gebhart/patrepeval huggingface dataset:
Dealing with contamination: enzymatic control of carryover contamination in PCR. (1993)

Life Technologies, Incorporated, Gaithersburg, Maryland 20884-9980 PCR produces an abundance of product DNA from traces of input DNA. It was apparent early that because it is so sensitive, PCR is especially susceptible to contamination. In a research setting (e.g., cloning a gene, preparing a probe), contamination is generally not a concern. However, if a primer pair is used many times, if the PCR is designed to be very sensitive, or if the presence or the absence of amplification of a target sequence will have diagnostic implications, then possible contamination must be eliminated for the PCR results to be meaningful. Contaminating DNA can originate from three sources: DNA from other test samples, DNA from experimental materials such as recombinant clones, or DNA generated by previous PCR amplification of the same target sequence. This last source of contamination, often called contamination, has proven to be the most troublesome source. Early users of PCR noted that carryover contaminat ion could be a significant problem owing to the abundance of DNA generated by PCR and the ease with which such DNA can be reamplified. (1'2) Detecting carryover contamination, e.g., by including negative control reactions, is essential. Prevention is clearly preferred, however, because correcting the problem can be costly and testing of samples will probably need to cease until a thorough clean-up can be effected. This will most likely mean discarding all suspected reagents, and cleaning, or even replacing, equipment. A last resort, one not always possible, is to change to a different primer pair, so as to amplify a different region of the target DNA. Two general approaches may be taken to control carryover contamination: physical isolation of PCR products from newly assembled reactions (see also Setting up a PCR Laboratory, pp. $2-$9) and design of the PCR so that products of a first PCR are not efficiently reamplifiable in a subsequent PCR. Physical measures to control carryover contaminat ion are listed in approximate order of difficulty and cost:
Selection of Anthrax Toxin Protective Antigen Variants That Discriminate between the Cellular Receptors TEM8 and CMG2 and Achieve Targeting of Tumor Cells (2007)

Anthrax toxin, a three-component protein toxin secreted by Bacillus anthracis, assembles into toxic complexes at the surface of receptor-bearing eukaryotic cells. The protective antigen (PA) protein binds to receptors, either tumor endothelial cell marker 8 (TEM8) or CMG2 (capillary morphogenesis protein 2), and orchestrates the delivery of the lethal and edema factors into the cytosol. TEM8 is reported to be overexpressed during tumor angiogenesis, whereas CMG2 is more widely expressed in normal tissues. To extend prior work on targeting of tumor with modified anthrax toxins, we used phage display to select PA variants that preferentially bind to TEM8 as compared with CMG2. Substitutions were randomly introduced into residues 605-729 of PA, within the C-terminal domain 4 of PA, which is the principal region that contacts receptor. Candidates were characterized in cellular cytotoxicity assays with Chinese hamster ovary (CHO) cells expressing either TEM8 or CMG2. A PA mutant having the substitutions R659S and M662R had enhanced specificity toward TEM8-overexpressing CHO cells. This PA variant also displayed broad and potent tumoricidal activity to various human tumor cells, especially to HeLa and A549/ATCC cells. By contrast, the substitution N657Q significantly reduced toxicity to TEM8 but not CMG2-overexpressing CHO cells. Our results indicate that certain amino acid substitutions within PA domain 4 create anthrax toxins that selectively kill human tumor cells. The PA R659S/M662R protein may be useful as a therapeutic agent for cancer treatment.
Gaucher disease: four families with previously undescribed mutations. (1996)

We describe four families with patients with type I Gaucher disease exhibiting previously undescribed mutations of the glucocerebrosidase gene. We found Cherokee Indian woman to have a G-->C substitution in cDNA nucleotide 354, predicting a lysine-->aspargine substitution in amino acid 79 of the processed protein. In a Greek family, we found an allele with a C-->T substitution in nucleotide 475 giving rise to an arginine-->tryptophan substitution at amino acid 120. In another non-Jewish European patient, we identified a C-->T substitution in nucleotide 1223, predicting a threonine-->methionine mutation in amino acid 369. We found two non-Jewish European children to have a C-->T mutation at nucleotide 1357, predicting termination at codon 414. Although siblings carry the same two glucocerebrosidase mutations, in these families as in others we noted considerable differences in severity of clinical manifestations. Finding the reason for these differences is an important goal in the study of Gaucher disease.
Breaking Down Barriers (2002)

The brain is guarded by a nearly impenetrable cellular barrier called the blood-brain barrier. A small but growing community of predominantly academic researchers is studying this barrier with an eye to improving drug delivery to the brain. Their research ranges from trying to better understand the basic biology to creating molecular Trojan horses that sneak anything from neural growth factors to therapeutic genes into the brain.
Effects of Acute and Chronic Stressors and CRF in Rat and Mouse Tests for Depression (2008)

Depressive illness is frequently associated with life stress. Corticotropin-releasing factor (CRF) is believed to be a key brain mediator of behaviors associated with stress, and abnormalities in the function of CRF have been associated with depression. Therefore, we have studied the effects of acute and chronic footshock and restraint in tests used in rodents to assess depression-like activity and antidepressant effects: the forced swim test in rats and mice, and the tail suspension test in mice. We also tested the effect of intracerebroventricular (icv) CRF administration. The results were complex. In the forced swim test in rats, acute footshock and restraint reduced floating, whereas chronic footshock increased floating as did icv CRF. However, chronic restraint induced opposite effects, decreasing floating in the forced swim test. The results from mice were significantly different. In the forced swim test, acute footshock and restraint decreased floating, while chronic footshock increased floating, and chronic restraint decreased floating as it did in rats. However, icv CRF decreased floating. The results from the tail-suspension test paralleled those from the forced swim test except that chronic footshock tended to decrease the time spent immobile. Thus in rats, the behavioral effects of the chronic footshock in the forced swim test could be explained by a desensitization of the CRF systems, either decreased activation of CRF, or desensitization of its receptors. However, such an effect cannot explain the responses to restraint, nor the behavioral effects of chronic footshock and restraint in mice.
English Text: System and structure (1992)

This book is a comprehensive introduction to text forming resources in English, along with practical procedures for analysing English texts and relating them to their contexts of use. It has been designed to complement functional grammars of English, building on the generation of discourse analysis inspired by Halliday and Hasan's Cohesion in English. The analyses presented were developed within three main theoretical and applied contexts: (i) educational linguistics (especially genre-based literacy programmes) (ii) critical linguistics (as manifested in the development of social semiotics) and (iii) computational linguistics (in dialogue with the various text generation projects based on systemic approaches to grammar and discourse). English Text's major contribution is to outline one way in which a rich semantically oriented functional grammar can be systematically related to a theory of discourse semantics, including deconstruction of contextual issues (i.e. register, genre and ideology). The chapters have been organized with the needs of undergraduate students in theoretical linguistics and postgraduate students in applied linguistics in mind.
Magnetoelectric Composites (2010)

In a composite of magnetostrictive and piezoelectric phases, mechanical strain mediates magnetoelectric (ME) coupling between the magnetic and the electric subsystems. This review discusses recent advances in the physics of ME interactions in layered composites and nanostructures and potential device applications. The ME phenomena of importance are giant low-frequency interactions and coupling when the electric and/or the magnetic subsystems show resonance, including electromechanical resonance (EMR) in the piezoelectric phase, ferromagnetic resonance (FMR) in the magnetic phase, and magnetoacoustic resonance at the overlap of EMR and FMR. Potential device applications for the composites are magnetic-field sensors, dual electric-field- and magnetic-field-tunable microwave and millimeter-wave devices, and miniature antennas.
ChemInform Abstract: ZUR GUANYLIERUNG VON AMINEN MIT O‐METHYL‐ISOHARNSTOFF‐SULFAT (1975)

Abstract Das durch Umsetzung von Cyanamid (I) mit Schwefelsäure und Methanol über die Verbindung (II) in ca. 80%iger Ausbeute erhältliche O‐Methyl‐isoharnstoff‐sulfat (III) reagiert mit den primären und sekundären Aminen (IV) in wäßriger Lösung zu den Guanidiniumsalzen (V).
Synthesis of Cyclopamine Using a Biomimetic and Diastereoselective Approach (2009)

From Homer to hedgehog: Cyclopamine, the first inhibitor of the hedgehog signaling pathway, causes cyclopia in embryos but in adults it is a potent anticancer drug. A concise biomimetic and diastereoselective synthesis of cyclopamine (2) starting from commercially available dehydroepiandrosterone (1) now also provides access to several analogues.
Will the Pig Solve the Transplantation Backlog? (2002)

The increasing shortage of human cadaveric organs for purposes of transplantation has become the critical limiting factor in the number of transplants performed each year. Some of this deficit is being met by the use of organs or partial organs from living donors, but this source is insufficient. Xenotransplantation-the transplantation of organs between species, namely from the pig to human-could provide a solution if immunologic and other associated problems could be solved. When a pig organ is transplanted into a primate, hyperacute rejection, induced by anti-pig antibody and mediated by complement and the coagulation system, develops rapidly. This immediate problem can now be overcome, but the return or persistence of anti-pig antibody leads to a delayed form of humoral rejection, acute humoral xenograft rejection, which leads to destruction of the organ within days or weeks. We review the various approaches being investigated to overcome this barrier. Whether they will also prevent subsequent acute cellular rejection remains unknown. Brief mention is made of the potential physiologic incompatibilities between pig and human organs, as well as the microbiologic safety aspects of xenotransplantation. Finally, the question of patient and societal acceptance of xenotransplantation is discussed.
Registration of real and CT-derived virtual bronchoscopic images to assist transbronchial biopsy (1998)

This paper describes research work motivated by an innovative medical application: computer-assisted transbronchial biopsy. This project involves the registration, with no external localization device, of a preoperative three-dimensional (3-D) computed tomography (CT) scan of the thoracic cavity (showing a tumor that requires a needle biopsy), and an intraoperative endoscopic two-dimensional (2-D) image sequence, in order to provide assistance in transbronchial puncture of the tumor. Because of the specific difficulties resulting from the data being processed, a multilevel strategy was introduced. For each analysis level, the relevant information to process and the corresponding algorithms were defined. This multilevel strategy, thus, provides the best possible accuracy. Original image processing methods were elaborated, dealing with segmentation, registration and 3-D reconstruction of the bronchoscopic images. In particular, these methods involve adapted mathematical morphology tools, a "daemon-based" registration algorithm, and a model-based shape-from-shading algorithm. This pilot study presents the application of these algorithms to recorded bronchoscopic video sequences for five patients. The preliminary results presented here demonstrate that it is possible to precisely localize the endoscopic camera within the CT data coordinate system. The computer can thus synthesize in near real-time the CT-derived virtual view that corresponds to the actual endoscopic view.
Computationally efficient, configurable, causal, real-time phase detection applied to local field potential oscillations (2015)

Neurological implantable devices with electrophysiological sensing capabilities may enable new medical therapies and diagnostics. Of specific interest is phase-dependent delivery of therapy-such as electrical stimulation-as a potential method to enhance therapy effectiveness in improving diseased or damaged physiological processes with respect to rhythmic biomarkers, while minimizing the average energy required to deliver the therapy. To address this need for phase-detection, within the constraints of device power limits, we have developed a computationally efficient, causal, real-time Fourier transform (RTFT) for use as a phase detection method that is both general and highly configurable. The application of this method to theta-band local field potentials recorded from the brains of sheep is demonstrated.
A tutorial on hidden Markov models and selected applications in speech recognition (1989)

This tutorial provides an overview of the basic theory of hidden Markov models (HMMs) as originated by L.E. Baum and T. Petrie (1966) and gives practical details on methods of implementation of the theory along with a description of selected applications of the theory to distinct problems in speech recognition. Results from a number of original sources are combined to provide a single source of acquiring the background required to pursue further this area of research. The author first reviews the theory of discrete Markov chains and shows how the concept of hidden states, where the observation is a probabilistic function of the state, can be used effectively. The theory is illustrated with two simple examples, namely coin-tossing, and the classic balls-in-urns system. Three fundamental problems of HMMs are noted and several practical techniques for solving these problems are given. The various types of HMMs that have been studied, including ergodic as well as left-right models, are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Mutations of RNA and protein sequences involved in human immunodeficiency virus type 1 packaging result in production of noninfectious virus (1990)

To identify RNA and protein sequences involved in packaging of human immunodeficiency virus type 1 (HIV-1), various mutations were introduced into the viral genome. Portions of the human immunodeficiency virus type 1 genome between the first splice donor site and the gag initiation codon were deleted to investigate the RNA packaging site (psi). Point mutations that alter cysteine residues in one or both zinc finger motifs of p7, a cleavage product of the gag precursor, were created to study the role of the gag zinc fingers in packaging. The psi site mutants and the gag mutants exhibited similar phenotypes. Cells transfected with the mutant genomes, while expressing normal levels of human immunodeficiency virus type 1 RNA and proteins, produced viral particles that were normal in protein content but lacked detectable viral RNA. These mutant virions were unable to productively infect cells. The combination of human immunodeficiency virus type 1 packaging mutations should minimize fortuitous assembly of infectious virus and may provide a means to produce noninfectious particles for candidate vaccines.
Glycoproteins of the lysosomal membrane. (1985)

Three glycoprotein antigens (120, 100, and 80 kD) were detected by mono- and/or polyclonal antibodies generated by immunization with highly purified rat liver lysosomal membranes. All of the antigens were judged to be integral membrane proteins based on the binding of Triton X-114. By immunofluorescence on normal rat kidney cells, a mouse monoclonal antibody to the 120-kD antigen co-stained with a polyclonal rabbit antibody that detected the 100- and 80-kD antigens as well as with antibodies to acid phosphatase, indicating that these antigens are preferentially localized in lysosomes. Few 120-kD-positive structures were found to be negative for acid phosphatase, suggesting that the antigen was not concentrated in organelles such as endosomes, which lack acid phosphatase. Immunoperoxidase cytochemistry also showed little reactivity in Golgi cisternae, coated vesicles, or on the plasma membrane. Digestion with endo-beta-N-acetylglucosaminidase H (Endo H) and endo-beta-N-acetylglucosaminidase F (Endo F) demonstrated that each of the antigens contained multiple N-linked oligosaccharide chains, most of which were of the complex (Endo H-resistant) type. The 120-kD protein was very heavily glycosylated, having at least 18 N-linked chains. It was also rich in sialic acid, since neuraminidase digestion increased the pI of the 120-kD protein from less than 4 to greater than 8. Taken together, these results strongly suggest that the glycoprotein components of the lysosomal membrane are synthesized in the rough endoplasmic reticulum and terminally glycosylated in the Golgi before delivery to lysosomes. We have provisionally designated these antigens lysosomal membrane glycoproteins lgp120, lgp100, lgp80.
EXUBERA®: Pharmaceutical Development of a Novel Product for Pulmonary Delivery of Insulin (2005)

Development of a product for pulmonary delivery of insulin presented significant technology challenges for this first-in-class pharmaceutical product. These included developing (a) a chemically stabilized protein, (b) a dry powder formulation exhibiting required aerosol physical characteristics, (c) low-dose powder filling and packaging technology, and (d) a mechanical device for powder dispersal and reliable dosing to the patient. The insulin drug is formulated using a novel excipient combination to create a powder with a high glass transition temperature (Tg). The high Tg minimizes insulin mobility (thus reactivity), enabling ambient storage conditions. The formulation composition results in minimal hygroscopicity, where customized packaging produced product ruggedness to humidity. The formulated insulin powder is manufactured by spray-drying. This technology was further engineered to produce the desired reproducible powder characteristics with tight control over particle size and moisture content. A solution step prior to drying assures homogeneity and minimizes dependence on the physical form of the components. Novel low-dose filling and packaging technology reproducibly meters milligram quantities of microfine powder to meet stringent quality requirements for dose control. The technology for accurate, uniform, high-throughput metering of drug powders allows for automation and is scaleable for commercial operations. Finally, the mechanical device design provides powder deagglomeration and dispersion processes in a reusable dry powder inhaler with unique characteristics. The device was designed to rely on patient-generated compressed air as the energy source. A sonic discharge of air through the novel TransJector reproducibly extracts, deagglomerates, and disperses the inhalation powder. A clear holding (spacer-type) chamber allows for patient feedback via dose visualization, and separates powder dispersal from the inspiratory effort. The EXUBERA [Pfizer (New York, NY) and sanofi-aventis (Paris, France)] product provides insulin into the bloodstream with similar reproducibly and effectiveness as subcutaneous injections.
Cases of Human Infertility are Associated with the Absence of P34H, an Epididymal Sperm Antigen1 (1996)

The interaction of spermatozoa with the zona pellucida is a critical step of fertilization. Specific sperm surface proteins involved in this process can be added or modified during epididymal transit. We have previously described a 34-kDa human epididymal sperm protein (P34H) that we proposed to be involved in sperm-zona pellucida interaction. In this study, Western blot analysis were performed to determine the level of P34H protein present on the spermatozoa of 16 men with idiopathic infertility. These levels were compared with the amount of P34H protein found in men of proven fertility. In addition, a sperm-zona pellucida binding assay was performed with spermatozoa from fertile and infertile men. Spermatozoa obtained from different semen samples from a given individual had similar P34H levels. However, the amount of P34H varied from one man to another. Nine of 16 infertile men had a P34H level that was less than 30% of the normal value based on a population of fertile men, while the remaining 7 males were in the normal range. Sperm from infertile subjects with a normal P43H determination bound to zonae pellucidae as efficiently as those from controls. However, spermatozoa from subjects with a low amount of P34H exhibited a dramatic diminution in their ability to interact with zonae pellucidae. Our results show that the quantity of the epididymal protein P34H varied from one male to another and that low levels of this epididymal sperm protein are associated with certain cases of idiopathic infertility. Results are discussed with regard to the function of human epididymis in sperm maturation.
Liver Hypertrophy (2012)

Preclinical toxicity studies have demonstrated that exposure of laboratory animals to liver enzyme inducers during preclinical safety assessment results in a signature of toxicological changes characterized by an increase in liver weight, hepatocellular hypertrophy, cell proliferation, and, frequently in long-term (life-time) studies, hepatocarcinogenesis. Recent advances over the last decade have revealed that for many xenobiotics, these changes may be induced through a common mechanism of action involving activation of the nuclear hormone receptors CAR, PXR, or PPARα. The generation of genetically engineered mice that express altered versions of these nuclear hormone receptors, together with other avenues of investigation, have now demonstrated that sensitivity to many of these effects is rodent-specific. These data are consistent with the available epidemiological and empirical human evidence and lend support to the scientific opinion that these changes have little relevance to man. The ESTP therefore convened an international panel of experts to debate the evidence in order to more clearly define for toxicologic pathologists what is considered adverse in the context of hepatocellular hypertrophy. The results of this workshop concluded that hepatomegaly as a consequence of hepatocellular hypertrophy without histologic or clinical pathology alterations indicative of liver toxicity was considered an adaptive and a non-adverse reaction. This conclusion should normally be reached by an integrative weight of evidence approach.