gebhart/patrepeval huggingface dataset:
High level antibody response to retrovirus‐associated but not to melanocyte lineage‐specific antigens in mice protected against B16 melanoma (1999)

Mice vaccinated with Mycobacterium tuberculosis Ag38 gene-transduced B16 melanoma cells showed significant protection from intravenous challenge with parental B16 melanoma cells. No cytotoxic T-cell activity was found against melanoma cells, although the endogenous presence of the mycobacterial gene induced a preferential Th1 response. After immunization, a low serological response against melanoma cells was detected, while a high titer of antibodies directed to parental B16 cells, mainly of IgG2a isotype, was found in protected mice after challenge. These antibodies exhibited complement-dependent cytotoxicity against melanoma cells in vitro, while in vivo, used in passive immunization, they induced a decrease in a number of experimental B16 lung metastases. Most of the antibodies were directed against endogenous murine leukemia viruses. No reactivity against melanocyte lineage-specific antigens was observed. In particular, no reactivity was found in sera from protected mice against tyrosinase-related protein 2 (TRP-2), either stably expressed in a non-melanoma cell line or obtained by in vitro transcription-translation, or against tyrosinase, TRP-1 and gp100 antigens immunoprecipitated from B16 cells. Thus, in the B16 murine model, the presence of dominant viral antigens induces a very strong humoral response that might be protective and may inhibit or mask the presence of minor clonotypes. Int. J. Cancer 83:107–112, 1999. © 1999 Wiley-Liss, Inc.
Novel FR-900493 Analogues That Inhibit the Outgrowth of <i>Clostridium difficile</i> Spores (2018)

The spectrum of antibacterial activity for the nucleoside antibiotic FR-900493 (<b>1</b>) can be extended by chemical modifications. We have generated a small focused library based on the structure of <b>1</b> and identified UT-17415 (<b>9</b>), UT-17455 (<b>10</b>), UT-17460 (<b>11</b>), and UT-17465 (<b>12</b>), which exhibit anti-<i>Clostridium difficile</i> growth inhibitory activity. These analogues also inhibit the outgrowth of <i>C. difficile</i> spores at 2× minimum inhibitory concentration. One of these analogues, <b>11</b>, relative to <b>1</b> exhibits over 180-fold and 15-fold greater activity against the enzymes, phospho-MurNAc-pentapeptide translocase (MraY) and polyprenyl phosphate-GlcNAc-1-phosphate transferase (WecA), respectively. The phosphotransferase inhibitor <b>11</b> displays antimicrobial activity against several tested bacteria including <i>Bacillus subtilis</i>, <i>Clostridium spp.</i>, and <i>Mycobacterium smegmatis</i>, but no growth inhibitory activity is observed against the other Gram-positive and Gram-negative bacteria. The selectivity index (Vero cell cytotoxicity/<i>C. difficile</i>antimicrobial activity) of <b>11</b> is approximately 17, and <b>11</b> does not induce hemolysis even at a 100 μM concentration.
A pH plate fluorosensor (optode) for early diagenetic studies of marine sediments (2002)

Pore water pH distributions are closely coupled to early diagenetic reactions and transport processes in surficial sediments. In this study, an optical plate fluorosensor for rapid two‐dimensional detection of H + concentration patterns in sediment pore waters was developed. The dual excitation (405/450 nm) single emission (520 nm) pH fluorophore HPTS (8‐hydroxypyrene 1, 3, 6, trisulfonic acid trisodium salt) was immobilized onto transparent, supporting sensor foils. Excitation/emission spectra of immobilized HPTS exhibited pH dependent shifts in seawater standards, and fluorescence excitation ratios were used for two‐wavelength, ratiometric detection of pH distributions in sediment and bottom water close to the sediment—water interface (pH ~ 6.5 to 8.5). Sensor foils were fixed to the inner sides of plastic box corers or glass plate aquaria containing sediment and overlying seawater. Equilibration with pore water occurred in seconds, and fluorescence response (excitation/emission) was scanned nondestructively using a monochrome, integrating CCD camera. The two‐dimensional sensor system has a vertical and horizontal resolution of 56 × 54 µm (5 × 5 pixels) applied over an image of 34 × 26 mm. Reproducibility and accuracy were best when foils were prepared from solutions of similar ionic strength to samples. Optical sensor pH distributions correlated well with high‐resolution, vertical distributions measured simultaneously with a minicombination pH electrode, and two‐dimensional pH patterns demonstrated directly the transport‐reaction heterogeneity associated with microtopography and biogenic structures in surface deposits and overlying waters close to the sediment—water interface. Sensor foils retained calibration characteristics for at least 50 d.
Synthetical experiments related to the indole alkaloids (1955)

K. T. Potts and R. Robinson, J. Chem. Soc., 1955, 2675 DOI: 10.1039/JR9550002675
Proteolysis of von Willebrand factor in therapeutic plasma concentrates (1994)

Therapeutic plasma concentrates containing vo Willebrand factor (vWF) lack the largest, most hemostatically active multimers. To evaluate whether this abnormality results from proteolysis during manufacturing, we have analyzed the subunit structure of vWF in several commercial products and found a marked reduction in the relative content of intact 225-kD subunit, paralleled by an increase in the proteolytic fragments normally present in plasma, particularly that of 176 kD. There was no heightened vWF fragmentation in blood-bank cryoprecipitate prepared from platelet-poor, single-donor plasma; in contrast, there was a marked degree of fragmentation in cryoprecipitate prepared from pooled plasmapheresis plasma representing the starting fraction for the production of commercial concentrates. In cryoprecipitate prepared experimentally from plasma containing varying numbers of platelets, the degradation of vWF was proportional to the platelet count, but was greatly diminished by adding protease inhibitors to the plasma. On the basis of these findings, we postulate that the loss of the largest vWF multimers in commercial products results from the use of poorly centrifuged plasmapheresis plasma containing an excessive number of residual platelets and leukocytes. These cells, lysing when plasma is frozen and thawed for the preparation of cryoprecipitate, may liberate proteolytic enzymes that cleave the vWF subunit and contribute to the degradation of the largest multimers. Our results should help devise new approaches for the preparation of more effective concentrates for the treatment of von Willebrand disease.
Model preconditioning by plane‐wave construction in geophysical estimation problems (2005)

We define plane‐wave construction (PWC), an operator for generating data aligned along predefined locally variable slopes, as the inverse of plane‐wave destruction, an operator used for measuring the slopes. PWC can be applied for efficient preconditioning of geophysical estimation problems. We demonstrate its application to coherency enhancing in seismic images and to seismic velocity estimation.
Purification of uridine diphosphate-galactose:glucosyl ceramide, beta 1-4 galactosyltransferase from human kidney. (1992)

A galactosyltransferase that transfers galactose from UDP-galactose to glucosylceramide was purified 440-fold to apparent homogeneity from normal human kidney "buffy coat" preparation employing detergent extraction, ultrafiltration, and Sepharose Q column chromatography. On reducing and nonreducing gels, the enzyme resolved into two bands with apparent molecular weights on the order of 60,000 and 58,000, respectively. The activity of the enzyme was also associated with these two bands following separation on polyacrylamide gels. Analytical isoelectric focusing revealed that the pI of this enzyme is approximately 4.55. Product characterization and substrate specificity studies employing chromatography, enzymatic digestion with various glycosidases, and use of a variety of glycosphingolipid substrates revealed that the major product synthesized by this enzyme was Cer1-1 beta Glc4-1Gal, and Cer1-1 beta Glc was the preferred substrate. Digestion of the 60- and 58-kDa proteins with Staphylococcus aureus (V-8) protease revealed at least six peptides having identical electrophoretic migration. This finding suggests that the two proteins may be related to each other. Western immunoblot assays revealed that the antibody against UDP-galactose:GlcCer, beta 1-4 galactosyltransferase (GalT-2) but not galactosyltransferase UDP-Gal:N-acetyl-D-glucosaminyl-glycopeptide 4-beta-D-galactosyltransferase (EC 2.4.1.38) (B-GT) immunoprecipitated (recognized) the kidney GalT-2. In contrast, antibody against B-GT did not immunoprecipitate GalT-2. Thus our data indicate that GalT-2 and B-GT are two distinct enzymes. The availability of the enzyme GalT-2 and corresponding antibody will allow functional studies in the near future.
Performance of phase-locked loop receiver in digital FM systems (2002)

We investigate a noncoherent detection technique based on a phase-locked loop (PLL) for wireless communication applications, with an emphasis on the Digital Enhanced Cordless Telephone (DECT) system. The performance of the PLL receiver in additive white Gaussian noise (AWGN) and interference-limited environments is simulated and compared to the performance of the limiter-discriminator detector (LD) and the differential detector (DD). The results indicate that a well-designed PLL receiver based on the selection of PLL parameters and post-detection filtering is a better candidate for the DECT than either LD or DD receiver.
A Scalable Architecture for System-on-Chip Interconnections (1999)

National audience
Highly-Selective Electronically-Tunable Cryogenic Filters Using Monolithic, Discretely-Switchable MEMS Capacitor Arrays (2005)

A low loss electronically tunable filter was demonstrated using HTS/Au MEMS switched capacitor arrays. The two-pole filter was tuned by simultaneously varying the capacitance of each resonator by equal amounts. A K factor of between 3,500 and 5,000 was demonstrated for single pole resonators. The total tuning range was about 25% with an average Q of 7,000 at 77 K.
How to Collect Segmentations for Biomedical Images? A Benchmark Evaluating the Performance of Experts, Crowdsourced Non-experts, and Algorithms (2015)

Analyses of biomedical images often rely on demarcating the boundaries of biological structures (segmentation). While numerous approaches are adopted to address the segmentation problem including collecting annotations from domain-experts and automated algorithms, the lack of comparative benchmarking makes it challenging to determine the current state-of-art, recognize limitations of existing approaches, and identify relevant future research directions. To provide practical guidance, we evaluated and compared the performance of trained experts, crowd sourced non-experts, and algorithms for annotating 305 objects coming from six datasets that include phase contrast, fluorescence, and magnetic resonance images. Compared to the gold standard established by expert consensus, we found the best annotators were experts, followed by non-experts, and then algorithms. This analysis revealed that online paid crowd sourced workers without domain-specific backgrounds are reliable annotators to use as part of the laboratory protocol for segmenting biomedical images. We also found that fusing the segmentations created by crowd sourced internet workers and algorithms yielded improved segmentation results over segmentations created by single crowd sourced or algorithm annotations respectively. We invite extensions of our work by sharing our data sets and associated segmentation annotations (http://www.cs.bu.edu/~betke/Biomedical Image Segmentation).
Desk Reference of Clinical Pharmacology (2007)

Since the publication of the bestselling first edition of CRC Desk Reference of Clinical Pharmacology, dramatic discoveries in molecular medicine along with rapid technological advances have revolutionized the diagnosis and resulted in new medications to be used in the treatment of a broad range of human diseases. To stay abreast of these ra
Polysaccharide Capsule and Sialic Acid-Mediated Regulation Promote Biofilm-Like Intracellular Bacterial Communities during Cystitis (2010)

Uropathogenic Escherichia coli (UPEC) is the leading cause of urinary tract infections (UTIs). A murine UTI model has revealed an infection cascade whereby UPEC undergoes cycles of invasion of the bladder epithelium, intracellular proliferation in polysaccharide-containing biofilm-like masses called intracellular bacterial communities (IBC), and then dispersal into the bladder lumen to initiate further rounds of epithelial colonization and invasion. We predicted that the UPEC K1 polysaccharide capsule is a key constituent of the IBC matrix. Compared to prototypic E. coli K1 strain UTI89, a capsule assembly mutant had a fitness defect in functionally TLR4(+) and TLR4(-) mice, suggesting a protective role of capsule in inflamed and noninflamed hosts. K1 capsule assembly and synthesis mutants had dramatically reduced IBC formation, demonstrating the common requirement for K1 polysaccharide in IBC development. The capsule assembly mutant appeared dispersed in the cytoplasm of the bladder epithelial cells and failed to undergo high-density intracellular replication during later stages of infection, when the wild-type strain continued to form serial generations of IBC. Deletion of the sialic acid regulator gene nanR partially restored IBC formation in the capsule assembly mutant. These data suggest that capsule is necessary for efficient IBC formation and that aberrant sialic acid accumulation, resulting from disruption of K1 capsule assembly, produces a NanR-mediated defect in intracellular proliferation and IBC development. Together, these data demonstrate the complex but important roles of UPEC polysaccharide encapsulation and sialic acid signaling in multiple stages of UTI pathogenesis.
Multimodality monitoring of the central nervous system using motor-evoked potentials (2008)

The literature supports the use of multimodality monitoring using all of the electrophysiological techniques that can provide intraoperative information about the neural structures at risk during the surgery.
The Figure of Merit in Amorphous Thermoelectrics (2002)

In some semiconductors, the mean free path can be greater for the phonons than for the charge carriers. When this is the case it is likely that the material will display a higher thermoelectric figure of merit in the amorphous rather than the crystalline form. Here we determine the general conditions that must hold for an amorphous material to be promising for thermoelectric applications. The most important quantity is undoubtedly the effective mass of the charge carriers. At room temperature it appears that this quantity is unlikely to be large enough for our purposes in any good thermoelectric material presently known. On the other hand, it seems quite possible that amorphous material may be useful in high-temperature thermoelectric generation. We suggest that our ideas may be demonstrated in amorphous or fine-grained skutterudites and half-Heusler alloys.
Disruption of Yeast Forkhead-associated Cell Cycle Transcription by Oxidative Stress (2004)

The effects of oxidative stress on yeast cell cycle depend on the stress-exerting agent. We studied the effects of two oxidative stress agents, hydrogen peroxide (HP) and the superoxide-generating agent menadione (MD). We found that two small coexpressed groups of genes regulated by the Mcm1-Fkh2-Ndd1 transcription regulatory complex are sufficient to account for the difference in the effects of HP and MD on the progress of the cell cycle, namely, G1 arrest with MD and an S phase delay followed by a G2/M arrest with HP. Support for this hypothesis is provided by fkh1fkh2 double mutants, which are affected by MD as we find HP affects wild-type cells. The apparent involvement of a forkhead protein in HP-induced cell cycle arrest, similar to that reported for Caenorhabditis elegans and human, describes a potentially novel stress response pathway in yeast.
Structure prediction and R115866 binding study of human CYP26A1: homology modelling, fold recognition, molecular docking and MD simulations (2008)

Abstract Two three-dimensional (3D) models of human cytochrome P450 26A1 (CYP26A1) were constructed using the programs Modeller and Sybyl-GeneFold, respectively. After refinement by molecular mechanics and molecular dynamics (MD) simulations, the two models were validated by structure analysis-validation online server. Subsequently, a flexible docking study was performed on the model constructed by GeneFold with the potent and specific inhibitor R115866 to examine the enzyme–inhibitor interactions. From the docking results, we can see R115866 interacts with amino acid residues at the active site by multiple hydrophobic interactions including the side chains of His111, Trp112, Ser115, Val116, Leu125, Ser126, Leu221, Phe222, Glu296, Phe299, Gly300, Glu303, Thr304, Pro371 and the cofactor heme. Trp112 and Thr304 form hydrogen bonds with R115866 and play important roles in stabilising the complex. This constructed CYP26A1 model may provide an opportunity to understand the action mode of the enzyme and could be useful in designing novel retinoic acid metabolism blocking agents (RAMBAs). Keywords: molecular modellingCYP26A1molecular dynamicsdockingR115866 Acknowledgement The MD simulations were carried out on the Sunway supercomputer platform at Beijing Institute of Pharmacology and Toxicology. We also acknowledge Professor Song Li for his support. Notes 1. http://www.expasy.org/tools/blast 2. SYBYL 6.91; Tripos Inc. (1699 South Hanley Road, St Louis, MO 63144, USA); http://www.tripos.com 3. http://nihserver.mbi.ucla.edu/SAVS/
Copper(I) Complexes derived from Mono- and Diphosphino-Boranes: Cu→B Interactions Supported by Arene Coordination (2009)

The monophosphino-boranes o-iPr2P(C6H4)BR2 (1: R = Ph and 3: R = Cy) and diphosphino-boranes [o-R2P(C6H4)]2BPh (5: R = Ph and 6: R = iPr) readily react with CuCl to afford the corresponding complexes {[o-iPr2P(C6H4)BPh2]Cu(μ-Cl)}2 2, {[o-iPr2P(C6H4)BCy2]Cu(μ-Cl)}2 4, {[o-Ph2P(C6H4)]2BPh}CuCl 7, and {[o-iPr2P(C6H4)]2BPh}CuCl 8. The presence of Cu→B interactions supported by arene coordination within complexes 2, 7, and 8 has been unambiguously evidenced by NMR spectroscopy and X-ray diffraction studies. The unique η2-BC coordination mode adopted by complexes 7 and 8 has been thoroughly analyzed by density-functional theory (DFT) calculations.
Connection between a Classical Separatrix and Quantum Inflection Point (2019)

ADVERTISEMENT RETURN TO ISSUEPREVViewpointNEXTConnection between a Classical Separatrix and Quantum Inflection PointStephen K. Knudson*Stephen K. KnudsonDepartment of Chemistry, College of William and Mary, Williamsburg, Virginia 23187, United States*E-mail: [email protected]More by Stephen K. Knudsonhttp://orcid.org/0000-0002-1607-2637Cite this: J. Phys. Chem. Lett. 2019, 10, 1, 26–29Publication Date (Web):January 3, 2019Publication History Received19 October 2018Accepted17 December 2018Published online3 January 2019Published inissue 3 January 2019https://pubs.acs.org/doi/10.1021/acs.jpclett.8b03201https://doi.org/10.1021/acs.jpclett.8b03201editorialACS PublicationsCopyright © 2019 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views669Altmetric-Citations-LEARN 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 PDF (821 KB) Get e-AlertscloseSUBJECTS:Computational chemistry,Electronic energy,Energy,Quantum number,Reaction products Get e-Alerts
3-D landmark detection and identification in the CAESAR project (2002)

One product of the Civilian American and European Surface Anthropometry Resource (CAESAR) project is the 3-D location of 72 landmarks on all of the thousands of subjects scanned in the survey. Several years of research was done to arrive at a method to quickly, accurately and consistently locate these landmarks. This paper describes the method, its development, and its results.
PPP Link Quality Monitoring (1996)

This document specifies an Internet standards track protocol for the Internet community, and requests discussion and suggestions for improvements.
Context-Aware Learning to Rank with Self-Attention (2020)

Learning to rank is a key component of many e-commerce search engines. In learning to rank, one is interested in optimising the global ordering of a list of items according to their utility for users.Popular approaches learn a scoring function that scores items individually (i.e. without the context of other items in the list) by optimising a pointwise, pairwise or listwise loss. The list is then sorted in the descending order of the scores. Possible interactions between items present in the same list are taken into account in the training phase at the loss level. However, during inference, items are scored individually, and possible interactions between them are not considered. In this paper, we propose a context-aware neural network model that learns item scores by applying a self-attention mechanism. The relevance of a given item is thus determined in the context of all other items present in the list, both in training and in inference. We empirically demonstrate significant performance gains of self-attention based neural architecture over Multi-LayerPerceptron baselines, in particular on a dataset coming from search logs of a large scale e-commerce marketplace, Allegro.pl. This effect is consistent across popular pointwise, pairwise and listwise losses.Finally, we report new state-of-the-art results on MSLR-WEB30K, the learning to rank benchmark.
Terahertz Near-Field Nanoscopy of Mobile Carriers in Single Semiconductor Nanodevices (2008)

We introduce ultraresolving terahertz (THz) near-field microscopy based on THz scattering at atomic force microscope tips. Nanoscale resolution is achieved by THz field confinement at the very tip apex to within 30 nm, which is in good agreement with full electro-dynamic calculations. Imaging semiconductor transistors, we provide first evidence of 40 nm (lambda/3000) spatial resolution at 2.54 THz (wavelength lambda=118 microm) and demonstrate the simultaneous THz recognition of materials and mobile carriers in a single nanodevice. Fundamentally important, we find that the mobile carrier contrast can be directly related to near-field excitation of THz-plasmons in the doped semiconductor regions. This opens the door to quantitative studies of local carrier concentration and mobility at the nanometer scale. The THz near-field response is extraordinary sensitive, providing contrast from less than 100 mobile electrons in the probed volume. Future improvements could allow for THz characterization of even single electrons or biomolecules.