gebhart/patrepeval huggingface dataset:
Role of HLA-A motifs in identification of potential CTL epitopes in human papillomavirus type 16 E6 and E7 proteins. (1994)

We have measured the binding affinity for five HLA-A alleles: HLA-A1 (A*0101), A2.1 (A*0201), A3 (A*0301), A11 (A*1101), and A24 (A*2401); of a set of all possible nonamer peptides (n = 240) of human papillomavirus type 16 E6 and E7 proteins. High affinity binding peptides were identified for each of the alleles, thus allowing us to select several candidates for CTL-based vaccines. Moreover, this unbiased set of peptides allowed an evaluation of the predictive value of HLA motifs derived either from the analysis of sequencing of pools of naturally processed peptides or from the binding analysis of polyalanine nonameric peptides that differed in the amino acids (aa) present at the anchor positions. Whereas pool sequencing-derived motifs were present in only 27% of high affinity binders, the more expanded motif, based on analysis of different aa substitutions at the anchor positions, was present in 73% of high affinity binders. Furthermore, it was found that the presence of anchor residues in a peptide was in itself not sufficient to determine binding to MHC class I molecules, because the majority of motif-containing peptides failed to bind to the relevant MHC. Finally, specific HLA motifs were used to predict peptide binders of 8, 10, and 11 aa in length. Several high affinity binding peptides were identified for each of the various peptide lengths, indicating a significant size heterogeneity in peptides capable of high affinity binding to HLA-A molecules.
“Clickable” polymersomes (2007)

Polymersomes, composed of amphiphilic polystyrene-block-poly(acrylic acid) (PS-b-PAA), with the periphery being covered with azide groups, were used for further functionalization using "click" chemistry.
Simultaneous spectral/spatial detection of edges for hyperspectral imagery: the HySPADE algorithm revisited (2012)

The hyperspectral/spatial detection of edges (HySPADE) algorithm, originally published in 2004 [1], has been modified and applied to a wider diversity of hyperspectral imagery (HSI) data. As originally described in [1], HySPADE operates by converting the naturally two-dimensional edge detection process based on traditional image analysis methods into a series of one-dimensional edge detections based on spectral angle. The HySPADE algorithm: i) utilizes spectral signature information to identify edges; ii) requires only the spectral information of the HSI scene data and does not require a spectral library nor spectral matching against a library; iii) facilitates simultaneous use of all spectral information; iv) does not require endmember or training data selection; v) generates multiple, independent data points for statistical analysis of detected edges; vi) is robust in the presence of noise; and vii) may be applied to radiance, reflectance, and emissivity data--though it is applied to radiance and reflectance spectra (and their principal components transformation) in this report. HySPADE has recently been modified to use Euclidean distance values as an alternative to spectral angle. It has also been modified to use an N x N-pixel sliding window in contrast to the 2004 version which operated only on spatial subset image chips. HySPADE results are compared to those obtained using traditional (Roberts and Sobel) edge-detection methods. Spectral angle and Euclidean distance HySPADE results are superior to those obtained using the traditional edge detection methods; the best results are obtained by applying HySPADE to the first few, information-containing bands of principal components transformed data (both radiance and reflectance). However, in practice, both the Euclidean distance and spectral angle versions of HySPADE should be applied and their results compared. HySPADE results are shown; extensions of the HySPADE concept are discussed as are applications for HySPADE in HSI analysis and exploitation.
Automatic generation of functional vectors using the extended finite state machine model (1996)

We present a method of automatic generation of functional vectors for sequential circuits. These vectors can be used for design verification, manufacturing testing, or power estimation. A high-level description of the circuit in VHDL or C is assumed available. Our method automatically transforms the high-level description of a circuit in VHDL or C into an extended finite state machine (EFSM) model that is used to generate functional vectors. The EFSM model is a generalization of the traditional state machine model. It is a compact representation of models with local data variables and preserves many nice properties of a traditional state machine model. The theoretical background of the EFSM model is addressed in this article. Our method guarantees that the generated vectors cover every statement in the high-level description at least once. Experimental results show that a set of comprehensive functional vectors for sequential circuits with more than a hundred flip-flops can be generated automatically in a few minutes of CPU time using our prototype system.
Association of alpha- and beta-subunits during the biosynthesis of beta-hexosaminidase in cultured human fibroblasts. (1984)

Subunit association of beta-hexosaminidase was studied in intact fibroblasts using antisera that discriminate between free and associated alpha-chains. These were anti-beta-hexosaminidase A (anti-alpha beta), which precipitated all alpha-chains, free or associated; anti-beta-hexosaminidase B (anti-beta beta), which precipitated those alpha-chains that were associated with beta; and anti-alpha-chains, which recognized only monomeric alpha-chains. After biosynthetic labeling, beta-hexosaminidase or its free alpha-subunit were immuno-precipitated from extracts of cells and medium with the aid of protein A-bearing Staphylococcus aureus, subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and visualized by fluorography. Pulse-chase labeling showed that the alpha-chains existed predominantly in the monomeric precursor form during the first 5 h, and then began to accumulate in the mature (lysosomal) associated alpha beta form. Precursor alpha beta complexes were secreted, along with some precursor alpha monomers; the latter were catalytically inert. Both alpha- and beta-chains were phosphorylated (a Golgi modification) prior to association. Thus alpha-beta association probably occurred in the Golgi area before transfer to lysosomes and before secretion. Cycloheximide inhibited the association and subsequent maturation of preformed alpha-chains, perhaps by causing a depletion of a pool of beta-chain precursor upstream from the site of subunit association. In fibroblasts from a patient with Sandhoff disease, that produced no beta-chains, the alpha-chains self-associated but their maturation was markedly decreased. We suggest that association with beta-chains is necessary not only for acquisition of catalytic activity but also for transport of alpha-chains to lysosomes.
A performance evaluation and examination of open-source erasure coding libraries for storage (2009)

Over the past five years, large-scale storage installa-tions have required fault-protection beyond RAID-5, leading to a flurry of research on and development of erasure codes for multiple disk failures. Numerous open-source implementations of various coding tech-niques are available to the general public. In this pa-per, we perform a head-to-head comparison of these implementations in encoding and decoding scenarios. Our goals are to compare codes and implementations, to discern whether theory matches practice, and to demonstrate how parameter selection, especially as it concerns memory, has a significant impact on a code’s performance. Additional benefits are to give storage system designers an idea of what to expect in terms of coding performance when designing their storage sys-tems, and to identify the places where further erasure coding research can have the most impact. 1
The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin (1988)

ADVERTISEMENT RETURN TO ISSUEPREVarticleNEXTThe OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambinWilliam L. Jorgensen and Julian Tirado-RivesCite this: J. Am. Chem. Soc. 1988, 110, 6, 1657–1666Publication Date (Print):March 1, 1988Publication History Published online1 March 1988Published inissue 1 March 1988https://pubs.acs.org/doi/10.1021/ja00214a001https://doi.org/10.1021/ja00214a001research-articleACS PublicationsCopyright © 1988 American Chemical SocietyRequest reuse permissionsArticle Views15043Altmetric-Citations4056LEARN 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
Loss of the tumorigenic phenotype with in vitro, but not in vivo, passaging of a novel series of human bronchial epithelial cell lines: possible role of an alpha 5/beta 1-integrin-fibronectin interaction. (1995)

We established an immortalized, nontumorigenic human bronchial epithelial cell line by transfection with the origin of replication-defective SV40 large T plasmid. This line spontaneously became tumorigenic at passage 184 (NL20T), although subsequent passages (passages 189, 200, and 205) failed to form tumors. The tumorigenic cell line NL20T was reinoculated back into athymic nude mice, and the two subsequently derived cell lines (NL20T-A and NL20T-B) have been passaged 85 times in vitro and remain tumorigenic. However, late-passage NL20T cells consistently lose their tumorigenicity when passaged in vitro on tissue culture plastic dishes (NL20T-n cells). Thus, two of the cell lines, NL20 and NL20T, reverted to the nontumorigenic phenotype reproducibly and spontaneously following serial passage on plastic tissue culture plates, whereas cells passaged in mice (NL20T-A and -B) did not. We used these nontumorigenic (NL20 and NL20T-n) and tumorigenic (early passage NL20T, NL20T-A, and NL20T-B) cells to study the role of the alpha 5/beta 1-integrin and attachment to fibronectin in tumorigenicity. The two nontumorigenic cell lines (NL20 and NL20T-n) attached slower to fibronectin-coated plates than the two tumorigenic cell lines in a cellular-extracellular matrix adhesion assay. Attachment was abrogated by exposure to a blocking antibody to the alpha 5/beta 1-integrin, the fibronectin receptor, in the two tumorigenic cell lines. Cell surface expression of the alpha 5/beta 1 cell surface protein by flow cytometry was highest in the tumorigenic NL20T and NL20T-A cells. NL20T-A cells were cultured with an antibody to alpha 5/beta 1 and inoculated s.c. into athymic nude mice; tumorigenicity of the NL20T-A cells was inhibited in a dose-dependent manner. Tumorigenicity was also inhibited partially with monoclonal antibodies to either alpha 5 or beta 1. A mixture of 10% tumorigenic NL20T-A cells and 90% nontumorigenic NL20 cells was cultured on plastic, type IV collagen, laminin, and fibronectin for 9 weeks. Only cells cultured on fibronectin formed tumors when inoculated s.c. into athymic nude mice. We conclude that these data are consistent with the hypothesis that neoplastic transformation in our original cell line arose from in vivo selection of a small mutant clone, which had arisen in culture and was selected subsequently in vivo but was lost with in vitro culture in NL20 cells, and that alpha 5/beta 1-integrin interaction with the extracellular matrix may play a role in tumorigenicity in our system.
MR spectroscopy quantitation: a review of frequency domain methods (2001)

There has been a vast increase in applications of magnetic resonance spectroscopy (MRS) in biomedical research during the last few years. This is not surprising since MRS provides both in vivo and in vitro a non-invasive tool for various biochemical and biomedical studies. There are also expectations that clinical MRS will have an important role as a diagnostic tool. An essential prerequisite for the future success of MRS for applicability in biomedical sciences will be accurate and biochemically relevant data analysis (at as high a level of automation as possible). This review briefly describes principles of the methodology available for advanced quantitative data analysis in the frequency domain. Various biomedical applications are discussed in order to illustrate the practical aspects of the analyses and to show the applicability and power of biochemical prior knowledge-based lineshape fitting analysis.
Application of computers in diabetes care-a review. II. Computers for decision support and education (1995)

This paper concludes a review of the contribution of information technology to diabetes care. The role of decision support tools for planning insulin therapy using various clinical algorithms, knowledge-based approaches and interactive simulations is discussed, and certain telemedicine approaches to therapy are considered. The validation and clinical evaluation of these tools is reviewed, as is the likely impact of the routine clinical application of implantable/non-invasive blood glucose monitoring devices. Finally, the application of computers as teaching tools is considered, and ways in which such educational approaches might be applied for disseminating the benefits of the Diabetes Control and Complications Trial more widely are discussed.
Optimization and Structural Characterization of W/Al2O3 Nanolaminates Grown Using Atomic Layer Deposition Techniques (2005)

W/Al2O3 nanolaminates were fabricated using atomic layer deposition (ALD) techniques. ALD of tungsten was performed using alternating exposures of WF6 and Si2H6. ALD of Al2O3 was performed using alternating exposures of Al(CH3)3 and H2O. The fabrication of optimum nanolaminates was very dependent on nucleation during the ALD of each layer. The nucleation of Al2O3 ALD on W surfaces and W ALD on Al2O3 surfaces was examined using quartz crystal microbalance investigations. Al2O3 ALD on W nucleated easily during the first Al(CH3)3/H2O reaction cycle. In contrast, W ALD nucleation on Al2O3 required multiple WF6/Si2H6 reaction cycles and was very sensitive to the Si2H6 exposure. The W ALD nucleation required at least six or seven WF6/Si2H6 reaction cycles. The optimum reaction parameters for nucleation were utilized to fabricate W/Al2O3 nanolaminates with a total targeted thickness of ∼1000 Å that were composed of various numbers of bilayers. Transmission electron microscopy (TEM) images revealed very well defined two-bilayer and four-bilayer W/Al2O3 nanolaminates grown at 177 °C. Depth-profile secondary ion mass spectrometry (SIMS) measurements confirmed the composition of the W/Al2O3 nanolaminates. Both the TEM and SIMS results showed that sharper interfaces were observed when W ALD nucleates on Al2O3, and rougher interfaces were observed when Al2O3 ALD nucleates on W. X-ray reflectivity (XRR) investigations indicated that the W/Al2O3 nanolaminates were much thicker than the ∼1000 Å target for the total thickness when the W/Al2O3 nanolaminates were composed of a larger number of bilayers. These results were consistent with much lower than expected film densities for the thin Al2O3 ALD nanolayers. Atomic force microscope studies revealed that the surface roughness of W/Al2O3 nanolaminates was lower at lower growth temperatures and lower at higher interfacial densities. XRR investigations also revealed a pronounced Bragg peak with a high X-ray reflectivity from 64-bilayer W/Al2O3 nanolaminates grown at 177 °C. The X-ray reflectivity of the 64-bilayer W/Al2O3 nanolaminates grown at 177 °C was constant versus annealing up to 500 °C. The reflectivity then dropped rapidly for annealing at ≥600 °C. This thermal instability will place some limits on the application of W/Al2O3 nanolaminates as thermal barrier coatings and X-ray mirrors.
Directed Positioning of Organometallic Fragments Inside a Calix[4]arene Cavity (1998)

A hemispherical diphosphane based on a calixarene allows encapsulation of reactive M-R fragments (M=transition metal; R=H, alkyl, CO) inside the calixarene cavity. The ruthenium complex 1 has an unprecedented sandwich structure that contains a CO ligand confined between two phosphane-substituted phenyl rings. The separation between the CO segment and the two aromatic rings is only 2.75 Å!
Quantification of fractional flow reserve based on angiographic image data (2011)

Coronary angiography provides excellent visualization of coronary arteries, but has limitations in assessing the clinical significance of a coronary stenosis. Fractional flow reserve (FFR) has been shown to be reliable in discerning stenoses responsible for inducible ischemia. The purpose of this study is to validate a technique for FFR quantification using angiographic image data. The study was carried out on 10 anesthetized, closed-chest swine using angioplasty balloon catheters to produce partial occlusion. Angiography based FFR was calculated from an angiographically measured ratio of coronary blood flow to arterial lumen volume. Pressure-based FFR was measured from a ratio of distal coronary pressure to aortic pressure. Pressure-wire measurements of FFR (FFR( P )) correlated linearly with angiographic volume-derived measurements of FFR (FFR( V )) according to the equation: FFR( P ) = 0.41 FFR( V ) + 0.52 (P-value < 0.001). The correlation coefficient and standard error of estimate were 0.85 and 0.07, respectively. This is the first study to provide an angiographic method to quantify FFR in swine. Angiographic FFR can potentially provide an assessment of the physiological severity of a coronary stenosis during routine diagnostic cardiac catheterization without a need to cross a stenosis with a pressure-wire.
Distribution of Amantadine‐Resistant H5N1 Avian Influenza Variants in Asia (2006)

We examined the distribution of genetic mutations associated with resistance to the M2 ion channel-blocking adamantane derivatives, amantadine and rimantadine, among H5N1 viruses isolated in Vietnam, Thailand, Cambodia, Indonesia, Hong Kong, and China. More than 95% of the viruses isolated in Vietnam and Thailand contained resistance mutations, but resistant mutants were less commonly isolated in Indonesia (6.3% of isolates) and China (8.9% of isolates), where human infection was recently reported. The dual mutation motif Leu26Ile-Ser31Asn (leucine-->isoleucine at aa 26 and serine-->asparagine at aa 31) was found almost exclusively in all resistant isolates from Vietnam, Thailand, and Cambodia, suggesting the biological selection of these mutations.
Molecular Engineering of the Band Gap of π‐Conjugated Systems: Facing Technological Applications (2007)

Abstract For almost two decades, the search of an intrinsically‐conductive organic metal has represented the major driving force for research on control of the band gap of extended π‐conjugated systems. However, the emergence of the application of π‐conjugated oligomers and polymers in field‐effect transistors, light‐emitting diodes, electrochromic devices and solar cells has introduced major changes in the chemistry of gap engineering. Besides controlled band gap, active materials for electronic and photonic applications must present appropriate absorption and/or emission properties, highest occupied and lowest unoccupied molecular orbital (HOMO and LUMO) energy levels and charge‐transport properties. The aim of this short review is to present an overview of the recent trends in this area in order to identify possible directions for future research. magnified image
Intracerebral infusion of an EGFR-targeted toxin in recurrent malignant brain tumors (2008)

The purpose of this study is to determine the maximum tolerated dose (MTD), dose-limiting toxicity (DLT), and intracerebral distribution of a recombinant toxin (TP-38) targeting the epidermal growth factor receptor in patients with recurrent malignant brain tumors using the intracerebral infusion technique of convection-enhanced delivery (CED). Twenty patients were enrolled and stratified for dose escalation by the presence of residual tumor from 25 to 100 ng/ml in a 40-ml infusion volume. In the last eight patients, coinfusion of (123)I-albumin was performed to monitor distribution within the brain. The MTD was not reached in this study. Dose escalation was stopped at 100 ng/ml due to inconsistent drug delivery as evidenced by imaging the coinfused (123)I-albumin. Two DLTs were seen, and both were neurologic. Median survival after TP-38 was 28 weeks (95% confidence interval, 26.5-102.8). Of 15 patients treated with residual disease, two (13.3%) demonstrated radiographic responses, including one patient with glioblastoma multiforme who had a nearly complete response and remains alive >260 weeks after therapy. Coinfusion of (123)I-albumin demonstrated that high concentrations of the infusate could be delivered >4 cm from the catheter tip. However, only 3 of 16 (19%) catheters produced intraparenchymal infusate distribution, while the majority leaked infusate into the cerebrospinal fluid spaces. Intracerebral CED of TP-38 was well tolerated and produced some durable radiographic responses at doses <or=100 ng/ml. CED has significant potential for enhancing delivery of therapeutic macromolecules throughout the human brain. However, the potential efficacy of drugs delivered by this technique may be severely constrained by ineffective infusion in many patients.
A Third Method of Generation and Detection of Single-Sideband Signals (1956)

This paper presents a third method of generation and detection of a single-sideband signal. The method is basically different from either the conventional filter or phasing method in that no sharp cutoff filters or wide-band 90° phase-difference networks are needed. This system is especially suited to keeping the signal energy confined to the desired bandwidth. Any unwanted sideband occupies the same band as the desired sideband, and the unwanted sideband in the usual sense is not present.
Technical report. An inexpensive densitometric analysis system using a Macintosh computer and a desktop scanner. (1994)

A brief description of the setup of an inexpensive densitometric analysis system is provided. This system uses a software package and scanner that can be obtained for a total of less than $1000 and that can be operated by any Macintosh computer, including a MacPlus. In the event that a scanner is already available, the software itself can be obtained for approximately $399. Several comparisons are presented of data obtained with this system, data obtained by other analytical methods and data obtained with more expensive, dedicated densitometric systems. These comparisons demonstrate the usefulness and accuracy of this system.