gebhart/patrepeval huggingface dataset:
User interface design for the Hyperties electronic encyclopedia (1987)

Printed books were an enormous stimulus to science, culture, commerce, and entertainment. Electronic books and hypertext systems may produce a similar stimulus in the next century, but current designs are poor. Typical screens are too small, too slow, too complicated, and too hard to read. With careful attention to the user interface and the underlying technology, we have a chance to create a new medium that is potentially more attractive and effective than printed books in many situations.
Nucleotide sequence of human endogenous retrovirus genome related to the mouse mammary tumor virus genome (1986)

We determined the complete nucleotide sequence of the human endogenous retrovirus genome HERV-K10 isolated as the sequence homologous to the Syrian hamster intracisternal A-particle (type A retrovirus) genome. HERV-K10 is 9,179 base pairs long with long terminal repeats of 968 base pairs at both ends; a sequence 290 base pairs long, however, was found to be deleted. It was concluded that a composite genome having the 290-base-pair fragment is the prototype HERV-K provirus gag (666 codons), protease (334 codons), pol (937 codons), and env (618 codons) genes. The size of the protease gene product of HERV-K is essentially the same as that of A- and D-type oncoviruses but nearly twice that of other retroviruses. A comparison of the deduced amino acid sequences encoded by the pol region showed HERV-K to be closely related to types A and D retroviruses and even more so to type B retrovirus. It was noted that the env gene product of HERV-K structurally resembles the mouse mammary tumor virus (type B retrovirus) env protein, and the possible expression of the HERV-K env gene in human breast cancer cells is discussed.
Biologic therapy for lymphoma (1999)

Biologic approaches to lymphoma treatment are now a practical reality rather than a vaguely perceived hope for the future. Interferon alfa seems to have been established as a life-extending therapy for selected patients with follicular lymphoma. Humanized anti-CD20 monoclonal antibody (rituximab) has an authentic 50% response rate in patients with follicular lymphoma, frequently works when given a second time, and is demonstrating what seems to be synergistic activity when combined with chemotherapy. Radioimmunoconjugates using iodine-131 and yttrium-90 as payload are producing responses in refractory and aggressive lymphomas. Vaccines and adoptive cellular therapies are also showing promising results in early phase clinical testing.
ChemInform Abstract: Nucleic Acid Models (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A quantitative Hpall-PCR assay to measure methylation of DNA from a small number of cells (1990)

Methylation-sensitive restriction enzymes and Southern blot analysis are commonly used to assay for DNA methylation, usually requiring DNA from about 105 cells. However sensitivity adequate for only a few hundred cells is needed in many cases, for example, the study of DNA methylation changes in germ cells or pre-implantation embryos. We earlier reported a sensitive PCR assay using primers that bracket a Hpall site; if the DNA is treated with HpaII prior to PCR, an amplified product is seen only from a methylated genomic template (1). We report here two improvements which make the assay quantitatively applicable to 100-300 cells, with as little as 10% DNA methylation detectable.
Characterization of cell envelope proteins of Staphylococcus epidermidis cultured in human peritoneal dialysate (1991)

The cell envelope protein profiles of Staphylococcus epidermidis cultured in used human peritoneal dialysate (HPD) differed markedly from those of cells cultured in nutrient broth. Compared with broth-grown cells, many cell wall proteins were repressed in HPD, although three proteins of 42, 48, and 54 kDa predominated and an iron-repressible 130-kDa protein was induced. Growth in HPD also resulted in expression of two cell membrane proteins of 32 and 36 kDa which were iron repressible. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and immunoblot analysis using monospecific polyclonal antisera raised against the 32- and 36-kDa proteins revealed considerable antigenic and molecular mass homology among 12 S. epidermidis isolates from patients with continuous ambulatory peritoneal dialysis-related peritonitis. The 32-kDa antiserum also cross-reacted with a 32-kDa S. aureus cell membrane protein. Immunoblots of S. epidermidis cell walls and membranes were also probed with normal human serum and serum and HPD from continuous ambulatory peritoneal dialysis patients. While the cell wall proteins of S. epidermidis appeared to be relatively poorly immunogenic, the 32- and 36-kDa membrane proteins reacted strongly with antibodies present in each of the body fluids evaluated. These results suggest that the highly conserved 32- and 36-kDa iron-repressible proteins are expressed during growth in vivo and may be involved in iron transport, since all 12 S. epidermidis strains examined also produced iron chelators.
Initial-phase optimization for bioremediation of munition compound-contaminated soils (1993)

We examined the bioremediation of soils contaminated with the munition compounds 2,4,6-trinitrotoluene (TNT), hexahydro-1,3,5-trinitro-1,3,5-triazine, and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetraazocine by a procedure that produced anaerobic conditions in the soils and promoted the biodegradation of nitroaromatic contaminants. This procedure consisted of flooding the soils with 50 mM phosphate buffer, adding starch as a supplemental carbon substrate, and incubating under static conditions. Aerobic heterotrophs, present naturally in the soil or added as an inoculum, quickly removed the oxygen from the static cultures, creating anaerobic conditions. Removal of parent TNT molecules from the soil cultures by the strictly anaerobic microflora occurred within 4 days. The reduced intermediates formed from TNT and hexahydro-1,3,5-trinitro-1,3,5-triazine were removed from the cultures within 24 days, completing the first stage of remediation. The procedure was effective over a range of incubation temperatures, 20 to 37 degrees C, and was improved when 25 mM ammonium was added to cultures buffered with 50 mM potassium phosphate. Ammonium phosphate buffer (50 mM), however, completely inhibited TNT reduction. The optimal pH for the first stage of remediation was between 6.5 and 7.0. When soils were incubated under aerobic conditions or under anaerobic conditions at alkaline pHs, the TNT biodegradation intermediates polymerized. Polymerization was not observed at neutral to slightly acidic pHs under anaerobic conditions. Completion of the first stage of remediation of munition compound-contaminated soils resulted in aqueous supernatants that contained no munition residues or aminoaromatic compounds.
Translational control in the endoplasmic reticulum stress response (2002)

From the perspective of protein biosynthesis, the endoplasmic reticulum (ER) can be viewed as a processing plant for folding and posttranslational modification of secreted and integral membrane proteins. At any given time, the load of client proteins that the ER must handle is set by developmental programs and modulated by physiological considerations. Specific signaling pathways and effector mechanisms have evolved to deal with the temporal and developmental variation in ER load experienced by different cells in mutlicellular organisms. The upstream signal that activates these pathways is referred to as ER stress and is defined functionally as an imbalance between the load of client proteins facing the ER and the organelle's ability to process that load. ER stress can be provoked by a variety of pathophysiological conditions, for example, ischemia, hyperhomocystinemia, viral infections, and mutations that impair client protein folding (1-4). However, the phenotypes of mutations affecting components of the ER stress-response machinery reveal that ER stress is also a normal physiological phenomenon (reviewed in ref.
Exchange interactions in quantum well subbands (1988)

It is shown that exchange interactions in the two-dimensional electron gas in quantum wells could cause observable effects on subband energies and intersubband transition energies. In the case of doped quantum wells, the intrasubband exchange interaction can produce an energy shift which is substantially larger than the direct Coulomb energy shift. Theoretical estimates of such shifts are compared with experimental measurements of the infrared photoconductivity of multiple quantum well AlGaAs/GaAs structures with wells doped at about 1018 cm−3.
Law and Medicine: Current Legal Issues. Michael Freeman, Andrew Lewis (2001)

1 University of Manchester
Cooperation of Invariant NKT Cells and CD4+CD25+ T Regulatory Cells in the Prevention of Autoimmune Myasthenia (2005)

CD1d-restricted NKT cells and CD4+CD25+ regulatory T (Treg) cells are thymus-derived subsets of regulatory T cells that have an important role in the maintenance of self-tolerance. Whether NKT cells and Treg cells cooperate functionally in the regulation of autoimmunity is not known. We have explored this possibility in experimental autoimmune myasthenia gravis (EAMG), an animal model of human myasthenia gravis, induced by immunization of C57BL/6 mice with the autoantigen acetylcholine receptor. We have demonstrated that activation of NKT cells by a synthetic glycolipid agonist of NKT cells, alpha-galactosylceramide (alpha-GalCer), inhibits the development of EAMG. alpha-GalCer administration in EAMG mice increased the size of the Treg cell compartment, and augmented the expression of foxp3 and the potency of CD4+CD25+ cells to inhibit proliferation of autoreactive T cells. Furthermore, alpha-GalCer promoted NKT cells to transcribe the IL-2 gene and produce IL-2 protein. Depletion of CD25+ cells or neutralization of IL-2 reduced the therapeutic effect of alpha-GalCer in this model. Thus, alpha-GalCer-activated NKT cells can induce expansion of CD4+CD25+ Treg cells, which in turn mediate the therapeutic effects of alpha-GalCer in EAMG. Induced cooperation of NKT cells and Treg cells may serve as a superior strategy to treat autoimmune disease.
Effect of Antiflagellar Human Monoclonal Antibody on Gut-Derived Pseudomonas aeruginosa Sepsis in Mice (1999)

We evaluated the effect of antiflagellar human monoclonal antibody on gut-derived Pseudomonas aeruginosa sepsis. Mice were given a suspension of P. aeruginosa SP10052 in their drinking water and were simultaneously treated with ampicillin (200 mg/kg of body weight) to disrupt the normal bacterial flora. Cyclophosphamide was then administered to induce leukopenia and translocation of the P. aeruginosa that had colonized the gastrointestinal tract, thereby producing gut-derived generalized sepsis. In this model, intraperitoneal injection of 100 microg of antiflagellar human monoclonal antibody (SC-1225) per mouse for 5 consecutive days significantly (P < 0.01) increased the survival rate compared with that for mice treated with bovine serum albumin (BSA). Treatment with SC-1225 significantly reduced the average number of viable bacteria in portal blood, liver, and heart blood compared with the average number after treatment with BSA. Furthermore, the presence in serum of the inflammatory cytokines tumor necrosis factor alpha and interleukin 6 were evaluated as markers of severity of infection, and the results showed that the levels of these cytokines in mice treated with SC-1225 were significantly decreased in comparison with those in BSA-treated control mice. Although there was no significant difference in the number of bacteria that colonized the intestine, SC-1225 treatment significantly increased bacterial opsonophagocytosis by cultured peritoneal macrophages from mice with or without cyclophosphamide pretreatment. Our results indicate that antiflagellar human monoclonal antibody SC-1225 protects mice against gut-derived sepsis caused by P. aeruginosa and suggest that such an effect is due to its opsonophagocytic activity and the reduced motility of the translocated bacteria once the bacteria move from the intestine into the bloodstream.
Rapid purification and properties of potassium-activated aldehyde dehydrogenase from Saccharomyces cerevisiae (1978)

A method for the purification of yeast K+-activated aldehyde dehydrogenase is presented which can be completed in substantially less time than other published procedures. The enzyme has a different N-terminal amino acid from preparations previously reported, and other small differences in amino acid content. These differences may be the result of differential proteolytic digestion rather than a different protein in vivo. A purification step involves the biospecific adsorption on affinity columns containing immobilized nucleotides in the absence of the substrate aldehyde. Direct binding studies with the coenzyme in the absence of aldehyde reveal 4 NAD sites per tetrameric molecule, each with a dissociation constant of 120 micron. These results conflict with properties of preparations previously reported and may conflict with kinetic models that have aldehyde as the leading substrate. Binding to Blue Dextran affinity columns suggests the presence of a dinucleotide fold in common with other dehydrogenases and kinases.
Toll-like Receptor 2 Down-regulation in Established Mouse Allergic Lungs Contributes to Decreased Mycoplasma Clearance (2008)

The established OVA-induced allergic airway inflammation impairs TLR2 expression and host defense cytokine (e.g., IL-6) production, and subsequently delays lung bacterial clearance. This could offer novel therapeutic strategies to reinstate TLR2 activation by using TLR2 ligands and/or blocking IL-4 and IL-13 to ameliorate persisting respiratory bacterial infections in allergic lungs.
Intravenous immunoglobulin for treating sepsis, severe sepsis and septic shock (2013)

Polyclonal IVIG reduced mortality among adults with sepsis but this benefit was not seen in trials with low risk of bias. Among neonates with sepsis, there is sufficient evidence that standard polyclonal IVIG, as adjunctive therapy, does not reduce mortality based on the inclusion of the large polyclonal IVIG trial on neonates. For Ig-M enriched IVIG, the trials on neonates and adults were small and the totality of the evidence is still insufficient to support a robust conclusion of benefit. Adjunctive therapy with monoclonal IVIGs remains experimental.
RBP1L1, a Retinoblastoma-Binding Protein-Related Gene Encoding an Antigenic Epitope Abundantly Expressed in Human Carcinomas and Normal Testis (2001)

RBP1L1 appears to be a molecular marker associated with a broad range of human malignancies.
Ultrafast reflective optical Kerr demultiplexer using polarisation rotation mirror (1992)

A novel all-optical Kerr switching scheme in a reflective mode is proposed and its stable 60Gbits operation at 1.307 μm demonstrated. The scheme uses a 90° polarisation rotation on reflection to compensate for birefringence phase turbulence in the Kerr media.
Cancer-Testis Genes Are Coordinately Expressed and Are Markers of Poor Outcome in Non–Small Cell Lung Cancer (2005)

Cancer-testis genes are coordinately expressed in NSCLC, and their expression is associated with advanced disease and poor outcome.
Solubilisation of gold by Cuhromobacterium violaceum (1985)

Abstract Chromobacterium violaceum , a cyanogenic bacterium, has been shown to solubilise up to 215 parts × 10 −6 gold from 1000 parts × 10 −6 of the pure metal after 40 days incubation in nutrient medium. Cyanide is produced during the growth and stationary phase of culture and the solubilised gold species has been shown to be the complex anion [Au(CN) 2 ] − .
Improving the management of Inherited Retinal Dystrophies by targeted sequencing of a population-specific gene panel (2016)

Next-generation sequencing (NGS) has overcome important limitations to the molecular diagnosis of Inherited Retinal Dystrophies (IRD) such as the high clinical and genetic heterogeneity and the overlapping phenotypes. The purpose of this study was the identification of the genetic defect in 32 Spanish families with different forms of IRD. With that aim, we implemented a custom NGS panel comprising 64 IRD-associated genes in our population, and three disease-associated intronic regions. A total of 37 pathogenic mutations (14 novels) were found in 73% of IRD patients ranging from 50% for autosomal dominant cases, 75% for syndromic cases, 83% for autosomal recessive cases, and 100% for X-linked cases. Additionally, unexpected phenotype-genotype correlations were found in 6 probands, which led to the refinement of their clinical diagnoses. Furthermore, intra- and interfamilial phenotypic variability was observed in two cases. Moreover, two cases unsuccessfully analysed by exome sequencing were resolved by applying this panel. Our results demonstrate that this hypothesis-free approach based on frequently mutated, population-specific loci is highly cost-efficient for the routine diagnosis of this heterogeneous condition and allows the unbiased analysis of a miscellaneous cohort. The molecular information found here has aid clinical diagnosis and has improved genetic counselling and patient management.
Intraventricular transplantation of oligodendrocyte progenitors into a fetal myelin mutant results in widespread formation of myelin (1999)

Transplantation of myelin-forming cells is a promising strategy for the treatment of myelin disorders. In this study, transplantation of glial cell progenitors into the cerebral ventricles of the embryonic myelin-deficient rat, a model of Pelizaeus-Merzbacher disease, was performed to assess the ability of these cells to incorporate into the developing brain and produce myelin. The donor cells migrated into the white and gray matter and produced myelin at widespread sites ranging from the corpus callosum and optic nerve to the cerebellum. These data suggest that myelin repair might be achieved by intraventricular delivery and transependymal incorporation of myelin-producing cells. Because these cells were genetically transduced to express a reporter gene, similar ex vivo manipulation with genes known to promote survival, migration, or proliferation of the transplanted cells could be used to enhance repair. Such a therapeutic strategy may be feasible in patients with inherited myelin disorders or in multiple sclerosis, particularly where the lesions are periventricular.
Effects of epinephrine in local anesthetic mixtures on hemodynamics and view quality during knee arthroscopy (2001)

We compared three different methods of anesthesia for outpatient knee arthroscopy in terms of perioperative surgical conditions, pain, and hemodynamics. In a prospective and double-blind study ( n=130) the patients were randomized into three groups. A 50-ml mixture composed of 20 ml 0.5% bupivacaine hydrochloride, 10 ml 2% lidocaine hydrochloride, and 20 ml 0.9% sodium chloride was prepared for local anesthesia. The knee joint was injected with 40 ml of the mixture. The portal sites were then injected with 10 ml of the mixture in group I. Using the same technique 250 micro g epinephrine was added to the same mixture in group II. In group III the knee joint was injected with 40 ml of the mixture, and only 50 micro g epinephrine was then added to 10 ml of the mixture left before the portal site injections. A tourniquet was not used. There were some statistically significant changes in hemodynamic data. Also the data on visual analogue scale scores, time of arthroscopy, and amount of liquid used for intra-articular flushing in group II and III were significantly lower than those in group I. According to our experience, bleeding in arthroscopy comes mostly from portal incision to intra-articular field, except when performing extensive synovial shaving, ligament reconstruction, and lateral retinacular release. Therefore, when hemostasis is obtained at portals, the arthroscopic view becomes clearer. We think that adding epinephrine to only portal site injections is sufficient to obtain a clear view and, furthermore, when carrying out arthroscopy in this manner, no significant changes are encountered in heart rate, mean arterial pressure, pain during arthroscopy, or time of arthroscopy.
Maximizing the Erythropoietin Response: Iron Strategies (2012)

Anemia is a significant cause of morbidity and lowers the quality of life of patients suffering from chronic kidney disease (CKD). Iron deficiency is the most important cause of erythropoietin (EPO) hyporesponsiveness in CKD. EPO administration significantly increases the costs of CKD management. It follows that paramount importance must be given to enhancing responsiveness to EPO thereby ensuring that the patient derives maximum benefit. Intravenous iron (IVI) administration has been used for decades to replenish body iron stores. Multiple preparations of Iron are available in the market. However, IVI administration is fraught with dangers like adverse drug reactions, susceptibility to infection, and, as recently postulated, direct cellular toxicity. Traditional approaches to IVI administration have focused on multiple administrations of lower doses for fear of adverse reactions. However, recent studies have demonstrated that higher doses can be safely administered in a single infusion, thereby reducing hospitalization costs and patient inconvenience. Newer preparations of IVI are relatively safer, easier to administer and efficacious. Preparations like Iron sucrose, ferumoxytol, ferric carboxymaltose and iron isomaltoside do not require test doses and allow higher doses to be administered at a time with cost and effect benefits.
Molecular Concepts Analysis Links Tumors, Pathways, Mechanisms, and Drugs (2007)

Global molecular profiling of cancers has shown broad utility in delineating pathways and processes underlying disease, in predicting prognosis and response to therapy, and in suggesting novel treatments. To gain further insights from such data, we have integrated and analyzed a comprehensive collection of "molecular concepts" representing > 2500 cancer-related gene expression signatures from Oncomine and manual curation of the literature, drug treatment signatures from the Connectivity Map, target gene sets from genome-scale regulatory motif analyses, and reference gene sets from several gene and protein annotation databases. We computed pairwise association analysis on all 13,364 molecular concepts and identified > 290,000 significant associations, generating hypotheses that link cancer types and subtypes, pathways, mechanisms, and drugs. To navigate a network of associations, we developed an analysis platform, the Molecular Concepts Map. We demonstrate the utility of the approach by highlighting molecular concepts analyses of Myc pathway activation, breast cancer relapse, and retinoic acid treatment.