gebhart/patrepeval huggingface dataset:
Synthesis and Antitumor Activity of Novel O-Carbamoylmethyloxime Derivatives of Radicicol (2003)

Radicicol (1), a macrocyclic antifungal antibiotic, is the lead compound of a novel class of heat shock protein 90 (Hsp90) inhibitors that result in the inhibition or degradation of Hsp90-associated proteins, such as v-src and Raf-1 kinases. New O-carbamoylmethyloxime derivatives of 1 were synthesized and evaluated for their in vitro antiproliferative activities against v-src- and K-ras-transformed cells and for their inhibitory activity against v-src tyrosine kinase. O-(Piperidinocarbonyl)methyloxime 9b, one of the most potent of these derivatives, exhibited more potent antiproliferative activity than 1 and its hydroxime KF25706 (2) and had an IC(50) of 25 nM for the inhibition of v-src kinase activity. Compound 9b was also found to decrease the Raf-1 protein level of KNRK5.2 cells. Furthermore, compound 9b exhibited significant antitumor activity when tested against MX-1 and A431 xenografts in nude mice.
Predicting the Future with Social Media (2010)

In recent years, social media has become ubiquitous and important for social networking and content sharing.And yet, the content that is generated from these websites remains largely untapped.In this paper, we demonstrate how social media content can be used to predict real-world outcomes.In particular, we use the chatter from Twitter.com to forecast box-office revenues for movies.We show that a simple model built from the rate at which tweets are created about particular topics can outperform market-based predictors.We further demonstrate how sentiments extracted from Twitter can be further utilized to improve the forecasting power of social media.
Security without identification: transaction systems to make big brother obsolete (1985)

The large-scale automated transaction systems of the near future can be designed to protect the privacy and maintain the security of both individuals and organizations.
An overview of limited feedback in wireless communication systems (2008)

It is now well known that employing channel adaptive signaling in wireless communication systems can yield large improvements in almost any performance metric. Unfortunately, many kinds of channel adaptive techniques have been deemed impractical in the past because of the problem of obtaining channel knowledge at the transmitter. The transmitter in many systems (such as those using frequency division duplexing) can not leverage techniques such as training to obtain channel state information. Over the last few years, research has repeatedly shown that allowing the receiver to send a small number of information bits about the channel conditions to the transmitter can allow near optimal channel adaptation. These practical systems, which are commonly referred to as limited or finite-rate feedback systems, supply benefits nearly identical to unrealizable perfect transmitter channel knowledge systems when they are judiciously designed. In this tutorial, we provide a broad look at the field of limited feedback wireless communications. We review work in systems using various combinations of single antenna, multiple antenna, narrowband, broadband, single-user, and multiuser technology. We also provide a synopsis of the role of limited feedback in the standardization of next generation wireless systems.
National survey of patterns of care for brain-tumor patients (1989)

An excellent response by participating institutions was realized in this survey of patterns of care for patients with primary brain tumors. Since the histopathology of the tumor is such a strong predictor of outcome and influences care so greatly, most analyses were performed not only on the overall series of patients but also by World Health Organization histological classification. Several factors that influence outcome were identified: tumor type, patient age, patient Karnofsky rating, tumor location, and therapy. Very few cases were coded as regards the American Joint Committee on Cancer clinical stage, and few potentially eligible cases were placed in investigative protocols. It behooves those centers providing investigative protocol opportunities to develop liaisons with practicing physicians nearby as well as at some distance and to provide an organizational framework that will make participation in these protocols practical for a larger segment of our brain-tumor patient population. Between 1980 and 1985, the increased use of magnetic resonance imaging in neuroradiology is apparent as well as the increased use of stereotactic biopsy and interstitial radiotherapy. Complications of therapy seem acceptably low. Five-year survival for benign brain tumor is high, while that for the most common primary tumor, glioblastoma multiforme, is only 5.5%. Some of the findings in this survey confirm those from the literature while others, particularly the pattern of care, represent new data.
Optimierung der biologischen Aktivität von kombinatorischen Verbindungsbibliotheken durch einen genetischen Algorithmus (1995)

An die Evolution angelehnt ist das Synthese‐ und Suchverfahren, mit dem von 160 000 möglichen Mehrkomponentenreaktionen vom Ugi‐Typ solche selektiert wurden, deren Produkte Thrombin inhibieren. So lieferte eine bereits in der 18. Generation erhaltene Reaktion die Verbindung 1 , die wesentliche Strukturmerkmale von bekannten Thrombininhibitoren aufweist und das Enzym wirksam hemmt ( K i = 0.22 μ M ). magnified image
Construction of atetR-IntegratedSalmonella entericaSerovar Typhi CVD908 Strain That Tightly Controls Expression of the Major Merozoite Surface Protein ofPlasmodium falciparumfor Applications in Human Vaccine Production (2002)

Attenuated Salmonella strains are an attractive live vector for delivery of a foreign antigen to the human immune system. However, the problem with this vector lies with plasmid segregation and the low level of expression of the foreign gene in vivo when constitutive expression is employed, leading to a diminished immune response. We have established inducible expressions of foreign genes in the Salmonella enterica serovar Typhi CVD908 vaccine strain using the tetracycline response regulatory promoter. To set up this system, a tetracycline repressor (tetR) was integrated into a defined Delta aroC locus of the chromosome via suicide plasmid pJG12/tetR-neo. To remove the neo gene conferring kanamycin resistance from the locus, a cre expression vector under the control of the tetracycline response promoter was transformed into the clone; expression of the Cre recombinase excised the neo gene and generated the end strain CVD908-tetR. Expression of the luciferase reporter gene in this strain is dependent on the presence of tetracycline in the medium and can be regulated up to 4,773-fold. Moreover, the tightly controlled expression of major merozoite surface protein 1 (MSP1) and parts of Plasmodium falciparum was achieved, and the product yield was increased when the inducible expression system was employed. Inoculation of bacteria harboring plasmid pZE11/MSP1(42) in mice produced the protein in liver and spleen controlled by the inducer. The persistence of the plasmid-carrying bacteria in mice was determined. Peak colonization of both liver and spleen was detected on the third day postinoculation and was followed by a decline in growth curves. After 14 days postinfection, the majority of the bacteria (>90%) recovered from the liver and spleen of the mice retained the plasmid when expression was induced; this clearly indicated that stability of the expression vector in vivo was improved by inducible expression. Establishment of the regulatory system in the vaccine strain may broaden the range of its use by enhancing plasmid stability and expression levels in vivo. Moreover, the availability of the vaccine strain inducibly expressing the entire MSP1 provides possibilities for examining its immunogenicity, particularly the cellular response in animal models.
In Situ Generation of Carbenes:  A General and Versatile Platform for Organocatalytic Living Polymerization (2003)

A metal-free, organocatalytic approach to living polymerization using N-heterocyclic carbenes as nucleophilic catalysts generated and used in situ in a single-pot process is detailed. The N-heterocyclic carbene catalyst platform is extremely versatile, as the nature of the substituents has a pronounced effect of catalyst stability and activity toward different substrates. The generation of imidazolium- and thiazaolium-based carbenes was accomplished from the reaction of the corresponding salts with the appropriate bases. This allowed the rapid screening of libraries of catalysts that provided a basic understanding of catalyst structure (sterics, electronics, etc.) with the polymerization rate, control, substrate, and range of molecular weights. The imidazole-based catalysts were significantly more active toward ROP than the thiazolium-based analogues. No appreciable differences between imidazol-2-ylidene and imidazolin-2-ylidene catalysts were observed. Less sterically demanding carbenes were found to be more active toward ring-opening polymerization (ROP) than their sterically encumbered analogues for lactone polymerization. These data prompted the investigation of ionic liquid as a precatalyst reservoir in a phase-transfer polymerization with an immiscible THF solution of monomer and initiator. In situ activation of the ionic liquid generates carbene that migrates to the organic phase effecting living ROP. Precatalyst (ionic liquid) regeneration terminates polymerization. This simple reaction/recycle protocol readily allows repetitive ROPs from the ionic liquid using commercially available materials.
Anti-inflammatory activities of cAMP-elevating agents: enhancement of IL-10 synthesis and concurrent suppression of TNF production (1998)

Interleukin-10 (IL-10) and tumor necrosis factor (TNF) exert key roles in some acute and chronic inflammatory diseases. In this study we investigated (1) the potency of different cAMP-elevating agents in enhancing IL-10 synthesis, (2) the involvement of protein kinase A in this enhancement, and (3) the mutual dependence of cAMP-enhanced IL-10 formation and cAMP-suppressed TNF synthesis. Rolipram, a specific phosphodiesterase inhibitor and cicaprost, a prostacyclin analogue, were applied as cAMP-elevating agents. The stable cAMP antagonist (Rp)-cAMPS was used to abrogate activation of protein kinase A. Human peripheral blood mononuclear cells were stimulated with lipopolysaccharide (LPS). TNF was quantified by radioimmunoassay, IL-10 by enzyme-linked immunosorbent assay, and mRNA by reverse transcriptase-polymerase chain reaction. After LPS stimulation alone 253+/-45 pg/mL IL-10 was synthesized, which increased to 644+/-117 pg/mL in the presence of 1 microM rolipram. (Rp)-cAMPS reversed this increase of IL-10 formation. In the same samples, the LPS-stimulated production of TNF was markedly attenuated by rolipram or cicaprost. A kinetic analysis revealed a significant increase in TNF production before IL-10 formation was detectable. These results demonstrate that (1) cAMP-elevating agents enhance IL-10 synthesis and suppress TNF production; (2) these regulative functions of cAMP-elevating agents are mediated by activation of protein kinases A; (3) suppression of TNF synthesis by cAMP in the early phase is not mediated by endogenous IL-10. Taken together, rolipram and cicaprost exert a dual regulatory function by enhancing IL-10 formation and attenuating TNF synthesis.
Introduction of soluble proteins into the MHC class I pathway by conjugation to an HIV tat peptide (1997)

Protection against most intracellular pathogens requires T cells that recognize pathogen-derived peptides in association with MHC class I molecules on the surface of infected cells. However, because exogenous proteins do not ordinarily enter the cytosol and access the MHC class I-processing pathway, protein-based vaccines that induce class I-restricted CTL responses have proved difficult to design. We have addressed this problem by conjugating proteins, such as OVA, to a short cationic peptide derived from HIV-1 tat (residues 49-57). When APC were exposed in vitro to such protein conjugates, they processed and presented the peptides in association with MHC class I molecules and stimulated CD8+ Ag-specific T cells. Moreover, Ag-specific CTLs were generated in vivo by immunizing mice with histocompatible dendritic cells that had been exposed to protein-tat conjugates.
Control of Postlaminectomy Scar Formation (1980)

Scar formation after laminectomy was evaluated in dogs treated with hemostatic agents, antiinflammatory drugs, or mechanical barriers. Microfibrillar collagen was found to be superior to gelatin foam. The antiinflammatory drugs delayed healing and frequently resulted in abscess formation, and eventually scar filled the defect. The fat grafts formed a viable mechanical barrier. Gelatin foam sponge was compared with microfibrillar collagen for hemostasis with free fat grafts in a clinical series of 50 patients. The latter technique was clearly superior.
Recognition by matching dense, oriented edge pixels (2002)

This paper describes techniques to perform efficient and accurate recognition in difficult domains by matching dense, oriented edge pixels. We model three-dimensional objects as the set of two-dimensional views of the object. Translation, rotation, and scaling of the views are allowed to approximate full three-dimensional motion. A modified Hausdorff measure is used to determine which transformations of each object model are reported as matches. The use of dense, oriented edge pixels allows us to achieve a low rate of false positives. Techniques to prune the search space are used to obtain a system that is efficient in practice. We give results of the system recognizing object views in intensity and infrared images.
cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate (2012)

Quantitative analyses of next-generation sequencing (NGS) data, such as the detection of copy number variations (CNVs), remain challenging. Current methods detect CNVs as changes in the depth of coverage along chromosomes. Technological or genomic variations in the depth of coverage thus lead to a high false discovery rate (FDR), even upon correction for GC content. In the context of association studies between CNVs and disease, a high FDR means many false CNVs, thereby decreasing the discovery power of the study after correction for multiple testing. We propose 'Copy Number estimation by a Mixture Of PoissonS' (cn.MOPS), a data processing pipeline for CNV detection in NGS data. In contrast to previous approaches, cn.MOPS incorporates modeling of depths of coverage across samples at each genomic position. Therefore, cn.MOPS is not affected by read count variations along chromosomes. Using a Bayesian approach, cn.MOPS decomposes variations in the depth of coverage across samples into integer copy numbers and noise by means of its mixture components and Poisson distributions, respectively. The noise estimate allows for reducing the FDR by filtering out detections having high noise that are likely to be false detections. We compared cn.MOPS with the five most popular methods for CNV detection in NGS data using four benchmark datasets: (i) simulated data, (ii) NGS data from a male HapMap individual with implanted CNVs from the X chromosome, (iii) data from HapMap individuals with known CNVs, (iv) high coverage data from the 1000 Genomes Project. cn.MOPS outperformed its five competitors in terms of precision (1-FDR) and recall for both gains and losses in all benchmark data sets. The software cn.MOPS is publicly available as an R package at http://www.bioinf.jku.at/software/cnmops/ and at Bioconductor.
Large-scale proteomic identification of S100 proteins in breast cancer tissues (2010)

This article reports for the first time the comparative proteomic screening of several S100 protein members among a large group of breast cancer patients. The results obtained strongly support the hypothesis that a significant deregulation of multiple S100 protein members is associated with breast cancer progression, and suggest that these proteins might act as potential prognostic factors for patient stratification. We propose that this may offer a significant contribution to the knowledge and clinical applications of the S100 protein family to breast cancer.
Radioimmunodetection of neuroblastoma with iodine-131-3F8: correlation with biopsy, iodine-131-metaiodobenzylguanidine and standard diagnostic modalities. (1991)

Iodine-131-3F8, a murine IgG3 monoclonal antibody specific for ganglioside GD2 was evaluated by radioimmunoscintigraphy in 42 patients with neuroblastoma. Comparison was made with 131I-metaiodobenzylguanidine (MIBG), 99mTc-methylene diphosphonate (MDP) bone scans, as well as computed axial tomography (CT) or magnetic resonance imaging (MRI). Iodine-131-3F8 detected more abnormal sites (283) than [131I] MIBG (138) or 99mTc-MDP (69), especially in patients with extensive disease. In 20 patients with soft-tissue tumors demonstrated by CT/MRI, 131I-3F8 detected the disease in 18. Upon surgical resection, two tumors interpreted as negative with 131I-3F8 imaging revealed ganglioneuroma, one showing microscopic foci of neuroblastoma. In contrast, 131I-3F8 imaging identified tumors that were confirmed histologically as neuroblastomas. In 26 patients with evidence of marrow disease by antibody scans, 14/26 had confirmation by iliac crest marrow aspirate/biopsy examinations. We conclude that 131I-3F8 scintigraphy has clinical utility in the management of patients with neuroblastoma by improving the sensitivity of tumor detection.
Will zigzag graphene nanoribbon turn to half metal under electric field? (2007)

At B3LYP level of theory, we predict that the half-metallicity in zigzag edge graphene nanoribbon (ZGNR) can be realized when an external electric field is applied across the ribbon. The critical electric field decreases with the increase of the ribbon width to induce the half-metallicity. Both the spin polarization and half-metallicity are removed when the edge state electrons fully transferred from one side to the other under very strong electric field. The electric field range under which ZGNR remains half-metallic increases with the ribbon width. Our study demonstrates a rich field-induced spin polarization behavior, which may lead to some important applications in spinstronics.
Respirable antisense oligonucleotides as novel therapeutic agents for asthma and other pulmonary diseases (1997)

Respirable antisense oligonucleotides (rAsONs) targeting discordantly expressed mediators of inflammation and/or bronchoconstriction and delivered to the lung via inhalation represent a new class of epigenetic-based therapeutics for asthma and other pulmonary diseases. The properties of these agents (solubility, chemical stability, rapid design based on primary DNA sequence information) combine synergistically with characteristics of the lung (non-invasive route of administration directly to the target organ, presence of uptake-modifying surfactant) to enhance the therapeutic potential of these oligonucleotide-based drugs. Their potential is further increased by the possibility of engineering antisense oligonucleotides whose effects are limited to the lung, reducing or avoiding the possibility of systemic toxicity.
Biomarkers Predicting Clinical Outcome of Epidermal Growth Factor Receptor–Targeted Therapy in Metastatic Colorectal Cancer (2009)

The monoclonal antibodies panitumumab and cetuximab that target the epidermal growth factor receptor (EGFR) have expanded the range of treatment options for metastatic colorectal cancer. Initial evaluation of these agents as monotherapy in patients with EGFR-expressing chemotherapy-refractory tumors yielded response rates of approximately 10%. The realization that detection of positive EGFR expression by immunostaining does not reliably predict clinical outcome of EGFR-targeted treatment has led to an intense search for alternative predictive biomarkers. Oncogenic activation of signaling pathways downstream of the EGFR, such as mutation of KRAS, BRAF, or PIK3CA oncogenes, or inactivation of the PTEN tumor suppressor gene is central to the progression of colorectal cancer. Tumor KRAS mutations, which may be present in 35%-45% of patients with colorectal cancer, have emerged as an important predictive marker of resistance to panitumumab or cetuximab treatment. In addition, among colorectal tumors carrying wild-type KRAS, mutation of BRAF or PIK3CA or loss of PTEN expression may be associated with resistance to EGFR-targeted monoclonal antibody treatment, although these additional biomarkers require further validation before incorporation into clinical practice. Additional knowledge of the molecular basis for sensitivity or resistance to EGFR-targeted monoclonal antibodies will allow the development of new treatment algorithms to identify patients who are most likely to respond to treatment and could also provide rationale for combining therapies to overcome primary resistance. The use of KRAS mutations as a selection biomarker for anti-EGFR monoclonal antibody (eg, panitumumab or cetuximab) treatment is the first major step toward individualized treatment for patients with metastatic colorectal cancer.
2016 Student Science Awards (2016)

Purpose To provide an opportunity for students to have their work recognized by a scientific society and to have it considered for publication in a peer-reviewed scientific journal. Eligibility The competition is open to any student currently enrolled in a degree program at a recognized educational institution.
An Attention Mechanism for Neural Answer Selection Using a Combined Global and Local View (2017)

We propose a new attention mechanism for neural based question answering, which depends on varying granularities of the input. Previous work focused on augmenting recurrent neural networks for question answering systems with simple attention mechanisms which are a function of the similarity between a question embedding and an answer embeddings across time. We extend this by making the attention mechanism dependent on a global embedding of the answer attained using a separate network. We evaluate our system on InsuranceQA, a large question answering dataset. Our model outperforms current state-of-the-art results on InsuranceQA. Further, we examine which sections of text our attention mechanism focuses on, and explore its performance across different parameter settings.
Polarization mode dispersion minimization in fiber-wound piezoelectric cylinders (1995)

We describe a technique for minimizing polarization mode dispersion (PMD) in broadband interferometry for use with phase modulators of the type formed by coiling nominally circular-core single-mode optical fiber onto piezoelectric cylinders. The technique involves using two piezoelectric elements, arranged to be optically orthogonal. We show that in the general case the two cylinders give rise to four distinct interferograms, but by careful alignment of the elements we reduce these to two coincident interferograms. Hence the large PMD of a single-element modulator is reduced to a negligible level.
Peptide therapeutics: current status and future directions (2014)

Peptides are recognized for being highly selective and efficacious and, at the same time, relatively safe and well tolerated. Consequently, there is an increased interest in peptides in pharmaceutical research and development (R&D), and approximately 140 peptide therapeutics are currently being evaluated in clinical trials. Given that the low-hanging fruits in the form of obvious peptide targets have already been picked, it has now become necessary to explore new routes beyond traditional peptide design. Examples of such approaches are multifunctional and cell penetrating peptides, as well as peptide drug conjugates. Here, we discuss the current status, strengths, and weaknesses of peptides as medicines and the emerging new opportunities in peptide drug design and development.