gebhart/patrepeval huggingface dataset:
Mouse Models of Human Cancer (2004)

Preface.Contributors.PART I: MOUSE HANDLING AND ENGINEERING.1. Approaches to Handling, Breeding, Strain Preservation, Genotyping, and Drug Administration for Mouse Models of Cancer (Dawnalyn Boggess, Kathleen A. Silva, Carlisle P. Landel, Larry Mobraaten, and John P. Sundberg).2. Pathology of Mouse Models of Cancer (Robert D. Cardiff).3. Intercurrent Infections in Genetically Engineered Mice (Stephen W. Barthold).4. Germline Modification Strategies (Silvia Grisendi and Pier Paolo Pandolfi).5. Somatic Cell Gene Transfer (Lene Uhrbom and Eric C. Holland).PART II: ORGAN SITE-SPECIFIC MOUSE MODELS OF HUMAN CANCER.6. Lung Cancer (Jonathan M. Kurie, Parviz Minoo, Stephen S. Hecht, Alexander Nikitin, and Franco J. DeMayo).7. Mammary Gland Cancer (Dalit Barkan, Cristina Montagna, Thomas Ried, and Jeffrey E. Green).8. Prostate Cancer (Katharine Ellwood-Yen and Charles Sawyers).9. Skin Cancer (Marcus Bosenberg).10. Ovarian Cancer (Sandra Orsulic).11. Peripheral Nervous System Tumors (David H. Gutmann, Arie Perry, Reshma Rangwala, and Larry S. Sherman).12. Central Nervous System Tumors (Andrew B. Lassman and Eric C. Holland).13. Myeloid Malignancies (Scott C. Kogan).14. Lymphoid Malignancies (Michael Teitell and Pier Paolo Pandolfi).PART III: GENERAL ISSUES IN CANCER BIOLOGY.15. Genetic Modifiers (David W. Threadgill, Kent W. Hunter, Fei Zou, and Kenneth F. Manly).16. Modeling Blood Vessel Formation in the Mouse (Robert Benezra, Shahin Rafii, and David Lyden).17. Metastasis (Dawn S. Chandler and Guillermina Lozano).18. Immunologic Study of Tumors in Mouse Models (Taha Merghoub and Alan N. Houghton).PART IV: IMAGING TECHNOLOGIES.19. Micro-Computed Tomography of Mouse Cancer Models (Jamey P. Weichert).20 .Magnetic Resonance Imaging in Mouse Cancer Models (Manickam Muruganandham and Jason A. Koutcher).21. Bioluminescent Imaging of Mouse Cancer Models (Christopher H. Contag).PART V: PRECLINICAL TRIALS.22 .Use of Magnetic Resonance Imaging for Evaluation of Treatment Response (Brian D. Ross, Thomas L. Chenevert, Bradford A. Moffat, Alnawaz Rehemtulla, Daniel E. Hall, Patrick McConville, and Jonathan Moody).23. Physiologically Based Pharmacokinetic and Pharmacodynamic Modeling (Raymond S. H. Yang, James E. Dennison, Melvin E. Andersen, Ying C. Ou, Kai H. Liao, and Brad Reisfeld).24. Trial Design and Biostatistics (Michael F. W. Festing).25. Cancer Drug Development in the Modern Era (William R. Sellers and Alex Matter).26. Preclinical Trials in Mouse Cancer Models (Brian Weiss and Kevin Shannon).Index.
Regulation of Transcription of themph(A) Gene for Macrolide 2′-Phosphotransferase I inEscherichia coli: Characterization of the Regulatory GenemphR(A) (2000)

The synthesis of macrolide 2'-phosphotransferase I [Mph(A)], which inactivates erythromycin, is inducible by erythromycin. The expression of high-level resistance to erythromycin requires the mph(A) and mrx genes, which encode Mph(A) and an unidentified protein, respectively. We have studied the mphR(A) gene, which regulates the inducible expression of mph(A). An analysis of the synthesis of Mph(A) in minicells and results of a complementation test indicated that mphR(A) is located downstream from mrx and that its product, MphR(A), represses the production of Mph(A). DNA sequencing indicated that the mph(A), mrx, and mphR(A) genes exist as a cluster that begins with mph(A) and that the deduced amino acid sequence of MphR(A) can adopt an alpha-helix-turn-alpha-helix structure. To study the regulation of gene expression by MphR(A), we performed Northern blotting and primer extension. A transcript of 2. 9 kb that corresponded to the transcript of mph(A) through mphR(A) was detected, and its level was elevated upon exposure of cells to erythromycin. Gel mobility shift assays and DNase I footprinting indicated that MphR(A) binds specifically to the promoter region of mph(A), and the amount of DNA shifted as a results of the binding of MphR(A) decreased as the concentration of erythromycin was increased. These results indicate that transcription of the mph(A)-mrx-mphR(A) operon is negatively regulated by the binding of a repressor protein, MphR(A), to the promoter of the mph(A) gene and is activated upon inhibition of binding of MphR(A) to the promoter in the presence of erythromycin.
Capacitorless DRAM Cell with Highly Scalable Surrounding Gate Structure (2006)

To overcome the scalability issues and process complexity of 1-transistor/1-capacitor DRAM cell, capacitorless 1-transistor (1T) DRAM cells have been recently proposed and investigated [1]. The mainstream 1T DRAM cell is a floating body transistor cell (FBC) which consists of a MOSFET with its body floating electrically. The FBC is implemented by a MOSFET formed on partially depleted silicon-on-insulator (PD-SOI).[2,3] Because the floating body is used as a storage node, the FBC does not require complicated processes for storage capacitor. Therefore, the FBC has a simple process and can be made below 4F
Human Dioxin-Inducible Cytochrome P 1 -450: Complementary DNA and Amino Acid Sequence (1985)

Induction of cytochrome P1-450 has been linked to susceptibility to certain chemically induced cancers in mouse and man. Treatment of the human cell line MCF-7 with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) results in high levels of aryl hydrocarbon (benzo[a]pyrene) hydroxylase (P1-450) activity. This cell line was used to isolate a human P1-450 full-length complementary DNA (cDNA) clone. The cDNA is 2566 nucleotides in length, encodes a polyadenylated messenger RNA (2.8 kilobases in length), and has a continuous reading frame producing a protein with 512 residues (molecular weight, 58,151). The human P1-450 cDNA and protein are 63 percent and 80 percent similar to mouse P1-450 cDNA and protein, respectively. Whereas the mouse TCDD-inducible P-450 gene subfamily has two members (P1-450 and P3-450), the human TCDD-inducible gene subfamily appears to have only one gene (P1-450).
Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene‐expression subtypes of breast cancer (2006)

Breast cancer is a leading cause of cancer-death among women, where the clinicopathological features of tumors are used to prognosticate and guide therapy. DNA copy number alterations (CNAs), which occur frequently in breast cancer and define key pathogenetic events, are also potentially useful prognostic or predictive factors. Here, we report a genome-wide array-based comparative genomic hybridization (array CGH) survey of CNAs in 89 breast tumors from a patient cohort with locally advanced disease. Statistical analysis links distinct cytoband loci harboring CNAs to specific clinicopathological parameters, including tumor grade, estrogen receptor status, presence of TP53 mutation, and overall survival. Notably, distinct spectra of CNAs also underlie the different subtypes of breast cancer recently defined by expression-profiling, implying these subtypes develop along distinct genetic pathways. In addition, higher numbers of gains/losses are associated with the "basal-like" tumor subtype, while high-level DNA amplification is more frequent in "luminal-B" subtype tumors, suggesting also that distinct mechanisms of genomic instability might underlie their pathogenesis. The identified CNAs may provide a basis for improved patient prognostication, as well as a starting point to define important genes to further our understanding of the pathobiology of breast cancer. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat
Room-temperature wafer bonding of Si to LiNbO3, LiTaO3and Gd3Ga5O12by Ar-beam surface activation (2001)

A room-temperature wafer bonding method using surface activation by Ar-beam sputter etching were applied to the bonding between dissimilar materials. LiNbO3, LiTaO3 and Gd3Ga5O12 wafers were successfully bonded to Si wafers without any heat treatment. This method is free from the various problems caused by the large thermal expansion mismatch between these materials during heat treatment in the conventional wafer bonding processes. The bond prepared by the Ar-beam treatment is so strong that fracture from inside the bulk materials is observed after the tensile test. The results of the bonding of Si wafers to both 128° Y-cut and Z-cut LiNbO3 wafers indicate that the influence of the crystal orientation on the bonding strength is negligible in this method. This method provides a very low damage bonding process for various material combinations regardless of any thermal expansion mismatch or crystal lattice mismatch.
Protein Region Important for Regulation of Lipid Metabolism in Angiopoietin-like 3 (ANGPTL3) (2003)

Angiopoietin-like 3 (ANGPTL3) is a secreted protein that is mainly expressed in the liver and regulates lipid metabolism by inhibiting the lipolysis of triglyceriderich lipoproteins. Using deletion mutants of human ANGPTL3, we demonstrated that the N-terminal coiled-coil domain-containing fragment-(17-207) and not the C-terminal fibrinogen-like domain-containing fragment-(207-460) increased the plasma triglyceride levels in mice. We also found that the N-terminal region 17-165 was required to increase plasma triglyceride levels in mice and that a substitution of basic amino acid residues in the region 61-66 of the fragment showed no increase in the plasma triglyceride levels and no inhibition of lipolysis by lipoprotein lipase. In addition, when we analyzed ANGPTL3 in human plasma, we detected cleaved fragments of ANGPTL3. By analyzing recombinant ANGPTL3 in mouse plasma, we found that it was cleaved at two sites, Arg221 downward arrow Ala222 and Arg224 downward arrow Thr225, which are located in the linker region between the coiled-coil domain and the fibrinogen-like domain. Furthermore, a cleavage-resistant mutant of ANGPTL3 was determined to be less active than wild-type ANGPTL3 in increasing mouse plasma triglyceride levels but not in inhibiting lipoprotein lipase activity. These findings suggest that the cleavage of ANGPTL3 is important for the activation of ANGPTL3 in vivo.
Reoxygenation of endothelial cells increases permeability by oxidant-dependent mechanisms. (1992)

We investigated the effects of hypoxia/reoxygenation exposure on the barrier function of endothelial cell monolayers. Bovine pulmonary microvessel endothelial cells were grown to confluence on microporous filters (0.8-microns pore diameter) and exposed to hypoxia (0.1% O2 or PO2 approximately 1 mm Hg) for 2, 4, 12, or 24 hours, followed by reoxygenation with room air for a period ranging from 16 seconds to 2 hours. The transendothelial clearance rate of 125I-albumin was measured to determine the permeability of endothelial monolayers. Permeability increased twofold or fivefold over control values after 1 hour of reoxygenation in monolayers that had been exposed to either 12 or 24 hours of hypoxia. The response occurred within 5 minutes of reoxygenation, increased maximally by 40 minutes, and remained elevated with continuous reoxygenation for up to 2 hours. The increase in permeability was associated with F-actin reorganization, a change to spindlelike cells, and injured mitochondria. Immunoblot analysis indicated that neither hypoxia alone nor reoxygenation changed CuZn superoxide dismutase (SOD), MnSOD, and catalase levels. However, release of superoxide anions (O2-) into the extracellular medium increased by twofold within 40-60 minutes of reoxygenation. Treatment of endothelial cells with CuZnSOD (100 units/ml) for the 24-hour hypoxia period prevented O2- generation and approximately 50% of the increase in permeability. Higher CuZnSOD concentrations (greater than or equal to 200 units/ml) were not protective. Treatment with catalase (100-1,000 units/ml) inhibited the reoxygenation-induced increase in permeability at the highest catalase concentration (1,000 units/ml), suggesting a critical role of hydrogen peroxide in mediating the response.(ABSTRACT TRUNCATED AT 250 WORDS)
Total synthesis of amphoteronolide B (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTotal synthesis of amphoteronolide BKyriacos C. Nicolaou, R. A. Daines, and T. K. ChakrabortyCite this: J. Am. Chem. Soc. 1987, 109, 7, 2208–2210Publication Date (Print):April 1, 1987Publication History Published online1 May 2002Published inissue 1 April 1987https://pubs.acs.org/doi/10.1021/ja00241a063https://doi.org/10.1021/ja00241a063research-articleACS PublicationsRequest reuse permissionsArticle Views784Altmetric-Citations38LEARN 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
Spinning and Processing Continuous Yarns from 4‐Inch Wafer Scale Super‐Aligned Carbon Nanotube Arrays (2006)

A flexible and elastic carbon coil (see figure) has been fabricated using a continuous yarn of carbon nanotube arrays. The processed yarn is both elastic and pliable and can be freely manipulated and molded to any desired shape that is retained after heat treatment. Owing to their highly ordered macroscopic structures, the good electrical and thermal conductivity of the nanotube components, and their good mechanical properties, these carbon nanostructures may find extensive use in a wide range of applications. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2089/2006/c2528_s.html or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
View-dependent refinement of multiresolution meshes with subdivision connectivity (2003)

We present a view-dependent level-of-detail algorithm for triangle meshes with subdivision connectivity. The algorithm is more suitable for textured meshes of arbitrary topology than existing progressive mesh-based schemes. It begins with a wavelet decomposition of the mesh, and, per frame, finds a partial sum of wavelets necessary for high-quality renderings from that frame's viewpoint. We present a screen-space error metric that measures both geometric and texture deviation and tends to outperform prior error metrics developed for progressive meshes. In addition, wavelets that lie outside the view frustum or in backfacing areas are eliminated. The algorithm takes advantage of frame-to-frame coherence for improved performance and supports geomorphs for smooth transitions between levels of detail.
Energy-Aware Scheduling of Virtual Machines in a Multiprocessor Environment (2006)

This thesis presents a new concept to schedule virtual machines in a multiprocessor environment due to their energy consumption. We propose to divide the process of energy-aware scheduling in a virtual machine environment into two parts: guestlevel scheduling and host-level scheduling. Thereby an energy-aware scheduler can benefit from the varying scheduling information available on both scheduling levels. At first we measure the energy consumption of threads and virtual machines. We suggest to use the energy consumption of threads and virtual machines in combination with energy budgets to come to scheduling decisions. Furthermore we elaborated the framework required to implement energy-aware scheduling policies on both scheduling levels. High scheduling accuracy because of fine-grained energy profiles for threads characterizes guest-level scheduling. Host-level scheduling is equipped with mechanisms to overcome non-energy-awareness or malfunctioning of guest operating systems. Additionally it supports a better exploration of energy capacities of all CPUs in a multiprocessor environment by migrating complete virtual machines. The flexible design of our framework supports the implementation of various energy-related scheduling policies, for example energy-aware balancing. Due to the two-leveled approach we can participate from fine-grained scheduling decisions on guest-level based on the energy consumption of threads as well as from scheduling decisions based on informations only available on host-level (for example the energy consumption of physical CPUs).
Radical-based neighboring segment matching method for on-line Chinese character recognition (1996)

A new approach to stroke-order and stroke-number free on-line handwritten Chinese character recognition is presented in this paper. In this new scheme, the decision rule of the segment attribute is used to characterize the segment sequence appearing in each Chinese character for recognizing connected-stroke and even cursive handwritten Chinese characters. A knowledge-based radical extraction method is proposed to perform the feature extraction before radical recognition stage. The top-level and bottom-level radical classification are adopted in the coarse classification stage to reduce the number of candidate characters. In order to develop a stroke order free system, the neighboring segment matching method is proposed. Experimental results show that the proposed scheme is an efficient solution for stroke-order and stroke-number free on-line Chinese character recognition. The recognition rate is 93.4% and the recognition speed is 0.6 second per character.
Stimuli responsive materials: new avenues toward smart organic devices (2005)

“Smart” patternable polymer-based materials that can be designed from various molecular building blocks show great potential, as they may be used in many fields, including nanotechnology, biochemistry, organic and physical chemistry, and materials science. The focus of this highlight will be on the basic design characteristics of practical Stimuli Responsive Materials (SRMs), the wide range of potential applications and the challenges to be accomplished in this rapidly expanding area. In particular, recent developments are described which are related to two of the many fundamental aspects of stimuli triggered responses: those that are photo-triggered and those that are solvent triggered. These selected state-of-the-art examples demonstrate the large scope and diversity in terms of activation mechanism, response time and property control.
Associations Between Hospital Length of Stay, 30‐Day Readmission, and Costs in ST‐Segment–Elevation Myocardial Infarction After Primary Percutaneous Coronary Intervention: A Nationwide Readmissions Database Analysis (2020)

Background Readmission after ST-segment-elevation myocardial infarction (STEMI) poses an enormous economic burden to the US healthcare system. There are limited data on the association between length of hospital stay (LOS), readmission rate, and overall costs in patients who underwent primary percutaneous coronary intervention for STEMI. Methods and Results All STEMI hospitalizations were selected in the Nationwide Readmissions Database from 2010 to 2014. From the patients who underwent primary percutaneous coronary intervention, we examined the 30-day outcomes including readmission, mortality, reinfarction, repeat revascularization, and hospital charges/costs according to LOS (1-2, 3, 4, 5, and >5 days) stratified by infarct locations. The 30-day readmission rate after percutaneous coronary intervention for STEMI was 12.0% in the anterior wall (AW) STEMI group and 9.9% in the non-AW STEMI group. Patients with a very short LOS (1-2 days) were readmitted less frequently than those with a longer LOS regardless of infarct locations. However, patients with a very short LOS had significantly increased 30-day readmission mortality versus an LOS of 3 days (hazard ratio, 1.91; CI, 1.16-3.16 [<i>P</i>=0.01]) only in the AW STEMI group. Total costs (index admission+readmission) were the lowest in the very short LOS cohort in both the AW STEMI group (<i>P</i><0.001) and the non-AW STEMI group (<i>P</i><0.001). Conclusions For patients who underwent primary percutaneous coronary intervention for STEMI, a very short LOS was associated with significantly lower 30-day readmission and lower cumulative cost. However, a very short LOS was associated with higher 30-day mortality compared with at least a 3-day stay in the AW STEMI cohort.
The Effect of Leukocyte Infiltration on Apoptosis in an In Vitro Thermal Injury Bioartificial Living Skin Equivalent Model (1999)

An in vitro bioartificial skin construct (BSC) model was studied to see how inflammatory infiltration affects apoptosis in skin that has been thermally injured. The BSC was used as a target organ. Control BSCs without leukocytes (CON) were burned (BCON) by scalding with phosphate-buffered saline heated to 70 degrees C for 6 seconds, and they were then cooled with room temperature phosphate-buffered saline for 15 seconds. Human alloimmunocytes were added to CON to create rejection cultures (REJ) and to BCON to create burned rejection cultures (BREJ). Slides were stained with hematoxylin and eosin and anti-Lewis antibody. In situ labeling of apoptosis was measured by terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL). Those sections that were immunostained for Lewis Y were analyzed for intensity stain index (ISI = [sigma P0 x I0]/ total tissue area in pixels). TUNEL was quantified with the following equation: no. of total apoptotic cells / total tissue area. Necrosis and blister formation in the epidermal layer were evident in BCON and BREJ. Pyknosis and nuclear fragmentation-indicators of apoptosis-were also present. Phagocytosis of keratinocytes by leukocytes was seen in REJ and BREJ. Immunostaining showed greater expression of Lewis Y antigen, as determined by ISI, in REJ as opposed to CON (58.2+/-2.3 vs. 36.4+/-2.3, respectively, P<.001), but no significant difference was found between BCON and BREJ (55.0+/-5.7 vs. 60.5+/-3.4, respectively) and REJ and BREJ (58.3+/-2.3 vs. 60.5+/-3.4, respectively). TUNEL staining indicated the presence of apoptosis as follows: REJ versus CON (0.0015+/-0.0002 vs. 0.0003+/-0.0001, respectively, P<.001); BREJ versus BCON (0.0031+/-0.0006 vs. 0.0018+/-0.0004, respectively, P<.05); REJ versus BREJ (0.0015+/-0.0002 vs. 0.0031+/-0.0006, respectively, P = .007). The presence of leukocytes and thermal injury induces apoptosis in BSC. The combination of these two variables results in increased apoptosis as determined by TUNEL. These findings suggest that a common pathway for skin injury may include inappropriate regulation of apoptosis exacerbated by a mechanism that includes inflammatory cellular infiltration.