL University of Illinois at Chicago, Chicago, ILView Profile Authors Info & Claims ACM SIGMOBILE Mobile Computing and Communications ReviewVolume 5Issue 2April 2001 pp 6–9https://doi.org/10.1145/584066.584072Online:01 April 2001Publication History 0citation365DownloadsMetricsTotal Citations0Total Downloads365Last 12 Months3Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Adaptation of a Surface Plasmon Resonance Biosensor with Microfluidics for Use with Small Sample Volumes and Long Contact Times (2001)

The efficient delivery of sample to surface-immobilized sites is a key element in biosensing. For a surface plasmon resonance (SPR) biosensor, this has been addressed by constant flow through a microfluidic system with a sample injection loop (Sjölander, S.; Urbaniczky, C. Anal. Chem. 1991, 63, 2338-2345). The present study describes an alternative mode of sample delivery without constant unidirectional flow. It was implemented on a commercial Biacore X SPR biosensor equipped with a microfluidic cartridge, but with the fluidic handling performed by an externally computer-controlled syringe pump. We demonstrate that sample volumes as low as 2 microL can be reproducibly positioned to cover the sensor surfaces, manipulated in a serial fashion, efficiently mixed by applying an oscillatory flow pattern, and fully recovered. Compared to the traditional continuous unidirectional flow configuration, we found very similar kinetic responses at high analyte concentrations and slightly slower responses at low concentrations, most likely due to depletion of analyte from the small sample volumes due to surface binding. With the antibody-antigen systems tested, binding parameters were obtained that are generally within 10% of those from conventional experiments. In the new configuration, biosensor experiments can be conducted without the usual constraints in the surface contact time that are correlated with sample volume and mass transport rate. This can translate to improved detection limits for slow reactions and can facilitate kinetic and thermodynamic binding studies.
Cutting Edge: An Inducible Sialidase Regulates the Hyaluronic Acid Binding Ability of CD44-Bearing Human Monocytes (1999)

Previous studies established that variable degrees and types of glycosylation can account for differences in the ability of CD44 to function as a receptor for hyaluronic acid. We have now used neuraminidase treatment to conclude that sialylation negatively regulates CD44 on the human monocytic cell line THP-1 and peripheral blood monocytes. Both of these cell types displayed increased receptor activity after overnight culture with LPS. Of particular interest, the sialidase inhibitor 2-deoxy-2, 3-dehydro-N-acetylneuraminic acid completely blocked the LPS induced recognition of hyaluronic acid by THP-1 cells. Furthermore, acquisition of this characteristic paralleled induction of one type of sialidase activity. Monocytes may be capable of enzymaticly remodeling cell surface CD44, altering their ability to interact with the extracellular matrix.
Synthesis and Photophysical Properties of Iridium(III) Bisterpyridine and Its Homologues:  a Family of Complexes with a Long-Lived Excited State (1999)

A new synthetic procedure has been developed which makes possible the preparation of IrLL‘3+ complexes (L, L‘ = terpyridine derivative) in good yields. In a first step, IrLCl3 is obtained under relatively mild conditions as an intermediate. Subsequent reaction with L‘ (a few minutes in refluxing ethylene glycol) affords IrLL‘3+. The electrochemical behavior and ground- and excited-state spectroscopic properties of four IrLL‘3+ complexes in nitrile solvents are reported. The X-ray structure of one of these complexes is also described. The complexes have been designed keeping in mind their incorporation in linearly arranged multicomponent arrays, according to a templating strategy based on the assembly of tpy-type ligands by the Ir(III) center. The complexes feature a high-lying level for the luminescent excited state (>2.5 eV), with a satisfactory room-temperature luminescence intensity (φem ≈ 10-2) and lifetime on the microsecond time scale. These favorable properties indicate that the Ir(III)-tpy center will not be the final recipient of the energy-harvesting processes in multipartite systems built around them. Temperature-dependent studies of the luminescence properties in the 95−298 K range indicate that the higher-lying levels of these complexes are not efficient pathways for deactivation of the luminescent states. For these reasons, it is concluded that the studied Ir-tpy-type complexes are well suited (i) to play the role of photoactive center and to gather photo- and electroactive units or (ii) to act as electron relays in linearly arranged multicomponent arrays.
Isolation of monoclonal antibodies specific for human c-myc proto-oncogene product. (1985)

Six monoclonal antibodies have been isolated from mice immunized with synthetic peptide immunogens whose sequences are derived from that of the human c-myc gene product. Five of these antibodies precipitate p62c-myc from human cells, and three of these five also recognize the mouse c-myc gene product. None of the antibodies sees the chicken p110gag-myc protein. All six antibodies recognize immunoblotted p62c-myc. These reagents also provide the basis for an immunoblotting assay by which to quantitate p62c-myc in cells.
Failure trends in a large disk drive population (2007)

It is estimated that over 90 % of all new information produced in the world is being stored on magnetic media, most of it on hard disk drives. Despite their importance, there is relatively little published work on the failure patterns of disk drives, and the key factors that affect their lifetime. Most available data are either based on extrapolation from accelerated aging exper-iments or from relatively modest sized field studies. Moreover, larger population studies rarely have the infrastructure in place to collect health signals from components in operation, which is critical information for detailed failure analysis. We present data collected from detailed observations of a large disk drive population in a production Internet services de-ployment. The population observed is many times larger than that of previous studies. In addition to presenting failure statis-tics, we analyze the correlation between failures and several parameters generally believed to impact longevity. Our analysis identifies several parameters from the drive’s self monitoring facility (SMART) that correlate highly with failures. Despite this high correlation, we conclude that mod-els based on SMART parameters alone are unlikely to be useful for predicting individual drive failures. Surprisingly, we found that temperature and activity levels were much less correlated with drive failures than previously reported. 1
Binaural cue coding-part II: schemes and applications (2003)

Binaural Cue Coding (BCC) is a method for multichannel spatial rendering based on one down-mixed audio channel and side information. The companion paper (Part I) covers the psychoacoustic fundamentals of this method and outlines principles for the design of BCC schemes. The BCC analysis and synthesis methods of Part I are motivated and presented in the framework of stereophonic audio coding. This paper, Part II, generalizes the basic BCC schemes presented in Part I. It includes BCC for multichannel signals and employs an enhanced set of perceptual spatial cues for BCC synthesis. A scheme for multichannel audio coding is presented. Moreover, a modified scheme is derived that allows flexible rendering of the spatial image at the receiver supporting dynamic control. All aspects of complete BCC encoder and decoder implementations are discussed, such as down-mixing of the input signals, low complexity estimation of the spatial cues, and quantization and coding of the side information. Application examples are given and the performance of the coder implementations are evaluated and discussed based on subjective listening test results.
Levodopa therapeutics: new treatment strategies. (1993)

Even though levodopa can provide effective therapy for symptomatic relief of parkinsonism, many patients deteriorate over time. This change may be related to a loss of storage capability for dopamine in the brain affected by parkinsonian changes. Some of the variability in drug action is determined by its peripheral pharmacokinetics. Methods that can enhance dose-by-dose effectiveness, including controlled-release preparations and enteral infusions, have practical applications for managing "wearing-off" or peak-effect problems.
Alginate Synthesis in Mucoid Pseudomonas aeruginosa: a Chromosomal Locus Involved in Control (1980)

Mucoid variants of Pseudomonas aeruginosa isolated in vitro or in vivo could be classified into two phenotypic groups based on whether alginate was produced on a chemically defined medium. Mucoid strains yielded lowe recombination frequencies than the non-mucoid parent when used as donors in FP2-mediated plate matings. The mucoid characteristic (muc) was co-inherited by a proportion of recombinants selected for the inheritance of chromosomal markers his-5075+ or cys-5605+. The results of further experiments using either a mucoid recipient or a mucoid donor carrying plasmid R68.45 suggested that the control of alginate production in P. aeruginosa involves at least one chromosomal locus.
Effect of heat shock protein 47 on collagen accumulation in keloid fibroblast cells (2007)

Combined with our previous histological results, we propose that overexpression of HSP47 in keloid fibroblast cells could induce excessive collagen accumulation by enhancing synthesis and secretion of collagen, which not only presents a possible mechanism of keloid formation, but also offers a therapeutic potential of RNA interference to HSP47 for the treatment of keloid and other fibroproliferative disorders.