gebhart/patrepeval huggingface dataset:
Progression of RAS-Mutant Leukemia during RAF Inhibitor Treatment (2012)

Vemurafenib, a selective RAF inhibitor, extends survival among patients with BRAF V600E-mutant melanoma. Vemurafenib inhibits ERK signaling in BRAF V600E-mutant cells but activates ERK signaling in BRAF wild-type cells. This paradoxical activation of ERK signaling is the mechanistic basis for the development of RAS-mutant squamous-cell skin cancers in patients treated with RAF inhibitors. We report the accelerated growth of a previously unsuspected RAS-mutant leukemia in a patient with melanoma who was receiving vemurafenib. Exposure to vemurafenib induced hyperactivation of ERK signaling and proliferation of the leukemic cell population, an effect that was reversed on drug withdrawal.
Intelligent vehicle technologies : theory and applications (2001)

'Intelligent Vehicle Technologies' covers the growing field of intelligent technologies, from intelligent control systems to intelligent sensors. Systems such as in-car navigation devices and cruise control are already being introduced into modern vehicles, but manufacturers are now racing to develop systems such as 'smart' cruise control, on-vehicle driver information systems, collision avoidance systems, vision enhancement and roadworthiness diagnostics systems.
Biological neural networks in invertebrate neuroethology and robotics (1994)

Second in a series emphasizing the interdisciplinary exchange of ideas central to advances in neural networks research. This book surveys neural control of movement and orientation, describes computer models of neural control circuits, and gives examples of actual robot implementations.
Fat free and 100% natural: seven food labelling tricks exposed (2014)

If you’re confused by food labels, you’re not alone. But don’t hold your breath for an at-a-glance food labelling system that tells you how much salt, fat and sugar each product contains. Australia’s proposed “health star rating” labelling scheme was put on hold in February, following pressure from the food industry. And it’s unclear whether the scheme will go ahead.
N-Methylamino acids in peptide synthesis. V. The synthesis of N-tert-butyloxycarbonyl, N-methylamino acids by N-methylation (1977)

The preparation of enantiomerically pure N-tert-butyloxycarbonyl,N-methylamino acids by N-methylation of the parent amino acid derivatives using sodium hydride and methyl iodide in tetrahydrofuran at room temperature is described for neutral amino acids including O-benzyl-protected threonine and tyrosine. Methylation of the O-benzylserine derivative under these conditions gives the N-methyldehydroalanine derivative. The β-elimination is completely suppressed, giving the corresponding N-methylserine derivative when the reaction is carried out at 5 °C. Other related data on N-methylation and N-methylamino acid derivatives are presented.
Hyaluronidase Activity of Rabbit Skin Wound Granulation Tissue Fibroblasts (1987)

The objective of this work was to identify and compare hyaluronidase activities of normal dermal and dermal wound granulation tissue fibroblasts. Direct evidence of the fibroblast as a source of tissue hyaluronidase was obtained. Fourth passage rabbit dermal fibroblasts were harvested on culture days 4, 8, 14, 18, and 22. Hyaluronidase activity and [35S]-sulfate- or [3H]-glucosamine-labeled glycosaminoglycans (GAGs) were monitored. Hyaluronidase assays were performed on medium and cellular fractions at the designated intervals. Enzyme activity of cellular fractions for both normal dermal and 14-day post-wound granulation tissue fibroblasts increased progressively through culture day 8. Thereafter (days 14-22), an eight-fold drop in cellular activity was coupled with cell death and emergence of hyaluronidase activity in medium fractions. Marked increases in degradation of secreted matrix components were concurrent with lysis-induced release of hyaluronidase. In this culture system, hyaluronidase activity was confined exclusively to cellular fractions and was released into the medium only under non-physiological conditions conducive to cellular death and lysis. Accordingly, this work suggests that previously reported skin wound hyaluronidases may be of fibroblastic origin and that susceptible GAGs are not degraded extracellularly, but, rather, must be internalized as a prerequisite to depolymerization.
How to Lose a Bond in Two Ways ― The Diradical/Zwitterion Dichotomy in Cycloaromatization Reactions (2013)

Abstract Cycloaromatization reactions decouple two electrons by breaking two π bonds to form only one σ bond and illustrate one of the most common mechanistic dichotomies in chemistry, namely the two ways of breaking a chemical bond: Zwitterionic or diradical. With a suitable choice of reaction conditions, substitution patterns, and catalysts, cycloaromatization processes can be redirected from the usual formation of a diradical towards a variety of zwitterionic pathways. This review illustrates the practical approaches for directing zwitterionic cycloaromatization reactions and lays the mechanistic foundations for the further development of this emerging field.
Application of a Radioimmunoassay (RIA) for Monitoring Immune Response to Porcine Zonae Pellucidae (1981)

Radioimmunoassay (RIA) methodology for purposes of monitoring immune response of female mice to injection with porcine zonae pellucidae was investigated. Titers of antibodies prepared against zonae pellucidae and, as measured by RIA, were compared to those obtained by the two frequently used zona antibody titration methods of (i) antibody produced precipitation layer formation on the zona surface (PPT titer), and (ii) indirect immunofluorescence (IF titer). RIA 30% binding and endpoint titers produced comparable immune profiles which indicated rapid rise in anti-zona activity occurring during the first 4 weeks following immunization, peak titer achieved between approximately 5 and 8 weeks followed by a very gradual decline in titer. Anti-zona titers remained at significantly high levels at 225 days following injection. RIA endpoint titers were approximately 200 times greater than the IF titers which, in turn, were 32-64 times greater than PPT titers. These data emphasize the greater sensitivity of the RIA over existing methodology for titrating zona antibodies and the feasibility for using RIA procedures for monitoring immune response following injection with zona material.
Evolution of Human and Non-human Primate CC Chemokine Receptor 5 Gene and mRNA (2000)

Polymorphisms in CC chemokine receptor 5 (CCR5), the major coreceptor of human immunodeficiency virus 1 (HIV-1) and simian immunodeficiency virus (SIV), have a major influence on HIV-1 transmission and disease progression. The effects of these polymorphisms may, in part, account for the differential pathogenesis of HIV-1 (immunosuppression) and SIV (natural resistance) in humans and non-human primates, respectively. Thus, understanding the genetic basis underlying species-specific responses to HIV-1 and SIV could reveal new anti-HIV-1 therapeutic strategies for humans. To this end, we compared CCR5 structure/evolution and regulation among humans, apes, Old World Monkeys, and New World Monkeys. The evolution of the CCR5 cis-regulatory region versus the open reading frame as well as among different domains of the open reading frame differed from one another. CCR5 cis-regulatory region sequence variation in humans was substantially higher than anticipated. Based on this variation, CCR5 haplotypes could be organized into seven evolutionarily distinct human haplogroups (HH) that we designated HHA, -B, -C, -D, -E, -F, and -G. HHA haplotypes were defined as ancestral to all other haplotypes by comparison to the CCR5 haplotypes of non-human primates. Different human and non-human primate CCR5 haplotypes were associated with differential transcriptional regulation, and various polymorphisms resulted in modified DNA-nuclear protein interactions, including altered binding of members of the NF-kappaB family of transcription factors. We identified novel CCR5 untranslated mRNA sequences that were conserved in human and non-human primates. In some primates, mutations at exon-intron boundaries caused loss of expression of selected CCR5 mRNA isoforms or production of novel mRNA isoforms. Collectively, these findings suggest that the response to HIV-1 and SIV infection in primates may have been driven, in part, by evolution of the elements controlling CCR5 transcription and translation.
Use of imiquimod 5% cream (Aldara™) in cats with multicentric squamous cell carcinoma in situ: 12 cases (2002–2005)* (2008)

Multicentric squamous cell carcinoma in situ (MSCCIS) is a variant of squamous cell carcinoma in cats, commonly referred to as Bowen's-like disease. Imiquimod 5% cream (Aldara) is a novel immune response modifier (IRM) that has been reported as a successful treatment for Bowen's disease in humans. The purpose of this study was to describe clinical findings, treatment protocols and survival in cats with MSCCIS treated with imiquimod 5% cream and to examine the effects of imiquimod 5% cream in cats with MSCCIS. The expression of papillomavirus group-specific antigen in the study population was also determined. From review of medical records, 12 cats were identified with a histologic diagnosis of MSCCIS and treatment with imiquimod 5% cream. Initial lesions responded to imiquimod 5% cream in all cats. Most cats (75%) developed new lesions. New lesions also responded to imiquimod 5% cream in all cats treated. Five cats (41%) had side effects suspected to be associated with the use of imiquimod 5% cream, including local erythema (25%), increased liver enzymes and neutropenia (8%), and partial anorexia and vomiting (8%). Kaplan-Meier median treatment duration and median survival time probabilities for cats in this study were 1189 days, respectively. A time to failure model was generated as many cats were censored from analysis well before the aforementioned projected median. This model resulted in a shorter median survival time of 243 days. No patient-related, tumour-related or treatment-related prognostic variables were identified. No expression for papilloma group-specific antigen was found. Imiquimod 5% cream appears to be well tolerated in the majority of cats, and further studies are warranted to further examine its usefulness in cats with this disease.
Eukaryotic Protein Disulfide Isomerase Complements Escherichia coli dsbA Mutants and Increases the Yield of a Heterologous Secreted Protein with Disulfide Bonds (1996)

Eukaryotic protein disulfide isomerase (PDI) is a 55-kDa enzyme with cysteine oxidoreductase, chaperone, and antichaperone activities that catalyzes disulfide formation and rearrangement in the eukaryotic endoplasmic reticulum. In Gram-negative bacteria, the formation of disulfide bonds in the periplasm is mediated by DsbA, a strong cysteine oxidase but an inefficient catalyst of disulfide bond isomerization with no known chaperone activity. We show that rat PDI (rPDI) secreted in the periplasmic space of Escherichia coli can catalyze the formation of disulfide bonds and complement several of the phenotypes of dsbA mutants. The function of rPDI was dependent on the dsbB gene, suggesting that the reoxidation of this eukaryotic enzyme involves direct interactions with bacterial redox proteins. Co-expression of rPDI increased the yield of bovine pancreatic trypsin inhibitor (BPTI) severalfold, an effect that was enhanced when reduced glutathione was added to the growth medium. Whereas PDI is thought to function primarily as an isomerase in the eukaryotic endoplasmic reticulum, rPDI failed to decrease the accumulation of two-disulfide folding intermediates of BPTI and thus did not appear to appreciably catalyze the rate-limiting step in the oxidative folding pathway of BPTI. These results demonstrate that expression of eukaryotic foldases in E. coli can be exploited to better understand their function in vivo and also to increase the yield of biotechnologically valuable proteins.
The ability of HIV type 1 to use CCR-3 as a coreceptor is controlled by envelope V1/V2 sequences acting in conjunction with a CCR-5 tropic V3 loop (1998)

Although infection by primary HIV type 1 (HIV-1) isolates normally requires the functional interaction of the viral envelope protein with both CD4 and the CCR-5 coreceptor, a subset of such isolates also are able to use the distinct CCR-3 receptor. By analyzing the ability of a series of wild-type and chimeric HIV-1 envelope proteins to mediate CCR-3-dependent infection, we have determined that CCR-3 tropism maps to the V1 and V2 variable region of envelope. Although substitution of the V1/V2 region of a CCR-3 tropic envelope into the context of a CCR-5 tropic envelope is both necessary and sufficient to confer CCR-3 tropism, this same substitution has no phenotypic effect when inserted into a CXCR-4 tropic HIV-1 envelope context. However, this latter chimera acquires both CCR-3 and CCR-5 tropism when a CCR-5 tropic V3 loop sequence also is introduced. These data demonstrate that the V1/2 region of envelope can, like the V3 loop region, encode a particular coreceptor requirement and suggest that a functional envelope:CCR-3 interaction may depend on the cooperative interaction of CCR-3 with both the V1/V2 and the V3 region of envelope.
On signal sequence polymorphisms and diseases of distribution. (1996)

We report a previously unappreciated property of the signals that target organelle-specific proteins to their subcellular sites of action. Such targeting sequences are shown to be polymorphic. We discovered this polymorphism when we cloned the mitochondrial manganese-containing superoxide dismutase from cell lines of normal individuals and patients with genetic diseases of premature aging and compared their sequences to each other and to those previously reported. The polymorphism consists of a single nucleotide change in the region of the DNA that encodes the signal sequence such that either an alanine or valine is present. Subsequently, eight cell lines were analyzed and all three possible combinations of the two signal sequences were observed. Such signal sequence polymorphisms could result in diseases of distribution, where essential proteins are not properly targeted, thereby leading to absolute or relative deficiencies of critical enzymes within specific cellular compartments. Progeria and related syndromes may be diseases of distribution.
AAV-Mediated Gene Therapy to the Isolated Limb in Rhesus Macaques (2010)

The development of a nonhuman primate (NHP) model for vascular delivery of therapeutic transgenes with adeno-associated viral (AAV) vectors is crucial for successfully treating muscular dystrophies. Current animal models for Duchenne muscular dystrophy (DMD) gene therapy have species limitations related to assessing function, immune response, and distribution of the micro- and minidystrophin transgenes in a clinically relevant manner. In addition, there are many forms of muscular dystrophy for which there are no available disease models. NHPs provide the ideal model to optimize vector delivery across a vascular barrier and provide accurate dose estimates for local or broadly targeted gene therapy studies. The vascular anatomy NHPs more clearly parallels humans providing an appropriate substrate for translational experiments. Here we outline the development of a rhesus macaque isolated focal limb perfusion (IFLP) protocol targeting the vascular bed of the gastrocnemius. This protocol serves as a model with broad implications for other muscle diseases along with the capability of targeting multiple muscle groups. To overcome the partial homogeneity between portions of the human microdystrophin transgene and those of the NHP dystrophin gene, we utilized a FLAG tag for tracking distribution of microdystrophin. We also provide methods for assessing transduction efficiency of microdystrophin.FLAG following the IFLP vascular delivery protocol.
EXPRESSION OF THE CATALYTIC SUBUNIT ASSOCIATED WITH TELOMERASE GENE IN HUMAN URINARY BLADDER CANCER (1999)

These findings indicate that the up-regulation of hEST2/hTRT gene expression may play a critical role in carcinogenesis of human urinary bladder cancers. RT-PCR for detecting expression of hEST2/hTRT gene is a powerful method for the screening and diagnosis of urinary bladder cancer.
Configurationally defined phosphorothioate-containing oligoribonucleotides in the study of the mechanism of cleavage of hammerhead ribozymes (1991)

The chemical synthesis is described of oligoribonucleotides containing a single phosphorothioate linkage of defined Rp and Sp configuration. The oligoribonucleotides were used as substrates in the study of the mechanism of cleavage of an RNA hammerhead domain having the phosphorothioate group at the cleavage site. Whereas the Rp isomer was cleaved only very slowly in the presence of magnesium ion, the rate of cleavage of the Sp isomer was only slightly reduced from that of the unmodified phosphodiester. This finding gives further evidence for the hypothesis that the magnesium ion is bound to the pro-R oxygen in the transition state of the hammerhead cleavage reaction. Also, inversion of configuration at phosphorus is confirmed for a two-stranded hammerhead.
Botulinum toxin injection into vocal cord in the treatment of malignant coprolalia associated with Tourette's syndrome (1996)

We describe a 13-year-old boy with Tourette's syndrome (TS) manifested chiefly by severe coprolalia, obsessive compulsive disorder, and attention deficit hyperactivity disorder. He was treated with unilateral injections of botulinum toxin to the vocal cord and experienced marked improvement in coprolalia as well as marked reduction in the premonitory urges associated with the vocal tics and coprolalia. As a result of the improvement, the patient was able to attend school and church and was able to socialize. Botulinum toxin may interfere with a sensory reflex arc required to perpetuate tics and coprolalia in TS, possibly by reducing local build-up of tension or muscle contraction in affected areas.
Glucocorticoid-mediated mineralocorticoid receptor activation and hypertension (2004)

Recently, mineralocorticoid receptor antagonists have been used in the randomized aldactone evaluation study (RALES) with spironolactone, the eplerenone post-AMI heart failure efficacy and survival study (EPHESUS), and in severe and postmyocardial infarct heart failure, respectively. These investigations cannot be understood on the basis of the present physiological knowledge and underscore the relevance of focusing on mineralocorticoid receptor activation by ligands other than aldosterone.
Hydrolysis of the Hen’s Perivitelline Layer by Cock Sperm in vitro (1977)

The intact perivitelline layer (PL) at ovulation or proximal magnum of the oviduct fail to show PL hydrolysis. It appears that the tertiary layers may mask PL sperm receptor sites, act as physical barriers not rendered penetrable by cock sperm acrosin or contain acrosomal enzyme inhibitors.
Vibration of Continuous Systems (2006)

Preface. Symbols. Chapter 1. Introduction: Basic Concepts and Terminology. Chapter 2. Vibration of Discrete Systems: Brief Review. Chapter 3. Derivation of Equations: Equilibrium Approach. Chapter 4. Derivation of Equations: Variation Approach. Chapter 5. Derivation of Equations: Integral Equation Approach. Chapter 6. Solution Procedure: Eigenvalue and Modal Analysis Approach. Chapter 7. Solution Procedure: Integral Transform Methods. Chapter 8. Transverse Vibration of Strings. Chapter 9. Longitudinal Vibration of Bars. Chapter 10. Torsional Vibration of Shafts. Chapter 11. Transverse Vibration of Beams. Chapter 12. Vibration of Circular Rings and Curved Beams. Chapter 13.Vibration of Membranes. Chapter 14. Transverse Vibration of Plates. Chapter 15. Vibration of Shells. Chapter 16. Elastic Wave Propagation. Chapter 17. Approximate Analytical Methods. A. Basic Equations of Elasticity. B. Laplace and Fourier Transforms. Index.
Remodeling in Asthma and Chronic Obstructive Pulmonary Disease (2006)

Airway and lung tissue remodeling and fibrosis play an important role in the development of symptoms associated with lung function loss in asthma and chronic obstructive pulmonary disease (COPD). In the past decades, much attention has been paid to the inflammatory cellular process involved in airway remodeling in these two diseases. However, it is increasingly clear that resident cells contribute to airway and lung tissue remodeling and to associated fibrosis as well. This article deals with some new aspects and discusses the role of vasculature and vascular endothelial growth factor in the development of airway obstruction and airway wall fibrosis in asthma and COPD. Moreover, it addresses the extracellular matrix (ECM) turnover as present in both asthma and COPD. All components of lung ECM (collagen, elastic fibers, proteoglycans) have been shown to be potentially altered in these two diseases. Finally, the interaction between transforming growth factor (TGF), Smad signaling, and TGF in the ECM turnover will be discussed. We propose that ECM damage and repair contribute to airway and lung tissue pathology and that the vasculature may enhance this process. The localization of this process is dependent on the etiology of the disease (i.e., allergen-driven in asthma and smoke-driven in COPD) and the local environment in which the pathologic process takes place.
On decoding BCH codes (1965)

The Gorenstein-Zierler decoding algorithm for BCH codes is extended, modified, and analyzed; in particular, we show how to correct erasures as well as errors, exhibit improved procedures for finding error and erasure values, and consider in some detail the implementation of these procedures in a special-purpose computer.
Alzheimer’s Disease And Inflammation: A Review Of Cellular And Therapeutic Mechanisms (2000)

1. Of the neurodegenerative diseases that cause dementia, Alzheimer's disease (AD) is the most common. Three major pathologies characterize the disease: senile plaques, neurofibrillary tangles and inflammation. We review the literature on events contributing to the inflammation and the treatments thought to target this pathology. 2. The senile plaques of AD consist primarily of complexes of the beta-amyloid protein. This protein is central to the pathogenesis of the disease. 3. Inflammatory microglia are consistently associated with senile plaques in AD, although the classic inflammatory response (immunoglobulin and leucocyte infiltration) is absent. beta-Amyloid fragments appear to mediate such inflammatory mechanisms by activating the complement pathway in a similar fashion to immunoglobulin. 4. Epidemiological studies have identified a reduced risk of AD in patients with arthritis and in leprosy patients treated with anti-inflammatory drugs. Longitudinal studies have shown that the consumption of anti-inflammatory medications reduces the risk of AD only in younger patients (< 75 years). 5. There is a considerable body of in vitro evidence indicating that the inflammatory response of microglial cells is reduced by non-steroidal anti-inflammatory drugs (NSAID). However, no published data are available concerning the effects of these medications on brain pathology in AD. 6. Cyclo-oxygenase 2 enzyme is constitutively expressed in neurons and is up-regulated in degenerative brain regions in AD. Non-steroidal anti-inflammatory drugs may reduce this expression. 7. Platelets are a source of beta-amyloid and increased platelet activation and increased circulating beta-amyloid have been identified in AD. Anti-platelet medication (including NSAID) would prevent such activation and its potentially harmful consequences. 8. Increased levels of luminal beta-amyloid permeabilizes the blood-brain barrier (BBB) and increases vasoconstriction of arterial vessels, paralleling the alterations observed with infection and inflammation. Cerebral amyloidosis is highly prevalent in AD, compromising the BBB and vasoactivity. Anti-inflammatory medications may alleviate these problems.