gebhart/patrepeval huggingface dataset:
Neutrophil dysfunction and increased susceptibility to infection (1995)

A critical evaluation of 3 years' experience using laboratory screening to detect neutrophil dysfunction is described. Neutrophil dysfunctions in patients with recurrent bacterial infections were investigated by using the following screening tests: (1) neutrophil chemotaxis towards N-formylmethionyl peptides (FMLP) and the complement fragment C5a; (2) neutrophil production of superoxide anions (O2-) in response to phorbol myristate acetate and opsonized zymosan particles; and (3) examination of May-Grünwald and myeloperoxidase cytochemical staining of peripheral blood smears. These tests were carried out in 100 patients suffering from infections and suspected of having altered neutrophil functional competence. A minority of patients was found to have well defined neutrophil dysfunction syndromes: chronic granulomatous disease (four cases), Chediak-Higashi disease (one case) and myeloperoxidase deficiency (one case). Of the remaining 94 patients, in whom infections localized to airways and/or skin predominated, 53 cases were found to have impaired chemotaxis (41 cases) or partial defects of the O2- production. Defects of chemotaxis toward FMLP and those towards both FLMP and C5a were the most frequent abnormalities. No defect was found in the other 41 patients. Moreover, impaired neutrophil chemotaxis was found in some patients with selective IgA deficiency (five cases) or immotile cilia syndrome (seven cases). The results suggest that (a) additional screening tests are required to ameliorate the efficiency of the diagnostic work-up of the patients suspected to have neutrophil dysfunction; and (b) further evaluation, also at the molecular level, should be considered at least in selected cases of non-classified neutrophil dysfunction in order to clarify diagnosis and plan rational therapeutic strategies.
DC-dielectrophoretic separation of microparticles using an oil droplet obstacle (2005)

A new dielectrophoretic particle separation method is demonstrated and examined in the following experimental study. Current electrodeless dielectrophoretic (DEP) separation techniques utilize insulating solid obstacles in a DC or low-frequency AC field, while this novel method employs an oil droplet acting as an insulating hurdle between two electrodes. When particles move in a non-uniform DC field locally formed by the droplet, they are exposed to a negative DEP force linearly dependent on their volume, which allows the particle separation by size. Since the size of the droplet can be dynamically changed, the electric field gradient, and hence DEP force, becomes easily controllable and adjustable to various separation parameters. By adjusting the droplet size, particles of three different diameter sizes, 1 microm, 5.7 microm and 15.7 microm, were successfully separated in a PDMS microfluidic chip, under applied field strength in the range from 80 V cm-1 to 240 V cm-1. A very effective separation was realized at the low field strength, since the electric field gradient was proved to be a more significant parameter for particle discrimination than the applied voltage. By utilizing low strength fields and adaptable field gradient, this method can also be applied to the separation of biological samples that are generally very sensitive to high electric potential.
A New, Effective Matrix Stimulation Diversion Technique (1995)

Summary This paper describes the theory and application of a new matrix stimulation diversion technique, maximized pressure differential and injection rates (MAPDIR), that uses injection rate as the key parameter to obtain sustained, planned bottomhole differential pressure, ∆p, levels. The technique, applicable wherever Darcy's law is valid (in sandstones and in unfractured or microfractured carbonatic reservoirs), favorably replaces diverting agents and extends to long intervals (&amp;gt; 100 ft) the main advantage provided by mechanical zone isolation for "selective stimulation," which is maximized ∆p. The use of slightly viscosified stimulation fluids can further extend the range of application and improve the economics by reducing both the amount of hydraulic power and the fluid volumes required for stimulation. A multilayered reservoir case illustrates the application of the MAPDIR technique. A new log-log plot of skin evolution vs. injected-acid volume shows significant damage removal trends and provides important information for matrix stimulation treatment optimization. Field experience includes the successful treatment of horizontal pay intervals of up to 460 ft. Because the real objective of diversion techniques is the effective removal of damage from the whole exposed pay, the meaning of "diversion" in this paper is not narrow (i.e., applicable only to diverting agents and ball sealers) but includes "placement" and "coverage" techniques, such as mechanical isolation, viscosified acids, and MAPDIR.
Solid‐phase synthesis of C‐terminal modified peptides (2003)

Solid-phase synthesis of biomolecules, of which peptides are the principal example, is well established. However, synthetic peptides containing modifications at the carboxy termini are often desired because of their potential therapeutic properties. As a result, there is a necessity for effective solid-phase strategies for the preparation of peptides with C-terminal end groups other than the usual carboxylic acid and carboxamide functionalities. The present article primarily reviews literature reports on methods for solid-phase synthesis of C-terminal modified peptides. In addition, general information about biological activities and/or synthetic applications of each individual class of peptide is also provided.
THE ENZYMOLOGY OF PROTEIN TRANSLOCATION ACROSS THE Escherichia coli PLASMA MEMBRANE (1991)

Converging physiological, genetic, and biochemical studies have established the salient features of preprotein translocation across the plasma membrane of Escherichia coli. Translocation is catalyzed by two proteins, a soluble chaperone and a membrane-bound translocase. SecB, the major chaperone for export, forms a complex with preproteins. Complex formation inhibits side-reactions such as aggregation and misfolding and aids preprotein binding to the membrane surface. Translocase consists of functionally linked peripheral and integral membrane protein domains. SecA protein, the peripheral membrane domain of translocase, is the primary receptor for the SecB/preprotein complex. SecA hydrolyzes ATP, promoting cycles of translocation, preprotein release, Δµ~H+-dependent translocation, and rebinding of the preprotein. The membrane-embedded domain of translocase is the SecY/E protein. It has, as subunits, the SeeY and SecE polypeptides. The SecY/E protein stabilizes and activates SecA and participates in binding it to the membrane. SecA recognizes the leader domain of preproteins, whereas both SecA and SecB recognize the mature domain. Many proteins translocate without requiring SecB, and some proteins do not need translocase to assemble into the plasma membrane. Translocation is usually followed by endoproteolytic cleavage by leader peptidase. The availability of virtually every pure protein and cloned gene involved in the translocation process makes E. coli the premier organism for the study of translocation mechanisms.
Functional genomics in Drosophila models of human disease (2012)

It is occasionally observed that common sporadic diseases have rare familial counterparts in which mutations at a single locus result in a similar disorder exhibiting simple Mendelian inheritance. Such an observation is often sufficient justification for the creation of a disease model in the fly. Whether the system is based on the over-expression of a toxic variant of a human protein or requires the loss of function of an orthologous fly gene, the consequent phenotypes can be used to understand pathogenesis through the discovery of genetic modifiers. Such genetic screening can be completed rapidly in the fly and in this review we outline how libraries of mutants are generated and how consequent changes in disease-related phenotypes are assessed. The bioinformatic approaches to processing the copious amounts of data so generated are also presented. The next phase of fly modelling will tackle the challenges of complex diseases in which many genes are associated with risk in the human. There is growing interest in the use of interactomics and epigenetics to provide proteome- and genome-scale descriptions of the regulatory dysfunction that results in disease.
Biologically and chemically optimized composites of carbonated apatite and polyglycolide as bone substitution materials (2000)

We report on the development and characterization of a new composite material consisting of amorphous carbonated apatite, Ca(5)(PO(4), CO(3))(3)(OH), and microstructured poly(hydroxyacetic acid), polyglycolide (PGA). This material is able to keep the pH of a surrounding solution within the physiological range (7.2-7.6). This was achieved by chemical fine-tuning of the counterplay between the acidic degradation of the polyester and the basic dissolution of calcium phosphate. Microporous samples with pore sizes of <1 microm and compact samples were prepared. The biological behavior was assayed in vitro by long-term osteoblast culture. Morphological and biochemical analyses of cell differentiation revealed excellent biocompatibility, leading to cell attachment, collagen and osteocalcin expression, and mineral deposition. This material could be of use as a biodegradable bone substitution material and as a scaffold for tissue engineering.
Inhibitory effects of interleukin-1 on growth hormone secretion in conscious male rats. (1995)

Although various pathophysiological effects of interleukin (IL) on the CRF-ACTH-adrenal axis and gonadotropin secretion have been studied extensively, the effects of IL on GH secretion still remain to be elucidated. We investigated the possible effects of IL on GH secretion in six groups of conscious rats. In four groups, IL was administered by continuous iv infusion and in the other two, by intracerebroventricular injection. Saline-treated rats served as controls for these groups. Sequential blood sampling was performed every 20 min in all groups, and the plasma GH concentration was determined by RIA. The expression of hypothalamic c-fos protein in a separate group was examined by immunohistochemistry. Continuous infusion of both IL-1 alpha and IL-1 beta (10 ng/min) significantly inhibited GH surges. The plasma IL-1 level was elevated to 2-3 ng/ml. Continuous iv infusion of IL-2 and IL-6 had no effect on GH secretion. The intracerebroventricular injection of both IL-1 alpha and IL-1 beta significantly inhibited GH surges, and the inhibitory effect was much greater for IL-1 beta than for IL-1 alpha. Continuous iv infusion of IL-1 beta markedly stimulated c-fos expression in specific hypothalamic nuclei, particularly in the paraventricular nucleus. These findings suggest that, in the rat, IL-1 inhibits GH secretion through its peripheral and central actions.
Deficiency of plasma protein S, protein C, or antithrombin III and arterial thrombosis. (1987)

Protein C and protein S are vitamin K-dependent coagulation factors that together act as an anticoagulant, and antithrombin III is a plasma protein that inhibits several activated factors in the coagulation cascade. Although deficiencies of any of these three proteins have been associated with deficiencies of these factors. We report one patient with a protein S deficiency, another with a protein C deficiency, and a third with an antithrombin III deficiency, each of whom who had extensive arterial thrombosis. We suggest that deficiencies of these proteins may constitute risk factors for arterial thrombosis.
Genetic Dissection of Dual Roles for the Transcription Factor six7 in Photoreceptor Development and Patterning in Zebrafish (2016)

The visual system of a particular species is highly adapted to convey detailed ecological and behavioral information essential for survival. The consequences of structural mutations of opsins upon spectral sensitivity and environmental adaptation have been studied in great detail, but lacking is knowledge of the potential influence of alterations in gene regulatory networks upon the diversity of cone subtypes and the variation in the ratio of rods and cones observed in numerous diurnal and nocturnal species. Exploiting photoreceptor patterning in cone-dominated zebrafish, we uncovered two independent mechanisms by which the sine oculis homeobox homolog 7 (six7) regulates photoreceptor development. In a genetic screen, we isolated the lots-of-rods-junior (ljrp23ahub) mutation that resulted in an increased number and uniform distribution of rods in otherwise normal appearing larvae. Sequence analysis, genome editing using TALENs and knockdown strategies confirm ljrp23ahub as a hypomorphic allele of six7, a teleost orthologue of six3, with known roles in forebrain patterning and expression of opsins. Based on the lack of predicted protein-coding changes and a deletion of a conserved element upstream of the transcription start site, a cis-regulatory mutation is proposed as the basis of the reduced expression of six7 in ljrp23ahub. Comparison of the phenotypes of the hypomorphic and knock-out alleles provides evidence of two independent roles in photoreceptor development. EdU and PH3 labeling show that the increase in rod number is associated with extended mitosis of photoreceptor progenitors, and TUNEL suggests that the lack of green-sensitive cones is the result of cell death of the cone precursor. These data add six7 to the small but growing list of essential genes for specification and patterning of photoreceptors in non-mammalian vertebrates, and highlight alterations in transcriptional regulation as a potential source of photoreceptor variation across species.
Thermal stability of Si/Si1−xGex/Si heterojunction bipolar transistor structures grown by limited reaction processing (1989)

The thermal stability of Si/500-Å-thick Si0.77Ge0.23 bilayers grown on Si by limited reaction processing is studied as a function of Si capping layer thickness. After annealing for 4 min at 850 °C, misfit dislocation spacings increase monotonically with cap thickness from 0.5 μm for an uncapped film to greater than 50 μm for a layer with a 500-Å-thick cap. Thus, an epitaxial Si cap of sufficient thickness prevents significant misfit dislocation formation during this anneal. Experimental observations are reported which indicate that the Si cap enhances thermal stability by inhibiting both dislocation nucleation and propagation. These results are very encouraging since they suggest that high-temperature processing of Si/Si1−xGex device structures may be possible without significant misfit dislocation formation.
Phospholipid polymer surfaces reduce bacteria and leukocyte adhesion under dynamic flow conditions (2005)

Persistence of infection can occur when the host immune response is compromised because of the presence of a foreign implant. Surface modification of biomaterials with phospholipid polymers may enhance biocompatibility and reduce incidence of infection by impeding bacterial and leukocyte adhesion. A rotating disk model, which generates shear stress from 0 to 18 dynes/cm(2), was used to characterize adhesion of neutrophils, monocytes, and bacteria in phosphate-buffered saline (PBS) or 25% human serum on polyethylene terephthalate surfaces coated with a phospholipid polymer, poly[omega-methacryloyloxyalkyl phosphorylcholine (MAPC)-co-n-butyl methacrylate (BMA)]. The material designated PMB30 contains a methylene chain length, (CH(2))(n), of n = 2, whereas PMHB30 contains a chain length of n = 6. In PBS, bacterial adhesion was shear stress dependent with the lowest bacterial density observed on PMB30. However, the presence of serum proteins eliminated shear stress and surface chemistry effects in addition to bacterial adhesion reduced to <10% of adhesion in PBS. Trends for leukocyte adhesion in serum demonstrated shear dependence with PMB30 exhibiting the lowest cell density throughout the range of shear stresses. In conclusion, modification of the polyethylene terephthalate surfaces with phospholipid polymers resulted in reduced bacterial and leukocyte adhesion. Furthermore, shortening the methylene chain length of the MAPC copolymer most effectively reduced adhesion.
Investigation of Electrostatic Interactions in Polyelectrolyte Multilayer Films:  Binding of Anionic Fluorescent Probes to Layers Assembled onto Colloids (1999)

The electrostatic binding of two anionic probe molecules, pyrenetetrasulfonic acid (4-PSA) and 6-carboxyfluorescein (6-CF), to poly(allylamine hydrochloride) (PAH)/poly(sodium 4-styrenesulfonate) (PSS) and poly(diallyldimethylammonium chloride) (PDADMAC)/PSS ultrathin multilayer films assembled onto polystyrene (PS) latex particles has been examined using fluorescence spectroscopy. At the probe concentrations studied, binding was observed only when the outermost layer was oppositely (positively) charged to the probe. The amount of probe bound was found to increase linearly with polyelectrolyte layer number up to about 11 layers (15 nm in thickness for the PAH/PSS films), with saturation binding occurring beyond 11 layers. The binding data reveal that a minimum of about 10−30% of the cationic charges of the polycations in the upper region of the multilayer films (where the probe binds) are not directly electrostatically utilized in the multilayer assembly process through ion-pair binding to oppositely charged sites on the polyanions. The removal of probe bound to multilayers of different thicknesses upon subsequent exposure to PSS has also been examined. Evidence that polyelectrolyte multilayer films are long-range electrostatically coupled systems is presented. The results obtained provide some insight into the role and extent of electrostatic interactions in polyelectrolyte multilayers.
Telling Humans and Computers Apart Automatically or How Lazy Cryptographers do AI (2002)

If you try to get a new email account at Yahoo, you’ll be asked to prove that you’re a human and not a computer. Why? Because a single computer program can get thousands of free email accounts per second. And that’s bad for Yahoo. But how do you prove to a computer that you’re a human? Proving that you’re a human to another human can be done using an idea from the 1950s: the Turing Test [11]. A human judge asks you a bunch of questions and decides, depending on your answers, whether he’s talking to a human or a computer. Proving that you’re a human to a computer is another matter. It requires a test (or a set of tests) that computers can grade, humans can pass, but paradoxically, computers can’t pass. In our lingo, it requires a captcha.
The complete amino acid sequence of the high molecular mass hemorrhagic protein HR1B isolated from the venom of Trimeresurus flavoviridis. (1990)

Hemorrhage is a common occurrence in a victim bitten by crotalid and viperid snakes, and hemorrhagic components in these various venoms have been isolated and characterized. Previously, we have shown that a low molecular weight hemorrhagic protein (HR2a, 202 amino acid residues) isolated from the venom of Trimeresurus flavoviridis is a member of a new subfamily of metalloproteinases. We now report the complete amino acid sequence of a high molecular mass hemorrhagic protein isolated from the same venom. This protein, HR1B, is a mosaic protein composed of 416 residues containing four asparagine-linked oligosaccharide chains. The amino-terminal half (residues 1-203) of HR1B contains a metalloproteinase domain, the sequence of which is 62% identical to that of HR2a and 52% identical to that of hemorrhagic toxin d isolated from Crotalus atrox venom. The most interesting finding is that the middle region (residues 204-300) of HR1B shows a striking similarity to disintegrins, Arg-Gly-Asp-containing platelet aggregation inhibitors, recently found in several viper venoms. Interestingly, however, this region of HR1B does not contain the Arg-Gly-Asp sequence which is known to be a putative binding site in the disintegrins for the platelet fibrinogen receptor, the glycoprotein IIb-IIIa complex. We also found that the carboxyl-terminal region (residues 213-336) of the middle part of HR1B shows 30% identity to residues 1543-1656 of von Willebrand factor and that the remaining region at the carboxyl-terminal end is unique and has a cysteine-rich sequence. These results suggest that the middle portion of HR1B, which shows structural similarities to the disintegrins and von Willebrand factor, may be important in synergistically stimulating hemorrhagic activity in the NH2-terminal metalloproteinase domain.
Deletion mapping of a retinal cone‐rod dystrophy: Assignment to 18q211 (1991)

Deletion of 18q211 was observed in a mentally retarded young man with electrophysiologically demonstrated cone-rod dystrophy, present since childhood. He had hypogonadism and a central postsynaptic hearing impairment. This is the first case of a chromosome deletion in a patient with a cone-rod dystrophy. Three patients with more distal deletions on chromosome 18 did not present retinal dystrophies. We suggest that one of the loci for cone-rod dystrophy may be located on chromosome 18 at q211-213. Reports of similar findings will be necessary for confirmation of this assumption.
A pilot study on the immunological effects of oral administration of donor major histocompatibility complex class II peptides in renal transplant recipients (2008)

Oral tolerance is an important physiological mechanism of immune hyporesponsiveness to dietary antigens and the commensal flora of the gastrointestinal tract. Feeding of alloantigens, therefore, has the potential to suppress undesirable immune responses after transplantation. To date, there are no published reports on the effects of such an approach in human transplant recipients. In the present pilot study, we demonstrate complete suppression of baseline indirect alloreactivity in patients with chronic renal allograft dysfunction following the oral feeding of low (0.5 mg/d) but not higher (1.0 and 5.0 mg/d) doses of donor major histocompatibility complex (MHC) class II peptides. The regimen was well tolerated with no evidence for sensitization to the donor antigen. Our results indicate that oral feeding of low dose donor MHC peptide may represent a safe and effective therapy to suppress indirect alloreactivity in renal transplant recipients with chronic allograft dysfunction and warrants further clinical investigation.
PET [11C]DASB Imaging of Serotonin Transporters in Patients with Alcoholism (2006)

Contrary to prior imaging reports using the nonselective ligand [(123)I]beta-CIT, we found no significant alterations of SERT density in alcoholic patients.
Color image quantization by pairwise clustering (2002)

This paper presents a new quantization method for color images. It uses a local error optimization strategy to generate near optimal quantization levels. The algorithm is simple to implement and produces results that are superior than those of other popular image quantization algorithms.