gebhart/patrepeval huggingface dataset:
Two critical periods of protein and glycoprotein synthesis in memory consolidation for visual categorization learning in chicks. (1998)

A protein synthesis inhibitor, anisomycin (ANI), and an inhibitor of glycoprotein synthesis, 2-deoxygalactose (2-D-gal), were used to investigate memory consolidation following visual categorization training in 2-day-old chicks. ANI (0.6 micromole/chick) and 2-D-gal (40 micromoles/chick) were injected intracerebrally at different time intervals from 1 hr before to 23 hr after the training. Retention was tested 24 hr post-training. Both ANI and 2-D-gal injections revealed two periods of memory sensitivity to pharmacological intervention. ANI impaired retention when injected from 5 min before to 30 min after the training or from 4 hr to 5 hr post-training, thus demonstrating that consolidation of long-term memory in this task requires two periods of protein synthesis. 2-D-Gal first produced an amnesia when it was injected in the interval from 5 min before to 5 min after the training. Injections made between 5 min and 5 hr post-training were without effect on the retention. The second period of memory impairment by 2-D-gal started at 5 hr post-training and lasted until 21 hr after the training. Administration of 2-D-gal made 23 hr after the training did not influence retention in the test at either 24 hr or 26 hr. These results are consistent with the hypothesis that two waves of protein and glycoprotein synthesis are necessary for the formation of long-term memory. The prolonged duration of performance impairment by 2-D-gal in the present task might reflect an extended memory consolidation period for a categorization form of learning.
Commercialized Multigene Predictors of Clinical Outcome for Breast Cancer (2008)

In the past 5 years, a number of commercialized multigene prognostic and predictive tests have entered the complex and expanding landscape of breast cancer companion diagnostics. These tests have used a variety of formats ranging from the familiar slide-based assays of immunohistochemistry and fluorescence in situ hybridization to the nonmorphology-driven molecular platforms of quantitative multiplex real-time polymerase chain reaction and genomic microarray profiling. In this review, 14 multigene assays are evaluated as to their scientific validation, current clinical utility, regulatory approval status, and estimated cost-benefit ratio. Emphasis is placed on two tests: oncotype DX and MammaPrint. Current evidence indicates that the oncotype DX test has the advantages of earlier commercial launch, wide acceptance for payment by third-party payors in the U.S., ease of use of formalin-fixed paraffin-embedded tissues, recent listing by the American Society of Clinical Oncology Breast Cancer Tumor Markers Update Committee as recommended for use, continuous scoring system algorithm, ability to serve as both a prognostic test and predictive test for certain hormonal and chemotherapeutic agents, demonstrated cost-effectiveness in one published study, and a high accrual rate for the prospective validation clinical trial (Trial Assigning Individualized Options for Treatment). The MammaPrint assay has the advantages of a 510(k) clearance by the U.S. Food and Drug Administration, a larger gene number, which may enhance further utility, and a potentially wider patient eligibility, including lymph node-positive, estrogen receptor (ER)-negative, and younger patients being accrued into the prospective trial (Microarray in Node-Negative Disease May Avoid Chemotherapy). A number of other assays have specific predictive goals that are most often focused on the efficacy of tamoxifen in ER-positive patients, such as the two-gene ratio test and the cytochrome P450 CYP2D6 genotyping assay.
Mutations of the p16 gene product are rare in prostate cancer (1997)

BACKGROUND The p16 gene product is a negative regulator of cell cycle and has been shown to be deleted or mutated in a number of tumor cell lines and primary tumors. The role of p16 in prostate cancer is not defined. Prostate cancer tissues and cell lines were evaluated for p16 gene alterations. METHODS Five metastatic prostate cancer cell lines were analyzed for p16 gene structure and its expression by Southern and Northern blot analyses. Forty-one DNA specimens from 18 microdissected primary tumor specimens, adjacent normal tissues, and cell lines were amplified by polymerase chain reaction for p16 protein coding and splice junction sequences. Mutations were analyzed by single strand conformation polymorphism and DNA sequencing. RESULTS DU 145 cell line exhibited a missense mutation in codon 84 (GAC to TAC). With the exception of previously reported polymorphism, no mutation was detected in p16 coding or splice junction sequences in primary prostate cancer specimens. CONCLUSIONS Inactivation of p16 gene by mutations in the protein coding sequence does not play a major role in the genesis of primary prostate cancer. Prostate 30:188–194, 1997. © 1997 Wiley-Liss, Inc.
Intraoperative Magnetic Tracker Calibration Using a Magneto-Optic Hybrid Tracker for 3-D Ultrasound-Based Navigation in Laparoscopic Surgery (2008)

This paper describes a ultrasound (3-D US) system that aims to achieve augmented reality (AR) visualization during laparoscopic surgery, especially for the liver. To acquire 3-D US data of the liver, the tip of a laparoscopic ultrasound probe is tracked inside the abdominal cavity using a magnetic tracker. The accuracy of magnetic trackers, however, is greatly affected by magnetic field distortion that results from the close proximity of metal objects and electronic equipment, which is usually unavoidable in the operating room. In this paper, we describe a calibration method for intraoperative magnetic distortion that can be applied to laparoscopic 3-D US data acquisition; we evaluate the accuracy and feasibility of the method by in vitro and in vivo experiments. Although calibration data can be acquired freehand using a magneto-optic hybrid tracker, there are two problems associated with this method--error caused by the time delay between measurements of the optical and magnetic trackers, and instability of the calibration accuracy that results from the uniformity and density of calibration data. A temporal calibration procedure is developed to estimate the time delay, which is then integrated into the calibration, and a distortion model is formulated by zeroth-degree to fourth-degree polynomial fitting to the calibration data. In the in vivo experiment using a pig, the positional error caused by magnetic distortion was reduced from 44.1 to 2.9 mm. The standard deviation of corrected target positions was less than 1.0 mm. Freehand acquisition of calibration data was performed smoothly using a magneto-optic hybrid sampling tool through a trocar under guidance by realtime 3-D monitoring of the tool trajectory; data acquisition time was less than 2 min. The present study suggests that our proposed method could correct for magnetic field distortion inside the patient's abdomen during a laparoscopic procedure within a clinically permissible period of time, as well as enabling an accurate 3-D US reconstruction to be obtained that can be superimposed onto live endoscopic images.
Solid‐Phase Edman Degradation (1971)

A modification of the Edman degradation is described whereby peptides are degraded sequentially on a solid support by a machine, the solid‐phase peptide sequencer. Reagents are pumped through a column containing the resin‐bound peptide, and the amino acid thiazolinones released after each degradative cycle are collected on a fraction collector for subsequent analysis. A complete cycle requires 2 h, and all operations are controlled automatically by a programmer. An improved peptide resin is described, to which peptides can be attached in yields ranging from about 70% for the 30 amino acid insulin B‐chain to nearly 100% for smaller peptides. Of the 18 amino acids examined so far, glycine, alanine, phenylalanine, tyrosine, valine, leucine, isoleucine, proline, methionine, asparagine, glutamine, histidine, lysine, threonine, serine and cysteic acid are degraded normally; the phenylthiohydantion of threonine is partially dehydrated and that of serine is almost completely destroyed by trifluoroacetic acid, however. The phenylthiohydantion of glutamic acid is not detected, because it remains bound by its γ‐carboxyl group to the resin. When aspartic acid is encountered in peptides, further degradation is completely blocked, presumably as a result of the β‐carboxyl group having formed a cyclic imide. Using the sequencer and unpurified reagents, it was possible to degrade entirely a 0.24 μmole sample of the 21 amino acid insulin A‐chain (oxidized) and to analyze the products within a 3‐day period. Degradative yields averaged 94% per cycle. Similarly, 0.1 μmole of the insulin B‐chain was degraded through 18 cycles before identification of the phenylthiohydantoins became ambiguous. The sequencer is simple in design and operation, and is inexpensive to construct. The scope and limitations of the method are discussed.
Mutagenesis of conserved 5' dements and transcription of a chicken H1 histone gene (1986)

In addition to readily identifiable TATA and CAAT boxes, chicken H1 histone genes contain a highly conserved G-rich region at about minus 80 and an A-rich H1 histone gene-specific motif some 120 bases upstream from the H1 mRNA cap site. The level of transcription from wild-type, 'G-box' and 'A-box' H1 deletion mutant templates was tested in Xenopus oocytes and in HeLa cells. Removal of the H1 gene-specific motif had no effect on H1 gene transcription in either assay system, whereas deletion of the G-rich sequence decreased H1 mRNA levels by about ten-fold in oocytes and in HeLa cells. At least in heterologous systems, the H1-gene specific A-rich region does not appear to influence the level of H1 gene transcription.
The role of class II molecules in human B cell activation. Association with phosphatidyl inositol turnover, protein tyrosine phosphorylation, and proliferation. (1990)

Cross-linking class II molecules on resting human B cells can initiate phosphatidyl inositol turnover and an increase in intracellular calcium concentration levels comparable with that seen with the cross-linking of surface Ig receptors. The calcium response is most evident on dense B cell fractions: buoyant cells are less responsive, even though the levels of class II expression are similar on dense and buoyant tonsillar B cells. Human B cell lines exhibit the same absence of correlation between intensity of the calcium signal and levels of surface class II expression, indicating that responsiveness is related to the state of differentiation of the cell rather than the amount of class II expressed. Cross-linking class II on normal B cells or B cell lines caused accumulation of inositol phosphates, suggesting class II induces calcium release from intracellular stores, rather than through direct regulation of calcium channels. The calcium response mediated through class II was completely abolished by bringing the protein tyrosine phosphatase, CD45, into close proximity with surface class II. This result indicated that protein tyrosine phosphorylation might regulate the signal transduced through this molecule. In support of this notion we found that tyrosine phosphorylation is induced when small dense tonsillar B cells are stimulated with either anti-Ig or with antibodies to class II. Finally, in B cell proliferation assays we show that cross-linking class II molecules on dense tonsillar B cells synergize strongly with suboptimal concentrations of PMA or IL-4. The significance of these results is discussed with regard to the cognate signal between B and T lymphocytes.
Interactions of troponin subunits: free energy of binary and ternary complexes (1987)

We have determined the free energy of formation of the binary complexes formed between skeletal troponin C and troponin T (TnC.TnT) and between troponin T and troponin I (TnT.TnI). This was accomplished by using TnC fluorescently modified at Cys-98 with N-(iodoacetyl)-N'-(5-sulfo-1-naphthyl)ethylenediamine for the first complex and TnI labeled at Cys-133 with the same probe for the other complex. The free energy of the ternary complex formed between troponin C and the binary complex TnT.TnI [TnC.(TnT.TnI)] was also measured by monitoring the emission of 5-(iodoacetamido)eosin attached to Cys-133 of the troponin I in TnT.TnI. The free energies were -9.0 kcal.mol-1 for TnC.TnT, -9.2 kcal.mol-1 for TnT.TnI, and -8.7 kcal.mol-1 for TnC.(TnT.TnI). In the presence of Mg2+ the free energies of TnC.TnT and TnC.(TnT.TnI) were -10.3 and -10.9 kcal.mol-1, respectively; in the presence of Ca2+ the corresponding free energies were -10.6 and -13.5 kcal.mol-1. Mg2+ and Ca2+ had negligible effect on the free energy of TnT.TnI. From these results the free energies of the formation of troponin from the three subunits were found to be -16.8 kcal.mol-1, -18.9 kcal.mol-1, and -21.6 kcal.mol-1 in the presence of EGTA, Mg2+, and Ca2+, respectively. Most of the free energy decrease caused by Ca2+ binding to the Ca2+-specific sites is derived from stabilization of the TnI-TnC linkage.(ABSTRACT TRUNCATED AT 250 WORDS)
Acquired resistance of a mammalian cell line to hypoxia-reoxygenation through cotransfection of Kir6.2 and SUR1 clones. (1998)

Reoxygenation after transient hypoxia is a common clinical condition that often causes greater tissue damage than persistent hypoxia itself. This warrants the development of a means to protect cells against hypoxia-reoxygenation injury. Adenosine triphosphate (ATP)-sensitive K+ (KATP) channels have been proposed to play an essential role in the mechanisms of endogenous cellular protection. Thus far, however, KATP channel proteins have not been exploited to generate an injury-resistant cellular phenotype by delivering KATP channel genes into injury-prone cells. A first step in this direction is the evaluation of the outcome of transferring genes encoding KATP channels into a KATP channel-deficient cell type exposed to metabolic stress. Untransfected COS-7 monkey kidney cells, which natively lack KATP channels, were found to be vulnerable to hypoxia-reoxygenation injury, which induced cytosolic Ca2+ loading, as measured by digital epifluorescent imaging. COS-7 cells cotransfected with KATP channel genes, Kir6.2 and SUR1, gained resistance to hypoxia-reoxygenation. This acquired resistance was abolished by glyburide, the KATP channel antagonist. We have previously shown that Kir6.2 and SUR1 physically associate to form a functional KATP channel, not reconstituted by either of the subunits alone. Transfection with individual channel subunits, Kir6.2 or SUR1, failed to produce resistance to hypoxia-reoxygenation induced Ca2+ loading. This is a first demonstration that transfer of KATP channel subunits can generate an injury-resistant cellular phenotype. The findings from this study may, thus, provide a framework for future therapeutic strategies based on gene delivery of KATP channel subunits in cells and tissues vulnerable to hypoxia-reoxygenation insults.
Abstract LB-109: MDV3100, an androgen receptor signaling inhibitor, inhibits tumor growth in breast cancer preclinical models regardless of estrogen receptor status (2012)

Abstract Background: The androgen receptor (AR) is detected by immunohistochemistry in approximately 75% of all invasive breast cancer, with ∼88% of estrogen receptor (ER) positive (ER+) tumors also expressing AR and ∼20 to 30% of ER negative (ER-) tumors also retaining AR expression. Potent inhibition of AR activity could be a therapeutic strategy in AR+ ER+ breast cancer. MDV3100 is an androgen receptor signaling inhibitor (ARSI), which inhibits AR activity via three mechanisms: 1) inhibition of androgen binding to AR, 2) inhibition of AR nuclear translocation, and 3) inhibition of nuclear AR-DNA binding; and has demonstrated an overall survival benefit in men with post-docetaxel prostate cancer. Methods: Two ER+/AR+ breast cancer cell lines, MCF7and BCK4 (recently derived from a pleurocentesis), were used to assess the proliferative effect of dihydrotestosterone (DHT) and estradiol (E2) in ovariectomized mice. MDV3100 was compared to bicalutamide and tamoxifen. Growth effects of MDV3100 on ER-/AR+ cells in tissue culture and in xenografts were also examined. Results: Both bicalutamide and MDV3100 inhibited DHT-mediated proliferation of ER+/AR+ cell lines. Although MDV3100 binds AR very effectively and does not bind ER, it inhibited E2-mediated proliferation. MDV3100 also blocked E2 mediated upregulation of AR, PR, and SDF-1. MDV3100 inhibited E2-stimulated tumor growth of MCF7 mammary xenografts as effectively as tamoxifen. With ER-/AR+ cells (MDA-MB-453), MDV3100 reduced DHT-induced nuclear translocation, cell growth in tissue culture and tumor growth in mouse orthotopic xenografts. Conclusions: MDV3100 blocked both DHT- and E2-mediated growth of breast cancer cells, whereas bicalutamide enhanced E2-mediated proliferation. MDV3100 may have unique therapeutic utility in patients with AR+ breast cancer, regardless of ER status. Funding: DOD Breast Cancer Program Idea Award BC074403, Avon Foundation for Women, and University of Colorado Cancer Center pilot project funds to JKR. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-109. doi:1538-7445.AM2012-LB-109
GeoSpaces/sup TM/-A virtual collaborative software environment for interactive analysis and visualization of geospatial information (2002)

Geographic information systems (GIS) software products have been available for the past two decades, offering the imagery and geospatial analyst mature and robust visualization and analysis capabilities. In recent years, tools for collaborating over the Internet with colleagues, family, and friends have emerged. Early capabilities supported simple chatting and instant messaging between two or more geographically dispersed collaborators, simultaneously and in real-time. More capable application sharing tools quickly followed, allowing multiple collaborators to read and write simultaneously within the same document. More recently, rich collaborative environments have emerged, providing robust resources such as file and data management, conferencing centers, electronic whiteboarding, automatic resource location, knowledge management tools, and many more bundled applications. A logical extension to these new Internet-based capabilities is to couple the mature GIS functionality with the emerging electronic whiteboarding tool concept, providing a geo-referenced, collaborative whiteboard. This paper describes such a new capability, called GeoSpace/sup TM/. General Dynamics Electronic Systems has developed and demonstrated GeoSpace/sup TM/ for operational use across a diverse set of applications. In this paper, we describe the underlying technical approach to process and share remotely sensed information within the context of a specific disaster assessment and management application.
Human SLPI inactivation after cigarette smoke exposure in a new in vivo model of pulmonary oxidative stress (2001)

The role of oxidative stress in inactivating antiproteases is the object of debate. To address this question, we developed an in vivo model of pulmonary oxidative stress induced by cigarette smoke (CS) in mice. The major mouse trypsin inhibitor contrapsin is not sensitive to oxidation, and the mouse secretory leukoprotease inhibitor (SLPI) does not inhibit trypsin. Instead, human recombinant (hr) SLPI inhibits trypsin and is sensitive to oxidation. Thus we determined the effect of CS in vivo on hrSLPI antiproteolytic function in the airways of mice. CS caused a significant decrease in total antioxidant capacity in bronchoalveolar lavage fluid (BALF) and significant changes in oxidized glutathione, ascorbic acid, protein thiols, and 8-epi-PGF(2alpha). Intratracheal hrSLPI significantly increased BALF antitryptic activity. CS induced a 50% drop in the inhibitory activity of hrSLPI. Pretreatment with N-acetylcysteine prevented the CS-induced loss of hrSLPI activity, the decrease in antioxidant defenses, and the elevation of 8-epi-PGF-(2alpha). Thus an inactivation of hrSLPI was demonstrated in this model. This is a novel model for studying in vivo the effects of CS oxidative stress on human protease inhibitors with antitrypsin activity.
A policy driven self-healing algorithm for context aware systems (2009)

This paper proposes a generic self-healing algorithm that automatically detects, diagnoses and repairs the problems appeared during the context aware systems' adaptation processes. The set, situation calculus and information system theories are used to define and formalize the concepts of context situation entropy and equivalent context situations together with a set of self-healing principles. These concepts and principles are used to generically define the self-healing algorithm. The self-healing property is enforced by monitoring the systems execution environment for: (i) evaluating the degree of fulfilling the context policies of the current context situation (context situation entropy), (ii) obtaining the equivalent context situations and (iii) determining the actions that have to be executed in order to keep the system in consistent functional states. The self-healing algorithm is validated on our RAP context model by enhancing it with a generic policy representation technique for run-time evaluation.
PECAN: Program Development Systems that Support Multiple Views (1985)

This paper describes the PECAN family of program development systems. PECAN supports multiple views of the user's program. The views can be representations of the program or of the corresponding semantics. The primary program view is a syntax-directed editor. The current semantic views include expression trees, data type diagrams, flow graphs, and the symbol table. PECAN is designed to make effective use of powerful personal machines with high-resolution graphics displays and is currently implemented on APOLLO workstations.
Mechanism of Cyclic Carbonate Synthesis from Epoxides and CO2 (2009)

Abstract Three interconnected catalytic cycles account for the title reaction catalyzed by a bimetallic aluminum(salen) complex and Bu 4 NBr. In the first, Bu 4 NBr acts as a nucleophile to activate the epoxide. In the second, Bu 3 N generated in situ serves to activate CO 2 . In the third, the aluminum(salen) complex brings the two activated species together so that the key bonds can be formed intramolecularly. magnified image
Silicon film thickness considerations in SOI-DTMOS (2002)

We study the body effect in silicon-on-insulator (SDI) devices to determine if enhanced drive currents can be obtained with a body bias equal to the supply voltage. We find that significantly enhanced drive currents are observed only when the film thickness is sufficiently large. We explain this phenomenon using two-dimensional (2-D) device simulations and conclude that a film thickness greater than 100 nm is required. This sets a criterion for SOI devices to be used as dynamic threshold MOSFETs.