gebhart/patrepeval huggingface dataset:
Potential of the Panama strain of Plasmodium vivax for the testing of malarial vaccines in Aotus nancymai monkeys. (2002)

Aotus monkeys were infected with a strain of Plasmodium vivax from Panama to determine its potential for the testing of malarial vaccines. After sporozoite inoculation, 3 splenectomized Aotus nancymai that had been infected previously with Plasmodium falciparum and P. vivax had prepatent periods of 13, 15, and 15 days with maximum parasite counts of 12,726/microl, 5,310/microl, and 9,180/microl. Three other A. nancymai previously infected with P. falciparum only had prepatent periods of 17, 15, and 15 days with maximum parasite counts of 44,460/microl, 31,500/microl, and 42,660/microl. One monkey with no previous history of infection had a prepatent period of 14 days after sporozoite inoculation, and a maximum parasite count of 100,000/microl; detectable parasitemia persisted for almost 500 days with 13 recognizable peaks in the parasite count. Anopheles dirus, Anopheles freeborni, Anopheles stephensi, and Anopheles quadrimaculatus mosquitoes were readily infected with the Panama strain.
Charged Gold Nanoparticles in Non-Polar Solvents: 10-min Synthesis and 2D Self-Assembly (2010)

We report a fast and highly reproducible chemical synthesis method for colloidal gold nanoparticles which are negatively charged in nonpolar solvents and coated with hydrophobic organic molecules. If a hexane droplet containing charged gold nanoparticles is mixed with a larger toluene droplet, nanoparticles immediately float to the air-toluene interface and form a close-packed monolayer film. After evaporation of the solvent molecules, the monolayer film of nanoparticles can be deposited to any substrate without any limit in size. The synthesis does not require a postsynthesis cleaning step, since the two immiscible liquid phases separate the reaction byproducts from gold nanoparticles and a minimal amount of coating molecules is used.
Convolution Filter Pruning for Transfer Learning on Small Dataset (2020)

In this paper, we propose a scheme to reduce the size of a pre-trained full-scale model with a domain-specific dataset. This scheme combines model compression and transfer learning. First, it identifies the sensitive parts of a full model using the target dataset. Then it applies transfer learning on the identified part of the network to construct a reduced and customized model. Our scheme can correct structure and parameters to prune for a target dataset, which makes the following transfer learning more efficient.We apply our scheme on image classification applications using convolutional neural networks. We observe that different image categories activate different filters, so we can identify sensitive parts of the model for different categories of images.We use VGG-16 (pre-trained by ImageNet dataset) as the full model and we apply transfer learning on two different datasets (Flowers-102 and Cats vs. Dogs). We apply three pruning criteria in our scheme. The accuracy of Flowers-102 dataset by the best criterion drops less than 2% while pruning 60% of the network. We also observe the effects of different settings of our scheme and examine their feasibility by experiments.
CD28 signals through acidic sphingomyelinase. (1995)

T cell receptor recognition of antigen can lead either to T lymphocyte differentiation and proliferation or to a state of unresponsiveness, which is dependent on whether appropriate costimulatory signals are provided to the mature T cell. We have investigated a novel intracellular signaling pathway provided by the costimulatory molecule CD28. CD28 engagement triggers the activation of an acidic sphingomyelinase (A-SMase), which results in the generation of ceramide, an important lipid messenger intermediate. A-SMase activation by CD28 occurred in resting as well as in activated primary T cells or leukemic Jurkat cells. In contrast, ligation of either CD3 or CD2 did not result in A-SMase activation. Overexpression of recombinant A-SMase in Jurkat T cells substituted for CD28 with regard to nuclear factor-kB activation. These data suggest that CD28 provides an important costimulatory signal by activation of an acidic sphingomyelinase pathway.
Expression of CD24 (BA-1) Predicts Monocytic Lineage in Acute Myeloid Leukemia (1994)

Fifty-seven cases of acute myeloid leukemia (AML), which had been subtyped by French-American-British morphologic and cytochemical criteria as myeloid (M1, M2) or monocytic (M4, M5), were retrieved from the files of the Division of Hematopathology, University of Iowa. Corresponding immunophenotyping data were reviewed with attention to the expression of CD14 (MY4) and CD24 (BA-1). Of 20 cases expressing CD24, 19 were M4 or M5, whereas all 14 cases expressing CD14 were of monocyte lineage. Therefore, CD14 was a highly specific (100%) but only moderately sensitive (58%) marker for distinguishing classes M1 or M2 from M4 or M5. By contrast and unexpectedly, CD24 was nearly as specific (97%), but more sensitive (79%) in marking M4 or M5 cells. This appears to be true even though CD24 is apparently not expressed on normal monocytes. When positive staining for either or both antibodies (CD24 or CD14) was considered indicative of a monocytic leukemia, the sensitivity of immunophenotyping in distinguishing M4/M5 from M1/M2 AML rose to 92%, while maintaining 97% specificity. The authors discuss a recent observation that may help explain the unexpected expression of CD24 in monocytic AML. They conclude that the usefulness of CD24 in identifying monocytic AML may exceed that of CD14, and that the use of CD24 and CD14 in combination improves the ability of flow cytometry to distinguish myeloid from monocytic acute leukemias.
Bacteriophage M13 Procoat Protein Inserts Into the Plasma Membrane as a Loop Structure (1987)

The major coat protein of bacteriophage M13 is synthesized as a precursor, the procoat, with a typical leader (signal) sequence of 23 residues at its NH2-terminus. A fusion protein that contains the NH2-terminal 141 residues of cytoplasmic ribulokinase and all but the first ten residues of M13 procoat was made. The fusion protein inserts into the plasma membrane of Escherichia coli and is processed by leader peptidase to give rise to a leader peptide of 155 residues and the mature coat protein of 50 residues. The NH2-terminus of the leader peptide remains in the cytoplasm and is protected from protease added to the medium outside of the cell. This indicates that M13 procoat inserts into the membrane as a loop structure and that the NH2-terminus of a leader peptide remains within the cytoplasm during membrane insertion.
Angiogenesis and angiogenesis inhibition: An overview (1997)

The study of angiogenesis attracts investigators from many different fields who find that regulation of blood vessel growth underlies a wide spectrum of biologic processes. These include reproduction, development, repair, angiogenic diseases, and cancer (Folkman, 1995).
MRP8/MRP14 impairs endothelial integrity and induces a caspase-dependent and -independent cell death program (2006)

Activated phagocytes express considerable amounts of MRP8 and MRP14, 2 calcium-binding S100 proteins forming stable heterodimers that are specifically secreted at inflammatory sites in many diseases. We previously reported that treatment of human microvascular endothelial cells with purified MRP8/MRP14 leads to loss of endothelial cell contacts. In this study, we demonstrate that MRP8/MRP14 complexes furthermore trigger cell death of endothelial cells after the onset of cell detachment. Morphologic analysis of dying endothelial cells revealed characteristic features of both apoptosis and necrosis. Furthermore, MRP8/MRP14 induced apoptotic caspase-9 and caspase-3 activation, DNA fragmentation, and membrane phosphatidylserine exposure in target cells. These events were independent of death receptor signaling and in part controlled by a mitochondrial pathway. Consistently, overexpression of antiapoptotic Bcl-2 abrogated caspase activation and externalization of phosphatidylserine; however, MRP8/MRP14 still induced plasma membrane damage and even DNA fragmentation. Thus, our results demonstrate that MRP8/MRP14 triggers cell death via caspase-dependent as well as -independent mechanisms. Excessive release of cytotoxic MRP8/MRP14 by activated phagocytes might therefore present an important molecular pathomechanism contributing to endothelial damage during vasculitis and other inflammatory diseases.
Truncated, branched, and/or cyclic analogs of neuropeptide Y: importance of the pancreatic peptide fold in the design of specific Y2 receptor ligands (1992)

Truncated, branched, and/or cyclic neuropeptide Y (NPY) analogues were tested for their ability to bind to the neuroblastoma cells, SK-N-MC (Y1 receptor) and SK-N-BE(2) (Y2 receptor). The design of such analogues was inspired by models of NPY based on the crystal structure of avian pancreatic polypeptide. The minimum length of the backbone was investigated using the following truncated analogues [binding affinity (nM) for Y1 and Y2 receptor subtypes respectively are given in parentheses]: des-AA10-17[D-Ala9]NPY (100, 0.9), des-AA7-23[D-Ala6]NPY (> 1000, 1.2), des-AA4-26[D-Ala3]NPY (> 1000, 120), cyclo(7,20)-des-AA10-17[Glu7,D- Ala9,D-Dpr20]NPY (100, nd), cyclo(2,27)-des-AA7-23[Glu2,D-Ala6,D-Dpr27]NPY (> 1000, 3.6), cyclo(2,30)- des-AA7-23[Glu2,D-Ala6,-D-Dpr30]NPY (> 1000, nd), cyclo(1,30)-des-AA4-26[Glu1,D-Ala3,D-Dpr30]NPY (> 1000, > 1000). A new family of branched NPY analogues corresponding to the partial deletion of the polyproline helix with conservation of the N-terminus was also examined: des-AA7-23[(Ac-NPY14-22)-epsilon-D-Lys6]NPY (> 1000, 2.1), des-AA7-23[(Ac-NPY7-22)-epsilon-D-Lys6]NPY (> 1000, 5.1), des-AA7-23-[(Ac-LEALEG-NPY14-22)-epsilon-D-Lys6]NPY (> 1000, 4.8). Finally, the role played by the flexible tail (residues 32-36) was studied with the following cyclic analogues: cyclo(30,34)-[Lys30,Glu34]NPY18-36 (> 1000, 360), cyclo(30,34)-[Orn30,Gly34]NPY18-36 (> 1000, 950), cyclo(30,34)-[Dpr30,Glu34]NPY18-36 (> 1000, 590), cyclo(33,36)-[Lys33,Glu36]NPY (> 1000, > 1000), cyclo(33,36)-[Lys33,Glu36]NPY18-36 (> 1000, > 1000). These results suggest that the Y1 receptor is highly discriminatory since deletion of residues 10-17, shown to have little effect on Y2 binding affinity, reduces Y1 affinity 50-fold. Bridging sites and constructs have been identified that may serve as useful leads in the design of more potent and selective analogues. We have identified two positions (9 and 6) where the introduction of a D amino acid is not detrimental to binding affinity. Whether this modification leads to the stabilization of a yet unidentified turn compatible with high Y2 receptor affinity will have to be determined by spectroscopic methods. Finally, stabilizing a putative alpha-helical conformation of the C-terminal heptapeptide of NPY18-36 has a deleterious effect on the Y1 and Y2 receptors.
Temperature Effects on Kinetic Parameters and Substrate Affinity of Cel7A Cellobiohydrolases (2015)

We measured hydrolytic rates of four purified cellulases in small increments of temperature (10-50 °C) and substrate loads (0-100 g/liter) and analyzed the data by a steady state kinetic model that accounts for the processive mechanism. We used wild type cellobiohydrolases (Cel7A) from mesophilic Hypocrea jecorina and thermophilic Rasamsonia emersonii and two variants of these enzymes designed to elucidate the role of the carbohydrate binding module (CBM). We consistently found that the maximal rate increased strongly with temperature, whereas the affinity for the insoluble substrate decreased, and as a result, the effect of temperature depended strongly on the substrate load. Thus, temperature had little or no effect on the hydrolytic rate in dilute substrate suspensions, whereas strong temperature activation (Q10 values up to 2.6) was observed at saturating substrate loads. The CBM had a dual effect on the activity. On one hand, it diminished the tendency of heat-induced desorption, but on the other hand, it had a pronounced negative effect on the maximal rate, which was 2-fold larger in variants without CBM throughout the investigated temperature range. We conclude that although the CBM is beneficial for affinity it slows down the catalytic process. Cel7A from the thermophilic organism was moderately more activated by temperature than the mesophilic analog. This is in accord with general theories on enzyme temperature adaptation and possibly relevant information for the selection of technical cellulases.
Using models of the myocyte for functional interpretation of cardiac proteomic data (2004)

There has been significant progress towards the development of highly integrative computational models of the cardiac myocyte over the past decade. Models now incorporate descriptions of voltage-gated ionic currents and membrane transporters, mechanisms of calcium-induced calcium release and intracellular calcium cycling, mitochondrial ATP production and its coupling to energy-requiring membrane transport processes and mechanisms of force generation. There is an extensive literature documenting both the reconstructive and predictive abilities of these models and there is no question that an interplay between quantitative modelling and experimental investigation has become a central component of modern cardiovascular research. As data regarding the cardiovascular proteome in both health and disease emerge, integrative models of the myocyte are becoming useful tools for interpreting the functional significance of changes in protein expression and post-translational modifications (PTMs). Data of particular importance include information on: (a) changes of expressed protein level, (b) changes of protein PTMs, (c) protein localization, and (d) protein-protein interactions, as it is often possible to incorporate and interpret the functional significance of such findings using computational models. We provide two examples of how models may be used in this fashion. In the first example, we show how information on altered expression of the sarcoplasmic reticulum Ca2+-ATPase, when interpreted through the use of a computational model, has provided key insights into fundamental mechanisms regulating cardiac action potential duration. In the second example, we show how information on the effects of phosphorylation of L-type Ca2+ channels, when interpreted through the use of a model, provides insights on how this post-translational modification alters the properties of excitation-contraction coupling and risk for arrhythmia.
In SituHybridization (2005)

Abstruct In situ hybridization is a method used to localize nucleic acid sequences in cells or tissue sections. The first in situ hybridization experiments were described by two groups of researchers in 1969, John et al. and Gall and Pardue (reviewed in ref. ). Radioactively labeled RNA probes were used to localize specific DNA sequences within the nuclei of Xenopus laevis ().
The value of multi-slice-computed tomography coronary angiography for risk stratification (2009)

Multi-slice-computed tomography coronary angiography (CTA) provides direct non-invasive anatomic assessment of the coronary arteries allowing for early identification of coronary artery disease (CAD). This information is useful for diagnosis of CAD, particularly the rule out of CAD. In addition, early identification of CAD with CTA may also be useful for risk stratification. The purpose of this review is to provide an overview of the current literature on the prognostic value of CTA and to discuss how the prognostic information obtained with CTA can be used to further integrate the technique into clinical practice. Non-invasive anatomic assessment of plaque burden, location, composition, and remodeling using CTA may provide prognostically relevant information. This information has been shown to be incremental to the Framingham risk score, coronary artery calcium scoring, and myocardial perfusion imaging. Characterization of atherosclerosis non-invasively has the potential to provide important prognostic information enabling a more patient-tailored approach to disease management. Future studies assessing outcome after CTA-based risk adjustments are needed to further understand the value of detailed non-invasive anatomic imaging.
Subretinal Semiconductor Microphotodiode Array (1998)

SMAs can be successfully implanted into the subretinal space and will generate current in response to light stimulation during an extended period of time.
Surface heat flux parameterization and the response of ocean general circulation models to high-latitude freshening (1994)

A global ocean general circulation model (OGCM) is forced using mixed boundary conditions (i.e. a restoring condition on the upper level temperature but using a fixed, specified surface salt flux). A freshwater flux anomaly is then applied over the western half of the sub-polar gyre in the northern North Atlantic. The response of the model is found to be dependent upon the details of the parameterization of the surface heat flux: In particular the “coupling strength” or Haney relaxation time is crucial. Responses range from a halocline catastrophe at short relaxation times (strong coupling) to a very modest perturbation at longer relaxation times (weaker coupling). An accurate parameterization is therefore required to properly model the evolution of the response. It is uncertain that the restorative condition is sufficiently realistic, especially in cases where a significantly different climatology is obtained. It is possible, for example, that the evolution could move from an unstable trajectory to a stable one if the parameters in the heat flux formulation are also allowed to evolve. This might help to explain why OGCMs under mixed boundary conditions are more sensitive than the observations suggest they should be. When a recovery does occur it does so on decadal time scales. It is therefore tempting to speculate that the positive feedback on the initial perturbation provided by the heat flux response plays a central role in the dynamics of North Atlantic variability, in a manner that is analogous to the wind-stress feedback in the El Ni±o, Southern Oscillation.
Late Results after Surgical Treatment of Renovascular Hypertension (1985)

During the period 1963-1980, 122 patients were operated on for renovascular hypertension at surgical department D, vascular section, Rigshospitalet, Copenhagen. Seventeen patients, with a median age of 24 years, had fibromuscular hyperplasia and 95 patients, with a median age of 48 years, had atherosclerosis. Twenty-four of the latter had bilateral renal artery lesions and 71 had unilateral disease. Ten patients had various other causes of renovascular hypertension. Operative mortality was 4.9%, decreasing to two per cent in the last 8 years. At discharge, 71% of the patients were normotensive without medication, 18% were improved, and 11% were unimproved. At follow-up in 1982, the actuarial 10-year survival rates for patients with unilateral and bilateral atherosclerotic disease were 65% and 48%, respectively. There was no difference between survival rates for patients with fibromuscular hyperplasia and an age- and sex-matched, population. Sixty-nine patients were reexamined with a median follow-up of 9 years. Of the survivors with atherosclerosis, 87% benefitted from the operation: 50% were normotensive without medication and 37% were improved. Of patients with fibromuscular hyperplasia, 93% benefitted from operation: 79% were normotensive and 14% were improved. The results support the value of surgery in patients with renal fibromuscular hyperplasia and to the long-term benefits of surgical treatment of patients with atherosclerotic renovascular disease.
Comparative study of maximum power point tracking algorithms (2002)

Abstract Maximum power point trackers (MPPTs) play an important role in photovoltaic (PV) power systems because they maximize the power output from a PV system for a given set of conditions, and therefore maximize the array efficiency. Thus, an MPPT can minimize the overall system cost. MPPTs find and maintain operation at the maximum power point, using an MPPT algorithm. Many such algorithms have been proposed. However, one particular algorithm, the perturb‐and‐observe (P&amp;O) method, claimed by many in the literature to be inferior to others, continues to be by far the most widely used method in commercial PV MPPTs. Part of the reason for this is that the published comparisons between methods do not include an experimental comparison between multiple algorithms with all algorithms optimized and a standardized MPPT hardware. This paper provides such a comparison. MPPT algorithm performance is quantified through the MPPT efficiency. In this work, results are obtained for three optimized algorithms, using a microprocessor‐controlled MPPT operating from a PV array and also a PV array simulator. It is found that the P&amp;O method, when properly optimized, can have MPPT efficiencies well in excess of 97%, and is highly competitive against other MPPT algorithms. Copyright © 2002 John Wiley &amp; Sons, Ltd.
Catalysis of protein folding by cyclophilins from different species (1991)

Cyclophilins are a class of ubiquitous proteins with yet unknown function. They were originally discovered as the major binding proteins for the immunosuppressant cyclosporin A. The only known catalytic function of these proteins in vitro is the cis/trans isomerization of Xaa-Pro bonds in oligopeptides. This became clear after the discovery that bovine cyclophilin is identical with porcine prolyl isomerase. This enzyme accelerates slow, proline-limited steps in the refolding of several proteins. Here we demonstrate that the cyclophilins from man, pig, Neurospora crassa, Saccharomyces cerevisiae, and Escherichia coli are all active as prolyl isomerases and as catalysts of protein folding. This evolutionary conservation suggests that catalysis of prolyl peptide bond isomerization may be an important function of the cyclophilins. It could be related with de novo protein folding or be involved in regulatory processes. Catalysis of folding is very efficient in the presence of the high cellular concentrations of prolyl isomerase.
Assessment of tobacco-specific N-nitrosamines in tobacco products. (1979)

Tobacco-specific nonvolatile N -nitrosamines in tobacco and in fresh mainstream and sidestream smoke of cigarettes and cigars were quantitatively determined with a thermal energy analyzer. The smoke was trapped in ascorbic acid solution buffered at pH 4.5 and extracted with dichloromethane, and the organic phase was chromatographed and analyzed by high-performance liquid chromatography-thermal energy analyzer methodology (sensitivity, 250 pg/injection). The nonvolatile nitrosamines were further enriched by repeated chromatography and positively identified by gas-liquid chromatography-mass spectrometry. [2′-14C] N ′-nitrosonornicotine served as internal standard for the quantitative analysis.

The tobacco of five different cigarettes contained between 0.22 and 7.0 ppm of the carcinogenic N ′-nitrosonornicotine, 0.13 and 0.74 ppm of the carcinogenic 4-( N -methyl- N -nitrosamino)-1-(3-pyridyl)-1-butanone, and 0.44 to 3.2 ppm of the newly identified N ′-nitrosoanatabine. In unaged mainstream and sidestream smoke of the same cigarettes, values ranged between 0.24 and 3.7 and 0.15 and 6.1 µg/cigarette for N ′-nitrosonornicotine, between 0.11 and 0.42 and 0.19 and 0.66 µg/cigarette for 4-( N -methyl- N -nitrosamino)-1-(3-pyridyl)-1-butanone, and between 0.33 and 4.6 and 0.15 and 1.5 µg/cigarette for N ′-nitrosoanatabine, respectively. The relatively high concentrations of these carcinogenic N -nitrosamines in sidestream smoke are discussed as possible tobacco-specific indicators for indoor pollution.