gebhart/patrepeval huggingface dataset:
MMPs and TIMP-1 are differentially expressed between acute murine excisional and laser wounds (2002)

Background and Objectives Matrix metalloproteinases (MMPs) and their physiological inhibitors, the tissue inhibitors of metalloproteinases (TIMPs) play significant roles in wound repair. The aim of this study was to determine whether MMP and TIMP-1 mRNA is differentially expressed between laser-created and excisional skin wounds. Study Design/Materials and Methods Full-thickness wounds were created on the dorsal surface of Balb/c mice by either excision of the skin or with a CO2 laser. Animals were sacrificed at days 1, 3, 5, 7, 10, and 13, and their wounds processed for RNA isolation or histology and immunohistochemistry. Results Northern hybridization for MMP-3, -10, -13, and TIMP-1 mRNA demonstrated higher expression on days 1, 3, and 5 in the laser wounds as compared to the excisional wounds. Histological evaluation revealed a two day delay in the resurfacing of laser wounds as compared to excisional wounds. Immunohistochemistry of Day 5 and 7 excisional and laser wounds showed MMP-3 within the epidermal compartment and the neo-dermis. No remarkable differences were noted in the spatial distribution patterns of MMP-3 between wound types. Conclusions Our findings demonstrate that MMPs and TIMP-1 mRNA expression is higher on days 1–5 post injury in full thickness laser-created wounds than in comparable same day excisional wounds. Lasers Surg. Med. 30:106–116, 2002. © 2002 Wiley-Liss, Inc.
Induction and large-scale expansion of CD8+ tumor specific cytotoxic T lymphocytes from peripheral blood lymphocytes by in vitro stimulation with CD80-transfected autologous melanoma cells. (1999)

Human melanoma cell lines may induce a specific T cell response against tumor cells in vitro. However, after repeated restimulation with autologous tumor cells, expansion of CTL is limited and often apoptosis of the T cells occurs. In order to improve conditions inducing primary T cell responses and thus allowing further expansion of tumor specific T cells for an adoptive transfer, we transfected human melanoma cells with the B7.1 gene (CD80), known to be a potent costimulatory molecule for T cell activation. CD80 expression on melanoma cells resulted in improved primary T cell activation, especially of CD8+ T cells. Furthermore, restimulation with CD80+ tumor cells gave rise to long term proliferating CD8+ T cell lines demonstrating an 100-fold expansion of T cells compared to the 20-30-fold increased numbers obtained with the controls (parental tumor cells +/- anti-CD28). T cells stimulated with CD80+ melanoma cells were found to display a MHC class I-restricted cytotoxic activity against the autologous tumor cells. In conclusion, these studies demonstrate the requirement of costimulation in generating large numbers of tumor specific T cells in vitro that may be used for an adoptive transfer in tumor immunotherapy.
Induction and Repression of Amidase Enzymes in Aspergillus nidulans (1970)

Aspergillus nidulans can grow on acetamide as both a carbon and nitrogen source and can also grow on formamide as a nitrogen source. Two distinct enzymes, an acetamidase and a formamidase, are produced. The control of the synthesis of these two enzymes in a wild-type strain was investigated. The formamidase is induced by acetamide and formamide and repressed by ammonia. The acetamidase is induced by formamide and acetamide, repressed by carbon metabolites derived from glucose and acetate, and repressed by ammonia. Repression of the acetamidase by ammonia depends on the carbon source; growth on glucose but not on acetate or acetamide allows repression to occur. The pattern of acetamidase repression is compared with that of histidine catabolic enzymes in various bacteria.
A New Polymer Concept for Coating of Vascular Stents Using PTFEP (poly(bis(trifluoroethoxy)phosphazene) to Reduce Thrombogenicity and Late In-Stent Stenosis (2005)

PTFEP nanocoating successfully showed thromboresistance and reduced late in-stent stenosis. Endothelialization was equal in both stent types. Studies in more human-like models and human feasibility studies in human arteries are encouraged.
Encapsulation of Implicit and Explicit Memory in Sequence Learning (1998)

Contrasts between implicit and explicit knowledge in the serial reaction time (SJRT) paradigm have been challenged because they have depended on a single dissociation; intact implicit knowledge in the absence of corresponding explicit knowledge. In the SRT task, subjects respond with a corresponding keypress to a cue that appears in one of four locations. The cue follows a repeating sequence of locations, and subjects can exhibit knowledge of the repeating sequence through increasingly rapid performance (an implicit test) or by being able to recognize the sequence (an explicit test). In our study, amnesic patients were given extensive SRT training. Their implicit and explicit test performance was compared to the performance of control subjects who memorized the training sequence. Compared with control subjects, amnesic patients exhibited superior performance on the implicit task and impaired performance on the explicit task. This crossover interaction suggests that implicit and explicit knowledge of the embedded sequence are separate and encapsulated and that they presumably depend on different brain systems.
The Human Type II 17β-Hydroxysteroid Dehydrogenase Gene Encodes Two Alternatively Spliced mRNA Species (1995)

The isozymes of the 17 beta-hydroxysteroid dehydrogenase (17 beta-HSD) gene family are responsible for the formation of the 17 beta-hydroxysteroids delta 5-androstene-3 beta,17 beta-diol, testosterone, 17 beta-estradiol, and dihydrotestosterone from their corresponding 17-ketosteroid precursors, thus playing a pivotal role in the formation of active sex steroids in both steroidogenic and peripheral target tissues. To clone the type II 17 beta-HSD gene, the full-length cDNA type II 17 beta-HSD was used as probe to screen a human leukocyte genomic DNA library. The type II 17 beta-HSD gene contains seven exons and spans > 40 kbp. The type II 17 beta-HSD gene encodes two alternatively spliced mRNAs that give rise to the previously identified type IIA 17 beta-HSD protein of 387 amino acids, as well as to a related 291-amino-acid type IIB 17 beta-HSD protein of unknown function. RNA blot analysis revealed the presence of a major 1.45-kb transcript that is abundant in placenta and endometrium. The mRNA cap site has been localized in a region between 179 and 167 nucleotides upstream of the ATG start codon by RNase protection and S1 nuclease mapping analyses. Cloning of the 17 beta-HSD type II gene provides us with the tools to study its transcriptional expression.
Myeloid-specific gene expression (1998)

The mononuclear phagocytes are recruited from bone marrow precursors to most tissues of the body, particularly during inflammation or immune stimulation. This combination of accessibility as stem cells and heterogenity of tissue locations makes the myeloid cell potentially important as a carrier of therapeutic agents. Understanding the regulation of transcription in myeloid cells is necessary for any future design of tissue-specific gene targeting vectors, particularly if there are inherent size limitations. Identified members of the C/EBP, Runt/PEBP2/CBF, and Ets families of transcription factors are critical for myeloid-specific gene expression and may have myeloid-restricted expression or myeloid-specific regulation in the hematopoietic system. AP-1, Sp1, and Myb appear to be important for myeloid-restricted expression in some cases. In addition, factors involved in the up-regulation of the level of gene expression when macrophages are activated by agents such as interferon-gamma and bacterial products have been identified. Some of the sequences to which these transcription factors bind in myeloid-restricted genes have been tested in cell lines and in transgenic mice and it is now possible to make an attempt to describe the characteristics of a myeloid-specific promoter.
Complete amino acid sequence of bovine plasminogen (1985)

The amino acid sequence of the single polypeptide chain of bovine plasminogen (786 residues, Mr 88092) was determined. Cleavage with CNBr yielded 13 fragments of which six originated from cleavage sites different from human plasminogen. Digestion with elastase gave three major fragments: kringles (1 + 2 + 3) and kringle 4, both with intact lysine binding sites, and mini-plasminogen. Subfragmentation was achieved mainly with 2-(2-nitrophenylsulfenyl)-3-methyl-3'-bromoindolenine (BNPS-skatole), Staphylococcus aureus V8 protease and trypsin. The sequences of fragments which were determined by automated Edman degradation, were aligned with overlapping sequences, or, in a few instances, by homology with the known sequence of human plasminogen. Sequence comparison with the human protein showed varying degrees of homology in the different functional and structural domains. The overall identity (78%) is practically the same as that found in those regions corresponding to the heavy (79%) and the light chain (80%) of plasmin. The average degree of identity among the kringles is 83%. Outside the kringle structures the extent of identity decreases, to 65% in the N-terminal region and to about 50% in the connecting strands between the kringles except for the strand between kringles 2 and 3, where only one out of 12 residues is exchanged. The results reported show that bovine plasminogen apparently contains the same structural and functional domains as human plasminogen. Bovine plasminogen also contains two carbohydrate moieties. The only partially substituted N-glycosidic site, Asn289, corresponds to partially glycosylated Asn288 in human plasminogen, whereas the O-glycosidic site of the human sequence, Thr345, is shifted to Ser339 in bovine plasminogen.
Efficient gene transfer into human hepatocytes by baculovirus vectors. (1995)

Viral vectors are the most efficient tools for gene delivery, and the search for tissue-specific infecting viruses is important for the development of in vivo gene therapy strategies. The baculovirus Autographa californica nuclear polyhedrosis virus is widely used as a vector for expression of foreign genes in insect cells, and its host specificity is supposed to be restricted to arthropods. Here we demonstrate that recombinant A. californica nuclear polyhedrosis virus is efficiently taken up by human hepatocytes via an endosomal pathway. High-level reporter gene expression from heterologous promoters was observed in human and rabbit hepatocytes in vitro. Mouse hepatocytes and some other epithelial cell types are targeted at a considerably lower rate. The efficiency of gene transfer by baculovirus considerably exceeds that obtained by calcium phosphate or lipid transfection. These properties of baculovirus suggest a use for it as a vector for liver-directed gene transfer but highlight a potential risk in handling certain recombinant baculoviruses.
Neuronal process outgrowth of human sensory neurons on monolayers of cells transfected with cDNAs for five human N-CAM isoforms. (1989)

Full length cDNAs for a variety of human N-CAM isoforms have been transfected into mouse L-cells and/or 3T3 cells. Three independent clones of each cell line that were shown to express human N-CAM were tested for their ability to support the morphological differentiation of sensory neurons. The cell surface expression of N-CAM isoforms, linked to the membrane directly by an integral transmembrane spanning domain or indirectly via covalent attachment to a glycosyl-phosphatidylinositol moiety, were consistently found to be associated with a significant increase in the morphological differentiation of both human and rat dorsal root ganglion neurons. Modification of the extracellular structure of both classes of N-CAM, consequent to the expression of a glycosylated 37-amino acid sequence normally found expressed exclusively in muscle N-CAM isoforms did not obviously affect the ability of transfected cells to support increased neuronal differentiation. 3T3 cells that were transfected with a full length cDNA encoding a secreted N-CAM isoform, and that have previously been shown to secrete N-CAM into the growth media rather than link it to the membrane did not significantly differ from control cells in their ability to support neuronal differentiation. These data provide direct evidence for both transmembrane and lipid-linked N-CAM isoforms being components of the regulatory machinery that determines neuronal morphology and process outgrowth.
Cellular Dynamics Visualized in Live Cells in Vitro and in Vivo by Differential Dual-Color Nuclear-Cytoplasmic Fluorescent-Protein Expression (2004)

We report here the genetic engineering of dual-color fluorescent cells with one color in the nucleus and the other in the cytoplasm that enables real-time nuclear-cytoplasmic dynamics to be visualized in living cells in vivo as well as in vitro. To obtain the dual-color cells, red fluorescent protein (RFP) was expressed in the cytoplasm of HT-1080 human fibrosarcoma cells, and green fluorescent protein (GFP) linked to histone H2B was expressed in the nucleus. Nuclear GFP expression enabled visualization of nuclear dynamics, whereas simultaneous cytoplasmic RFP expression enabled visualization of nuclear cytoplasmic ratios as well as simultaneous cell and nuclear shape changes. Thus, total cellular dynamics can be visualized in the living dual-color cells in real time. The parental HT-1080 and the derived dual-color clones had similar cell proliferation rates, suggesting that expression of GFP and/or RFP does not affect cell cycle progression. The cell cycle position of individual living cells was readily visualized by the nuclear-cytoplasmic ratio and nuclear morphology. Real-time induction of apoptosis was observed by nuclear size changes and progressive nuclear fragmentation. Mitotic cells were visualized by whole-body imaging after injection in the mouse ear. Common carotid artery injection of dual-color cells and a reversible skin flap enabled the external visualization of the dual-color cells in microvessels in the mouse brain where extreme elongation of the cell body as well as the nucleus occurred. Dual-color cells in various positions of the cell cycle were visualized in excised mouse lungs after tail-vein injection of the dual-color cells. In the lung, the dual-color cells were observed frequently juxtaposing their nuclei, suggesting a potential novel form of cell-cell communication. The dual-color cells thus are a useful tool for visualizing living-cell dynamics in vivo as well as in vitro. Drugs that could specifically perturb these processes can now be readily screened in real time in vivo.
Fundamentals of Computer Graphics, Fourth Edition (2015)

Drawing on an impressive roster of experts in the field, Fundamentals of Computer Graphics, Fourth Edition offers an ideal resource for computer course curricula as well as a user-friendly personal or professional reference. Focusing on geometric intuition, the book gives the necessary information for understanding how images get onto the screen by using the complementary approaches of ray tracing and rasterization. It covers topics common to an introductory course, such as sampling theory, texture mapping, spatial data structure, and splines. It also includes a number of contributed chapters from authors known for their expertise and clear way of explaining concepts. Highlights of the Fourth Edition Include: Updated coverage of existing topics Major updates and improvements to several chapters, including texture mapping, graphics hardware, signal processing, and data structures A text now printed entirely in four-color to enhance illustrative figures of concepts The fourth edition of Fundamentals of Computer Graphics continues to provide an outstanding and comprehensive introduction to basic computer graphic technology and theory. It retains an informal and intuitive style while improving precision, consistency, and completeness of material, allowing aspiring and experienced graphics programmers to better understand and apply foundational principles to the development of efficient code in creating film, game, or web designs.
High-Intensity Ultrasonics: Theory and Industrial Applications (1999)

Presenting a comprehensive description of the theory and physics of high-intensity ultrasound, this book also deals with a wide range of problems associated with the industrial applications of ultrasound, mainly in the areas of metallurgy and mineral processing. The book is divided into three sections, and Part I introduces the reader to the theory and physics of high-intensity ultrasound. Part II considers the design of ultrasonic generators, mechanoacoustic radiators and other vibrational systems, as well as the control of acoustic parameters when vibrations are passed into a processed medium. Finally, Part III describes problems associated with various uses of high-intensity ultrasound in metallurgy. The applications of high-intensity ultrasound for metal shaping, thermal and thermochemical treatment, welding, cutting, refining, and surface hardening are also discussed here. This comprehensive monograph will provide an invaluable source of information, which has been largely unavailable in the West until now.
Human Galectin-3 Is a Novel Chemoattractant for Monocytes and Macrophages (2000)

Galectin-3 is a beta-galactoside-binding protein implicated in diverse biological processes. We found that galectin-3 induced human monocyte migration in vitro in a dose-dependent manner, and it was chemotactic at high concentrations (1.0 microM) but chemokinetic at low concentrations (10-100 nM). Galectin-3-induced monocyte migration was inhibited by its specific mAb and was blocked by lactose and a C-terminal domain fragment of the protein, indicating that both the N-terminal and C-terminal domains of galectin-3 are involved in this activity. Pertussis toxin (PTX) almost completely blocked monocyte migration induced by high concentrations of galectin-3. Galectin-3 caused a Ca2+ influx in monocytes at high, but not low, concentrations, and both lactose and PTX inhibited this response. There was no cross-desensitization between galectin-3 and any of the monocyte-reactive chemokines examined, including monocyte chemotactic protein-1, macrophage inflammatory protein-1alpha, and stromal cell-derived factor-1alpha. Cultured human macrophages and alveolar macrophages also migrated toward galectin-3, but not monocyte chemotactic protein-1. Finally, galectin-3 was found to cause monocyte accumulation in vivo in mouse air pouches. These results indicate that galectin-3 is a novel chemoattractant for monocytes and macrophages and suggest that the effect is mediated at least in part through a PTX-sensitive (G protein-coupled) pathway.
O-Glycosylation of the Tail Domain of Neurofilament Protein M in Human Neurons and in Spinal Cord Tissue of a Rat Model of Amyotrophic Lateral Sclerosis (ALS) (2005)

Mammalian neurofilaments (NFs) are modified by post-translational modifications that are thought to regulate NF assembly and organization. Whereas phosphorylation has been intensely studied, the role of another common modification, the attachment of O-linked N-acetylglucosamine (GlcNAc) to individual serine and threonine residues, is hardly understood. We generated a novel monoclonal antibody that specifically recognizes an O-glycosylated epitope in the tail domain of NF-M and allows determination of the glycosylation state at this residue. The antibody displays strong species preference for human NF-M, shows some reactivity with rat but not with mouse or bovine NF-M. By immunohistochemistry and Western blot analysis of biopsy-derived human temporal lobe tissue we show that immunoreactivity is highly enriched in axons parallel to hyperphosphorylated NFs. Treatment of cultured neurons with the GlcNAcase inhibitor PUGNAc causes a 40% increase in immunoreactivity within 1 h, which is completely reversible and parallels the total increase in cellular O-GlcNAc modification. Treatment with the mitogen-activated protein kinase kinase inhibitor PD-98059 leads to a similar increase in immunoreactivity. In spinal cord tissue of a transgenic rat model for amyotrophic lateral sclerosis, immunoreactivity is strongly decreased compared with wild-type animals while phosphorylation is increased. The data suggest that hyperphosphorylation and tail domain O-glycosylation of NFs are synchronously regulated in axons of human neurons in situ and that O-glycosylation of NF-M is highly dynamic and closely interweaved with phosphorylation cascades and may have a pathophysiological role.
Self-adjusting binary search trees (1985)

The splay tree, a self-adjusting form of binary search tree, is developed and analyzed. The binary search tree is a data structure for representing tables and lists so that accessing, inserting, and deleting items is easy. On an n -node splay tree, all the standard search tree operations have an amortized time bound of O (log n ) per operation, where by “amortized time” is meant the time per operation averaged over a worst-case sequence of operations. Thus splay trees are as efficient as balanced trees when total running time is the measure of interest. In addition, for sufficiently long access sequences, splay trees are as efficient, to within a constant factor, as static optimum search trees. The efficiency of splay trees comes not from an explicit structural constraint, as with balanced trees, but from applying a simple restructuring heuristic, called splaying , whenever the tree is accessed. Extensions of splaying give simplified forms of two other data structures: lexicographic or multidimensional search trees and link/cut trees.
Stem Cells: A New Paradigm in Medical Therapeutics (2010)

Even though the stem cells have been studied for decades, only during the past few years has there been an overwhelming proliferation of publications covering isolation, cultivation and utilization of the body's master cells. This paper attempts to summarize the recent studies in the field of stem cells. A number of studies have reported the existence of multipotent stem cells in the cord, cord blood, placenta, bone marrow, brain, heart, teeth, skin, liver, hair follicles and many other tissues and organs, giving rise to cell types other than their tissue of origin. Increased therapeutic use of stem cells has resulted in scientific methods of collection, testing, processing and storage of these cells, with minimal cell damage and differentiation. Cell expansion, bioreactors and tissue engineering are employed extensively to improve the cell dose and outcome. Stem cell infusion, transplantation and implantation are accepted curative therapies for many malignant and non-malignant conditions. Stem cell therapies also provide alternative solutions for the repair and regeneration of various tissues and organs. There has been a dramatic improvement in the understanding of immunosuppressive properties of stem cells on various immune cell types. Stem cells are found to secrete angiogenic cytokines that increase neovascularization. They bring the promise of curing a disease state as these cells normally regenerate tissues in a healthy organism. Stem cell transplantation, in isolation or in combination with other procedures, has been found to be effective. Stem cell therapy is also seen as a possible alternative for the treatment of different diseases such as juvenile diabetes, amyotrophic lateral sclerosis, cerebral palsy, stroke, spinal cord injury and Parkinson's disease. Regenerative medicine using human stem cells is one of the new and promising fields for treating various intractable diseases and damaged organs.
XVI.—The nitration of β-naphthoic acid and some new amino- and nitro-naphthoic acids (1926)

H. A. Harrison and F. A. Royle, J. Chem. Soc., 1926, 129, 84 DOI: 10.1039/JR9262900084