gebhart/patrepeval huggingface dataset:
Selection of scFv Phages on Intact Cells Under Low pH Conditions Leads to a Significant Loss of Insert-Free Phages (2001)

Display of functional antibody fragments on the surface of filamentous bacteriophages allows fast selection of specific phage antibodies against a variety of target antigens. However, enrichment of single chain variable fragment (scFv)-displaying phages is often hampered by the abundance of bacteriophages lacking antibody fragments. Moderate adhesive binding activities and production advantages of these "empty" phages results in their subsequent enrichment during selection on target cells. To date, very limited effort has been made to develop strategies removing nonspecific binding phages during the selection processes. To efficiently reduce insert-free phages when panning on intact cells, we increased the washing stringency by lowering the pH of the buffer with citric acid. Under standard washing procedures (pH 7.4), only approximately 73% of recovered phages were insert-free after three rounds of selection. Using stringent washing procedures (pH 5.0), approximately 12% of recovered phages contained no scFv. Using this protocol, we have cloned an antibody fragment from a mouse/human hybridoma cell line directed against the disialoganglioside GD2. This study confirms that selection of phage antibodies on cells is efficiently enhanced by assays augmenting the stringency to remove nonspecific binding phages.
In situ hybridization demonstration of poly‐adenylated RNA sequences in formalin‐fixed paraffin sections using a biotinylated oligonucleotide poly d(T) probe (1989)

An in situ hybridization technique has been developed for assessing poly(A)+ RNA preservation in routine pathology specimens. The method detects poly-adenylated RNA sequences in tissue sections using a biotinylated polydeoxythymidine (poly d(T)) probe. The probe was prepared from single-stranded 25-30 base oligo d(T) and was biotinylated using the enzyme terminal deoxynucleotide transferase with biotin-11-dUTP and dTTP in the ratio 1:4. The hybridization protocol uses varying concentrations of proteinase K to unmask mRNA sequences and the biotin-labelled hybrids are demonstrated after hybridization under standard conditions by the application of streptavidin and biotinylated alkaline phosphatase. Alkaline phosphatase was visualized using a Fast Red naphthol-capture method and the sections were counterstained with haematoxylin. The results have confirmed that the method is specific for poly(A)+ RNA and shows that poly(A)+ RNA can be demonstrated in routine formalin-fixed sections using non-radioactive techniques with retention of morphology. It also provides a means of optimizing the hybridization conditions for specific mRNA probes and produces a staining pattern demonstrating the relative level of poly(A)+ RNA per cell which may reveal new information about cell activity and tissue function.
Protective effect of Fluosol-DA in acute cerebral ischemia. (1981)

Fluosol-DA (Perfluorochemical Blood Substitutes) are small particle fluorocarbons suspended in an emulsion and have a high propensity for carrying oxygen and carbon dioxide. Fluosol-DA was investigated for the modification of acute focal cerebral ischemia and compared to mannitol. A total of 36 adult cats were divided into 3 groups and had transorbital microtourniquet ligation of the middle cerebral artery (MCA). Control animals were given intravenous isotonic saline. Animals in the experimental groups were treated with either intravenous Fluosol-DA or mannitol. All animals were nursed in an oxygen chamber and 4 cats from each group were sacrificed at 1, 3 and 6 hours after MCA occlusion. The results of macroscopic and histological examination of the brain suggested Fluosol-DA had a definite protective effect on acute focal cerebral ischemia which was in keeping with the observed neurological outcome. It is suggested that Fluosol-DA may support flow in the microcirculation and that the small particles of Fluosol-DA may be able to reach the area of ischemia via collaterals by decreasing blood viscosity, preventing narrowing of the arteriolar and capillary lumen and increasing the cerebral blood flow.
Synthesis of [F-18]-1-amino-3-fluorocyclobutane-1-carboxylic acid (FACBC): a PET tracer for tumor delineation (1999)

Fluorine-18 labeled 1-amino-3-fluorocyclobutane-1-carboxylic acid (FACBC), a new tumor-avid amino acid, was synthesized for positron emission tomography. [18F]FACBC was prepared with high specific activity by nucleophilic displacement with an overall radiochemical yield of 12% (EOB). Synthesis of the triflate precursor was accomplished in nine steps starting from the reaction of benzyl bromide with epichlorohydrin which gave 1-chloro-2-benzyloxy-3-brompropane. A key step involves conversion of 3-benzyloxy-cyclobutane-1,1-dicarboxylate diamide to a mixture of diastereomeric 2-benzyloxycyclobutane hydantoins. Copyright © 1999 John Wiley & Sons, Ltd.
Pyridine Is an Organocatalyst for the Reductive Ozonolysis of Alkenes (2012)

Whereas the cleavage of alkenes by ozone typically generates peroxide intermediates that must be decomposed in an accompanying step, ozonolysis in the presence of pyridine directly generates ketones or aldehydes through a process that neither consumes pyridine nor generates any detectable peroxides. The reaction is hypothesized to involve nucleophile-promoted fragmentation of carbonyl oxides via formation of zwitterionic peroxyacetals.
Formation of crystals of the insecticidal proteins of Bacillus thuringiensis subsp. aizawai IPL7 in Escherichia coli (1989)

Escherichia coli JM103 cells harboring expression plasmid pTB1 or pKC6 synthesized the 130- and 135-kilodalton insecticidal proteins, respectively, of Bacillus thuringiensis subsp. aizawai IPL7, and both products accumulated as cytoplasmic inclusion bodies. Amorphous inclusions which contained contaminating proteins, together with the corresponding insecticidal proteins, were formed in cultures at 37 degrees C, but bipyramidal crystals practically free of contaminants were observed at 30 degrees C. Although 9.8% of the amino acids were substituted between these two proteins, both protein crystals had the same shape as those of the parental B. thuringiensis strain, which produced both proteins.
Platelet transfusion therapy (2001)

Platelet transfusions were first introduced in the 1960s as a separate component for transfusion. Since then, the use of platelet transfusions has continued to increase, with current concerns focused on the appropriate use of this therapy for thrombocytopenic patients or those with platelet dysfunction.
Simple method for focusing x rays using tapered capillaries (1988)

A new method of focusing x rays is described using appropriately tapered capillaries. The x rays are incident on the inner surface of the capillary below the critical glancing angle and reflect due to total external reflection. By appropriately narrowing the capillary, the x rays can thus be focused in a broad band of energies. The theory of the effect and optimum taper is described. A measurement verifying the focusing capability of the method is presented. The method appears practical for focusing bending magnet synchrotron radiation around 8 keV down to a diameter of 10 mum from an initial dimension of 1-mm(2) incident cross section with an attenuation of the total energy of ~2, i.e., an increase in the intensity per unit area of 6.5 x 10(3). Greater focusing is possible with softer x rays and from undulator sources. The wide-ranging applicability of the technique is discussed.
Synthesis of a phenyl thio-β-d-galactopyranoside library from 1,5-difluoro-2,4-dinitrobenzene: discovery of efficient and selective monosaccharide inhibitors of galectin-7 (2005)

The galectins are a family of [small beta]-galactoside-binding proteins that have been implicated in cancer and inflammation processes. Herein, we report the synthesis of a library of 28 compounds that was tested for binding to galectins-1, -3, -7, -8N and -9N. An aromatic nucleophilic substitution reaction between 1,5-difluoro-2,4-dinitrobenzene and a galacto thiol gave 5-fluoro-2,4-dinitrophenyl 2,3,4,6-tetra-O-acetyl-1-thio-beta-D-galactopyranoside. This versatile intermediate was then modified in a two dimensional manner: either by further substitution of the second fluoride by amines or thiols, or by reduction of the nitro groups and acylation of the resulting amines, or both. Deacetylation then gave a library of aromatic beta-galactosides that showed variable inhibitory activity against the different galectins, as shown by screening with a fluorescence-polarisation assay. Particularly efficient inhibitors were found against galectin-7, while less impressive enhancements of inhibitor affinity over methyl beta-D-galactopyranoside were found for galectin-1, -3, -8N and -9N. The best inhibitors against galectin-7 showed significantly higher affinity (K(d) as low as 140 microM) than both beta-methyl galactoside (K(d) 4.8 mM) and the unsubstituted beta-phenyl thiogalactoside (non-inhibitory). The best inhibitors against galectin-7 were poor against the other galectins and thus have potential as structurally simple and selective tools for dissecting biological functions of galectin-7.
Number of Walls Controlled Synthesis of Millimeter-Long Vertically Aligned Brushlike Carbon Nanotubes (2007)

Millimeter (mm) long vertically aligned carbon nanotubes (CNTs) were grown by the catalyst assisted thermal chemical vapor deposition (CVD) technique. The continuous growth of CNTs as long as 7 mm was observed after 12 h of deposition by adjusting the growth parameters for making the catalyst active for a long time. The direct dependence of the number of walls of mm-long CNTs on the Fe catalyst thickness was observed. The successful syntheses of single-walled nanotubes (SWNTs), double-walled nanotubes (DWNTs), and multiwalled nanotubes (MWNTs) with high percentages (∼80%) were achieved by varying the catalyst layer thickness. The effect of Al2O3 buffer layer was found to be critical for this controlled synthesis, which has been discussed in detail. The possible growth mechanism is also discussed to better understand this phenomenon.
Induction of Endothelial Cell Chemotaxis by Sphingosine 1-Phosphate and Stabilization of Endothelial Monolayer Barrier Function by Lysophosphatidic Acid, Potential Mediators of Hematopoietic Angiogenesis (1999)

Angiogenesis, the formation of new blood vessels, is an important component of restoration of hematopoiesis after BMT, but the mediators involved in hematopoietic angiogenesis have not been identified. We examined the influence of the lipid growth factors, phosphatidic acid (PA), lysophosphatidic acid (LPA), and sphingosine 1-phosphate (S1P), on several angiogenic properties of endothelial cells, including migration and stabilization of vascular barrier integrity. In a previous study, PA was found to disrupt the permeability of established endothelial monolayers, an early event in the angiogenic response that liberates cells for subsequent mobilization. In the present study, both PA and LPA weakly induced the chemotactic migration of endothelial cells from an established monolayer. The chemotactic response induced by PA and LPA was similar in intensity to that observed with optimal levels of the known protein endothelial cell chemoattractants, basic fibroblast growth factor (bFGF) and vascular endothelial growth factor (VEGF). A markedly greater chemotactic response was effected by nanomolar concentrations of S1P, indicating that this platelet-derived factor plays an important role in a key aspect of angiogenesis, chemotactic migration of endothelial cells. The chemotactic response to S1P was completely inhibited by preincubation of endothelial cells with antisense oligonucleotides to the high-affinity S1P receptor, Edg-1. In addition, chemotaxis of endothelial cells to S1P was inhibited by preincubation of cells with specific inhibitors of tyrosine kinases, but inhibitors of phosphatidylinositol 3' kinase had little effect. Finally, LPA effectively stabilized endothelial monolayer barrier function, a late event in angiogenesis. Thus, the phospholipid growth factors, PA, S1P, and LPA, display divergent and potent effects on angiogenic properties of endothelial cells and angiogenic differentiation of endothelial cells potentially act in tandem to effectively induce neovascularization. These mediators may thus exert important roles in restoration of hematopoiesis, as they facilitate blood vessel formation at sites of transplanted stem cells, allowing the progeny of engrafted progenitors to move from marrow sinusoids to the peripheral vasculature.
Decreased Lung Fibroblast Growth Factor 18 and Elastin in Human Congenital Diaphragmatic Hernia and Animal Models (2007)

Impaired septation in CDH is associated with decreased FGF18 expression and elastic fiber deposition. Simultaneous correction of FGF18 and elastin defects by TO and vitamin A suggests that defective elastogenesis may result, at least partly, from FGF18 deficiency.
Surface-Enhanced Raman Scattering and Atomic Force Microscopy of Brass Electrodes in Sulfuric Acid Solution Containing Benzotriazole and Chloride Ion (1993)

Three different methods were used to roughen brass (Cu/Zn = 67/33) electrodes in 0.5 M H 2 SO 4 containing 1.0 mM benzotriazole (BTAH): (1) polarization at +0.05 V vs. saturated calomel for 5 min; (2) immersion in the above solution for six hours; and (3) oxidation-reduction cycling in the presence of chloride ion. The surfaces prepared by the first two methods exhibited surface-enhanced Raman scattering (SERS) spectra of the polymeric complex [Cu(I)BTA] n . The SERS spectrum obtained from electrodes prepared by the third method is very similar to that of [CU(I)C1BTAH] 4 . Examination of the electrodes by atomic force microscopy (AFM) showed that a large number of grain boundary sites are formed by the roughening processes. This effect is attributed to the loss of zinc, which occurs during corrosion of the mirror-like, polished brass electrode surface in the sulfuric acid solution.
Vaccination against typhoid fever: present status. (1994)

Typhoid fever remains an underestimated important health problem in many developing countries, causing more than 600,000 deaths annually in the world. Because of the reactogenicity of the parenteral, killed whole-cell vaccine, research has been oriented towards vaccination orally using live organisms and purified antigen. Live vaccine Ty21a, given by the oral route, has been extensively tested in several studies in developing countries. Its liquid formulation was the most effective, providing more than 60% protection after 7 years of follow-up. A Vi polysaccharide vaccine has been elaborated and provided more than 65% protection; after 3 years of follow-up the Vi antibody level was still at a high level. These two vaccines are therefore candidates for use in public health control programmes. Before such use, however, they need further evaluation for safety and protective efficacy when administered to the EPI-targeted age groups. The question of whether typhoid fever vaccines interfere with the response to simultaneously administered measles vaccine must also be studied. New live vaccines, given by the oral route in one dose, have been constructed through genetic engineering. The first results are promising, but they must be improved before use in a large-scale study. These strains could be used as live vector to deliver foreign antigens to the intestinal mucosa.
Characterization of a Lidless Form of the Molecular Chaperone DnaK (2001)

The C-terminal, polypeptide binding domain of the 70-kDa molecular chaperone DnaK is composed of a unique lidlike subdomain that appears to hinder steric access to the peptide binding site. We have expressed, purified, and characterized a lidless form of DnaK to test the influence of the lid on the ATPase activity, on interdomain communication, and on the kinetics of peptide binding. The principal findings are that loss of the lid creates an activated form of DnaK which is not equivalent to ATP-bound DnaK. For example, at 25 degrees C the NR peptide (NRLLLTG) dissociates from the ADP and ATP states of DnaK with observed off-rate constants of 0.001 and 4.8 s(-1), respectively. In contrast, for DnaK that lacks most of the helical lid, residues 518-638, the NR peptide dissociates with observed off-rate constants of 0.1 and 188 s(-1). These results show that the loss of the lid does not interfere with interdomain communication, that the beta-sandwich peptide binding domain can exist in two discrete conformations, and that the lid functions to increase the lifetime of a DnaK.peptide complex. We discuss several mechanisms to explain how the lid affects the lifetime of a DnaK.peptide complex.
Matching the crystallographic structure of ribosomal protein S7 to a three-dimensional model of the 16S ribosomal RNA (1998)

Two recently published but independently derived structures, namely the X-ray crystallographic structure of ribosomal protein S7 and the "binding pocket" for this protein in a three-dimensional model of the 16S rRNA, have been correlated with one another. The known rRNA-protein interactions for S7 include a minimum binding site, a number of footprint sites, and two RNA-protein crosslink sites on the 16S rRNA, all of which form a compact group in the published 16S rRNA model (despite the fact that these interactions were not used as primary modeling constraints in building that model). The amino acids in protein S7 that are involved in the two crosslinks to 16S rRNA have also been determined in previous studies, and here we have used these sites to orient the crystallographic structure of S7 relative to its rRNA binding pocket. Some minor alterations were made to the rRNA model to improve the fit. In the resulting structure, the principal positively charged surface of the protein is in contact with the 16S rRNA, and all of the RNA-protein interaction data are satisfied. The quality of the fit gives added confidence as to the validity of the 16S rRNA model. Protein S7 is furthermore known to be crosslinked both to P site-bound tRNA and to mRNA at positions upstream of the P site codon; the matched S7-16S rRNA structure makes a prediction as to the location of this crosslink site within the protein molecule.
A theory of shape by space carving (1999)

In this paper we consider the problem of computing the 3D shape of an unknown, arbitrarily-shaped scene from multiple photographs taken at known but arbitrarily-distributed viewpoints. By studying the equivalence class of all 3D shapes that reproduce the input photographs, we prove the existence of a special member of this class, the photo hull, that (1) can be computed directly from photographs of the scene, and (2) subsumes all other members of this class. We then give a provably-correct algorithm called Space Carving, for computing this shape and present experimental results on complex real-world scenes. The approach is designed to (1) build photorealistic shapes that accurately model scene appearance from a wide range of viewpoints, and (2) account for the complex interactions between occlusion, parallax, shading, and their effects on arbitrary views of a 3D scene.
Effect of Out-of-Hospital Pediatric Endotracheal Intubation on Survival and Neurological Outcome (2000)

These results indicate that the addition of out-of-hospital ETI to a paramedic scope of practice that already includes BVM did not improve survival or neurological outcome of pediatric patients treated in an urban EMS system.
The C1q Family of Proteins: Insights into the Emerging Non-Traditional Functions (2012)

Research conducted over the past 20 years have helped us unravel not only the hidden structural and functional subtleties of human C1q, but also has catapulted the molecule from a mere recognition unit of the classical pathway to a well-recognized molecular sensor of damage-modified self or non-self antigens. Thus, C1q is involved in a rapidly expanding list of pathological disorders - including autoimmunity, trophoblast migration, preeclampsia, and cancer. The results of two recent reports are provided to underscore the critical role C1q plays in health and disease. First is the observation by Singh et al. (2011) showing that pregnant C1q-/- mice recapitulate the key features of human preeclampsia that correlate with increased fetal death. Treatment of the C1q-/- mice with pravastatin restored trophoblast invasiveness, placental blood flow, and angiogenic balance and, thus, prevented the onset of preeclampsia. Second is the report by Hong et al. (2009) which showed that C1q can induce apoptosis of prostate cancer cells by activating the tumor suppressor molecule WW-domain containing oxydoreductase (WWOX or WOX1) and destabilizing cell adhesion. Downregulation of C1q on the other hand, enhanced prostate hyperplasia and cancer formation due to failure of WOX1 activation. C1q belongs to a family of structurally and functionally related TNF-α-like family of proteins that may have arisen from a common ancestral gene. Therefore C1q not only shares the diverse functions with the tumor necrosis factor family of proteins, but also explains why C1q has retained some of its ancestral "cytokine-like" activities. This review is intended to highlight some of the structural and functional aspects of C1q by underscoring the growing list of its non-traditional functions.
Dynamics of microglial activation: A confocal time-lapse analysis in hippocampal slices (2001)

The dynamics of microglial cell activation was studied in freshly prepared rat brain tissue slices. Microglia became activated in the tissue slices, as evidenced by their conversion from a ramified to amoeboid form within several hours in vitro. To define better the cytoarchitectural dynamics underlying microglial activation, we performed direct three-dimensional time-lapse confocal imaging of microglial cells in live brain slices. Microglia in tissue slices were stained with a fluorescent lectin conjugate, FITC-IB(4), and stacks of confocal optical sections through the tissue were collected repeatedly at intervals of 2-5 min for several hours at a time. Morphometric analysis of cells from time-lapse sequences revealed that ramified microglia progress to amoeboid macrophages through a stereotypical sequence of steps. First, in the withdrawal stage, the existing ramified branches of activating microglia do not actively extend or engulf other cells, but instead retract back (mean rate, 0.5-1.5 microm/min) and are completely resorbed into the cell body. Second, in the motility stage, a new set of dynamic protrusions, which can exhibit cycles of rapid extension and retraction (both up to 4 microm/min), abruptly emerges. Sometimes new processes begin to emerge even before the old branches are completely withdrawn. Third, in the locomotory stage, microglia begin translocating within the tissue (up to 118 microm/h) only after the new protrusions emerge. We conclude that the rapid conversion of resting ramified microglia to active amoeboid macrophages is accomplished not by converting quiescent branches to dynamic ones, but rather by replacing existing branches with an entirely new set of highly motile protrusions. This suggests that the ramified branches of resting microglia are normally incapable of rapid morphological dynamics necessary for activated microglial function. More generally, our time-lapse observations identify changes in the dynamic behavior of activating microglia and thereby help define distinct temporal and functional stages of activation for further investigation.