gebhart/patrepeval huggingface dataset:
Endosomal proteolysis of internalized proteins (1996)

Endosomal proteases have been implicated in the degradation of internalized regulatory peptides involved in the control of metabolic pathways and in the processing of intracellular antigens for cytolytic immune responses. Processing in the endocytic vesicles is regulated by changes in endosomal acidity due to the presence of an ATP-dependent proton pump which modulates protease activity, protein unfolding and receptor-ligand interactions. A limited number of proteases appear to reside in endosomes which do not contain the full complement of active proteases capable of completely degrading all internalized polypeptides. Retention of some acid hydrolases in endosomes is apparently related to their association with undefined endosomal membrane receptors. The limited number of proteases and the pH gradient from neutral to acidic (pH 7 to 5) within endosomes make possible a selective and controlled processing environment in comparison to lysosomes. The full set of endo- and exopeptidases that break down proteins to amino acids are active later in the pathway in lysosomes.
Ruminal acetogens and their potential to lower ruminant methane emissions (1999)

Ruminant methane is a major contributor to the anthropogenic greenhouse gas inventories of Australia and New Zealand. Direct intervention in the rumen offers one means for controlling ruminant methane emissions. In this respect, acetogenic bacteria (acetogens) normally present in the rumen are of interest because they have the potential to provide an alternative sink for H2, an essential intermediate in the formation of methane. Although little is known about the populations of acetogens in grazing ruminants, studies on ruminants fed diets containing concentrates or conserved forages indicate that the rumen contains a diversity of acetogens and that some of these have the potential to act as hydrogenotrophs in place of methanogens. This paper describes the current understanding of ruminal acetogens and outlines potential applications of acetogens in methane mitigation strategies. Strategies which use acetogens to outcompete and displace methanogens are considered less likely to be successful than strategies which use acetogens to maintain low H2 levels in the rumen following suppression of methanogens. However, the former cannot be completely discounted at present.
Effects of Fluvalinate and Coumaphos on Queen Honey Bees (Hymenoptera: Apidae) in Two Commercial Queen Rearing Operations (2002)

We conducted research on the potential impacts of fluvalinate and coumaphos on honey bee, Apis mellifera L., queen viability and health. Queens were reared in colonies that had been treated with differing amounts of both fluvalinate and coumaphos. Pre- and posttreatment samples of both wax and bees were collected from all of the colonies and analyzed for total concentrations of fluvalinate and coumaphos. All queens were measured for queen weight, ovarial weight, and number of sperm in the spermathecae. The queens treated with high doses of fluvalinate weighed significantly less than low-dose or control queens, but otherwise appeared to develop normally. The highest fluvalinate concentrations were observed in the wax and queen cells of the high-dose group. The developing queens in colonies treated with as little as one coumaphos-impregnated strip for more than 24 h suffered a high mortality rate. Several of the queens showed sublethal effects from the coumaphos, including physical abnormalities and atypical behavior. The queens exposed to coumaphos weighed significantly less and had lower ovary weights than the control group queens. The highest coumaphos concentrations were observed in the queen cells and wax of the high-dose groups.
Hypoglycemic effect of isoleucine involves increased muscle glucose uptake and whole body glucose oxidation and decreased hepatic gluconeogenesis (2007)

Isoleucine, a branched chain amino acid, plays an important role in the improvement of glucose metabolism as evidenced by the increase of insulin-independent glucose uptake in vitro. This study evaluated the effect of isoleucine on glucose uptake and oxidation in fasted rats and on gluconeogenesis in vivo and in vitro. Oral administration of isoleucine decreased the plasma glucose level by 20% and significantly increased muscle glucose uptake by 71% without significant elevation of the plasma insulin level compared with controls at 60 min after administration. Furthermore, expiratory excretion of 14CO2 from [U-14C]glucose in isoleucine-administered rats was increased by 19% compared with controls. Meanwhile, isoleucine decreased AMP levels in the liver but did not affect hepatic glycogen synthesis. Under insulin-free conditions, isoleucine significantly inhibited glucose production when alanine was used as a glucogenic substrate in isolated hepatocytes. This inhibition by isoleucine was also associated with a decline in mRNA levels for phosphoenolpyruvate carboxykinase and glucose-6-phosphatase (G6Pase) and a decreased activity of G6Pase in isolated hepatocytes. These findings suggest that a reduction of gluconeogenesis in liver, along with an increase of glucose uptake in the muscle, is also involved in the hypoglycemic effect of isoleucine. In conclusion, isoleucine administration stimulates both glucose uptake in the muscle and whole body glucose oxidation, in addition to depressing gluconeogenesis in the liver, thereby leading to the hypoglycemic effect in rats.
Word association norms, mutual information, and lexicography (1990)

The term word association is used in a very particular sense in the psycholinguistic literature. (Generally speaking, subjects respond quicker than normal to the word nurse if it follows a highly associated word such as doctor. ) We will extend the term to provide the basis for a statistical description of a variety of interesting linguistic phenomena, ranging from semantic relations of the doctor/nurse type (content word/content word) to lexico-syntactic co-occurrence constraints between verbs and prepositions (content word/function word). This paper will propose an objective measure based on the information theoretic notion of mutual information, for estimating word association norms from computer readable corpora. (The standard method of obtaining word association norms, testing a few thousand subjects on a few hundred words, is both costly and unreliable.) The proposed measure, the association ratio, estimates word association norms directly from computer readable corpora, making it possible to estimate norms for tens of thousands of words.
Regulation of age-related macular degeneration-like pathology by complement factor H (2015)

Complement factor H (CFH) is a major susceptibility gene for age-related macular degeneration (AMD); however, its impact on AMD pathobiology is unresolved. Here, the role of CFH in the development of AMD pathology in vivo was interrogated by analyzing aged Cfh(+/-) and Cfh(-/-) mice fed a high-fat, cholesterol-enriched diet. Strikingly, decreased levels of CFH led to increased sub-retinal pigmented epithelium (sub-RPE) deposit formation, specifically basal laminar deposits, following high-fat diet. Mechanistically, our data show that deposits are due to CFH competition for lipoprotein binding sites in Bruch's membrane. Interestingly and despite sub-RPE deposit formation occurring in both Cfh(+/-) and Cfh(-/-) mice, RPE damage accompanied by loss of vision occurred only in old Cfh(+/-) mice. We demonstrate that such pathology is a function of excess complement activation in Cfh(+/-) mice versus complement deficiency in Cfh(-/-) animals. Due to the CFH-dependent increase in sub-RPE deposit height, we interrogated the potential of CFH as a previously unidentified regulator of Bruch's membrane lipoprotein binding and show, using human Bruch's membrane explants, that CFH removes endogenous human lipoproteins in aged donors. Thus, advanced age, high-fat diet, and decreased CFH induce sub-RPE deposit formation leading to complement activation, which contributes to RPE damage and visual function impairment. This new understanding of the complicated interactions of CFH in AMD-like pathology provides an improved foundation for the development of targeted therapies for AMD.
Recombinant toxins for the treatment of cancer. (2003)

Recombinant toxins are proteins made by genetic engineering consisting of a toxin fused to a ligand which binds selectively to a target cell. Recombinant toxins used for cancer treatment generally contain either a growth factor or a recombinant fragment of a monoclonal antibody fused to a truncated bacterial toxin, derived either from Pseudomonas exotoxin or from diphtheria toxin. One recombinant toxin containing human interleukin (IL)-2 and truncated diphtheria toxin (DAB389-IL-2, denileukin diftitox or Ontak; Seragen Inc) is approved for clinical use in advanced stage cutaneous T-cell lymphoma. Recombinant toxins containing truncated Pseudomonas exotoxin and fragments of anti-CD22 and anti-CD25 monoclonal antibodies have induced remissions in chemotherapy-resistant hematological malignancies, particularly hairy cell leukemia, and are currently undergoing experimental testing. The number of approved recombinant toxins for the treatment of cancer is expected to increase in the coming years.
Airway humidification in mechanically ventilated neonates and infants (1997)

Passive airway humidification by a heat and moisture exchanger is effective in mechanically ventilated neonates and infants over a 6-hr period. However, the performance and safety of a heat and moisture exchanger in prolonged mechanical ventilation remain to be proven.
Regulated Expression of a Tumor-Associated Antigen Reveals Multiple Levels of T-Cell Tolerance in a Mouse Model of Lung Cancer (2008)

Maximizing the potential of cancer immunotherapy requires model systems that closely recapitulate human disease to study T-cell responses to tumor antigens and to test immunotherapeutic strategies. We have created a new system that is compatible with Cre-LoxP-regulatable mouse cancer models in which the SIY antigen is specifically overexpressed in tumors, mimicking clinically relevant TAAs. To show the utility of this system, we have characterized SIY-reactive T cells in the context of lung adenocarcinoma, revealing multiple levels of antigen-specific T-cell tolerance that serve to limit an effective antitumor response. Thymic deletion reduced the number of SIY-reactive T cells present in the animals. When potentially self-reactive T cells in the periphery were activated, they were efficiently eliminated. Inhibition of apoptosis resulted in more persistent self-reactive T cells, but these cells became anergic to antigen stimulation. Finally, in the presence of tumors overexpressing SIY, SIY-specific T cells required a higher level of costimulation to achieve functional activation. This system represents a valuable tool in which to explore sources contributing to T-cell tolerance of cancer and to test therapies aimed at overcoming this tolerance.
The Fusion Glycoprotein of Human Respiratory Syncytial Virus Facilitates Virus Attachment and Infectivity via an Interaction with Cellular Heparan Sulfate (2000)

Human respiratory syncytial virus (RSV) F glycoprotein (RSV-F) can independently interact with immobilized heparin and facilitate both attachment to and infection of cells via an interaction with cellular heparan sulfate. RSV-glycosaminoglycan (GAG) interactions were evaluated using heparin-agarose affinity chromatography. RSV-F from A2- and B1/cp-52 (cp-52)-infected cell lysates, RSV-F derived from a recombinant vaccinia virus, and affinity-purified F protein all bound to and were specifically eluted from heparin columns. In infectivity inhibition studies, soluble GAGs decreased the infectivity of RSV A2 and cp-52, with bovine lung heparin exhibiting the highest specific activity against both A2 (50% effective dose [ED(50)] = 0.28 +/- 0.11 microg/ml) and cp-52 (ED(50) = 0.55 +/- 0. 14 microg/ml). Furthermore, enzymatic digestion of cell surface GAGs by heparin lyase I and heparin lyase III but not chondroitinase ABC resulted in a significant reduction in cp-52 infectivity. Moreover, bovine lung heparin inhibited radiolabeled A2 and cp-52 virus binding up to 90%. Taken together, these data suggest that RSV-F independently interacts with heparin/heparan sulfate and this type of interaction facilitates virus attachment and infectivity.
The Effect of Cache on the Performance of a Multi-Threaded Pipelined RISC Processor (1991)

This paper examines the effects of multithreaded pipelining on the CPI (cycles per instruction) of a RISC processor. The desired CPI in a conventional (single-threaded) RISC processor is one instruction per cycle. However, the CPI is typically more than one because of data hazards, control hazards, and resource hazards in the pipeline.
Microsphere resonator mode characterization by pedestal anti-resonant reflecting waveguide coupler (2000)

The stripline pedestal anti-resonant reflecting optical waveguide (SPARROW) is an efficient and robust coupling device for silica microsphere whispering-gallery-mode excitation. The concept incorporates alternating layers of Si and SiO/sub 2/, designed to isolate the mode of the sphere and the waveguide from the dielectric substrate. Experimental characterizations of this coupling technique are presented, including displacement measurements, and whispering-gallery-mode intensity mapping. Power extraction efficiencies of over 98% are reported.
Molecular Tongs Containing Amino Acid Mimetic Fragments:  New Inhibitors of Wild-Type and Mutated HIV-1 Protease Dimerization (2006)

We have designed, synthesized, and evaluated the inhibitory activity and metabolic stability of new peptidomimetic molecular tongs based on a naphthalene scaffold for inhibiting HIV-1 protease dimerization. Peptidomimetic motifs were inserted into one peptidic strand to make it resistant to proteolysis. The peptidic character of the molecular tongs can be decreased without changing the way they inhibit dimerization. Mutated HIV-1 proteases are also vulnerable to dimerization inhibitors, and the multimutated protease ANAM-11 is twice as sensitive to the inhibitor compared to wild-type protease. Thus, the metabolic stability of antidimeric molecular tongs can be increased without compromising their ability to inhibit wild-type and mutated HIV-1 proteases in vitro.
In Vivo Adenovirus-Mediated Suicide Gene Therapy of Orthotopic Bladder Cancer (2000)

These studies were undertaken to determine the feasibility, safety, and efficacy of suicide gene therapy using adenoviral-mediated herpes simplex virus thymidine kinase (ADV/RSV-tk) and the prodrug ganciclovir (GCV) in an orthotopic murine bladder cancer model. We utilized a replication-defective adenoviral construct containing the beta-galactosidase gene as a control and the herpes simplex virus thymidine kinase gene as the therapeutic vector under the transcription control of the Rous sarcoma virus long terminal repeat promoter. Intravesically created, orthotopic bladder tumors were established in syngeneic C3H/He female mice. India ink injection and beta-galactosidase studies were performed to determine if transurethral administration, direct tumor injection, or the combination was the most efficient route of virus administration. Optimal dosing of ADV/RSV-tk was determined by direct tumor injection with increasing viral doses and treatment with GCV. Treatment efficacy, long-term survival, and toxicity were determined in separate but similar controlled experiments. Growth curve studies demonstrated reliable tumor formation by 14 days. Direct transvesical tumor injection resulted in the best distribution and intratumor gene expression as measured by X-gal staining. Dose-ranging experiments demonstrated an optimal viral dose of 5 x 10(8) plaque-forming units and a greater than twofold reduction in tumor growth for the animals treated with ADV/RSV-tk compared to controls. Efficacy studies demonstrated a greater than threefold reduction in tumor growth. No clinical or gross pathologic toxicity was detected. Long-term survival results suggested a survival benefit for the treatment animals compared to controls. We conclude that ADV/RSV-tk in combination with GCV provides effective therapy for orthotopic murine bladder cancer by significantly inhibiting tumor growth with limited toxicity to the host. These data provide further support for testing this suicide gene therapy strategy in human Phase I trials.
Potential safety issues in the use of the hormone melatonin in paediatrics (2015)

Melatonin is a hormone produced by the pineal gland during the night in response to light/dark information received by the retina and its integration by the suprachiasmatic nucleus. When administered to selected populations of adults, in particular those displaying delayed sleep phase disorder, melatonin may advance the time of sleep onset. It is, however, being increasingly prescribed for children with sleep disorders despite the fact that (i) it is not registered for use in children anywhere in the world; (ii) it has not undergone the formal safety testing expected for a new drug, especially long-term safety in children; (iii) it is known to have profound effects on the reproductive systems of rodents, sheep and primates, as well as effects on the cardiovascular, immune and metabolic systems; and (iv) there is the potential for important interactions with drugs sometimes prescribed for children. In this review, I discuss properties of melatonin outside its ability to alter sleep timing that have been widely ignored but which raise questions about the safety of its use in infants and adolescents.
Molecular Mechanisms of Amyloidosis (2003)

Amyloidosis affects millions of people, as a cause of Alzheimer's disease or a complication of dialysis, and also causes rare conditions. The many forms of the disorder have one underlying principle: misfolded proteins. Prompt, correct diagnosis is essential, especially in the inherited forms of amyloidosis. This article reviews the molecular basis of various types of amyloidosis and proposes new ways of treating these disorders.
Monoclonal T-Cell Receptors: New Reagents for Cancer Therapy (2007)

Adoptive transfer of antigen-specific T lymphocytes is an effective form of immunotherapy for persistent virus infections and cancer. A major limitation of adoptive therapy is the inability to isolate antigen-specific T lymphocytes reproducibly. The demonstration that cloned T-cell receptor (TCR) genes can be used to produce T lymphocyte populations of desired specificity offers new opportunities for antigen-specific T-cell therapy. TCR gene-modified lymphocytes display antigen-specific function in vitro, and were shown to protect against virus infection and tumor growth in animal models. A recent trial in humans demonstrated that TCR gene-modified T cells persisted in all and reduced melanoma burden in 2/15 patients. In future trials, it may be possible to use TCR gene transfer to equip helper and cytotoxic T cells with new antigen-specificity, allowing both T-cell subsets to cooperate in achieving improved clinical responses. Sequence modifications of TCR genes are being explored to enhance TCR surface expression, while minimizing the risk of pairing between introduced and endogenous TCR chains. Current T-cell transduction protocols that trigger T-cell differentiation need to be modified to generate "undifferentiated" T cells, which, upon adoptive transfer, display improved in vivo expansion and survival. Both, expression of only the introduced TCR chains and the production of naïve T cells may be possible in the future by TCR gene transfer into stem cells.
A single postnatal injection of oxytocin rescues the lethal feeding behaviour in mouse newborns deficient for the imprinted Magel2 gene (2010)

The onset of feeding at birth is a vital step for the adaptation of the neonate to extra uterine life. Prader-Willi syndrome (PWS) is a complex neurogenetic disorder caused by the alteration of several imprinted contiguous genes including MAGEL2. PWS presents with various clinical manifestations, including poor suckling behaviour and feeding problems in neonates. Hypothalamic defects have been proposed, but the pathophysiological mechanisms remain poorly understood. Here, we report that a Magel2-deficient mouse with 50% neonatal mortality had an altered onset of suckling activity and subsequent impaired feeding, suggesting a role of MAGEL2 in the suckling deficit seen in PW newborns. The hypothalamus of Magel2 mutant neonates showed a significant reduction in oxytocin (OT). Furthermore, injection of a specific OT receptor antagonist in wild-type neonates recapitulated the feeding deficiency seen in Magel2 mutants, and a single injection of OT, 3-5 h after birth, rescued the phenotype of Magel2 mutant pups, allowing all of them to survive. Our study illustrates the crucial role of feeding onset behaviour after birth. We propose that OT supply might constitute a promising avenue for the treatment of feeding difficulties in PW neonates and potentially of other newborns with impaired feeding onset.
Comparison of Antibody Concentrations and Protective Activity of Respiratory Syncytial Virus Immune Globulin and Conventional Immune Globulin (1994)

Relative to conventional immune globulins (IG, 13 lots), IGs prepared from donors with high activity by microneutralization assay to respiratory syncytial virus (RSVIG, 8 lots) had significantly higher neutralizing antibodies to 6 RSV strains (mean enrichment, 5.2-fold; range, 2.6- to 10.0-fold). In contrast, IgG antibody concentrations to whole RSV, fusion protein, or glycoproteins of A and B strains were similar in RSVIG and IG. Treatment of cotton rats with RSVIG at 0.5 g/kg 24 h before RSV challenge reduced RSV by 99% in the lungs (P < .001). RSVIG at 5.0 g/kg reduced RSV by 99% in the nose. IG at 5.0 g/kg had efficacy similar to that of RSVIG at 0.5 g/kg. Serum plaque-reduction neutralization titers of 1/390 resulted in 99% reduction of lung RSV and titers of 1/3500 resulted in 99% reduction in nose RSV. Relative to IG, RSVIG is enriched selectively in RSV neutralizing antibodies and has approximately 10 times greater protective activity in cotton rats.
Spinal cord injury in rat (2000)

We tested the hypothesis that transplantation of bone marrow stromal cells (MSCs) into the spinal cord after a contusion injury promotes functional outcome. Rats (n = 31) were subjected to a weight driven implant injury. MSCs or phosphate buffered saline was injected into the spinal cord 1 week after injury. Sections of tissue were analyzed by double-labeled immunohistochemistry for MSC identification. Functional outcome measurements using the Basso-Beattie-Bresnehan score were performed weekly to 5 weeks post-injury. The data indicate significant improvement in functional outcome in animals treated with MSC transplantation compared to control animals. Scattered cells derived from MSCs expressed neural protein markers. These data suggest that transplantation of MSCs may have a therapeutic role after spinal cord injury.