gebhart/patrepeval huggingface dataset:
Human Epidermal Growth Factor Receptor 2 Testing in Breast Cancer (2023)

HER2 testing guidelines have focused on identifying HER2 protein overexpression or gene amplification in breast cancer to identify patients for therapies that disrupt HER2 signaling. This update acknowledges a new indication for trastuzumab deruxtecan when HER2 is not overexpressed or amplified but is immunohistochemistry (IHC) 1+ or 2+ without amplification by in situ hybridization. Clinical trial data on tumors that tested IHC 0 are limited (excluded from DESTINY-Breast04), and evidence is lacking that these cancers behave differently or do not respond similarly to newer HER2 antibody-drug conjugates. Although current data do not support a new IHC 0 versus 1+ prognostic or predictive threshold for response to trastuzumab deruxtecan, this threshold is now relevant because of the trial entry criteria that supported its new regulatory approval. Therefore, although it is premature to create new result categories of HER2 expression (eg, HER2-Low, HER2-Ultra-Low), best practices to distinguish IHC 0 from 1+ are now clinically relevant. This update affirms prior HER2 reporting recommendations and offers a new HER2 testing reporting comment to highlight the current relevance of IHC 0 versus 1+ results and best practice recommendations to distinguish these often subtle differences. Additional information is available at www.asco.org/breast-cancer-guidelines.
Design and fabrication of band pass filters based on a dielectric E-plane waveguide (2002)

The small-size waveguide made of high-permittivity ceramic is analyzed by using two kinds of approximate approaches. Based on these analysis results, BPFs are designed and fabricated. The characteristics of the fabricated BPFs agree well with the prediction with minor differences corresponding to each design method.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
CaM kinase augments cardiac L-type Ca<sup>2+</sup>current: a cellular mechanism for long Q-T arrhythmias (1999)

Early afterdepolarizations (EAD) caused by L-type Ca2+ current (ICa, L) are thought to initiate long Q-T arrhythmias, but the role of intracellular Ca2+ in these arrhythmias is controversial. Rabbit ventricular myocytes were stimulated with a prolonged EAD-containing action potential-clamp waveform to investigate the role of Ca2+/calmodulin-dependent protein kinase II (CaM kinase) in ICa,L during repolarization. ICa,L was initially augmented, and augmentation was dependent on Ca2+ from the sarcoplasmic reticulum because the augmentation was prevented by ryanodine or thapsigargin. ICa,L augmentation was also dependent on CaM kinase, because it was prevented by dialysis with the inhibitor peptide AC3-I and reconstituted by exogenous constitutively active CaM kinase when Ba2+ was substituted for bath Ca2+. Ultrastructural studies confirmed that endogenous CaM kinase, L-type Ca2+ channels, and ryanodine receptors colocalized near T tubules. EAD induction was significantly reduced in current-clamped cells dialyzed with AC3-I (4/15) compared with cells dialyzed with an inactive control peptide (11/15, P = 0.013). These findings support the hypothesis that EADs are facilitated by CaM kinase.
Optical diffuse reflectance of Black Silicon and its isotropicity (2016)

In this work the reflectance factor and the directional properties of the diffuse reflectance of Black Silicon (B-Si) structure fabricated using cryogenic deep reactive ion etching are investigated. The reflectance is measured by observing the scattered power pattern for different incidence and scattering angles in comparison with ideal diffuse reflectance (Lambertian) reference. The measurements are conducted at the visible and near-infrared wavelengths of 650 nm and 1500 nm up to 2400 nm. Interestingly, the B-Si structure exhibits a tendency to isotropic diffuse reflectance pattern rather than the Lambertian one, which may be of interest for a variety of applications including photonic solar cell and thermal radiators.
Eosinophil accumulation induced by human interleukin-8 in the guinea-pig in vivo. (1993)

Interleukin-8 (IL-8) is a neutrophil chemoattractant cytokine. Initially IL-8 appeared to exhibit specificity for neutrophils over other cells of the immune system. However, several recent studies have shown that this mediator can also activate other leucocyte types in vitro. In this study we have used an in vivo model of local [111In]leucocyte accumulation in the guinea-pig and an in vitro assay of leucocyte activation (changes in cytosolic-free Ca2+) to investigate the eosinophil chemoattractant activity of IL-8. The intradermal injection of recombinant human (rh)IL-8 induced a dose-dependent accumulation of intravenously administered [111In]eosinophils into the skin sites over 4 hr. Time-course experiments revealed that this cell infiltration was delayed in onset, occurring between 1 and 2 hr after injection of IL-8. The delay may indicate that IL-8 operates via an indirect mechanism. In contrast, eosinophil accumulation induced by the complement fragment C5a occurred within the first hour following injection. Other human cytokines, IL-1, IL-3, IL-5, tumour necrosis factor (TNF) and granulocyte-macrophage colony-stimulating factor (GM-CSF), were not eosinophil chemoattractants in this in vivo test system. Direct activation of eosinophils by IL-8 was demonstrated in vitro by a transient elevation in cytoplasmic-free Ca2+ levels where it was less potent than either rhC5a or leukotriene B4 (LTB4). Experiments using [111In]neutrophils in vivo indicated that rhIL-8 and rhC5a were similar in potency in inducing local neutrophil infiltration into guinea-pig skin. The demonstration of the eosinophil chemoattractant activity of IL-8 in vivo raises the possibility that this cytokine, or a structurally related molecule, contributes towards eosinophil infiltration in a number of inflammatory conditions such as asthma, helminthic infections and adult respiratory distress syndrome.
The use of cell phone technology in activity and travel data collection (2005)

This paper was transferred from the original CD ROM created for this conference. The material on the CD ROM was published using Adobe Acrobat technology. The original CD ROM was produced by Document Transformation Technologies Postal Address: PO Box 560 Irene 0062 South Africa. Tel.: +27 12 667 2074 Fax: +27 12 667 2766 E-mail: doctech@doctech.co.za URL: http://www.doctech.co.za
Resilience in multilayer networks (1999)

The integration of different technologies such as ATM, SDH, and WDM in multilayer transport networks raises many questions regarding the coordination of the individual network layers. Especially in the area of network survivability, much can be gained by a better alignment of the healing actions taken by different network layers in case of outages. Survivability issues encountered in a multilayer environment include, among others: how to identify the original failure cause, how to appoint for each failure a layer responsible for its healing, how to let different layers interwork, and how to provide spare resources in an efficient way.
The alpha-lytic protease gene of Lysobacter enzymogenes. The nucleotide sequence predicts a large prepro-peptide with homology to pro-peptides of other chymotrypsin-like enzymes. (1988)

alpha-Lytic protease is a 19.8-kDa protein secreted from the Gram-negative bacterium Lysobacter enzymogenes. We have cloned and sequenced the gene for this serine protease. The nucleotide sequence contains an open reading frame which codes for the 198-residue mature enzyme and a potential prepro-peptide, also of 198 residues. The COOH-terminal 49 residues of the pro-peptide are significantly homologous to the propeptides of Streptomyces griseus proteases A and B. We suggest that this pro-peptide region facilitates formation of the active enzyme. A region bridging the NH2-terminal pre- and pro-peptides is homologous to a maize inhibitor of serine proteases. We speculate that this region inhibits enzymatic activity of the prepro-enzyme.
Increased Production of Transforming Growth Factor‐α in Psoriatic Epidermis (1991)

To elucidate the involvement of transforming growth factor-alpha (TGF-alpha) in the pathogenesis of psoriasis, we measured TGF-alpha levels in the extracts from six normal epidermis and four psoriatic involved epidermis samples by enzyme-linked sorbent assay using monoclonal antibody specific for TGF-alpha. The amount of TGF-alpha in the extracts of normal epidermis was 1.45 +/- 1.06 ng/g of wet tissue, while the amount in psoriatic involved epidermis was 6.71 +/- 0.75 ng/g of wet tissue. The TGF-alpha level in psoriatic involved epidermis was thus 4.62 fold higher than that of normal epidermis (P less than 0.001). TGF-alpha binds to epidermal growth factor receptors and functions as an autocrine growth factor for epidermal keratinocytes. Therefore, the increased levels of TGF-alpha may be involved in the induction or the maintenance of hyperproliferation of psoriatic epidermal keratinocytes.
Hyperthermic Effects of Gold Nanorods on Tumor Cells (2007)

Plasmon-resonant gold nanorods, which have large absorption cross sections at near-infrared frequencies, are excellent candidates as multifunctional agents for image-guided therapies based on localized hyperthermia. The controlled modification of the surface chemistry of the nanorods is of critical importance, as issues of cell-specific targeting and nonspecific uptake must be addressed prior to clinical evaluation. Nanorods coated with cetyltrimethylammonium bromide (a cationic surfactant used in nanorod synthesis) are internalized within hours into KB cells by a nonspecific uptake pathway, whereas the careful removal of cetyltrimethylammonium bromide from nanorods functionalized with folate results in their accumulation on the cell surface over the same time interval. In either case, the nanorods render the tumor cells highly susceptible to photothermal damage when irradiated at the nanorods' longitudinal plasmon resonance, generating extensive blebbing of the cell membrane at laser fluences as low as 30 J/cm2.
ScanRanker: Quality Assessment of Tandem Mass Spectra via Sequence Tagging (2011)

In shotgun proteomics, protein identification by tandem mass spectrometry relies on bioinformatics tools. Despite recent improvements in identification algorithms, a significant number of high quality spectra remain unidentified for various reasons. Here we present ScanRanker, an open-source tool that evaluates the quality of tandem mass spectra via sequence tagging with reliable performance in data from different instruments. The superior performance of ScanRanker enables it not only to find unassigned high quality spectra that evade identification through database search but also to select spectra for de novo sequencing and cross-linking analysis. In addition, we demonstrate that the distribution of ScanRanker scores predicts the richness of identifiable spectra among multiple LC-MS/MS runs in an experiment, and ScanRanker scores assist the process of peptide assignment validation to increase confident spectrum identifications. The source code and executable versions of ScanRanker are available from http://fenchurch.mc.vanderbilt.edu.
Polyp Detection in Colonoscopy Video using Elliptical Shape Feature (2007)

Early detection of polyps and cancers is one of the most important goals of colonoscopy. Computer-based analysis of video files using texture features, as has been proposed for polyps of the stomach and colon, has two major limitations: this method uses a fixed size analysis window and relies heavily on a training set of images for accuracy. To overcome these limitations, we propose a new technique focusing on shape instead of texture in this paper. The proposed polyp region detection method is based on the elliptical shape that is common for nearly all small colon polyps.
Amino Acid Based Phosphoramidite Ligands for the Rhodium‐Catalyzed Asymmetric Hydrogenation (2009)

Abstract Two sets of amino acid based phosphoramidite ligands with either a BINOL backbone (S b ‐ 1a – e and R b ‐ 1a ) or a flexible biphenol backbone ( 2a – c and 2f ) were synthesized and evaluated in the rhodium‐catalyzed hydrogenation of different functionalized alkenes: dimethyl itaconate ( 3 ), methyl 2‐acetamidoacrylate ( 4 ), methyl α‐acetamidocinnamate ( 5 ) and N ‐(3,4‐dihydro‐2‐naphthalenyl)acetamide ( 6 ). The amino acid fragment can be modified at three positions (R 1 –R 3 ) giving rise to modular ligands. Initial experiments varying the R 1 position of the amino acid fragment, showed that the valine‐based phosphoramidite ligand S b ‐ 1b forms the most selective rhodium catalyst for three of the four substrates of the current study. The modifications at the other positions (R 2 and R 3 ) tweaked the ligand structure such that enhanced selectivities were obtained; up to 97 % ee is obtained for the asymmetric hydrogenation of 4 with S b ‐ 1e . For ligands with two sources of chirality match/mismatch effects are observed, the diastereoisomer S b ‐ 1b giving higher selectivity than the diastereoisomer R b ‐ 1b for most of the substrates. The set of phosphoramidite ligands having the flexible and cheap biphenol backbone is developed to study the ability of the amino acid derivatives as the sole source of chirality in the ligand to steer enantioselectivity in rhodium‐catalyzed hydrogenation. This study shows their capacity to compete with their BINOL‐based analogues and even to outclass them depending on the substrate evaluated. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)
Reconstruction of baseline JPEG coded images in error prone environments (2000)

In this paper, a two-stage method for the reconstruction of missing data in the transmission of baseline JPEG coded images in error prone environments is proposed. In the first stage, we estimate the values of the missing DC coefficients. As effects of errors in estimating the missing DC values will appear as a number of stripes across the image, a technique for removing such stripes is also developed. In the second stage, the data of missing blocks is reconstructed by exploiting the correlation between adjacent blocks. Simulation results intricate that our reconstruction method performs very well. The two key contributions of our method are that it does not assume nondifferential encoding of the DC coefficients, and that it performs well in the reconstruction of diagonal edges.
Monitoring the Growth of a Bacteria Culture by MALDI-MS of Whole Cells (1999)

We have probed the time evolution of a growing bacteria culture by extracting samples periodically and performing matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) on whole cells. The mass spectra generated by this method contain tens of peaks in the 3-11-kDa mass range. Cultures of E. coli strain K-12 were grown in two types of containers and at two nutrient concentrations and sampled periodically from 6 to 84 h after inoculation. The relative intensities of several of the stronger peaks vary quite dramatically as a function of time. These temporal characteristics must be taken into account when MALDI-MS is applied to identify bacteria. The results also suggest that MALDI-MS can be used to follow the aging of a bacteria culture.
Optical properties of ZnSe diffractive optical elements for spot array generation (2000)

The diffractive optical element (DOE) is a revolutionary technology for sophisticated optical systems. It has recently been launched within the optical industry, which is constantly seeking improvements over conventional optics. We have designed and fabricated three types of binary-phase DOE and a 4-level phase DOE for spot array generation. The surface relief of a ZnSe substrate was patterned and etched by using photolithography and reactive ion etching (RIE) technologies. The optical properties of anti-reflection coated samples were then examined by measuring the intensity distribution of the converging beams and the results compared with the calculated beam propagation.
Halogen dance reactions—A review (2007)

Halogen Dance (HD) reactions are a useful tool for synthetic chemists as they enable access to positions in aromatic and heteroaromatic systems for subsequent functionalization which are often difficult to address by other methods, hence, allowing entry to versatile scaffolds. While the method can be extremely useful, this transformation is often neglected upon designing synthetic sequences. This may be largely attributed to the lack of comprehensive reference works covering the general principles and outlining the versatility and limitations of the technique. The following review tries to present HD reactions in a clear and concise manner in order to convince more chemists of its advantages. It covers the field of HD reactions from their first observation in 1951 until the present. The important contributions leading to the elucidation of the mechanism are briefly outlined followed by a detailed mechanistic section and a discussion of factors which influence HD reactions. Finally, an overview of HD reactions on various carbocyclic and heterocyclic ring systems and its applications in the synthesis of complex compounds is given.
Towards Effective Runtime Trace Generation Techniques in the .NET Framework (2006)

Effective runtime trace generation is vital for und erstanding, analyzing, and maintaining large scale applications. In this paper two cross-language trace generation m ethods are introduced for the .NET platform. The no nintrusive methods are based on the .NET Debugging and Profiling Infrastructure; consequently, neither additional development tools, nor the .NET Framework SDK is required to be installed on the target system. Both m ethods are applied to a test set of real-size executables and compared by performance and applicability.
Effect of melatonin on kidney cold ischemic preservation injury. (2013)

Melatonin is a potent free radical scavenger of reactive oxygen species, nitric oxide synthase inhibitor and a well-known antioxidant secreted from pineal gland. This hormone has been reported to protect tissue from oxidative damage. In this study, we aim to investigate the effect of melatonin on kidney cold ischemia time when added to preservation solution. Thirty male Wistar albino rats were divided equally into three groups; Ringer Lactate (RL) solution, University of Wisconsin (UW) solution with and without melatonin. The serum Lactate Dehydrogenase (LDH) activities of the preservation solutions at 2(nd), 24(th), 36(th), and 48(th) hours were determined. Tissue malondialdehyde (MDA) levels were also measured and a histological examination was performed at 48(th) hour. Melatonin that added to preservation solution prevented enzyme elevation and decreased lipid peroxidation in preservation solution when compared to the control group (p<0.05). The histological examination revealed that UW solution containing melatonin significantly prevented the kidney from pathological injury (p<0.05). Melatonin added to preservation solutions such as UW solution seemed to protect the tissue preserved effectively from cold ischemic injury for up to 48 hour.
Abstract A19: Imprime PGG<sup>®</sup>, a soluble β-1,3/1,6 immunomodulatory glucan, induces enhanced antitumor activity in an in vivo pancreatic tumor model when combined with cetuximab and gemcitabine. (2012)

Advances in targeted therapeutics, such as the anti-Epidermal Growth Factor Receptor (EGFR) MAb, cetuximab (Erbitux®), have dramatically changed treatment options for many cancers. Disappointingly, cetuximab administered with standard-of-care gemcitabine, failed to improve survival in pancreatic cancer (PC), a fatal disease with very few treatment options. About 90% of PCs that express EGFR also contain activating KRAS mutations making it resistant to anti-EGFR therapies. Imprime PGG®, a yeast-derived pathogen-associated molecular pattern, is a soluble β-1,3/1,6 glucan that primes innate immune cells to recognize and kill MAb targeted tumor cells. Objective: To determine the anti-tumor potential of Imprime PGG® in combination with cetuximab +/- gemcitabine in a standard pancreatic cancer xenograft model. Method: Briefly, Balb/c nude mice were inoculated s.c. with 3 x 10 6 EGFR + , KRAS-mutant, MiaPaCa-2 tumor cells. When tumors reached ~50-70 mm 3 , mice were randomized into different treatment groups and administered Imprime PGG®, cetuximab, or gemcitabine, or combinations thereof, 3x/ week for 4 weeks. Tumor measurements were performed twice per week until the tumor volume reached 3000 mm 3 , after which the mice were euthanized. Study endpoints were change in tumor volume and overall survival. Results: Tumor growth data on day +38 demonstrated gemcitabine alone to have significant inhibitory effects (47%; p=0.027) compared to placebo treated mice. The addition of Imprime PGG® or cetuximab to gemcitabine therapy further enhanced tumor inhibition (64% and 88% respectively; p 80 days). Conclusion: In summary, Imprime PGG® combination treatment with cetuximab and gemcitabine induced significant anti-tumor activity, with delay in tumor growth and prolongation of survival in immunodeficient mice with KRAS-mutant pancreatic tumors. Based on these observations, we propose the novel combination treatment with Imprime PGG®, cetuximab, and gemcitabine as a promising new strategy in PC treatment for humans. Work supported by funds from the NCI (Contract # HHSN261201000118C). In vivo work performed at CrownBio. Citation Format: Mary A. Antonysamy, Yumi Yokoyama, Arkadiusz Z. Dudek, Nadine Ottoson, William Grossman. Imprime PGG ® , a soluble β-1,3/1,6 immunomodulatory glucan, induces enhanced antitumor activity in an in vivo pancreatic tumor model when combined with cetuximab and gemcitabine. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Progress and Challenges; Jun 18-21, 2012; Lake Tahoe, NV. Philadelphia (PA): AACR; Cancer Res 2012;72(12 Suppl):Abstract nr A19.
Chemistry of oxaziridines. 3. Asymmetric oxidation of organosulfur compounds using chiral 2-sulfonyloxaziridines (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemistry of oxaziridines. 3. Asymmetric oxidation of organosulfur compounds using chiral 2-sulfonyloxaziridinesFranklin A. Davis, Robert H. Jenkins Jr., Sami B. Awad, Orum D. Stringer, William H. Watson, and Jean GalloyCite this: J. Am. Chem. Soc. 1982, 104, 20, 5412–5418Publication Date (Print):October 1, 1982Publication History Published online1 May 2002Published inissue 1 October 1982https://pubs.acs.org/doi/10.1021/ja00384a028https://doi.org/10.1021/ja00384a028research-articleACS PublicationsRequest reuse permissionsArticle Views1139Altmetric-Citations82LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts