gebhart/patrepeval huggingface dataset:
A New Method toward Microengineered Surfaces Based on Reactive Coating (2001)

By using chemical vapor deposition (CVD) a range of substrates can be coated with a highly reactive polymer containing pentafluorophenol ester groups. A biotin-modified pattern is generated on the substrate by microcontact printing; such a pattern interacts specifically with fluorescein-conjugated streptavidin and thereby the pattern becomes observable with fluorescence microscopy.
Predicting visible differences in high dynamic range images: model and its calibration (2005)

New imaging and rendering systems commonly use physically accurate lighting information in the form of high-dynamic range (HDR) images and video. HDR images contain actual colorimetric or physical values, which can span 14 orders of magnitude, instead of 8-bit renderings, found in standard images. The additional precision and quality retained in HDR visual data is necessary to display images on advanced HDR display devices, capable of showing contrast of 50,000:1, as compared to the contrast of 700:1 for LCD displays. With the development of high-dynamic range visual techniques comes a need for an automatic visual quality assessment of the resulting images. In this paper we propose several modifications to the Visual Difference Predicator (VDP). The modifications improve the prediction of perceivable differences in the full visible range of luminance and under the adaptation conditions corresponding to real scene observation. The proposed metric takes into account the aspects of high contrast vision, like scattering of the light in the optics (OTF), nonlinear response to light for the full range of luminance, and local adaptation. To calibrate our HDR VDP we perform experiments using an advanced HDR display, capable of displaying the range of luminance that is close to that found in real scenes.
O5-Methyl-(.+-.)-(2'R,3'S)-psorospermin (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTO5-Methyl-(.+-.)-(2'R,3'S)-psorosperminDavid K. Ho, Ann T. McKenzie, Stephen R. Byrn, and John M. CassadyCite this: J. Org. Chem. 1987, 52, 3, 342–347Publication Date (Print):February 1, 1987Publication History Published online1 May 2002Published inissue 1 February 1987https://pubs.acs.org/doi/10.1021/jo00379a005https://doi.org/10.1021/jo00379a005research-articleACS PublicationsRequest reuse permissionsArticle Views260Altmetric-Citations30LEARN 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
DNA repair factor XPC is modified by SUMO-1 and ubiquitin following UV irradiation (2005)

Nucleotide excision repair (NER) is the major DNA repair process that removes diverse DNA lesions including UV-induced photoproducts. There are more than 20 proteins involved in NER. Among them, XPC is thought to be one of the first proteins to recognize DNA damage during global genomic repair (GGR), a sub-pathway of NER. In order to study the mechanism through which XPC participates in GGR, we investigated the possible modifications of XPC protein upon UV irradiation in mammalian cells. Western blot analysis of cell lysates from UV-irradiated normal human fibroblast, prepared by direct boiling in an SDS lysis buffer, showed several anti-XPC antibody-reactive bands with molecular weight higher than the original XPC protein. The reciprocal immunoprecipitation and siRNA transfection analysis demonstrated that XPC protein is modified by SUMO-1 and ubiquitin. By using several NER-deficient cell lines, we found that DDB2 and XPA are required for UV-induced XPC modifications. Interestingly, both the inactivation of ubiquitylation and the treatment of proteasome inhibitors quantitatively inhibited the UV-induced XPC modifications. Furthermore, XPC protein is degraded significantly following UV irradiation in XP-A cells in which sumoylation of XPC does not occur. Taken together, we conclude that XPC protein is modified by SUMO-1 and ubiquitin following UV irradiation and these modifications require the functions of DDB2 and XPA, as well as the ubiquitin-proteasome system. Our results also suggest that at least one function of UV-induced XPC sumoylation is related to the stabilization of XPC protein.
A performance methodology for commercial servers (2000)

This paper discusses a methodology for analyzing and optimizing the performance of commercial servers. Commercial server workloads are shown to have unique characteristics which expand the elements that must be optimized to achieve good performance and require a unique performance methodology. The steps in the process of server performance optimization are described and include the following: 1. Selection of representative commercial workloads and identification of key characteristics to be evaluated. 2. Collection of performance data. Various instrumentation techniques are discussed in light of the requirements placed by commercial server workloads on the instrumentation. 3. Creation of input data for performance models on the basis of measured workload information. This step in the methodology must overcome the operating environment differences between the instance of the measured system under test and the target system design to be modeled . 4. Creation of performance models. Two general types are described: high-level models and detailed cycle-accurate simulators. These types are applied to model the processor, memory, and I/O system. 5. System performance optimization. The tuning of the operating system and application software is described. Optimization of performance among commercial applications is not simply an exercise in using traces to maximize the processor MIPS. Equally significant are items such as the use of probabilities to reflect future workload characteristics, software tuning, cache miss rate optimization, memory management, and I/O performance. The paper presents techniques for evaluating the performance of each of these key contributors so as to optimize the overall performance and cost/performance of commercial servers.
Marketed therapeutic antibodies compendium (2012)

Therapeutic monoclonal antibodies (mAbs) are currently being approved for marketing in Europe and the United States, as well as other countries, on a regular basis. As more mAbs become available to physicians and patients, keeping track of the number, types, production cell lines, antigenic targets, and dates and locations of approvals has become challenging. Data are presented here for 34 mAbs that were approved in either Europe or the United States (US) as of March 2012, and nimotuzumab, which is marketed outside Europe and the US. Of the 34 mAbs, 28 (abciximab, rituximab, basiliximab, palivizumab, infliximab, trastuzumab, alemtuzumab, adalimumab, tositumomab-I131, cetuximab, ibrituximab tiuxetan, omalizumab, bevacizumab, natalizumab, ranibizumab, panitumumab, eculizumab, certolizumab pegol, golimumab, canakinumab, catumaxomab, ustekinumab, tocilizumab, ofatumumab, denosumab, belimumab, ipilimumab, brentuximab) are currently marketed in Europe or the US. Data for six therapeutic mAbs (muromonab-CD3, nebacumab, edrecolomab, daclizumab, gemtuzumab ozogamicin, efalizumab) that were approved but have been withdrawn or discontinued from marketing in Europe or the US are also included.
T7 lytic phage‐displayed peptide libraries exhibit less sequence bias than M13 filamentous phage‐displayed peptide libraries (2006)

We investigated whether the T7 system of phage display could produce peptide libraries of greater diversity than the M13 system of phage display due to the differing processes of lytic and filamentous phage morphogenesis. Using a bioinformatics-assisted computational approach, collections of random peptide sequences obtained from a T7 12-mer library (X(12)) and a T7 7-mer disulfide-constrained library (CX(7)C) were analyzed and compared with peptide populations obtained from New England BioLabs' M13 Ph.D.-12 and Ph.D.-C7C libraries. Based on this analysis, peptide libraries constructed with the T7 system have fewer amino acid biases, increased peptide diversity, and more normal distributions of peptide net charge and hydropathy than the M13 libraries. The greater diversity of T7-displayed libraries provides a potential resource of novel binding peptides for new as well as previously studied molecular targets. To demonstrate their utility, several of the T7-displayed peptide libraries were screened for streptavidin- and neutravidin-binding phage. Novel binding motifs were identified for each protein.
Synergism of EGFR and c-Met pathways, cross-talk and inhibition, in non-small cell lung cancer (2008)

There was a synergistic effect of EGF and HGF on proliferation, downstream activation of signal transduction and an additive effect seen on motility. These studies show that a combination of HGF and EGF tyrosine kinase inhibitors on NSCLC, could potentially be targeted in a synergistic fashion.
OneNet: Joint Domain, Intent, Slot Prediction for Spoken Language Understanding (2018)

In practice, most spoken language understanding systems process user input in a pipelined manner; first domain is predicted, then intent and semantic slots are inferred according to the semantic frames of the predicted domain. The pipeline approach, however, has some disadvantages: error propagation and lack of information sharing. To address these issues, we present a unified neural network that jointly performs domain, intent, and slot predictions. Our approach adopts a principled architecture for multitask learning to fold in the state-of-the-art models for each task. With a few more ingredients, e.g. orthography-sensitive input encoding and curriculum training, our model delivered significant improvements in all three tasks across all domains over strong baselines, including one using oracle prediction for domain detection, on real user data of a commercial personal assistant.
Cytokines in Neuroinflammation and Alzheimers Disease (2004)

Inflammation has been reported in numerous neurodegenerative disorders such as Parkinson's disease, stroke and Alzheimer's disease (AD). In AD, the inflammatory response is mainly located to the vicinity of amyloid plaques. Cytokines, such as Interleukin-1 (IL-1), Interleukin-6 (IL-6), Tumor Necrosis Factor alpha (TNF-alpha) and Transforminng Growth Factor beta (TGF-beta) have been clearly involved in this inflammatory process. Although their expression is induced by the presence of amyloid-beta peptide, these cytokines are also able to promote the accumulation of amyloid-beta peptide. Altogether, IL-1, IL-6, TNF-alpha and TGF-beta should be considered as key players of a vicious circle leading to the progression of the disease.
Use of polymerase chain reaction to detect heterozygous familial hypercholesterolemia. (1990)

We used a modification of the polymerase chain reaction (PCR), involving two pairs of oligonucleotide primers, to detect a mutation in the low-density lipoprotein (LDL) receptor gene, commonly occurring among patients with familial hypercholesterolemia (FH) in Finland. This mutation, called FH-Helsinki, involves a large (about 9500 base pairs, bp) deletion in the LDL receptor gene extending from intron 15 to exon 18. For the PCR, one pair of primers was designed to cover both sides of the deletion in its immediate vicinity. In the presence of the deletion, the primers were brought close enough to each other to allow the amplification and electrophoretic detection of a 300-bp amplification product. In the absence of the deletion, no amplification occurred and this band accordingly was not visible in the gel. To render the interpretation of the results unequivocal, we designed a second pair of oligonucleotide primers. This pair of primers allowed another amplification product (158 bp) to appear in samples containing a normal exon 17, i.e., in DNA specimens from healthy subjects and FH heterozygotes with or without the FH-Helsinki deletion. The technique is easy to perform, avoids the use of radioactive reagents, and is applicable to the detection of any extensive DNA deletion.
Shot-boundary detection: unraveled and resolved? (2002)

Partitioning a video sequence into shots is the first step toward video-content analysis and content-based video browsing and retrieval. A video shot is defined as a series of interrelated consecutive frames taken contiguously by a single camera and representing a continuous action in time and space. As such, shots are considered to be the primitives for higher level content analysis, indexing, and classification. The objective of this paper is twofold. First, we analyze the shot-boundary detection problem in detail and identify major issues that need to be considered in order to solve this problem successfully. Then, we present a conceptual solution to the shot-boundary detection problem in which all issues identified in the previous step are considered. This solution is provided in the form of a statistical detector that is based on minimization of the average detection-error probability. We model the required statistical functions using a robust metric for visual content discontinuities (based on motion compensation) and take into account all (a priori) knowledge that we found relevant to shot-boundary detection. This knowledge includes the shot-length distribution, visual discontinuity patterns at shot boundaries, and characteristic temporal changes of visual features around a boundary. Major advantages of the proposed detector are its robust and sequence-independent performance, while there is also the possibility to detect different types of shot boundaries simultaneously. We demonstrate the performance of our detector regarding two most widely used types of shot boundaries: hard cuts and dissolves.
Comparable Worth and the Fair Pay Act of 1994 (1996)

Comparable Worth
DNA topoisomerase I-targeting drugs as radiation sensitizers. (1999)

Combination chemoradiation, alone or as an adjuvant to surgery, has been shown to improve treatment outcomes in a number of human malignancies, but may be limited by normal tissue toxicities. A primary challenge in radiation oncology is the development of drugs that can selectively enhance the cytotoxicity of ionizing radiation against tumor cells. Mammalian DNA topoisomerase I is the major cytotoxic target of a number of newly developed anticancer drugs that have shown efficacy against solid tumors, including colon cancer, ovarian cancer, lung cancer, cancer of the head and neck, and pediatric cancers. Topoisomerase I-targeting drugs exert their cytotoxic effect by producing enzyme-mediated DNA damage, rather than by directly inhibiting enzyme catalytic activity. DNA topoisomerase I recently has been established as a biochemical mediator of radiosensitization in cultured mammalian cells by camptothecin derivatives. Interestingly, this sensitization appears to be schedule-dependent, cell cycle phase-specific, cell line-dependent, and not strictly dependent on drug cytotoxicity. Clinical chemoradiation trials using camptothecin derivatives are currently ongoing. Future studies aimed at better understanding the underlying mechanisms of molecular radiosensitization with topoisomerase I-targeting drugs are pivotal to the clinical application of these agents, as well as in guiding the development of more effective radiosensitizers.
Intestinal Adaptation (1978)

THE mucosal lining of the intestinal tract is in a constant state of renewal. Enteric* epithelium has the fastest rate of turnover† for any tissue in the body, exceeded only by a few rapidly growing malignant tumors.1 Nonetheless, proliferation of epithelial cells may be further accelerated by a number of stimuli, notably partial intestinal resection. Survival of animals and man is possible after the loss of most of the small bowel, and postoperative diarrhea and malabsorption tend to improve with time. Clearly, the gut, like the liver and kidney, has both a functional reserve and a . . .
Retinal Degeneration in Choroideremia: Deficiency of Rab Geranylgeranyl Transferase (1993)

Rab geranylgeranyl transferase (GG transferase) is a two-component enzyme that attaches 20-carbon isoprenoid groups to cysteine residues in Rab proteins, a family of guanosine triphosphate-binding proteins that regulate vesicular traffic. The mutant gene in human choroideremia, an X-linked form of retinal degeneration, encodes a protein that resembles component A of rat Rab GG transferase. Lymphoblasts from choroideremia subjects showed a marked deficiency in the activity of component A, but not component B, of Rab GG transferase. The deficiency was more pronounced when the substrate was Rab3A, a synaptic vesicle protein, than it was when the substrate was Rab1A, a protein of the endoplasmic reticulum. The data imply the existence of multiple component A proteins, one of which is missing in choroideremia.
Variational inverse parameter estimation in a cohesive sediment transport model: An adjoint approach (2003)

Parameter estimation in the sediment deposition and resuspension process is an important issue in numerical modeling of suspended sediment transport. The sediment settling velocity and resuspension rate are two critical parameters controlling the sediment exchange process between the water column and sediment bed. In this paper a variational inverse data assimilation scheme for estimation of the sediment settling velocity and resuspension rate is developed and tested with a three‐dimensional cohesive sediment transport model. The sediment settling velocity and resuspension rate are treated as poorly known parameters in the model and are estimated by the variational inverse scheme using an adjoint approach. A limited‐memory quasi‐Newtonian conjugate gradient algorithm is used in the minimization process. The variational inverse model is tested in the James River estuary in Virginia by identical twin experiments. Numerical experimental results show that variational inverse data assimilation is a useful tool for retrieving poorly known parameters in a cohesive sediment transport model.
Suppression of Coronary Artery Spasm by the Rho-Kinase Inhibitor Fasudil in Patients With Vasospastic Angina (2002)

Fasudil was effective in preventing ACh-induced coronary artery spasm and resultant myocardial ischemia in patients with vasospastic angina. We suggest that this Rho-kinase inhibitor may be a novel therapeutic intervention to treat ischemic coronary syndromes caused by coronary artery spasm.
Nutritional Requirements and Antibiotic Resistance Patterns ofHelicobacterSpecies in Chemically Defined Media (2006)

The growth of the gastric pathogen Helicobacter pylori in the absence of serum remains challenging, and nutritional requirements have only partially been defined, while almost nothing is known about nutritional requirements of other Helicobacter spp. Although previous data showed that H. pylori grows in the chemically defined medium F-12, but not in other tissue culture media examined, the specific components responsible for growth were not entirely understood. Here we describe the optimization of amino acids, metals, and sodium chloride for H. pylori. Iron, zinc, and magnesium were critical for growth; copper was not required. Optimization of sodium chloride was further beneficial. Nutritional requirements and antibiotic resistance patterns of several other Helicobacter spp. revealed that all except H. felis grew in serum-free, unsupplemented F-12. All Helicobacter spp. were resistant to at least six antimicrobial agents when cultured in the presence of serum. However, in the absence of serum, H. pylori, H. mustelae, and H. muridarum became sensitive to polymyxin B and/or trimethoprim. Much of the data were obtained using a convenient ATP assay to quantify growth. H. pylori has surprisingly few absolute requirements for growth: 9 amino acids, sodium and potassium chloride, thiamine, iron, zinc, magnesium, hypoxanthine, and pyruvate. These data suggest that H. pylori and other Helicobacter spp. are not as fastidious as previously thought. The data also suggest that chemically defined media described herein could yield the growth of a wide range of Helicobacter spp., allowing a more detailed characterization of Helicobacter physiology and interactions with host cells.
Hypoxia-Adenosinergic Immunosuppression: Tumor Protection by T Regulatory Cells and Cancerous Tissue Hypoxia (2008)

Cancerous tissue protection from tumor-recognizing CD8(+) and CD4(+) T cells (antitumor T cells) limits the therapeutic potential of immunotherapies. We propose that tumor protection is to a large extent due to (a) inhibition of antitumor T cells by hypoxia-driven accumulation of extracellular adenosine in local tumor microenvironment and due to (b) T regulatory cell-produced extracellular adenosine. The adenosine triggers the immunosuppressive signaling via intracellular cyclic AMP-elevating A2A adenosine receptors (A2AR) on antitumor T cells. In addition, the activated antitumor T cells in hypoxic tumor microenvironment could be inhibited by elevated levels of immunosuppressive hypoxia-inducible factor-1alpha. Complete rejection or tumor growth retardation was observed when A2AR has been genetically eliminated or antagonized with synthetic drug or with natural A2AR antagonist 1,3,7-trimethylxanthine (caffeine). The promising strategy may be in combining the anti-hypoxia-adenosinergic treatment that prevents inhibition of antitumor T cells by tumor-produced and T regulatory cell-produced adenosine with targeting of other negative regulators, such as CTL antigen-4 blockade. Observations of tumor rejection in mice and massive prospective epidemiologic studies support the feasibility of anti-hypoxia-adenosinergic combined immunotherapy.
Maintenance therapy in multiple myeloma (2009)

The treatment of multiple myeloma (MM) has changed dramatically in the past twenty years with the introduction of high-dose therapy plus autologous stem-cell transplantation (ASCT) in younger patients and, more recently, of three novel agents (thalidomide, bortezomib, and lenalidomide). When conventional chemotherapy was the only available possibility, complete responses (CR) were very rare and the objective of maintenance was to prolong remission duration by continuing the same type of treatment that induced the initial response. With recent therapeutic improvements, CR achievement becomes a realistic goal that, in most cases, is significantly correlated with the outcome (1). Therefore, both the nature and the impact of maintenance therapy have changed. Maintenance therapy is based currently on novel agents, and its objective is not only to control the clone but also to further decrease the tumor burden and improve the quality of response. A number of randomized studies show a benefit from maintenance therapy with novel agents (until now, mostly thalidomide), at least in terms of response rate and progression-free survival (PFS). However, there is still a debate as concerns the impact on overall survival (OS) and the optimal administration of maintenance therapy.