gebhart/patrepeval huggingface dataset:
Recognition of Tumor-Specific Proteins in Human Cancer (1997)

Cancer is a disease of all ages and even though cancer is not a common disease in\nyounger people, cancer is recognized as one of the most imp0l1ant causes of death at\nany age. In fact, when considering the main death causes in people younger than thirty\nyears, cancer is second only to accidents. Beyond the age of thirty years, the number\nof deaths from cancer increases upon aging, gradually at first, rising simply later on.\nApm1 from cancer causing death, the disease is fem'ed because patients who suffer\nfrom cancer are often condemned to a long and painful terminal illness.\nBased on their frequency of occurrence, cancers are traditionally categorized as either\nepithelial cancers (approximately 85% of all human cancers) or non-epithelial cancers\n(approximately 15% of all human cancers). Cancers arising from epithelial cells (i.e.\ncells lining the body cavities and skin) are called cm'Cinomas (Latin: km'kinos - crab or\nlobster; oma - swelling), while those arising from non-epithelial cells are further\nsubdivided according to the tissue and cell type from which they originate. Thus,\nsarcomas are derived from connective tissue or muscle cells (Greek: sarx - meat),\nwhile leukemias are derived from hematopoietic cells (Greek: leucos - white; haimablood).\nOther non-epithelial cancers include the ones deJived fi'Om cells ofthe nervous\nsystem and germinal or embryonal cells.
Organic molecules as mediators and catalysts for photocatalytic and electrocatalytic CO2reduction (2012)

Reduction of CO(2) by electrochemical and photoelectrochemical methods to produce carbon-rich fuels is a heavily pursued research theme. Most of the current efforts are focused on the development of transition-metal-based catalysts. In this tutorial review, we present an overview of the development of organic molecules as mediators and catalysts for CO(2) reduction. Four classes of organic molecules are discussed: tetraalkylammonium salts, aromatic esters and nitriles, ionic liquids, and pyridinium derivatives. It is shown that reactions mediated or catalyzed by these organic molecules can be competitive compared to their metal-catalyzed counterparts, both in terms of product selectivity and energy efficiency.
Determinants for Membrane Association of the Hepatitis C Virus RNA-dependent RNA Polymerase (2001)

The hepatitis C virus (HCV) RNA-dependent RNA polymerase (RdRp), represented by nonstructural protein 5B (NS5B), is believed to form a membrane-associated RNA replication complex together with other nonstructural proteins and as yet unidentified host components. However, the determinants for membrane association of this essential viral enzyme have not been defined. By double label immunofluorescence analyses, NS5B was found in the endoplasmic reticulum (ER) or an ER-like modified compartment both when expressed alone or in the context of the entire HCV polyprotein. The carboxyl-terminal 21 amino acid residues were necessary and sufficient to target NS5B or a heterologous protein to the cytosolic side of the ER membrane. This hydrophobic domain is highly conserved among 269 HCV isolates analyzed and predicted to form a transmembrane alpha-helix. Association of NS5B with the ER membrane occurred by a posttranslational mechanism that was ATP-independent. These features define the HCV RdRp as a new member of the tail-anchored protein family, a class of integral membrane proteins that are membrane-targeted posttranslationally via a carboxyl-terminal insertion sequence. Formation of the HCV replication complex, therefore, involves specific determinants for membrane association that represent potential targets for antiviral intervention.
Lysyl Oxidase Is Required for Vascular and Diaphragmatic Development in Mice (2003)

Lysyl oxidase (LOX) is an enzyme responsible for the cross-linking of collagen and elastin both in vitro and in vivo. The unique functions of the individual members of this multigene family have been difficult to ascertain because of highly conserved catalytic domains and overlapping tissue expression patterns. To address this problem of functional and structural redundancy and to determine the role of LOX in the development of tissue integrity, Lox gene expression was deleted by targeted mutagenesis in mice. Lox-targeted mice (LOX(-/-)) died soon after parturition, exhibiting cardiovascular instability with ruptured arterial aneurysms and diaphragmatic rupture. Microscopic analysis of the aorta demonstrated fragmented elastic fiber architecture in homozygous mutant null mice. LOX activity, as assessed by desmosine (elastin cross-link) analysis, was reduced by approximately 60% in the aorta and lungs of homozygous mutant animals compared with wild type mice. Immature collagen cross-links were decreased but to a lesser degree than elastin cross-links in LOX(-/-) mice. Thus, lysyl oxidase appears critical during embryogenesis for structural stability of the aorta and diaphragm and connective tissue development.
System Structure Analysis: Clustering with Data Bindings (1985)

This paper examines the use of cluster analysis as a tool for system modularization. Several clustering techniques are discussed and used on two medium-size systems and a group of small projects. The small projects are presented because they provide examples (that will fit into a paper) of certain types of phenomena. Data bindings between the routines of the system provide the basis for the bindings. It appears that the clustering of data bindings provides a meaningful view of system modularization.
Activated Akt promotes increased resting T cell size, CD28‐independent T cell growth, and development of autoimmunity and lymphoma (2003)

The mechanisms that regulate basal T cell size and metabolic activity are uncertain. Since the phosphatidylinositol-3 phosphate kinase (PI3 K) and Akt (PKB) pathway has been shown in model organisms to regulate both cell size and metabolism, we generated transgenic mice expressing a constitutively active form of Akt (myristoylated Akt, mAkt) in T cells. Naive transgenic T cells were enlarged and had increased rates of glycolysis compared to control T cells. In addition, mAkt transgenic T cells resisted death-by-neglect upon in vitro culture. Upon activation, mAkt-transgenic T cells were less dependent than control cells on costimulation through CD28 and could both grow rapidly and secrete cytokines in the absence of CD28 ligation. In addition, transgenic expression of mAkt led to the accumulation of CD4 T cells and B cells with age. Many aged mAkt-transgenic mice also developed autoimmunity with immunoglobulin deposits on kidney glomeruli and displayed increased incidence of lymphoma. Together, these data show that Akt activation is sufficient to increase basal T cell size and metabolism. Enhancement of T cell metabolism by Akt and more rapid CD28-independent T cell growth may contribute to the accumulation of excess immune cells and the development of lymphoma and autoimmunity.
CAG repeat expansions and schizophrenia: association with disease in females and with early age-at-onset (1995)

An increase in the severity of schizophrenia through consecutive generations (anticipation) has been found in some studies of families with affected members. Anticipation in five neurological disorders is known to arise from the expansion of CAG repeats between generations of affected individuals. The 'repeat expansion detection' method was used to screen individual genomes for the size of such expansions in a sample of schizophrenic and normal subjects. Comparison of the frequency distribution of CAG expansions observed in schizophrenic patients to that for normal subjects, showed that there are significantly more expansions in patients (p = 0.048). When male and female subjects are considered separately, there is a highly significant difference in the distribution of repeat sizes found between affected and normal females (p = 0.0023) but no significant difference between affected and normal males. Overall there is a 28% excess of expansions observed in affected versus normal females, and their presence confers a relative risk of 4.12 (p < 0.005). In contrast, the frequency distribution of age-at-onset with respect to repeat size is nearly the same in male and female patients and, when the sexes are combined, the larger (CAG)69-136 expansions are associated with a younger age-at-onset (p = 0.02).
Managing tissue heating in laser therapy to enable double-blind clinical study (2006)

Laser devices in clinical applications must eventually be tested via clinical trials. An essential component in clinical trials is the double-blind study whereby the patient and the treating physician have no knowledge as to whether a given treatment is active or placebo. In pharmaceuticals, the problem is easily addressed. With laser therapy this can be very challenging. For some optical therapies, laser heating of tissue, by even as little as a few degrees can indicate to the patient and/or the physician that the device is active, un-blinding the study. This problem has been analyzed for a specific laser therapy using a combination of clinical data, analytical methods, finite element modeling, and laboratory testing. The methods used arrived at a solution, but not necessarily one that could have been predicted easily. This paper will present a model of tissue heating and the methods used to mask the effects from the laser in an effort to make active treatment and placebo indistinguishable.
Studying the Interaction of α-Gal Carbohydrate Antigen and Proteins by Quartz-Crystal Microbalance (2003)

The interaction of alpha-galacosyl antigen and its binding protein (anti-Gal antibody) has been studied by quartz crystal microbalance through a SAM immobilization technique which overcomes the nonspecific interactions and molecule trapping for current piezoelectric biosensors.
The Authorization Service of Tivoli Policy Director (2005)

This paper presents the Authorization Service provided by Tivoli Policy Director (PD) and its use by PD family members as well as third-party applications. Policies are defined over an object namespace and stored in a database, which is managed via a management console and accessed through an Authorization API. The object namespace abstracts from heterogeneous systems and thus enables the definition of consistent policies and their centralized management. ACL inheritance and delegated management allow these policies to be managed efficiently. The Authorization API allows applications with their own access control requirements to decouple authorization logic from application logic. By intercepting the traffic over well-defined communication protocols (TCP/IP HTTP IIOP and others), PD family members establish a single entry point to enforce enterprise policies that regulate access to corporate data.
Silicon nitride films on silicon for optical waveguides (1977)

Silicon nitride (Si(3)N(4)) thin film optical waveguides with propagation losses of less than 0.1 dB/cm for the TE(0) mode at lambda(0) = 6328 A have been successfully grown by low-pressure chemical vapor deposition. Silicon wafers 5 cm in diameter were used as substrates, and the Si(3)N(4) was separated from the substrate by a steamoxide SiO(2) buffer layer. Propagation losses are examined for the various waveguide modes, and their dependence on waveguide parameters and wavelength are discussed and compared with exact calculations. Leakage into the silicon substrate is shown to be a major loss mechanism, especially at longer wavelengths and for higher mode numbers.
The use of spectroscopic techniques in the study of DNA stability (2000)

Accurate determination of nucleic acid thermodynamics has become increasingly important in understanding biological function as well as applications in biotechnology and pharmaceuticals. Knowledge of the thermodynamics of DNA hybridization and secondary structure formation is necessary for understanding DNA replication fidelity (1), mismatch repair efficiency (2) and the mechanism of DNA triplet repeat diseases (3). In addition, RNA folding thermodynamics are an important aspect of understanding ribozyme catalysis, as well as understanding the regulation of protein expression, mRNA stability and the mechanism of protein synthesis by the ribosome (4). With the genome sequencing era upon us (5), it will increasingly become important to predict the folding and hybridization thermodynamics of DNA and RNA, so that accurate diagnostic tests for genetic and infectious diseases can be developed. Thus, there is a need to develop a database of accurate thermodynamic parameters for different nucleic acid folding motifs (4). This chapter describes practical aspects of the application of UV absorbance temperature profiles to determine the thermodynamics of nucleic acid structural transitions. Protocols and practical advice are presented for issues not normally addressed in the primary literature but that are crucial for the determination of reliable thermodynamics, such as sequence design, sample preparation, choice of buffer, protocols for determining strand concentrations and mixing strands, design of microvolume cuvettes and cell holder, instrumental requirements, data analysis methods, and sources of error. References to the primary literature and reviews are also provided where appropriate.
Phase I trial of the histone deacetylase inhibitor, depsipeptide (FR901228, NSC 630176), in patients with refractory neoplasms. (2002)

The MTD of depsipeptide given on a day-1 and -5 schedule every 21 days is 17.8 mg/m(2). The DLTs are fatigue, nausea, vomiting, and transient thrombocytopenia and neutropenia. Whereas cardiac toxicity was anticipated based on preclinical data, there was no evidence of myocardial damage. However, reversible ECG changes with ST/T wave flattening were regularly observed. Biologically active serum concentrations were achieved, and 1 patient obtained a partial response. The recommended Phase II dose is 17.8 mg/m(2) administered on day 1 and 5 of a 21-day cycle.
Deeper Understanding of Biological Tissue: Quantitative Correlation of MALDI-TOF and Raman Imaging (2013)

In order to achieve a comprehensive description of biological tissue, spectral information about proteins, lipids, nucleic acids, and other biochemical components need to be obtained concurrently. Different analytical techniques may be combined to record complementary information of the same sample. Established techniques, which can be utilized to elucidate the biochemistry of tissue samples are, for instance, MALDI-TOF-MS and Raman microscopic imaging. With this contribution, we combine these two techniques for the first time. The combination of both techniques allows the utilization and interpretation of complementary information (i.e., the information about the protein composition derived from the Raman spectra with data of the lipids analyzed by the MALDI-TOF measurements). Furthermore, we demonstrate how spectral information from MALDI-TOF experiments can be utilized to interpret Raman spectra.
Experience with the Vero cell line. (1998)

The Vero cell line has been managed with the Cell Bank system to produce at the 142nd passage IPV, OPV and rabies vaccines since 1982 by Pasteur Mérieux Serums & Vaccins (PMsv). The safety of the cell line was regularly validated at the Working Cell Bank (WCB) level according to the WHO and European Pharmacopoeia requirements for absence of bacteria, fungi, mycoplasma and viruses. A special emphasis was devoted to research on the absence of simian viruses (SV40, SIV, Retro-D virus and simian CMV). All these specific researches were negative. At a low level of passage, the Vero cells are not tumorigenic. Vaccines have been prepared in low passage level Vero cells and together with the excellent downstream purification have resulted in excellent safety as attested by pharmacovigilance of more than 100 million doses of IPV during 12 years, more than 20 million doses of rabies vaccine during 10 years and more than 1 billion of OPV during eight years.
AN OUTBREAK OF CRYPTOSPORIDIUM DIARRHEA IN A PEDIATRIC HOSPITAL (1991)

Navarrete, Susana M.D.; Stetler, Harrison C. M.D.; Avila, Carlos M.D.; Garcia Aranda, José Alberto M.D.; Santos-Preciado, José I. M.D. Author Information
Molecular topography imaging by intermembrane fluorescence resonance energy transfer (2002)

Fluorescence resonance energy transfer (FRET) between lipid-linked donor and acceptor molecules in two apposing lipid bilayer membranes is used to resolve topographical features at an intermembrane junction. Efficient energy transfer occurs when the membranes are apposed closely, which creates an image, or footprint, that maps the contact zone and reveals nanometer-scale topographical structures. We experimentally characterize intermembrane FRET by using a supported membrane junction consisting of a glass-supported lipid membrane, onto which a second membrane is deposited by rupture of a giant vesicle. A series of membrane junctions containing different glycolipids (phosphatidylinositol and ganglioside G(M1)), protein (cholera toxin), and lipid-linked polyethylene glycol are studied. The carbohydrate and protein components influence the intermembrane separation. Differential FRET efficiency is clearly distinguishable for each case. Quantitative analysis of the FRET efficiency yields measurements of intermembrane-separation distances that agree precisely with structural data on G(M1) and cholera toxin. The lateral arrangement of molecular species on the membrane surface thus can be discerned by their influence on membrane spacing without the need for direct labeling of the molecule of interest. In the case of polyethylene glycol lipid-containing membrane junctions, imaging by intermembrane FRET reveals spontaneously forming patterns that are not visible in conventional fluorescence images.
Immunolocalization of Estrogen Receptor β in the Mouse Brain: Comparison with Estrogen Receptor α (2003)

Estrogen receptor alpha (ER alpha) and ER beta are members of the steroid nuclear receptor family that modulate gene transcription in an estrogen-dependent manner. ER mRNA and protein have been detected both peripherally and in the central nervous system, with most data having come from the rat. Here we report the development of an ER beta-selective antibody that cross-reacts with mouse, rat, and human ER beta protein and its use to determine the distribution of ER beta in the murine brain. Further, a previously characterized polyclonal antibody to ER alpha was used to compare the distribution of the two receptors in the first comprehensive description of ER distribution specifically in the mouse brain. ER beta immunoreactivity (ir) was primarily localized to cell nuclei within select regions of the brain, including the olfactory bulb, cerebral cortex, septum, preoptic area, bed nucleus of the stria terminalis, amygdala, paraventricular hypothalamic nucleus, thalamus, ventral tegmental area, substantia nigra, dorsal raphe, locus coeruleus, and cerebellum. Extranuclear-ir was detected in several areas, including fibers of the olfactory bulb, CA3 stratum lucidum, and CA1 stratum radiatum of the hippocampus and cerebellum. Although both receptors were generally expressed in a similar distribution through the brain, nuclear ER alpha-ir was the predominant subtype in the hippocampus, preoptic area, and most of the hypothalamus, whereas it was sparse or absent from the cerebral cortex and cerebellum. Collectively, these findings demonstrate the region-selective expression of ER beta and ER alpha in the adult ovariectomized mouse brain. These data provide an anatomical framework for understanding the mechanisms by which estrogen regulates specific neural systems in the mouse.
Evidence for Lipid-Dependent Structural Changes in Specific Domains of Apolipoprotein B100 (1998)

The structural organization and stability of apoB100 in complexes containing triglyceride (TG) and phospholipid have been examined. LDL was delipidated to form aqueous soluble apoB100-TG complexes that retain approximately 70% of LDL TG, but contain no other lipids. The apoB100-TG complexes exhibited reduced amphipathic alpha-helical content (17%) and net negative charge (-2.9 mV) as compared to native LDL-apoB100 (49% and -6 mV, respectively). Of 28 anti-apoB monoclonal antibodies tested, 15 showed partial or full reactivity with apoB100-TG. The immunoreactive epitopes of apoB100-TG were restricted to those situated in either the amino terminal globular domain (4 of 6) or in regions of apoB100 that are predicted to be composed of amphipathic beta-strands (11 of 13). Incubation of the apoB100-TG complex with palmitoyloleoylphosphatidylcholine (POPC) spontaneously (< 10 min) formed homogeneous lipoproteins (20 nm) that contained approximately 300 molecules of POPC per particle (apoB100-PC). Phospholipidation of apoB100-TG complexes partially recovered the alpha-helical content (34%) and net negative charge (-4.9 mV) of the native LDL and restored resistance of apoB100 to denaturation by guanidine HCl (5.8 M). Addition of phospholipids to apoB100-TG also increased the immunoreactivity of specific epitopes that are located primarily in regions of apoB100 that are thought to be constituted of amphipathic beta-strands. The effects of TG and phospholipid on apoB100 conformation appear to be highly domain-specific. On the basis of these results, we propose that the beta-strands of apoB100 may represent a nonflexible lipid-associating backbone, while the amphipathic alpha-helical domains may represent flexible lipid-binding regions that allow the particle to accommodate varying amounts of lipid.