gebhart/patrepeval huggingface dataset:
A phase II nonrandomized study of nab-paclitaxel plus carboplatin in patients with recurrent platinum-sensitive ovarian or primary peritoneal cancer. (2010)

5011 Background: Paclitaxel in combination with carboplatin is effective salvage therapy for the treatment of recurrent ovarian cancer. The purpose of this study was to evaluate the antitumor activity of nanoparticle albumin-bound paclitaxel (nab-paclitaxel) plus carboplatin in patients with recurrent platinum-sensitive ovarian or primary peritoneal carcinoma. Methods: Patients with measurable disease received nab-paclitaxel 100 mg/m2 on days 1, 8, and 15 of each 28-day cycle and carboplatin AUC 5 intravenously on day 1. Patients were to be treated for at least 6 cycles. Efficacy was measured by objective response rate (ORR) per RECIST, progression-free survival (PFS), and overall survival (OS). Patients were followed every 3 months for 2 years. Results: Forty eligible patients with median age of 62 years (range 43 - 81) were enrolled; 28 patients had ovarian cancer stage IIIC, 9 had stage IIB/IIIB or IIC, and 3 had stage IV disease. Most were Caucasian (83%), most had ECOG status of 0 (88%), and all had received prior taxane/platinum chemotherapies. The median (standard deviation [STDV]) platinum-free interval was 13 (8) months. The median number of cycles with nab-paclitaxel plus carboplatin was 6 (range 3-48). Of 38 patients who were evaluable (2 did not receive treatment), 15 (39%) had a complete response (CR), 15 (39%) had a partial response (PR) for an ORR of 79%. Seven (18%) patients had stable disease (SD), 1 (3%) patient had disease progression (PD). The median (STDV) PFS was 13 (11) months and median (STDV) OS was 30 (13) months. The most common grade ≥ 3 adverse events were neutropenia (43%), fatigue (33%), hypersensitivity reaction to carboplatin (18%), anemia (10%), thrombocytopenia (5%), and nausea (5%). Of the 40 patients enrolled, 11 patients have completed 2 years of follow-up, 15 patients have died, 13 patients are still being followed, and 1 patient is still receiving treatment after more than 2 years. Conclusions: With a 97% disease control rate (CR + PR + SD), the combination of nab-paclitaxel plus carboplatin had significant antitumor activity and was reasonably tolerated in patients with platinum-sensitive recurrent ovarian cancer. No significant financial relationships to disclose.
Randomized clinical trial of preoperative oral versus intravenous iron in anaemic patients with colorectal cancer (2017)

Intravenous iron did not reduce the blood transfusion requirement but was more effective than oral iron at treating preoperative anaemia and iron deficiency in patients undergoing colorectal cancer surgery.
Integration of a nanostructured dielectrophoretic device and a surface-enhanced Raman probe for highly sensitive rapid bacteria detection (2015)

This work reports a synergistic approach to the concentration, detection and kinetic monitoring of pathogens through the integration of nanostructured dielectrophoresis (DEP) with nanotag-labelled Surface Enhanced Raman Spectroscopy (SERS). A nanoelectrode array made of embedded Vertically Aligned Carbon Nanofibers (VACNFs) at the bottom of a microfluidic chip was used to effectively capture and concentrate nanotag-labelled E. coli DHα5 cells into a 200 μm × 200 μm area on which a Raman laser probe was focused. The SERS nanotags were based on iron oxide-gold (IO-Au) core-shell nanoovals (NOVs) of ∼50 nm size, which were coated with a QSY21 Raman reporter and attached to E. coli through specific immunochemistry. The combination of the greatly enhanced Raman signal by the SERS nanotags and the effective DEP concentration significantly improved the detection limit and speed. The SERS signal was measured with both a confocal Raman microscope and a portable Raman probe during DEP capture, and was fully validated with fluorescence microscopy measurements under all DEP conditions. The SERS measurements were sensitive enough to detect a single bacterium. A concentration detection limit as low as 210 cfu ml(-1) using a portable Raman system was obtained with a DEP capture time of only ∼50 s. These results demonstrate the potential to develop a compact portable system for rapid and highly sensitive detection of specific pathogens. This system is reusable, requires minimum sample preparation, and is amenable to field applications.
Identification of DNA binding proteins in vaccinia virus by DNA‐protein crosslinking (1993)

DNA binding proteins of vaccinia virus (VV) virions, strain LIVP, have been studied by their covalent crosslinking to DNA, using two-dimensional gel retardation electrophoresis of crosslinked DNA and proteins as well as the 'protein image' hybridization assay. Five proteins with molecular masses of 16, 25, 27, 41 and 54 kDa, respectively, associated with all analysed DNA sequences, including early and late genes and their promoters, have been identified.
Synthesis and Establishment of Stereochemistry of the Unusual Polyoxazole—Thiazole Based Cyclopeptide YM‐216391 Isolated from Streptomyces nobilis. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis (2008)

Small non-protein-coding RNAs (ncRNAs) have systematically been studied in various model organisms from Escherichia coli to Homo sapiens. Here, we analyse the small ncRNA transcriptome from the pathogenic filamentous fungus Aspergillus fumigatus. To that aim, we experimentally screened for ncRNAs, expressed under various growth conditions or during specific developmental stages, by generating a specialized cDNA library from size-selected small RNA species. Our screen revealed 30 novel ncRNA candidates from known ncRNA classes such as small nuclear RNAs (snRNAs) and C/D box-type small nucleolar RNAs (C/D box snoRNAs). Additionally, several candidates for H/ACA box snoRNAs could be predicted by a bioinformatical screen. We also identified 15 candidates for ncRNAs, which could not be assigned to any known ncRNA class. Some of these ncRNA species are developmentally regulated implying a possible novel function in A. fumigatus development. Surprisingly, in addition to full-length tRNAs, we also identified 5'- or 3'-halves of tRNAs, only, which are likely generated by tRNA cleavage within the anti-codon loop. We show that conidiation induces tRNA cleavage resulting in tRNA depletion within conidia. Since conidia represent the resting state of A. fumigatus we propose that conidial tRNA depletion might be a novel mechanism to down-regulate protein synthesis in a filamentous fungus.
The Many Faces of H89: A Review (2006)

H89 is marketed as a selective and potent inhibitor of protein kinase A (PKA). Since its discovery, it has been used extensively for evaluation of the role of PKA in the heart, osteoblasts, hepatocytes, smooth muscle cells, neuronal tissue, epithelial cells, etc. Despite the frequent use of H89, its mode of specific inhibition of PKA is still not completely understood. It has also been shown that H89 inhibits at least 8 other kinases, while having a relatively large number of PKA-independent effects which may seriously compromise interpretation of data. Thus, while recognizing its kinase inhibiting properties, it is advised that H89 should not be used as the single source of evidence of PKA involvement. H-89 should be used in conjunction with other PKA inhibitors, such as Rp-cAMPS or PKA analogs.
Metalorganic chemical vapor deposition of tungsten nitride for advanced metallization (1996)

In this study, the physical and electrical properties of tungsten nitride thin films deposited by thermal decomposition of bis(tertbutylimido)bis(tertbutylamido)tungsten have been investigated. The films have an excellent step coverage over high aspect-ratio contact holes as well as a low carbon concentration. Strong W–N double bonds in the precursor preserved the nitrogen atoms during the pyrolysis process. This method subsequently yielded low-resistivity films. A decrease in film resistivity from 4300 to 620 μΩ cm corresponded to an increase in the deposition temperature from 500 to 650 °C. X-ray diffraction (XRD) and wavelength dispersive spectroscopy (WDS) results indicated that the as-deposited films have face centered cubic (fcc) phase polycrystalline structures with excessive nitrogen atoms.
Conformational Changes in G-CSF/Receptor Complex As Investigated by Isotope-Edited FTIR Spectroscopy (1997)

Conformations of G-CSF and the extracellular domain of its receptor as well as their complex have been investigated by employing isotope-edited FTIR spectroscopy. To determine unambiguously the protein conformations of G-CSF and the receptor in the complex, we have prepared uniformly 13C/15N isotope labeled G-CSF to resolve its amide I' band from that of the receptor in the IR spectrum of the complex. By comparing the IR spectra of the isotope-labeled G-CSF and the receptor with that of the complex, we have provided spectral evidence that the AB loop region involving the unique 310 helix segment of G-CSF likely undergoes a conformational change to a regular alpha-helix upon binding to the receptor. The IR data also indicate a possible minor increase in alpha-helical conformation for the receptor in the complex. Furthermore, FTIR spectra of G-CSF, the receptor, and their complex demonstrate clearly that protein conformations of both G-CSF and the receptor have been dramatically stabilized by complex formation. Specifically, the melting transition (Tm value) of the alpha-helix in G-CSF is increased by nearly 30 degrees C and that of the beta-strand in the receptor by nearly 15 degrees C in the G-CSF/receptor complex. We estimate from the current FTIR data that the native conformations of approximately 15% of all receptor residues are stabilized by G-CSF binding. On the other hand, the entire alpha-helical content of G-CSF appears to be stabilized in the complex. Together, these results indicate that formation of the ligand/receptor complex results in not only conformational changes in the receptor but also significant structural changes in the ligand. This adds insight to the general consensus that binding of ligand to cytokine receptors induces mostly structural changes in the receptor which lead to receptor oligomerization and signal transduction. The current data also suggest a possible physiological role of the 310 helix present in G-CSF for its receptor binding activity.
Abstract 213: Novel NOTCH3 activating mutations identified in tumors sensitive to OMP-59R5, a monoclonal antibody targeting the Notch2 and Notch3 receptors. (2013)

Abstract The Notch signaling pathway, driven by four Notch family receptors (NOTCH1-4) and five canonical Notch ligands (DLL1, DLL3, DLL4, JAG1, and JAG2) in humans, critically regulates key functions during embryonic development as well as stem cell maintenance and differentiation in adult tissues. Altered Notch signaling activity has been documented in many types of cancers; depending on the tumor type, Notch signaling can be oncogenic or tumor suppressing. Activating mutations in NOTCH1 have been identified in hematopoietic cancers including T-cell acute lymphoblastic leukemia and chronic lymphoblastic leukemia. With the advance in high-throughput genomic sequencing platforms, mutations in the NOTCH genes have also been identified in solid tumors, albeit at much lower frequencies. Here we report for the first time the identification of two activating mutations in NOTCH3. One is a frameshift mutation in the PEST domain, and the other a frameshift mutation in the ankyrin (ANK) domain. The PEST frameshift mutation leads to the production of C-terminally truncated NOTCH3 protein, and by Western Blotting of nuclear fractions of tumor tissues and Immunohistochemistry (IHC) we show that this mutant NOTCH3 accumulates stably in the nuclei of the breast tumor in which it was identified. Breast xenograft tumors carrying this mutation are highly sensitive to OMP-59R5, a ligand-blocking antibody targeting the Notch2 and Notch3 receptors, suggesting that the mutation, although activating, is still ligand dependent. Consistent with this finding, expression of this mutant NOTCH3 constructed by site-directed mutagenesis exhibits higher baseline activity compared to wild type NOTCH3 and is equally responsive to ligands in in vitro NOTCH reporter assays. We are not able to observe increased nuclear accumulation of the ANK frameshift mutant NOTCH3 in the colon tumor in which it was identified. However, in vitro the ANK mutant NOTCH3 has higher baseline activity than wild-type NOTCH3 in the absence of ligands and remains highly responsive to ligands. The colon xenograft tumors carrying this NOTCH3 ANK mutation are also sensitive to OMP-59R5 in in vivo efficacy studies. Taken together our data suggest that NOTCH3 is oncogenic in certain subtypes of tumors, and tumors with these activating mutations may predictive sensitivity to therapeutic antibodies targeting the receptor. Citation Format: Breanna Wallace, Min Wang, Chris Muriel, Jennifer Cain, Belinda Cancilla, Jalpa Shah, Jie Wei, Austin Gurney, John Lewicki, Aaron Sato, Tim Hoey, Tracy Tang, Ann M. Kapoun. Novel NOTCH3 activating mutations identified in tumors sensitive to OMP-59R5, a monoclonal antibody targeting the Notch2 and Notch3 receptors. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 213. doi:10.1158/1538-7445.AM2013-213
Fossil Fuels as a Source of Mercury Pollution (1971)

The upper limit of the quantity of mercury released by weathering processes is approximately 230 metric tons per year. The quantity of mercury released by burning of coal is estimated to be of the order of 3000 tons per year, a quantity comparable to that emitted as waste from industrial processes.
Reduction of dislocation in GaN epitaxial layer grown on (111)-oriented Silicon by using InN inter-layer (2009)

Abstract not Available.
Detection of human parvovirus B19 DNA by using the polymerase chain reaction (1990)

The polymerase chain reaction (PCR) was investigated for detecting human parvovirus B19 (B19) DNA in sera. Three pairs of oligonucleotides were evaluated as primers. The best oligonucleotide pair spanned 699 nucleotides, including the region common to VP1 and VP2. After PCR amplification of B19 DNA in serum, a 699-nucleotide DNA fragment was detected on agarose gels. This DNA fragment was B19 DNA, because after Southern transfer it hybridized to a 19-nucleotide internal probe and contained a single PstI cleavage site. Dot blot hybridization with a radiolabeled cloned portion of the B19 genome as a probe was compared with PCR. PCR was 10(4) times more sensitive than dot blot hybridization and, with an internal radiolabeled probe, 10(7) times more sensitive than dot blot hybridization. Of 29 serum specimens from 18 patients with proven B19 infections, 24 were PCR positive. None of 20 serum samples from uninfected controls were positive. Of 22 serum samples positive for immunoglobulin M to B19, PCR detected B19 DNA in 17. Seven serum samples lacking immunoglobulin M were PCR positive. PCR detected B19 DNA in urine, amniotic fluid, pleural fluid, ascites, and leukocyte extracts. PCR is a rapid and simple method for diagnosing infections with human parvovirus B19 but must be combined with serologic tests for immunoglobulin M to B19, especially when testing only a single serum sample.
Intraperitoneal immunization against necrobacillosis in experimental animals. (1978)

This paper studies dislocation induced internal stresses as introduced in a strain gradient crystal plasticity approach. The need for a second-order crystal plasticity approach is motivated in the context of the analysis of free-standing metal films used in radio-frequency micro-electro-mechanical systems (RFMEMS). The presented second-order framework incorporates the influence of inter- and intragranular deformation inhomogeneities in the constitutive description, generally assumed to be the basic origin of scale dependent behaviour and associated size effects. Focusing on the dynamic loading of thin RF-MEMS films, attention is given to dislocation induced kinematical hardening effects. The corresponding internal stresses are discussed withrespect to their contribution to the solution of the underlying elasto-plastic framework which implicitly accounts for elastic incompatibilities. Within theloading regime of interest, the response in loading–unloading–reloading and cyclic loading is assessed.
Efficient creation of statistics over query expressions (2004)

Query optimizers use base-table statistics to derive statistics on the subplans that are enumerated during optimization. In practice, traditional optimizers rely on a number of simplifying assumptions, which can compromise the accuracy of cardinality estimates. To address this limitation, we had earlier introduced SITs, which are statistics built over query expressions, and we explained how a traditional optimizer can judiciously use SITs to sidestep the problem of inaccurate estimates. A significant challenge that was not addressed was how to build SITs efficiently in a database system. We present a family of techniques to create SITs. These techniques differ from each other in the trade-off they present between accuracy and efficiency of creation. We also present techniques to efficiently create multiple SITs by taking advantage of the commonalities among their generating query expressions.
A Dual-Function Wheeled Probe for Tissue Viscoelastic Property Identification during Minimally Invasive Surgery (2007)

This paper proposes a novel approach for the identification of tissue properties in-vivo using a force sensitive wheeled probe. The purpose of such a device is to compensate a surgeon for a portion of the loss of haptic and tactile feedback experienced during robotic-assisted minimally invasive surgery. Initially, a testing facility for validating the concept ex-vivo was developed and used to characterize two different testing modalities - static (1-DOF) tissue indentation and rolling (2-DOF) tissue indentation. As part of the static indentation experiments a mathematical model was developed to classify tissue condition based on changes in mechanical response. The purpose of the rolling indentation tests was to detect tissue abnormalities, such as tumors, which are difficult to isolate under static testing conditions. During such tests, the test-rig was capable of detecting simulated miniature buried masses at depths of 12mm. Based on these experiments a portable device capable of carrying out similar tests in-vivo was developed. The device was designed to be operated through a trocar port and its key feature is the ability to transition between static indentation and rolling indentation modalities without retracting and changing the tool.
Control of Monolayer Assembly Structure by Hydrogen Bonding Rather Than by Adsorbate−Substrate Templating (1999)

Stratified amide-containing self-assembled monolayers (SAMs) provide opportunities for investigating the fundamental dependence of supramolecular structure upon molecular constitution. We report a series of amide-containing alkanethiol SAMs (Cn-1AT/Au, n = 9, 11−16, 18) in which the hydrophobic overlayer thickness is systematically varied and the thickness of the polar region is held constant. The results from X-ray photoelectron spectroscopy, contact angle goniometry, reflective IR spectroscopy, and electrochemical measurements provide a consistent structural picture of the series. The amide underlayers in all the SAMs are well-ordered and extensively hydrogen bonded. However, the alkyl chains are disordered below n = 15. Comparison of the assembly structures shows that the chain length threshold for alkyl ordering is several methylenes higher than in n-alkanethiol SAMs. This indicates that alkyl chains adjacent to an amide underlayer are destabilized as compared to n-alkanethiols and that the amide underlayer destructively interferes with alkyl close packing as compared to the Au(111)−sulfur template. However, the amide regions of the SAMs are all well-ordered, showing that the amide sublayer acts as a “template” that is independent of alkyl chain length. The amide region dominates over gold−sulfur epitaxy in establishing the structure of these assemblies, and the amide−alkyl boundary provides an example of a “rigid−elastic” buried organic interface. Implications of these studies for molecular control of bulk properties, lipid-linked protein structure and function, buried organic interfaces in other systems, rationally designed ordered multilayers, and hybrid supramolecular systems are discussed.
Eosinophils, eosinophil ribonucleases, and their role in host defense against respiratory virus pathogens (2001)

Eosinophils remain among the most enigmatic of cells, as our appreciation of their detrimental activities--e.g., asthma and allergic disease--far outweighs our understanding of their beneficial effects. Among the major secretory effector proteins of eosinophils are the ribonucleases eosinophil-derived neurotoxin (EDN) and eosinophil cationic protein (ECP) in primates and their orthologs, the eosinophil-associated ribonucleases (EARs) in rodents. The rapid diversification observed among these ribonucleases suggested that the ultimate target(s) might be similarly efficient at generating sequence diversity while maintaining an unalterable susceptibility to ribonucleolytic cleavage. This has prompted us to consider a role for these proteins and by extension, for eosinophils, in host defense against single-stranded RNA virus pathogens. We detail our studies of the antiviral activity of eosinophils and eosinophil ribonucleases against respiratory syncytial virus (RSV) in vitro and the related, natural rodent pathogen, pneumonia virus of mice (PVM), in vivo, and consider the possibility that antiviral host defense and the dysregulated responses leading to asthma represent opposing sides of an eosinophil-mediated double-edged sword.
Practical Challenges for Digital Watermarking Applications (2002)

The field of digital watermarking has recently seen numerous articles covering novel techniques, theoretical studies, attacks, and analysis. In this paper, we focus on an emerging application to highlight practical challenges for digital watermarking applications. Challenges include design considerations, requirements analysis, choice of watermarking techniques, speed, robustness, and the tradeoffs involved. We describe common attributes of watermarking systems and discuss the challenges in developing real world applications. Our application uses digital watermarking to connect ordinary toys to the digital world. The application captures important aspects of watermarking systems and illustrates some of the design issues faced.
The effect of local anaesthetics on synoviocytes: a possible indirect mechanism of chondrolysis (2012)

0.5 % bupivacaine with epinephrine caused a significant increase in cell death of the synoviocytes, while 0.5 % bupivacaine alone produced cell injury and a significant release of matrix metalloproteinases, which may also lead to indirect injury of the surrounding chondrocytes. These results may help explain the onset of chondrolysis observed in patients who have been treated with intra-articular local anaesthetics.