gebhart/patrepeval huggingface dataset:
The Cancer Chemotherapy Drug Etoposide (VP-16) Induces Proinflammatory Cytokine Production and Sickness Behavior–like Symptoms in a Mouse Model of Cancer Chemotherapy–Related Symptoms (2006)

Cancer chemotherapy-related symptoms such as fatigue, malaise, loss of interest in social activities, difficulty concentrating, and changes in sleep patterns can lead to treatment delays, dose reductions, or termination and have a profound effect on the physical, psychosocial, and economic aspects of quality of life. Clinicians have long suspected that these symptoms are similar to those associated with "sickness behavior," which is triggered by the production of the inflammatory cytokines IL-1beta, TNF-alpha, and IL-6 by macrophages and other cells of the innate immune system in response to immune challenge. The p38 mitogen-activated protein kinase (p38 MAPK) plays a central role in the production of these cytokines and consequently the induction of sickness behavior. Several cancer chemotherapy drugs have been shown to activate p38 MAPK, but whether these drugs can also induce the production of inflammatory cytokines to cause sickness behavior is unknown. The aim of this study was to determine whether the cancer chemotherapy drug etoposide (VP-16), which is known to activate p38 MAPK, could induce inflammatory cytokine production by murine macrophages and sickness-like behaviors when injected into mice. VP-16 activated p38 MAPK and induced IL-6 production in murine macrophages in a p38 MAPK- dependent manner. VP-16 administration rapidly increased serum levels of IL-6 in healthy mice and induced sickness-like behaviors as evidenced by a decrease in food intake, body weight, hemoglobin level, and voluntary wheel-running activity. These findings support the idea that the induction of IL-1beta, TNF-alpha, and IL-6 by cancer chemotherapy drugs underlies the fatigue and associated symptoms experienced by people undergoing cancer chemotherapy.
Adaptive runtime partitioning of AMR applications on heterogeneous clusters (2001)

This paper presents the design and evaluation of an adaptive, system sensitive partitioning and load balancing framework for distributed structured adaptive mesh refinement applications on heterogeneous and dynamic cluster environments. The framework uses system capabilities and current system state to select and tune appropriate partitioning parameters (e.g. partitioning granularity, load per processor) to maximize overall application performance.
PARTIAL HEPATECTOMY REDUCES THE ENDOTOXIN-INDUCED PEAK CIRCULATING LEVEL OF TUMOR NECROSIS FACTOR IN RATS (1996)

The pro-inflammatory cytokine tumor necrosis factor (TNF) is dramatically and transiently elevated in the circulation during endotoxic and septic shock and is a primary mediator in the pathogenesis of the sepsis syndrome. TNF peaks in the circulation 90 min after endotoxin administration with little variation, even among species. The specific cells, tissues, or organs that produce the high circulating level of TNF in septic shock remain unknown. The most likely sources are macrophage-laden tissues such as the liver and the spleen and circulating blood leukocytes. This study evaluated whether the liver is an important source producing the TNF spike 90 min after endotoxin. To test this hypothesis, we measured the peak circulating level of TNF following an endotoxin injection in rats subjected to a two-thirds hepatectomy versus sham-operated controls. Hepatechectomized rats produced 64% less TNF after endotoxin than controls (857 + or - 143 pg/mL plasma vs. 2410 + or - 491, respectively; p < .01). In contrast, splenectomy did not significantly after peak TNF levels versus sham-operated controls following an endotoxin injection (1380 + or - 148 pg/mL plasma vs. 1710 + or - 291). Furthermore, incubation of rat blood with endotoxin for 90 min did not significantly increase TNF above controls. These experiments demonstrate an important role for the liver in producing the high circulating levels of TNF after an endotoxin injection and suggest that hepatic-specific cytokine modulation deserves study for a therapeutic benefit in septic shock.
Automated 3-D Intraretinal Layer Segmentation of Macular Spectral-Domain Optical Coherence Tomography Images (2009)

With the introduction of spectral-domain optical coherence tomography (OCT), much larger image datasets are routinely acquired compared to what was possible using the previous generation of time-domain OCT. Thus, the need for 3-D segmentation methods for processing such data is becoming increasingly important. We report a graph-theoretic segmentation method for the simultaneous segmentation of multiple 3-D surfaces that is guaranteed to be optimal with respect to the cost function and that is directly applicable to the segmentation of 3-D spectral OCT image data. We present two extensions to the general layered graph segmentation method: the ability to incorporate varying feasibility constraints and the ability to incorporate true regional information. Appropriate feasibility constraints and cost functions were learned from a training set of 13 spectral-domain OCT images from 13 subjects. After training, our approach was tested on a test set of 28 images from 14 subjects. An overall mean unsigned border positioning error of 5.69+/-2.41 microm was achieved when segmenting seven surfaces (six layers) and using the average of the manual tracings of two ophthalmologists as the reference standard. This result is very comparable to the measured interobserver variability of 5.71+/-1.98 microm.
Palladium-Catalyzed Aerobic Dehydrogenation of Substituted Cyclohexanones to Phenols (2011)

Aromatic molecules are key constituents of many pharmaceuticals, electronic materials, and commodity plastics. The utility of these molecules directly reflects the identity and pattern of substituents on the aromatic ring. Here, we report a palladium(II) catalyst system, incorporating an unconventional ortho-dimethylaminopyridine ligand, for the conversion of substituted cyclohexanones to the corresponding phenols. The reaction proceeds via successive dehydrogenation of two saturated carbon-carbon bonds of the six-membered ring and uses molecular oxygen as the hydrogen acceptor. This reactivity demonstrates a versatile and efficient strategy for the synthesis of substituted aromatic molecules with fundamentally different selectivity constraints from the numerous known synthetic methods that rely on substitution of a preexisting aromatic ring.
All-transretinoic acid as a novel therapeutic strategy for Alzheimer’s disease (2009)

Retinoic acid, an essential factor derived from vitamin A, has been shown to have a variety of functions including roles as an antioxidant and in cellular differentiation. Since oxidative stress and dedifferentiation of neurons appear to be common pathological elements of a number of neurodegenerative disorders, we speculated that retinoic acid may offer therapeutic promise. In this vein, recent compelling evidence indicates a role of retinoic acid in cognitive activities and anti-amyloidogenic properties. Here, we review the actions of retinoic acid that indicate that it may have therapeutic properties ideally served for the treatment of neurodegenerative diseases such as Alzheimer's disease.
A 4-Output Single-Inductor DC-DC Buck Converter with Self-Boosted Switch Drivers and 1.2A Total Output Current (2008)

Minimizing power consumption in multi-processor systems requires the use of multiple supplies with a wide range of regulated voltages and currents. Since one inductor per DC-DC converter is expensive, there is an increasing interest in single-inductor-multiple-output (SIMO) DC-DC converters. Recent research results report a SIMO boost converter and various boost or buck converters with two outputs. This 0.5mum CMOS system is a four- output, single-inductor buck converter with independent regulation of each output.
Anti-CD3 × Anti-Epidermal Growth Factor Receptor (EGFR) Bispecific Antibody Redirects T-Cell Cytolytic Activity to EGFR-Positive Cancers In vitro and in an Animal Model (2006)

Abstract Purpose: Targeting epidermal growth factor receptor (EGFR) overexpressed by many epithelial-derived cancer cells with anti-EGFR monoclonal antibodies (mAb) inhibits their growth. A limited number of clinical responses in patients treated with the anti-EGFR mAb, (cetuximab), may reflect variability in EGFR type or signaling in neoplastic cells. This study combines EGFR-targeting with the non-MHC–restricted cytotoxicity of anti-CD3 activated T cells (ATC) to enhance receptor-directed cytotoxicity. Experimental Design: ATC from normal and patient donors were expanded ex vivo. Specific cytolytic activity of ATC armed with anti-CD3 × anti-EGFR (EGFRBi) against EGFR-expressing cancer cells derived from lung, pancreas, colon, prostate, brain, skin, or EGFR-negative breast cancer cells was evaluated in 51Cr release assays. In vivo studies comparing tumor growth delay induced by EGFRBi-armed ATCs or cetuximab were done in severe combined immunodeficient/Beige mice (SCID-Beige) bearing COLO 356/FG pancreatic and LS174T colorectal tumors. Results: At effector/target ratios from 3.125 to 50, both EGFRBi-armed normal and patient ATC were significantly more cytotoxic, by 23% to 79%, against EGFR-positive cells over ATC, cetuximab, anti-CD3 alone, or ATC armed with irrelevant BiAb directed at CD20. EGFRBi-armed ATC also secreted significantly higher levels of some TH1/TH2 cytokines compared with ATC alone. In mice, i.v. infusions of EGFRBi-armed ATC (0.001 mg equivalent/infusion) were equally effective as cetuximab (1 mg/infusion) alone for significantly delaying growth of established COLO 356/FG but not LS174T tumors compared with mice that received ATC alone or vehicle (P &amp;lt; 0.001). Conclusions: Combining EGFR antibody targeting with T cell–mediated cytotoxicity may overcome some limitations associated with EGFR-targeting when using cetuximab alone.
Evaluation of implantable glucose enzyme-based sensors with extracorporal blood shunt. (1988)

This paper presents several methods and instruments developed for the characterization of enzymatic membranes and enzyme electrodes: 1. amplitude and response time of steady-state and transient responses to glucose, automatically determined with an Apple II based workstation, 2. enzyme electrode response to in vitro simulated I.V.G.T.T. and to in vivo I.V.G.T.T. when connected to an extracorporal blood shunt of conscious rats.
Terlipressin bolus induces systemic vasoconstriction in septic shock* (2004)

Terlipressin may be useful for sepsis-induced vasodilation.
Acute Myeloid Leukemia (2001)

Through the hard work of a large number of investigators, the biology of acute myeloid leukemia (AML) is becoming increasingly well understood, and as a consequence, new therapeutic targets have been identified and new model systems have been developed for testing novel therapies. How these new therapies can be most effectively studied in the clinic and whether they will ultimately improve cure rates are questions of enormous importance. In this article, Dr. Jacob Rowe presents a summary of the current state-of-the-art therapy for adult AML. His contribution emphasizes the fact that AML is not a single disease, but a number of related diseases each distinguished by unique cytogenetic markers which in turn help determine the most appropriate treatment. Dr. Jerald Radich continues on this theme, emphasizing how these cytogenetic abnormalities, as well as other mutations, give rise to abnormal signal transduction and how these abnormal pathways may represent ideal targets for the development of new therapeutics. A third contribution by Dr. Frederick Appelbaum describes how AML might be made the target of immunologic attack. Specifically, strategies using antibody-based or cell-based immunotherapies are described including the use of unmodified antibodies, drug conjugates, radioimmunoconjugates, non-ablative allogeneic transplantation, T cell adoptive immunotherapy and AML vaccines. Finally, Dr. John Dick provides a review of the development of the NOD/SCID mouse model of human AML emphasizing both what it has taught us about the biology of the disease as well as how it can be used to test new therapies. Taken together, these reviews are meant to help us understand more about where we are in the treatment of AML, where we can go and how we might get there.
Nerve growth factor induces the genes for two proteins related to a family of calcium-binding proteins in PC12 cells. (1988)

Differential hybridization of a cDNA library from rat pheochromocytoma PC12 cells with cDNA probes from naive PC12 cells and from PC12 cells exposed to nerve growth factor for 7 days identified cDNA sequences of two genes induced by NGF. The mRNA species detected by these cDNA sequences, designated 42A and 42C, reached maximal levels after 24 hr of treatment with NGF and were still significantly higher than control levels after 7 days. Epidermal growth factor transiently induced both mRNAs but at much lower levels. The mRNAs code for 95- (42C) and 101- (42A) amino acid residue peptides whose sequences are homologous to those of a family of calcium-binding proteins including the S-100 protein. The conservation of primary and secondary structure between 42A, 42C, and the other proteins suggests a possible role for them in the regulation of cell growth and differentiation.
Ultrasonic wave propagation in cancellous and cortical bone: Prediction of some experimental results by Biot’s theory (1992)

Pulse transmission ultrasound was used to determine the longitudinal wave speed along the direction of trabecular alignment in 32 water-saturated anisotropic tibial bovine cancellous bone samples and in one cortical bone sample also from the bovine tibia. These results are compared to published ultrasound wave-speed data obtained from bovine femoral specimens. Nonlinear regression was used to fit Biot's theory to the data. The correlation coefficient for regression analysis between the experimental ultrasound velocities and the velocities predicted by Biot's theory was r = 0.78.
The Influence of Drilling Variables on Barite Sag (1996)

Abstract Barite sag is a significant variation in mud density caused by the settlement of barite or other weight material in high-angle wells. The wide fluctuations in mud weight can lead to severe operational problems, including well-control, induced wellbore instability, downhole mud losses, and stuck pipe. A laboratory flow loop has been used to evaluate the influence of key drilling parameters on barite sag. Results show that the highest sag occurs at angles in the region 60-75°, particularly at low annular velocities. Drillpipe rotation is shown to be particularly beneficial in minimising barite settlement. Rotation also assists in re-distributing barite deposits formed on the low side of the hole. Data from the tests clearly demonstrate the interdependence of drillpipe eccentricity, rotation, and mud flow rate. Results from the study have been combined with field observations to develop guidelines to minimise barite sag and manage the associated risks. The conclusions of the study are that barite sag can be minimised by attention to detail at the planning and execution stages of drilling a well. In particular, recommendations in four key areas are addressed: well planning, mud properties and testing, operational practices, and wellsite monitoring procedures.
Achieving Stable Human Stem Cell Engraftment and Survival in the CNS: Is the Future of Regenerative Medicine Immunodeficient? (2011)

There is potential for a variety of stem cell populations to mediate repair in the diseased or injured CNS; in some cases, this theoretical possibility has already transitioned to clinical safety testing. However, careful consideration of preclinical animal models is essential to provide an appropriate assessment of stem cell safety and efficacy, as well as the basic biological mechanisms of stem cell action. This article examines the lessons learned from early tissue, organ and hematopoietic grafting, the early assumptions of the stem cell and CNS fields with regard to immunoprivilege, and the history of success in stem cell transplantation into the CNS. Finally, we discuss strategies in the selection of animal models to maximize the predictive validity of preclinical safety and efficacy studies.
Biochemical Isolation of Insoluble Tau in Transgenic Mouse Models of Tauopathies (2012)

Tau is a highly soluble microtubule-associated protein (MAP) that is abundant in the central nervous system and expressed mainly in neuronal axons. Intracellular aggregates of insoluble tau protein are present in a group of neurodegenerative diseases called tauopathies, which include Alzheimer's disease. Numerous transgenic mouse models of tauopathies have been produced in the last decade, and analysis of insoluble tau in these animals has provided a powerful tool to understand the development of tau pathology. In this short chapter, we aim at reviewing the two main isolation methods, sarkosyl and formic acid extraction (and their variations), used for the biochemical isolation of insoluble tau in transgenic mouse models of tauopathy, and discuss their advantages and drawbacks.
OBSERVATIONS OF EQUINES, HUMANS AND DOMESTIC AND WILD VERTEBRATES DURING THE 1969 EQUINE EPIZOOTIC AND EPIDEMIC OF VENEZUELAN ENCEPHALITIS IN GUATEMALA1 (1972)

Thirteen strains of Venezuelan (equine) encephalitis (VE) virus were isolated from bloods and nasal or throat swabs taken from ill equines and humans in Guatemala during July-September 1969. Five of five human virus strains tested differed slightly from a prototypic endemic Mexican-Guatemalan strain in plaque-reduction neutralization tests. Virus titers ranged to 104,5 and 103.0 SMicLD50/0.01 ml of equine and human blood, respectively, and 101.5 and 105.5 of equine nasal swab and human throat swab specimens. Absence of detectable virus in acute-phase bloods correlated with presence of VE virus antibody in equine sera whereas it correlated with absence of convalescent antibody responses in human sera. Based on epidemiologic observations and antibody tests of relatively small samples at selected study sites, it was estimated that about 35% of equines died from VE virus infection during the epizootic in Guatemala, 5% were mildly ill, and at least 10% were inapparently infected. About 3 to 4% of humans had been infected by VE or an antigenically closely-related arbovirus before the epizootic, 5 to 10% had mild, non-encephalitic febrile VE virus disease and 0 to 3% had inapparent infection with VE virus. Post-epizootic sera from dogs and cattle contained VE virus hemag-glutination inhibition (HI) and neutralization (N) antibodies, and a few sera from pigs and bats, but none from domestic fowl, wild birds or rodents had HI antibodies. Since no outbreaks of disease occurred in these animals during the epizootic, the possibility that some of them might have been silent amplifiers of VE virus was considered.
Intrathecal Baclofen for Severe Spinal Spasticity (1990)

PENN, R. D.; SAVOY, S. M.; CORCOS, D.; LATASH, M.; GOTTLIEB, G.; PARKE, B.; KROIN, J. S. Author Information
<title>Resource-driven content adaptation</title> (2006)

Recent trends have created new challenges in the presentation of multimedia information. First, large, high-resolution video displays are increasingly popular. Meanwhile, many mobile devices, such as PDAs and mobile telephones, can display images and videos on small screens. One obvious issue is that content designed for a large display is inappropriate for a small display. Moreover, wireless bandwidth and battery lifetime are precious resources for mobile devices. In order to provide useful content across systems with different resources, we propose "resource-driven content adaptation" by augmenting the content with metadata that can be used to display or render the content based on the available resources. We are investigating several problems related to resource-driven content adaptation. These include: adaptation of the presented content based on available resources- display resolution, bandwidth, processor speed, quality of services, and energy. Content adaptation may add or remove information based on available resources. Adaptive content can utilize resources more effectively but also present challenges in resource management, content creation, transmission, and user perception.
Flow of thermoplastics in an annular die under parallel oscillations (1990)

Abstract A sound wave extrusion system has been developed. This system includes a single screw extruder and an annular die having an internal surface oscillating in the sound frequency range. Oscillating shear flow has been imposed in the direction parallel to the main pressure flow. The die characteristics and average melt temperature at the exit from the die for several thermoplastics have been measured with and without imposition of oscillations. Modeling of parallel superposition of sound oscillations upon pressure flow has been performed using the Leonov viscoelastic constitutive equation. Three cases are considered: (i) the process is isothermal and the change in die pressure is only due to a nonlinear interaction of oscillatory and pressure flow; (ii) the process is nonisothermal and adiabatic, and pressure reduction is due to the nonlinear interaction and the dissipation of oscillatory energy leading to the temperature rise in polymer melts; (iii) the process is nonisothermal with heat transfer due to transient heat conduction and the dissipation of oscillatory energy. Pressure reduction occurs due to both nonlinear interaction and temperature rise. It is found that case (i) cannot explain the observed die pressure reduction, while case (ii) describes those data only at high flow rates. The theoretical results from case (iii) are found to be in qualitative agreement with experimental observations. Generally, the theoretical results of case (iii) are better than those of cases (i) and (ii).
<title>Measurements of the principal axis and phase retardation using a new circular polariscope and the Senarmont setup</title> (2005)

Measurements of the principal axis and phase retardation using a new circular polariscope and the Senarmont setup with electro-optic modulation is presented. In the first step of measurements, we use the electro-optic modulated circular heterodyne interferometer and the phase-lock technique to precisely measure the principal axis angle. After removing the first quarter-wave plate in the first setup, a Senarmont setup is designed to determine the phase retardation also using the phase-lock technique. The simple phase extraction algorithm for the principal axis angle and the phase retardation measurement is presented. The average absolute errors of the principal axis angle and the phase retardation of the &lambda;/8-wave plate are determined to be only 0.468<sup>0</sup> and 0.23%.
The Protein Protocols Handbook (2009)

Since the second edition of this book was published in 2002 there have, of course, been continual methodological developments in the field of protein chemistry. Consequently, for this third edition, I introduced 57 chapters/protocols not present in the second edition, significantly updated a number of chapters remaining from the second edition and increased the overall length of the book from 164 to 208 chapters. The new chapters are generally spread across the various sections of the book, but in particular we have expanded the section on post-translational modifications to reflect the increasing importance of these modifications in understanding of protein function.