gebhart/patrepeval huggingface dataset:
apoB-100 has a pentapartite structure composed of three amphipathic alpha-helical domains alternating with two amphipathic beta-strand domains. Detection by the computer program LOCATE. (1994)

Due to the great length of apolipoprotein (apo) B-100, the localization of lipid-associating domains in this protein has been difficult. To address this question, we developed a computer program called Locate that searches amino acid sequences to identify potential amphipathic alpha-helixes and beta-strands by using sets of rules for helix and strand termination. A series of model chimeric protein test datasets were created by tandem linking of amino acid sequences of multiple proteins containing four different secondary structural motifs: motif A (exchangeable plasma apolipoproteins); motif G (globular alpha-helical proteins); motif C (coiled-coil alpha-helical proteins); and motif B (beta pleated-sheet proteins). These four test datasets, as well as randomly scrambled sequences of each dataset, were analyzed by Locate using increasingly stringent parameters. Using intermediately stringent parameters under which significant numbers of amphipathic helixes were found only in the unscrambled motif A, two dense clusters of putative lipid-associating amphipathic helixes were located precisely in the middle and at the C-terminal end of apoB-100 (a sparse cluster of class G* helixes is located at the N-terminus). The dense clusters are located between residues 2103 through 2560 and 4061 through 4338 and have densities of 2.4 and 2.2 amphipathic helixes per 100 residues, respectively; under these conditions, motif A has a density of 1.4 amphipathic helixes per 100 residues. These two domains correspond closely to the two major apoB-100 lipid-associated domains at residues 2100 through 2700 and 4100 through 4500 using the principle of releasability of tryptic peptides from trypsin-treated intact low-density lipoprotein. The classes of amphipathic helixes identified within these two putative lipid-associating domains are considerably more diverse than those found in the exchangeable plasma apolipoproteins. Interestingly, apoB-48 terminates at the N-terminal edge of the middle cluster. By using a similar strategy for analysis of amphipathic beta-strands, we discovered that the two gap regions between the three amphipathic helix clusters are highly enriched in putative amphipathic beta-strands, while the three amphipathic helical domains are essentially devoid of this putative lipid-associating motif. We propose, therefore, that apoB-100 has a pentapartite structure, NH2-alpha 1-beta 1-alpha 2-beta 2-alpha 3-COOH, with alpha 1 representing a globular domain.
EP-2104R: A Fibrin-Specific Gadolinium-Based MRI Contrast Agent for Detection of Thrombus (2008)

Thrombus (blood clot) is implicated in a number of life threatening diseases, e.g., heart attack, stroke, pulmonary embolism. EP-2104R is an MRI contrast agent designed to detect thrombus by binding to the protein fibrin, present in all thrombi. EP-2104R comprises an 11 amino acid peptide derivatized with 2 GdDOTA-like moieties at both the C- and N-terminus of the peptide (4 Gd in total). EP-2104R was synthesized by a mixture of solid phase and solution techniques. The La(III) analogue was characterized by and 1D and 2D NMR spectroscopy and was found to have the expected structure. EP-2104R was found to be significantly more inert to Gd(III) loss than commercial contrast agents. At the most extreme conditions tested (pH 3, 60 degrees C, 96 hrs), less than 10% of Gd was removed from EP-2104R by a challenge with a DTPA based ligand, while the commercial contrast agents equilibrated within minutes to hours. EP-2104R binds equally to two sites on human fibrin (Kd = 1.7 +/- 0.5 microM) and has a similar affinity to mouse, rat, rabbit, pig, and dog fibrin. EP-2104R has excellent specificity for fibrin over fibrinogen (over 100-fold) and for fibrin over serum albumin (over 1000-fold). The relaxivity of EP-2104R bound to fibrin at 37 degrees C and 1.4 T was 71.4 mM(-1) s(-1) per molecule of EP-2104R (17.4 per Gd), about 25 times higher than that of GdDOTA measured under the same conditions. Strong fibrin binding, fibrin selectivity, and high molecular relaxivity enable EP-2104R to detect blood clots in vivo.
Identifying the Mechanism of Biosensing with Carbon Nanotube Transistors (2007)

Carbon nanotube transistors have outstanding potential for electronic detection of biomolecules in solution. The physical mechanism underlying sensing however remains controversial, which hampers full exploitation of these promising nanosensors. Previously suggested mechanisms are electrostatic gating, changes in gate coupling, carrier mobility changes, and Schottky barrier effects. We argue that each mechanism has its characteristic effect on the liquid gate potential dependence of the device conductance. By studying both the electron and hole conduction, the sensing mechanisms can be unambiguously identified. From extensive protein-adsorption experiments on such devices, we find that electrostatic gating and Schottky barrier effects are the two relevant mechanisms, with electrostatic gating being most reproducible. If the contact region is passivated, sensing is shown to be dominated by electrostatic gating, which demonstrates that the sensitive part of a nanotube transistor is not limited to the contact region, as previously suggested. Such a layout provides a reliable platform for biosensing with nanotubes.
A Novel FMR1 PCR Method for the Routine Detection of Low Abundance Expanded Alleles and Full Mutations in Fragile X Syndrome (2010)

The novel PCR technology can accurately categorize the spectrum of FMR1 alleles, including alleles previously considered too large to amplify; reproducibly detect low abundance full mutation alleles; and correctly infer homozygosity in female samples, thus greatly reducing the need for sample reflexing to Southern blotting.
Bone Marrow-Derived Progenitor Cells Contribute to Experimental Choroidal Neovascularization (2003)

This study is the first to demonstrate that bone marrow-derived progenitor cells are a source of endothelial and smooth musclelike cells in CNV.
Chemical treatment enhances skipping of a mutated exon in the dystrophin gene (2011)

Duchenne muscular dystrophy (DMD) is a fatal muscle wasting disease caused by a loss of the dystrophin protein. Control of dystrophin mRNA splicing to convert severe DMD to a milder phenotype is attracting much attention. Here we report a dystrophinopathy patient who has a point mutation in exon 31 of the dystrophin gene. Although the mutation generates a stop codon, a small amount of internally deleted, but functional, dystrophin protein is produced in the patient cells. An analysis of the mRNA reveals that the mutation promotes exon skipping and restores the open reading frame of dystrophin. Presumably, the mutation disrupts an exonic splicing enhancer and creates an exonic splicing silencer. Therefore, we searched for small chemicals that enhance exon skipping, and found that TG003 promotes the skipping of exon 31 in the endogenous dystrophin gene in a dose-dependent manner and increases the production of the dystrophin protein in the patient's cells.
Fibrin Glue Alone and Skeletal Myoblasts in a Fibrin Scaffold Preserve Cardiac Function after Myocardial Infarction (2004)

Current efforts in cardiac tissue engineering center around the use of scaffolds that deliver cells to the epicardial surface. In this study, we examined the effects of fibrin glue as an injectable scaffold and wall support in ischemic myocardium. The left coronary artery of rats was occluded for 17 min, followed by reperfusion. Echocardiography was performed 8 days after infarction. One to 2 days later, either 0.5% bovine serum albumin (BSA) in phosphate-buffered saline, fibrin glue alone, skeletal myoblasts alone, or skeletal myoblasts in fibrin glue were injected into the ischemic left ventricle. Echocardiography was again performed 5 weeks after injection. The animals were then sacrificed and the hearts were fresh frozen and sectioned for histology and immunohistochemistry. Both the fractional shortening (FS) and infarct wall thickness of the BSA group decreased significantly after 5 weeks (p = 0.0005 and 0.02, respectively). In contrast, both measurements for the fibrin glue group, cells group, and cells in fibrin glue group did not change significantly (FS: p = 0.18, 0.89, and 0.19, respectively; wall thickness: p = 0.40, 0.44, 0.43, respectively). Fibrin glue is capable of preserving infarct wall thickness and cardiac function after a myocardial infarction in rats and may be useful as a biomaterial scaffold for myocardial cell transplantation.
The action of proteolytic enzymes on N,N-dimethyl proteins. Basis for a microassay for proteolytic enzymes. (1969)

N,N-Dimethyl proteins were prepared by reductive methylation of their amino groups with formaldehyde and NaBH4. Proteolysis of these alkylated proteins by trypsin, α-chymotrypsin, subtilisin, pepsin, and fungal protease was determined by direct measurement of the bonds split, with the use of trinitrobenzenesulfonic acid to determine directly the appearance of new terminal amino groups. The low blank values obtained with N,N-dimethyl proteins has resulted in a greatly increased sensitivity and accuracy not possible with unmodified proteins. On the basis of these studies, an assay of proteolytic activity is described, with N,N-dimethylcasein or N,N-dimethylhemoglobin as substrate, which is from 10 to several hundred times more sensitive than the standard caseinolytic assay of Kunitz.
Clinical and laboratory features of calcium-sensing receptor disorders: a systematic review (2004)

Mutations in the calcium-sensing receptor gene (CaSR) may result in disorders of calcium homeostasis manifesting as familial benign hypocalciuric hypercalcaemia (FBHH), neonatal severe hyperparathyroidism (NSHPT) or autosomal dominant hypocalcaemia with hypercalciuria (ADHH). FBHH may have a population prevalence as high as one in 16 000, and ADHH one in 70 000. NSHPT is very rare. The FBHH condition is usually asymptomatic. Parathyroidectomy does not result in normal serum calcium, and no active treatment is indicated. To differentiate FBHH from primary hyperparathyroidism (PHPT), a guideline which includes measurement of serum calcium, intact parathyroid hormone (PTH), magnesium and fasting urinary calcium excretion is proposed. Screening of family members for hypercalcaemia, and occasionally a search for mutations in the CaSR gene, may be required. The NSHPT condition may manifest with hypercalcaemia, (usually) very elevated serum PTH concentration, subperiosteal erosions and fractures. Milder cases may be managed medically, but respiratory failure, extreme hypercalcaemia and failure to thrive are indications for early parathyroidectomy. The ADHH condition may result in asymptomatic hypocalcaemia, but some affected family members have minor symptoms, and a minority experience seizures in infancy which can recur into adulthood. A significant proportion of cases previously reported as idiopathic hypoparathyroidism (IHP) may in fact be due to mutations in the CaSR gene. In a moderately hypocalcaemic patient with no other clearly discernible cause, an elevated urine calcium:creatinine ratio is suggestive of ADHH, as is the presence of a first-degree relative with hypocalcaemia. If treatment with vitamin D analogues is undertaken, serum and urine calcium should be monitored, advice which applies equally to ADHH and IHP.
Electrospray ionization mass spectrometry and ion mobility analysis of the 20S proteasome complex (2005)

Mass spectrometry and gas phase ion mobility [gas phase electrophoretic macromolecule analyzer (GEMMA)] with electrospray ionization were used to characterize the structure of the noncovalent 28-subunit 20S proteasome from Methanosarcina thermophila and rabbit. ESI-MS measurements with a quadrupole time-of-flight analyzer of the 192 kDa alpha7-ring and the intact 690 kDa alpha7beta7beta7alpha7 are consistent with their expected stoichiometries. Collisionally activated dissociation of the 20S gas phase complex yields loss of individual alpha-subunits only, and it is generally consistent with the known alpha7beta7beta7alpha7 architecture. The analysis of the binding of a reversible inhibitor to the 20S proteasome shows the expected stoichiometry of one inhibitor for each beta-subunit. Ion mobility measurements of the alpha7-ring and the alpha7beta7beta7alpha7 complex yield electrophoretic diameters of 10.9 and 15.1 nm, respectively; these dimensions are similar to those measured by crystallographic methods. Sequestration of multiple apo-myoglobin substrates by a lactacystin-inhibited 20S proteasome is demonstrated by GEMMA experiments. This study suggests that many elements of the gas phase structure of large protein complexes are preserved upon desolvation, and that methods such as mass spectrometry and ion mobility analysis can reveal structural details of the solution protein complex.
Human CD40‐ligand: molecular cloning, cellular distribution and regulation of expression by factors controlling IgE production (1993)

Here we report the cloning of the cDNA for human CD40-Ligand (CD40-L) from a CD4-positive T cell clone. The deduced amino acid sequence predicts a type II membrane protein of 261 amino acids. Northern blot and FACS analysis of PBMNC revealed that the human CD40-L can be detected on T cells and is absent from B cells and monocytes. The human CD40-L is expressed on both CD4- and CD8-positive T cells, (CD45R0+) and (CD45RA+) subsets. We observed that IL-4, an inducer of IgE production, upregulated CD40-L mRNA level while IFN gamma, an inhibitor of IgE synthesis, reduced the expression of CD40-L mRNA. These data suggest a the correlation between human CD40-L expression and IgE production.
Analytical model of magnetic nanoparticle transport and capture in the microvasculature (2006)

An analytical model is presented for predicting the transport and capture of therapeutic magnetic nanoparticles in the human microvasculature. The nanoparticles, with surface bound drug molecules, are injected into the vascular system upstream from malignant tissue, and are captured at the tumor site using a local applied magnetic field. The applied field is produced by a rare-earth cylindrical magnet positioned outside the body. An analytical expression is derived for predicting the trajectory of a particle as it flows through the microvasculature in proximity to the magnet. In addition, a scaling relation is developed that enables the prediction of the minimum particle radius required for particle capture. The theory takes into account the dominant magnetic and fluidic forces, which depend on the position and properties of the magnet, the size and magnetic properties of the nanoparticles, the dimensions of the microvessel, the hematocrit level of the blood, and the flow velocity. The model is used to study noninvasive drug targeting, and the analysis indicates that submicron particles can be directed to tumors that are several centimeters from the field source.
Inhibition of peptidyl-prolyl cis/trans isomerase activity by substrate analog structures: thioxo tetrapeptide-4-nitroanilides (1995)

The ubiquitous cyclophilins belong to peptidyl-prolyl cis/trans isomerases (PPIases; EC 5.2.1.8). They are able to catalyze the cis/trans isomerization about peptidyl-prolyl amide bonds. The mode of action of human cytosolic cyclophilin (Cyp18cy) has been studied on substrate analog tetrapeptide-4-nitroanilides containing the thioxo peptidyl-prolyl bond. Five peptides of the general structure Ala-Xaa-psi [CS-N]-Pro-Phe-NH-Np (Xaa = Gly, Ala, (S)-2-aminobutyric acid, Phe, and Leu) containing the thioxo peptidyl-prolyl bond were synthesized. The kcat values for the chymotryptic cleavage of 4-nitroanilide bond of the thioxo tetrapeptide-4-nitroanilides ranged from 1.7 to 9.0 s-1 and were sufficiently high to analyze the conformational equilibria by isomer-specific proteolysis. The rate constants of the cis/trans isomerization of the thioxo peptidyl-prolyl bond were found to be 25-100-fold lower due to the O/S substitution. Cyp18cy binds both thioxo peptides and oxo peptides in similar manner in the active center but cannot utilize the sulfur analogs as substrates. Instead, competitive inhibition occurs, which was further characterized for Ala-Gly-psi[CS-N]-Pro-Phe-NH-Np. The inhibition was nearly independent of the pH value in the range of pH 4.5-9, exhibiting apparent Ki values ranging from 200 to 600 microM. In comparison to Ala-Gly-trans-psi[CS-N]-Pro-Phe-NH-Np, the cis thioxo peptide Ala-Gly-cis-psi[CS-N]-Pro-Phe-NH-Np was found to possess an approximately 30-fold higher affinity for the active site of the enzyme. Thus, in the presence of stoichiometric amounts of Cyp18cy, the total amount of Ala-Leu-cis-psi[CS-N]-Pro-Phe-NH-Np in solution, detectable by isomer-specific proteolysis, was considerably enhanced.
Enzyme-Immunoassay: A Powerful Analytical Tool (1980)

This paper reviews various aspects of enzyme-immunoassay (EIA). Firstly it summarizes the principles of tests in which use is made of labelled antigen or antibody. Since these constitute essential reagents in EIA they are discussed next. Many assay principles call for a bound/free separation. The various methods to accomplish this are therefore briefly discussed. Very important are the characteristics of EIA: specificity, sensitivity, precision and practicability, the latter including reagent stability, performance requirements, assay times and automation potential. Finally, fields of application are listed and some more recent developments are mentioned.
Combination Antiplatelet Therapy with Aspirin and Clopidogrel: The Role of Antecedent and Concomitant Doses of Aspirin (2007)

Before addition of clopidogrel, aspirin 325 mg has a tendency to provide stronger platelet inhibition than aspirin 81 mg. However, when clopidogrel and aspirin are used in combination, the higher aspirin dose does not translate into superior antiplatelet action. Given that the existing body of evidence supports the comparable efficacy and, particularly, superior safety of lower versus higher doses of aspirin, aspirin 81 mg should be the dose used in combination with clopidogrel.
Ultrasonic tissue characterization of blood during stasis and thrombosis with a real-time linear-array backscatter imaging system (1993)

Quantitative integrated backscatter imaging of blood during stasis and coagulation is feasible using a clinically applicable real-time integrated backscatter imager. Ultrasonic tissue characterization of thrombi may provide data on thrombus age, composition, and stability, which may assist diagnosis and treatment.
Use of Zona Drilling for Safe and Effective Biopsy of Murine Oocytes and Embryos1 (1990)

With the mouse as a model, we have used zona drilling to devise procedures for safe removal of the first polar body or one or more blastomeres from cleaving embryos. These methods require minimal disruption of the zona pellucida and little or no direct contact between microtools and the materials to be biopsied. Of 175 eggs subjected to the polar body biopsy procedure, 1 was killed, and 165/174 survivors were fertilized (94.8%). For blastomere biopsy, embryos from the 2- to 16-cell stage were incubated in a chelating medium containing 100 mM sucrose for at least 30 min. The zonae were then drilled, and one or more blastomeres were "pushed" out through the hole by pressure exerted against the zona at some distance from the drilling site. In all 85 embryos biopsied, one or more additional intact blastomeres were successfully removed. Moreover, 83/84 biposied embryos that were subsequently cultured developed into blastocysts (98.8%). Although acid Tyrode's solution was used in this study, mechanical methods of zona opening were also effective. The data indicate that oocyte and embryo biopsy assisted by zona drilling is safe and does not appear to affect fertilization or development, and as such, it is applicable to genetic diagnostic procedures.
A Comparison of the Pathogenesis and Antigenicity of Infectious Canine Hepatitis Virus and the A26/61 Virus Strain (Toronto) (1970)

SUMMARY The antigenic characteristics of the Toronto A26/61 canine adenovirus (A26/61) and infectious canine hepatitis ( ich ) virus were compared by use of hemagglutination-inhibition ( hi ), serum-virus neutralization ( sn ), and complement-fixation ( cf ) tests. The 7 canine adenoviruses studied comprised 2 distinct homogeneous antigenic groups typified by classical ich virus and the A26/61 virus. The pathogenicity of an A26/61 virus strain (C955L) was compared to the pathogenicity of a virulent ich virus in young dogs. In contrast to classical infectious hepatitis produced by the ich virus, the C955L virus produced respiratory disease varying in severity from rhinitis to fatal bronchopneumonia. The respiratory disease encompassed both a kennel cough syndrome and a distemper-like condition. Infected dogs developed specific antibodies. The C955L virus was recovered for 5 to 10 days from throats and rectums of all dogs given the virus and for 1 to 4 days from heparinized plasma of 9 of 14 dogs. The A26/61 strain, C955L, appeared to differ from the ich strain in tissue tropism. Virus was recovered most frequently from tissues of the respiratory system and, to a lesser extent, from tissues of the digestive system from dogs given the C955L virus. Virus was infrequently isolated from kidneys, liver, or gallbladder. Pathologic changes were most remarkable in tissues of the respiratory system and consisted of a proliferative, interstitial pneumonia with necrotizing bronchitis and bronchiolitis. Intranuclear inclusion bodies were present in epithelial cells of the nasal and bronchial mucosa as well as alveolar septal cells.
Epitaxial Growth of SiC on Silicon on Insulator Substrates with Ultrathin Top Si Layer by Hot-Mesh Chemical Vapor Deposition (2008)

The epitaxial growth of SiC on silicon-on-insulator (SOI) substrates with an ultrathin (<10 nm) top Si layer by hot-mesh chemical vapor deposition (CVD) was investigated. This method utilizes heated tungsten wires arranged in a mesh, which promotes the high decomposition efficiency of H2 gas. Using the hot-mesh CVD method, SiC epitaxial films were successfully grown on SOI substrates without voids being formed, which are formed readily in thin (<100 nm) top Si layers at temperatures above 800 °C. Some micropatterns for micro-electro-mechanical systems were fabricated on SiC on insulator (SiCOI) structure substrates by reactive ion etching and wet etching.
Polymer-Based Therapeutics (2009)

Polymeric materials have been applied in therapeutic applications, such as drug delivery and tissue regeneration, for decades owing to their biocompatibility and suitable mechanical properties. In addition, select polymer-drug conjugates have been used as bioactive pharmaceuticals owing to their increased drug efficacy, solubility, and target specificity compared with small-molecule drugs. Increased synthetic control of polymer properties has permitted the production of polymer assemblies for the targeted and controlled delivery of drugs, and polymeric sequestrants take advantage of their lack of solubility for the sequestration of target molecules in vivo. In more recent studies reviewed in greater detail here, the properties of polymers that distinguish them from small-molecule drugs, such as their high molecular weight and their ability to display multiple pendant moieties, have been specifically exploited for activating cellular targets or inhibiting the binding of pathogens. The elucidation of relevant structure-function relationships in investigations of this kind has relied on the combination of living polymerization methods with chemical conjugation methods, and protein engineering methods have shown increasing potential in the manipulation of architectural features of such polymer therapeutics. Garnering a detailed understanding of the various mechanisms by which multivalent polymers engage biological targets is certain to expand the role of polymers as therapeutics, by enabling highly specific activities of designed polymers in the biological environment.