gebhart/patrepeval huggingface dataset:
Simian virus 40-transformed adherent cells from human long-term marrow cultures: cloned cell lines produce cells with stromal and hematopoietic characteristics (1987)

Adherent cells from long-term marrow cultures from 23 individuals were transformed with wild-type simian virus 40 (SV40). After transformation, cloned cell lines were developed that even after rigorous subcloning invariably produced both stromal cells and round cells. The stromal cells expressed cytoskeletal filaments similar to those of long-term marrow culture adherent cells and produced interstitial and basal lamina collagen types. The round cells had the electron microscopic appearance of primitive hematopoietic cells and when examined with cytochemical stains and monoclonal antibodies to hematopoietic differentiation antigens had reaction patterns suggestive of cells from several lineages. Most round cells expressed the pan- hematopoietic T-200 determinant, and lesser percentages expressed the early T cell antigens CD-1 and CD-3, HLA-DR determinants, the monocytic antigen recognized by Leu M3, and the myeloid antigens detected by monoclonal antibodies 1G10 and 12.8. In addition, when plated in semisolid medium in the presence of a source of colony-stimulating activity, up to 11% of the cells formed colonies consisting of blastlike cells that also expressed hematopoietic cell surface determinants. The data suggest that adherent cells in long-term marrow cultures contain a cell that after transformation by SV40 obligately produces cells with hematopoietic as well as stromalike features.
Rationale for using new lipid emulsions in parenteral nutrition and a review of the trials performed in adults (2009)

Lipids traditionally used in parenteral nutrition are based on n-6 fatty acid-rich vegetable oils such as soyabean oil. This practice may not be optimal because it may present an excessive supply of linoleic acid. Alternatives to the use of soyabean oil include its partial replacement by so-called medium-chain TAG (MCT), olive oil or fish oil, either alone or in combination. Lipid emulsions containing MCT are well established, but those containing olive oil and fish oil, although commercially available, are still undergoing trials in different patient groups. Emulsions containing olive oil or fish oil are well tolerated and without adverse effects in a wide range of adult patients. An olive oil-soyabean oil emulsion has been used in quite small studies in critically-ill patients and in patients with trauma or burns with little real evidence of advantage over soyabean oil or MCT-soyabean oil. Fish oil-containing lipid emulsions have been used in adult patients post surgery (mainly gastrointestinal). This approach has been associated with alterations in patterns of inflammatory mediators and in immune function and, in some studies, a reduction in the length of stay in the intensive care unit and in hospital. One study indicates that peri-operative administration of fish oil may be superior to post-operative administration. Fish oil has been used in critically-ill adults. Here, the influence on inflammatory processes, immune function and clinical end points is not clear, since there are too few studies and those that are available report contradictory findings. One important factor is the dose of fish oil required to influence clinical outcomes. Further studies that are properly designed and adequately powered are required in order to strengthen the evidence base relating to the use of lipid emulsions that include olive oil and fish oil in critically-ill patients and in patients post surgery.
Cellular oxygen sensing by mitochondria: old questions, new insight (2000)

Hypoxia elicits a variety of adaptive responses at the tissue level, at the cellular level, and at the molecular level. A physiological response to hypoxia requires the existence of an O(2) sensor coupled to a signal transduction system, which in turn activates the functional response. Although much has been learned about the signaling systems activated by hypoxia, no consensus exists regarding the nature of the underlying O(2) sensor or whether multiple sensors exist. Among previously considered mechanisms, heme proteins have been suggested to undergo allosteric modification in response to O(2) binding or release at different PO(2) levels. Other studies suggest that ion channels may change conductance as a function of PO(2), allowing them to signal the onset of hypoxia. Still other studies suggest that NADPH oxidase may decrease its generation of reactive O(2) species (ROS) during hypoxia. Recent data suggest that mitochondria may function as O(2) sensors by increasing their generation of ROS during hypoxia. These oxidant signals appear to act as second messengers in the adaptive responses to hypoxia in a variety of cell types. Such observations contribute to a growing awareness that mitochondria do more than just generate ATP, in that they initiate signaling cascades involved in adaptive responses to hypoxia and that they participate in the control of cell death pathways.
The physics of Schottky barriers? (1970)

A review is given of the physical processes which determine the height of the barrier and the current-voltage relationship in a metal-semiconductor Schottky barrier.
Practical neural network recipes in C (1993)

This text serves as a cookbook for neural network solutions to practical problems using C++. It will enable those with moderate programming experience to select a neural network model appropriate to solving a particular problem, and to produce a working program implementing that network. The book provides guidance along the entire problem-solving path, including designing the training set, preprocessing variables, training and validating the network, and evaluating its performance. Though the book is not intended as a general course in neural networks, no background in neural works is assumed and all models are presented from the ground up
BAY 43-9006 Inhibition of Oncogenic RET Mutants (2006)

BAY 43-9006 is a powerful inhibitor of the RET kinase. Its potential as a therapeutic tool for RET-positive thyroid tumors, including those expressing V804 mutations merits study.
Detection of Subpopulations in Near-Infrared Reflectance Analysis (1988)

In typical near-infrared multivariate statistical analyses, samples with similar spectra produce points that cluster in a certain region of spectral hyperspace. These clusters can vary significantly in shape and size due to variation in sample packings, particle-size distributions, component concentrations, and drift with time. These factors, when combined with discriminant analysis using simple distance metrics, produce a test in which a result that places a particular point inside a particular cluster does not necessarily mean that the point is actually a member of the cluster. Instead, the point may be a member of a new, slightly different cluster that overlaps the first. A new cluster can be created by factors like low-level contamination or instrumental drift. An extention added to part of the BEAST (Bootstrap Error-Adjusted Single-sample Technique) can be used to set nonparametric probability-density contours inside spectral clusters as well as outside, and when multiple points begin to appear in a certain region of cluster-hyperspace the perturbation of these density contours can be detected at an assigned significance level. The detection of false samples both within and beyond 3 SDs of the center of the training set is possible with this method. This procedure is shown to be effective for contaminant levels of a few hundred ppm in an over-the-counter drug capsule, and is shown to function with as few as one or two wavelengths, suggesting its application to very simple process sensors.
Magnetic Resonance in Medicine (2006)

Magnetic Resonance in Medicine is an international journal devoted to the publication of original investigations concerned with all aspects of the development and use of nuclear magnetic resonance and electron paramagnetic resonance techniques for medical applications.
An artificial neural networks for approximating polynomial functions (2003)

The authors use polynomial function as a common base to measure the capacity of a feedforward artificial neural network (FANN) with a finite number of hidden nodes. They show that there is a relationship between the capacity of a FANN in approximating polynomial functions and the number of hidden nodes used in the FANN. A procedure for realizing a FANN in approximating polynomial functions is described. Two examples are given to show the procedure. Several experiments are reported, verifying that a FANN with a certain number of hidden nodes has the capability to learn a given polynomial function. The experiments also showed that the proposed algorithm for training a FANN performs accurately.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Enhancement of fluid filtration across tumor vessels: Implication for delivery of macromolecules (1999)

Cancer therapies using genes and other macromolecules might realize their full clinical potential if they could be delivered to tumor tissue in optimal quantities. Unfortunately, the compromised circulation within tumors poses a formidable resistance to adequate and uniform penetration of these agents. Previously, we have proposed elevated interstitial fluid pressure (IFP) as a major physiological barrier to delivery of macromolecules. Here we postulate that modulation of tumor microvascular pressure (MVP) and associated changes in IFP would enhance macromolecular delivery into a solid tumor. To test our hypothesis, we altered tumor MVP by either periodic injection or continuous infusion of angiotensin II (AII) and measured the resulting changes in IFP and uptake of macromolecules. We used the nicotinyl hydrazine derivative of human polyclonal IgG (HYNIC-IgG) as a nonspecific macromolecule and CC49 antibody as a specific macromolecule. We found that both chronic and periodic modulation of tumor MVP enhances transvascular fluid filtration, leading to a 40% increase in total uptake of the specific antibody within 4 hr of its administration. Conversely, neither continuous nor periodic infusion of AII induced any increase in uptake of nonspecific antibodies. Strategies to improve delivery of macromolecules and limitations of this approach are identified.
Cyclopalladated Ferrocenylimine as Efficient Catalyst for the Syntheses of Arylboronate Esters (2010)

Abstract The cyclopalladated ferrocenylimine I and its phosphine adducts IIa–f were prepared and evaluated in the borylation of aryl halides. The tricyclohexylphosphine adduct IIb exhibited highly catalytic activity for the coupling of aryl and heteroaryl bromides containing various functional groups with low catalyst loading (2 mol%). Aryl and heteroaryl chlorides were smoothly converted into the corresponding boronates in the presence of the monophosphinobiaryl ligand (XPhos) adduct IIf . It was proposed that palladacycle was only a reservoir of the catalytically active species from the investigation on the reaction mechanism.
Role of B cells as antigen-presenting cells in vivo revisited: antigen-specific B cells are essential for T cell expansion in lymph nodes and for systemic T cell responses to low antigen concentrations (2001)

Studies in B cell-deficient mice generated by continuous injection of anti-mu antibodies (muSM) showed that T cell priming in lymph nodes was dependent on antigen presentation by B cells. This concept has recently become controversial since a wide range, from complete deficiency to near normal T cell responses, was reported in studies carried out with B cell-deficient mice generated by gene disruption (muMT). In this study we show that in the absence of B cells, T cell responses are greatly reduced in all the available muMT mouse strains although responses in muMT of the C57BL/6 background (which were used for most studies with muMT) were much more variable and could reach up to 42% of control. In contrast, T cell responses in muMT --> F(1) bone marrow chimeras which have the same phenotype as muMT were totally impaired, suggesting a principle difference between mice developing without B cells (muMT mice) and muSM which are made B cell deficient only after birth. Normal T cell priming was completely restored by reconstitution of muMT and muMT --> F(1) mice with syngeneic B cells. Interestingly, only B cell populations containing antigen-specific B cells were capable of reconstituting T cell responses. Monoclonal B cells taken from Ig transgenic mice could not reconstitute responses to an irrelevant antigen. We also found that B cells were also required for systemic T cell priming when antigen concentrations were limiting but were not required for priming (for T cell help) when mice were immunized with a high antigen dose.
Effects of pH Gradients on Liposomal Charge States Examined by Capillary Electrophoresis (2002)

Liposomes have been used for biomimetic containers and to study phenomena ranging from photosynthetic systems to membrane fusion and dynamics. An important aspect of many preparations and in biological processes is the presence of a pH gradient across the membrane. Here, experiments were conducted using capillary electrophoresis to investigate the effects of this gradient on liposomes composed of phosphatidic acid, phosphatidylcholine, and cholesterol. pH gradients for the liposomes were created by titration of the exterior buffer; then the electrophoretic properties were analyzed by capillary electrophoresis and the size was measured by laser light scattering. Our results show that the presence of a pH gradient has a significant effect on the electrophoretic migration of liposome samples, induced principally by a change in effective charge. The differences in charge for the liposome samples are evaluated with regard to acid−base equilibria, which is shown to be inadequate to describe the dynamics of the system. A more complex capacitive theory incorporating elements of the Overbeek−Booth theory and the relaxation effect appears to more effectively describe the results and could aid in predicting liposome behavior under various pH gradient conditions.
Solving partial differential equations in real-time using artificial neural network signal processing as an alternative to finite-element analysis (2003)

Finite element methods (FEM) have been widely utilized for evaluating partial differential equations (PDEs). Although these methods have been highly successful, they require time-consuming procedures to build numerous volumetric elements and solve large-size linear systems of equations. In this paper, a new signal processing method is utilized to solve PDEs numerically by using an artificial neural network. We investigate the theoretical aspects of this approach and show that the numerical computation can be formulated as a machining learning problem and implemented by a supervised function approximation neural network. We also show that, for the case of the Poisson equation, the solution is unique and continuous with respect to the boundary surface. We apply this method to bio-potential computation where the solution of a standard volume conductor is mapped to the solutions of a set of volume conductors in different shapes.
The TIGRFAMs database of protein families (2003)

TIGRFAMs is a collection of manually curated protein families consisting of hidden Markov models (HMMs), multiple sequence alignments, commentary, Gene Ontology (GO) assignments, literature references and pointers to related TIGRFAMs, Pfam and InterPro models. These models are designed to support both automated and manually curated annotation of genomes. TIGRFAMs contains models of full-length proteins and shorter regions at the levels of superfamilies, subfamilies and equivalogs, where equivalogs are sets of homologous proteins conserved with respect to function since their last common ancestor. The scope of each model is set by raising or lowering cutoff scores and choosing members of the seed alignment to group proteins sharing specific function (equivalog) or more general properties. The overall goal is to provide information with maximum utility for the annotation process. TIGRFAMs is thus complementary to Pfam, whose models typically achieve broad coverage across distant homologs but end at the boundaries of conserved structural domains. The database currently contains over 1600 protein families. TIGRFAMs is available for searching or downloading at www.tigr.org/TIGRFAMs.
Zero-error function computation in sensor networks (2009)

We consider the problem of data harvesting in wireless sensor networks. A designated collector node seeks to compute a function of the sensor measurements. For a directed graph G = (V ,¿) on the sensor nodes, we wish to determine the optimal encoders on each edge which achieve zero-error block computation of the function at the collector node. Our goal is to characterize the rate region in R <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">|¿|</sup> . We start with the two node problem, and determine a necessary and sufficient condition for the encoder that yields the optimal alphabet, from which we then calculate the minimum worst case and average case complexity. We then extend this result to trees and derive a necessary and sufficient condition for the encoder on each edge. The further extension of these results to directed acyclic graphs is not immediate. We provide an outer bound on the rate region by finding the disambiguation requirements for each cut, and describe examples where this outer bound is tight. Finally, we consider a collocated network of nodes with a specified order of transmission. We determine a necessary and sufficient condition for each encoder which is based on the transmissions received, and show that the average case complexity of computing a type-threshold function is ¿(1), in comparison to the worst case complexity of ¿(log n).
Renal mineralocorticoid receptors and hippocampal corticosterone-binding species have identical intrinsic steroid specificity. (1983)

There is current evidence for two classes of hippocampal glucocorticoid receptors (GR)--one classical, [3H]dexamethasone [( 3H]Dex)-binding sites in glial cells, and the other [3H]corticosterone-preferring sites in neuronal cells. In the presence of 1 microM of the synthetic glucocorticoid RU26988 (11 beta, 17 beta-dihydroxy-17 alpha-propynylandrost-1,4,6,-trien-3-one) to exclude tracer from [3H]Dex sites, hippocampal cytosol from adrenalectomized/ovariectomized Sprague-Dawley rats binds [3H]Dex to sites (Kd at 4 degrees C, 0.77 X 10(-9) M; 65 fmol/mg of protein) with the following order of specificity: aldosterone (Aldo) = 9 alpha-fluorocortisol (9 alpha F-cortisol) = deoxycorticosterone (DOC) = corticosterone greater than cortisol much greater than Dex; [3H]Aldo, [3H]DOC, and [3H]corticosterone binding show identical specificity in the presence of RU26988. Addition of 1% adrenalectomized/ovariectomized rat plasma (but not plasma heated at 56 degrees C for 30 min) alters the specificity to: 9 alpha F-cortisol greater than or equal to Aldo greater than or equal to DOC much greater than Dex greater than or equal to corticosterone greater than or equal to cortisol, consistent with sequestration of DOC, corticosterone, and cortisol by transcortin and similar to classical mineralocorticoid receptor (MR) binding of [3H]Aldo in renal cytosol (9 alpha F-cortisol greater than or equal to Aldo greater than or equal to DOC much greater than corticosterone greater than or equal to cortisol greater than or equal to Dex). Separation of other renal binders from transcortin by hydroxylapatite adsorption established the intrinsic specificity of [3H]Aldo binding to MR as: DOC greater than or equal to Aldo greater than or equal to 9 alpha F-cortisol greater than or equal to corticosterone greater than cortisol much greater than Dex, parallel to that of the [3H]corticosterone-binding sites in hippocampus. These studies suggest (i) that hippocampal [3H]corticosterone-binding sites and renal MR may have identical intrinsic specificity for steroids, with apparent specificity differences the result of tissue-specific sequestration of naturally occurring steroids other than Aldo and (ii) that an identical steroid-binding species may thus be occupied under physiological conditions by a mineralocorticoid in one tissue (kidney) and a glucocorticoid in another (hippocampus).
Do DNA repair systems affect N4-hydroxycytidine-induced mutagenesis? (1983)

It was tested whether mutations induced in E. coli by N4-hydroxycytidine (oh4Cyd): (i) undergo mutation frequency decline (MFD) when synthesis of protein is arrested, and (ii) are influenced by polA1, polA107 or xth mutations. It was also investigated whether oh4Cyd may provoke SOS response and prophage lambda induction. All these processes may involve the action of repair enzymes. It has been shown that none of these processes or repair enzymes affects oh4Cyd-induced mutagenesis.
The absorption and effect of dietary supplementation with omega‐3 fatty acids on serum leukotriene B4, in patients with cystic fibrosis (1994)

The substitution of omega-3 (n-3) fatty acids for omega-6 (n-6) fatty acids generates eicosanoids with diminished inflammatory effects. As the lungs of patients with cystic fibrosis (CF) are in a state of chronic inflammation in which increased amounts of eicosanoids are found, n-3 supplementation may reduce this level of inflammation and result in clinical improvement. The absorption and clinical effects of n-3 vs. n-6 fatty acids in CF were measured in a prospective, randomized, double-blind, crossover study in which 14 patients with CF (age: 6-16 years, mean 10.5 years; baseline Shwachman-Brasfield scores: 41-88, mean 76.7) received 6 weeks of n-3 ethyl ester concentrate from menhaden oil (100-131 mg/kg/day, mean 112.8) or n-6 fatty acids from safflower oil (102-132 mg/kg/day, mean 113.3), followed by a washout period of 6 weeks, and then 6 weeks of the other supplement. Analysis by gas chromatography showed that n-3 supplementation resulted in increased eicosapentaenoic acid (20:5n-3) in platelet phospholipids, from 0.14 to 2.16%, P < 0.05 and in increased docosahexaenoic acid (22:6n-3), from 1.33 to 3.72%, P < 0.05. Clinical effects were evaluated at weeks 0, 6, 12, and 18, and analyzed for differences among the n-3, n-6, and washout periods. No adverse effects were reported or observed. No statistically significant differences were found (ANOVA, P > 0.05) in Shwachman-Brasfield scores, sweat test, weight change, or forced expiratory volume and flow (FEV1, FEF25-75%, and FVC) percentiles. Tumor necrosis factor was not measurable in any serum sample. Serum leukotriene B4 (LTB4) levels were significantly reduced by n-3 fatty acids, mean reduction (-177 pg/mL) compared to n-6 fatty acids (+63 pg/mL) P < 0.05. These results show that both n-3 fatty acids are absorbed and incorporated into platelet phospholipids in patients with CF and reduced serum LTB4. No significant clinical differences or adverse effects were found.
Antimicrobial peptide killing of African trypanosomes (2011)

The diseases caused by trypanosomes are medically and economically devastating to the population of Sub-Saharan Africa. Parasites of the genus Trypanosoma infect both humans, causing African sleeping sickness, and livestock, causing Nagana. The development of effective treatment strategies has suffered from severe side effects of approved drugs, resistance and major difficulties in delivering drugs. Antimicrobial peptides (AMPs) are ubiquitous components of immune defence and are being rigorously pursued as novel sources of new therapeutics for a variety of pathogens. Here, we review the role of AMPs in the innate immune response of the tsetse fly to African trypanosomes, catalogue trypanocidal AMPs from diverse organisms and highlight the susceptibility of bloodstream form African trypanosomes to killing by unconventional toxic peptides.