gebhart/patrepeval huggingface dataset:
Arterial baroreflex control of muscle sympathetic nerve activity under orthostatic stress in humans (2012)

The mechanisms by which blood pressure is maintained against the orthostatic stress caused by gravity's effect on the fluid distribution within the body are important issues in physiology, especially in humans who usually adopt an upright posture. Peripheral vasoconstriction and increased heart rate (HR) are major cardiovascular adjustments to orthostatic stress and comprise part of the reflex response elicited via the carotid sinus and aortic baroreceptors (arterial baroreflex: ABR) and cardiopulmonary stretch receptors (cardiopulmonary baroreflex). In a series of studies, we have been characterizing the ABR-mediated regulation of cardiovascular hemodynamics and muscle sympathetic nerve activity (MSNA) while applying orthostatic stress in humans. We have found that under orthostatic stress, dynamic carotid baroreflex responses are modulated as exemplified by the increases in the MSNA, blood pressure, and HR responses elicited by carotid baroreflex unloading and the shorter period of MSNA suppression, comparable reduction and faster recovery of mean arterial blood pressure (MAP) and greater HR response to carotid baroreflex stimulation. Our results also show that ABR-mediated beat-to-beat control over burst incidence, burst strength and total MSNA is progressively modulated as orthostatic stress is increased until induction of syncope, and that the sensitivity of ABR control over the aforementioned MSNA variables is substantially reduced during the development of syncope. We suggest that in humans, the modulation of ABR function under orthostatic stress may be one of the mechanisms by which blood pressure is maintained and orthostatic hypotension limited, and impairment of ABR control over sympathetic vasomotor activity leads to the severe hypotension associated with orthostatic syncope.
Application of molecular biology-based methods to the diagnosis of infectious diseases (1996)

The basis for effective treatment and cure of a patient is the rapid diagnosis of the disease and its causative agent, which is founded on the analysis of the clinical symptoms coupled with laboratory tests. As we approach the 21st century, clinicians are becoming increasingly able to diagnose and treat diseases at the molecular level. The rapid development of new methods and techniques in the area of molecular biology has gained new insights into the genetic and structural features of a considerable number of human pathogens. These results obtained by intensive basic research are currently leading to improved diagnostic procedures. Basically, there are four different possibilities for laboratory diagnosis of infections: 1. direct detection of the pathogens (e.g., microscopy and/or culture), 2. detection of protein components of the pathogens with the help of specific antibodies (e.g., antigen capture ELISA) 3. IgA-, IgM- and IgG-specific detection of antibodies directed against a given pathogen and changes in their corresponding titer, and as the most sensitive method, 4. specific detection of nucleic acids (e.g., PCR) of the pathogens. Here, the human immunodeficiency virus (HIV) and Mycobacterium tuberculosis are serving as examples to review the recent developments as well as the future perspectives in molecular biology-based laboratory diagnosis.
Cooperative Interactions of Hemoglobin (1975)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Absolute bioavailability and stereoselective pharmacokinetics of doxepin (2002)

1. Commercial doxepin contains geometric isomers in the proportions Z:E = 15:85. Z-doxepin and its metabolite Z-N-desmethyldoxepin are both active antidepressants, whereas the corresponding E-isomers are less active therapeutically. 2. The present pharmacokinetic study was a balanced, randomized, two-treatment, two-period, two-sequence crossover design in which 12 healthy male volunteers were given single doses of commercial doxepin intravenously and orally on two occasions separated by a washout period. 3. A two-compartment model with no lag time and first-order elimination fitted the plasma concentration-time curves after intravenous dosing. Pharmacokinetic parameters estimated from the model were comparable with those estimated by non-compartmental methods. 4. All pharmacokinetic parameters displayed a wide between-subject variability. Both isomers of doxepin showed large volumes of distribution and relatively short half-lives in plasma, suggestive of extensive distribution and/or tissue binding. The mean fraction absorbed after oral administration was 0.29 for each isomer. Renal clearances of each isomer were very low after either oral or intravenous dosing, although all four analytes were quantifiable in the urine for prolonged periods. 5. After oral dosing, plasma concentrations of the doxepin isomers remained roughly in the ratio Z:E = 15:85, whereas those of N-desmethyldoxepin were closer to 1:1 in all but two outliers, who had high levels E-N-desmethyldoxepin.
Bone Grafts & Bone Substitutes (1992)

Part 1 Basic science of bone graft healing: introduction to bone grafting different forms of bone grafts radiographic assessment of bone grafts biology of vascularized bone grafts cartilage-derived growth factors embryologic aspects of bone grafts bone morphogenetic protein tissue-response to bone-derived implants biologic principles of bone induction - application to bone grafts role of transforming growth factor critical sites for new bone formation the role of bone marrow in osteogenesis animal models in bone research the role of the periosteum in bone grafting the role of osteoclasts induced new bone formation in extraction apparatus the role of pulsed electromagnetic fields in bone grafting electrical stimulation of bone induction and grafting acquisition and banking of bone allografts the role of prostaglandins in bone formation primate model - evaluation of bone substitution in craniofacial reconstruction. Part 2 Bone substitution: calcium sulfate composite bone grafts metallic implants bioactive bone substitutes bone grafting in total hip replacement and implant interface. Part 3 Clinical application: maxillofacial surgery computer-assisted fabrication for bone grafting vascularized bone grafts craniofacial surgery the Ilizarov bone transport system orthopaedic surgery reconstructive microsurgery trauma surgery otolaryngology - head and neck surgery.
Design and Synthesis of an Orally Active Metabotropic Glutamate Receptor Subtype-2 (mGluR2) Positive Allosteric Modulator (PAM) That Decreases Cocaine Self-Administration in Rats (2010)

The modification of 3'-((2-cyclopentyl-6,7-dimethyl-1-oxo-2,3-dihydro-1H-inden-5-yloxy)methyl)biphenyl-4-carboxylic acid (BINA, 1) by incorporating heteroatoms into the structure and replacing the cyclopentyl moiety led to the development of new mGluR2 positive allosteric modulators (PAMs) with optimized potency and superior druglike properties. These analogues are more potent than 1 in vitro and are highly selective for mGluR2 vs other mGluR subtypes. They have significantly improved pharmacokinetic (PK) properties, with excellent oral bioavailability and brain penetration. The benzisothiazol-3-one derivative 14 decreased cocaine self-administration in rats, providing proof-of-concept for the use of mGluR2 PAMs for the treatment of cocaine dependence.
Point Decoration of Silicon Nanowires: An Approach Toward Single‐Molecule Electrical Detection (2014)

Probing interactions of biological systems at the molecular level is of great importance to fundamental biology, diagnosis, and drug discovery. A rational bioassay design of lithographically integrating individual point scattering sites into electrical circuits is capable of realizing real-time, label-free biodetection of influenza H1N1 viruses with single-molecule sensitivity and high selectivity by using silicon nanowires as local reporters in combination with microfluidics. This nanocircuit-based architecture is complementary to more conventional optical techniques, but has the advantages of no bleaching problems and no fluorescent labeling. These advantages offer a promising platform for exploring dynamics of stochastic processes in biological systems and gaining information from genomics to proteomics to improve accurate molecular and even point-of-care clinical diagnosis.
Intracellular Delivery of siRNA by Polycationic Superparamagnetic Nanoparticles (2012)

The siRNA transfection efficiency of nanoparticles (NPs), composed of a superparamagnetic iron oxide core modified with polycationic polymers (poly(hexamethylene biguanide) or branched polyethyleneimine), were studied in CHO-K1 and HeLa cell lines. Both NPs demonstrated to be good siRNA transfection vehicles, but unmodified branched polyethyleneimine (25 kD) was superior on both cell lines. However, application of an external magnetic field during transfection (magnetofection) increased the efficiency of the superparamagnetic NPs. Furthermore, our results reveal that these NPs are less toxic towards CHO-K1 cell lines than the unmodified polycationic-branched polyethyleneimine (PEI). In general, the external magnetic field did not alter the cell's viability nor it disrupted the cell membranes, except for the poly(hexamethylene biguanide)-modified NP, where it was observed that in CHO-K1 cells application of the external magnetic field promoted membrane damage. This paper presents new polycationic superparamagnetic NPs as promising transfection vehicles for siRNA and demonstrates the advantages of magnetofection.
Uptake of cell wall peptides by Salmonella typhimurium and Escherichia coli (1987)

During bacterial growth, cell wall peptides are released from the murein and reused for the synthesis of new cell wall material. Mutants defective in peptide transport were unable to reutilize cell wall peptides, demonstrating that these peptides are taken up intact into the cytoplasm prior to reincorporation into murein. Furthermore, cell wall peptide recycling was shown to play an important physiological role; peptide transport mutants which were unable to recycle these peptides showed growth defects under appropriate conditions. Using mutants specifically defective in each of the three peptide transport systems, we showed that the uptake of cell wall peptides was mediated solely by the oligopeptide permease (Opp) and that neither the dipeptide permease (Dpp) nor the tripeptide permease (Tpp) played a significant role in this process. Our data indicate that the periplasmic oligopeptide-binding protein has more than one substrate-binding site, each with different though overlapping specificities.
The target landscape of clinical kinase drugs (2017)

Kinase inhibitors are important cancer therapeutics. Polypharmacology is commonly observed, requiring thorough target deconvolution to understand drug mechanism of action. Using chemical proteomics, we analyzed the target spectrum of 243 clinically evaluated kinase drugs. The data revealed previously unknown targets for established drugs, offered a perspective on the "druggable" kinome, highlighted (non)kinase off-targets, and suggested potential therapeutic applications. Integration of phosphoproteomic data refined drug-affected pathways, identified response markers, and strengthened rationale for combination treatments. We exemplify translational value by discovering SIK2 (salt-inducible kinase 2) inhibitors that modulate cytokine production in primary cells, by identifying drugs against the lung cancer survival marker MELK (maternal embryonic leucine zipper kinase), and by repurposing cabozantinib to treat FLT3-ITD-positive acute myeloid leukemia. This resource, available via the ProteomicsDB database, should facilitate basic, clinical, and drug discovery research and aid clinical decision-making.
Epitope-specific antibody response is controlled by immunoglobulin VH polymorphisms (2014)

Autoantibody formation is essential for the development of certain autoimmune diseases like rheumatoid arthritis (RA). Anti-type II collagen (CII) antibodies are found in RA patients; they interact with cartilage in vivo and are often highly pathogenic in the mouse. Autoreactivity to CII is directed to multiple epitopes and conserved between mice and humans. We have previously mapped the antibody response to CII in a heterogeneous stock cohort of mice, with a strong association with the IgH locus. We positioned the genetic polymorphisms and determined the structural requirements controlling antibody recognition of one of the major CII epitopes. Polymorphisms at positions S31R and W33T of the associated variable heavy chain (VH) allele were identified and confirmed by gene sequencing. The Fab fragment binding the J1 epitope was crystallized, and site-directed mutagenesis confirmed the importance of those two variants for antigen recognition. Back mutation to germline sequence provided evidence for a preexisting recognition of the J1 epitope. These data demonstrate a genetic association of epitope-specific antibody responses with specific VH alleles, and it highlights the importance of germline-encoded antibodies in the pathogenesis of antibody-mediated autoimmune diseases.
Pharyngeal Narrowing and Closing Pressures in Patients with Obstructive Sleep Apnea (1993)

Based on previous studies, we hypothesized that the pharynx collapses at multiple sites in most patients with obstructive sleep apnea (OSA). The purpose of this study was to document, in a population of apneic subjects, the site(s) of narrowing and closing pressure of the hypotonic pharynx. We endoscopically examined the pharynx in 45 OSA patients during sleep while they received nasal continuous positive airway pressure (CPAP), which produces hypotonia of pharyngeal muscles. Intrapharyngeal images and pressures were obtained at the end of expiration during single-breath tests (SBT). The fractional narrowing (FN) of each pharyngeal segment (nasopharynx, oropharynx, and hypopharynx) was calculated as the relative change in area when nasal airway pressure was reduced from a pressure that held the pharynx fully distended to the pressure at which the airway closed. The frequency distribution of FN for the nasopharynx was skewed toward larger values, and the frequency was relatively evenly distributed for the oropharynx and hypopharynx. A site having FN greater than 0.75 was defined as a site of primary narrowing, and a site showing FN 0.25 to 0.75 was defined as a site of secondary narrowing. The nasopharynx was a site of primary narrowing in 80% of patients, and two or more sites of narrowing were commonly observed (82%). Four categories of combined narrowing were identified: (1) primary narrowing only at the nasopharynx (18%); (2) primary narrowing at the nasopharynx plus other sites of secondary narrowing (40%); (3) primary narrowing at the nasopharynx plus other sites of primary narrowing (22%); and (4) other patterns (20%).(ABSTRACT TRUNCATED AT 250 WORDS)
Viral infections of the gastrointestinal tract (1994)

Impact of Diarrheal Diseases Worldwide, Caryn Bern and Roger I. Glass Pathophysiology of Viral Diarrhea, Harley W. Moon Immunology of the Gastrointestinal Tract, Debra A. Tristram and Pearay L. Ogray Virus-Specific Cellular Immune Response to Intestinal Infection, Paul H. Offit Electron Microscopy for the Detection of Gastroenteritis Viruses, Frances W. Doane Natural History of Human Rotavirus Infections, Ruth F. Bishop The Rotavirus Proteins, Nora M. Mattion, Jean Cohen, and Mary K. Estes Assays for Detecting Human Rotavirus, Robert H. Yolken and James A. Wilde Animal Rotaviruses, Linda J. Saif, Blair I. Rosen, and Anil V. Parwani Non-Group A Rotaviruses, Janice C. Bridger Jennerian and Modified Jennerian Approach to Vaccination Against Rotavirus Diarrhea in Infants and Young Children: An Introduction, Albert Z. Kapikian Bovine Rotavirus-Based Rotavirus Vaccines in Humans, Timo Vesikari Rhesus Rotavirus-Based Human Rotavirus Vaccines and Observations on Selected Non-Jennerian Approaches to Rotavirus Vaccination, Albert Z. Kapikian Norwalk and Norwalk-like Viruses, Albert Z. Kapikian Enteric Adenoviruses, Goran Wadell, Annika Allard, Mats Johansson, Lennart Svensson, and Ingrid Uhnoo Caliciviruses, W. David Cubitt Astrovirus Gastroenteritis, John B. Kurtz The Toroviruses: Bovine (Breda Virus) and Equine (Berne Virus) and the Torovirus-like Agents of Humans and Animals, Gerald N. Woode Human Coronaviruses, E. Owen Caul Enteric Coronaviruses of Animals, Maurice Pensaert, Paul Callebaut, and Eric Cox Bacterial Diarrheas, James P. Nataro and Myron M. Levine Treatment of Diarrheal Diseases, R. Bradley Sack and G. H. Rabbani
Nonnative Capping Structure Initiates Helix Folding in an Annexin I Fragment. A 1H NMR Conformational Study (1995)

A 21-residue peptide, P1AQFD5ADELR10AAMKG15LGTDE20D, corresponding to the (helix A)-loop motif of the second repeat of human annexin I, was synthesized and studied by 2D proton NMR. The conformational properties of the peptide were characterized at different temperatures in pure aqueous solution and in a TFE/H2O (1:4 v/v) mixture. In pure aqueous solution, the peptide adopts a preferred conformation, comprising both elements of native and nonnative structures. A high alpha helix content is present in the DADELRA segment, which corresponds to an initiation site in the middle of the native alpha helix sequence. At the N-terminus flanking region, a particular nonnative folding is revealed by the J(NH-CH alpha) coupling constants and a set of unusual NOE connectivities which correspond to a helix interrupt at the first D residue. Addition of relatively small amount of TFE restores the native helix fold at the C-terminus but not at the N-terminus. On the contrary, the nonnative N-terminus structure is clearly stabilized by TFE. Our data indicate that this structure comprises (i) an Asp5-x-x-Glu8 N-terminal capping box, as recently named by Harper and Rose [Harper, E. T., & Rose, G. D. (1993) Biochemistry 32, 7605-7609], (ii) a (i,i + 3) Asp7-x-x-Arg10 salt bridge, and (iii) a hydrophobic cluster centered on Phe4 which mainly interacts with Leu9 but also with Ala2, Ala6, and Ala12 in a dynamic way. This structure is rather stable since it is still observed at 293 K in aqueous solution and 313 K in the presence of TFE. It constitutes a very potent initiation site of the alpha helix structure. This is, however, a nonnative structure involving highly conserved residues in the whole annexin family and thus may play an important role in the folding pathway as a transient "compacting helper".
CpG DNA increases primary malignant B cell expression of costimulatory molecules and target antigens (2001)

Multiple factors, including expression of costimulatory molecules, antigen-presenting molecules, and target antigens, likely impact the efficacy of antibody therapy and other approaches to the immunotherapy of B cell malignancy. Unmethylated CpG-dinucleotides in select base contexts ("CpG motifs") that resemble sequences found in bacterial DNA are potent immunostimulatory agents capable of inducing a complex immune response, including a strong B cell stimulus. We examined the effect of a potent human CpG oligonucleotide (CpG ODN 2006) on different types of primary human malignant B cells and reactive follicular hyperplasia. CpG oligodeoxynucleotide (CpG ODN), but not control (non-CpG ODN), increased the expression of costimulatory molecules (CD40, CD80, CD86, CD54) on malignant B cells without altering the phenotype of B cells obtained from reactive follicular hyperplasia. CpG ODN also enhanced expression of class I and class II MHC in most samples. CD20 expression was increased in response to CpG ODN, most notably in B-CLL and marginal zone lymphoma. An inverse correlation was found between baseline expression of CD20 and CD40 and their expression after exposure to CpG ODN, thus the most significant increase in expression of these molecules was found in those samples that had the lowest baseline levels. In conclusion, CpG ODN can lead to increasing expression of molecules involved in costimulation, antigen presentation, and as targets for antibody-based therapy and deserve further evaluation as potential immunotherapeutic agents for B cell malignancy.
RAVI, a proposed standard for the interchange of audio/visual interactive applications (1990)

RAVI (representation for audio/visual interactive applications), a set of specifications proposed as a standard for the interchange of audio/visual interactive applications (AVIs), is presented. RAVI was designed to meet the functional requirements of an AVI. RAVI consists of an interchange format and a set of functional operators (formulation). Protocols for a RAVI system are defined to allow communication between distributed subsystems. RAVI profiles allow compatible implementation of restricted sets of functionalities. As far as possible, the RAVI specifications use existing standards and are being submitted to ISO and CCITT for discussion. Products are commercially available, and a number of applications has already been developed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Peptide:glycosaminoglycan hybrid hydrogels as an injectable intervention for spinal disc degeneration (2016)

Degeneration of the spinal discs is a major cause of back pain. During the degeneration process, there is a loss of glycosaminoglycans (GAGs) from the proteoglycan-rich gel in the disc's nucleus, which adversely alters biomechanical performance. Current surgical treatments for back pain are highly invasive and have low success rates; there is an urgent need for minimally-invasive approaches that restore the physiological mechanics of the spine. Here we present an injectable peptide:GAG hydrogel that rapidly self-assembles <i>in situ</i> and restores the mechanics of denucleated intervertebral discs. It forms a gel with comparable mechanical properties to the native tissue within seconds to minutes depending on the peptide chosen. Unlike other biomaterials that have been proposed for this purpose, these hybrid hydrogels can be injected through a very narrow 25 G gauge needle, minimising damage to the surrounding soft tissue, and they mimic the ability of the natural tissue to draw in water by incorporating GAGs. Furthermore, the GAGs enhance the gelation kinetics and thermodynamic stability of peptide hydrogels, significantly reducing effusion of injected material from the intervertebral disc (GAG leakage of 8 ± 3% after 24 h when peptide present, compared to 39 ± 3% when no peptide present). In an <i>ex vivo</i> model, we demonstrate that the hydrogels can restore the compressive stiffness of denucleated bovine intervertebral discs. Compellingly, this novel biomaterial has the potential to transform the clinical treatment of back pain by resolving current surgical challenges, thus improving patient quality of life.