gebhart/patrepeval huggingface dataset:
Anopheles stephensi and Toxorhynchites amboinensis: Aseptic Rearing of Mosquito Larvae on Cultured Cells (1982)

Aseptic larvae of Anopheles stephensi and Toxorhynchites amboinensis were reared on a continuous cell line (RU TAE 12 V) from the mosquito, T. amboinensis, that grew in suspension as multicellular vesicles. Surface-sterilized eggs were hatched in a 24-well plate containing 0.2 ml of Leibovitz's L-15 medium per well and incubated in a humidified atmosphere. Toxorhynchites amboinensis eggs of 36 hr or older were placed singly to assure hatching and avoid cannibalism. Hatching rates were over 80%. All larval instars were maintained in L-15 medium at 28 C with a 12-hr photoperiod. Anopheles stephensi larvae were reared in 25-cm2 tissue culture flasks containing 10 ml of L-15 medium with 30 to 50 first and second instar larvae or 10 third and fourth instar larvae per flask. Toxorhynchites amboinensis larvae remained in the 24-well plate in 1.5 ml of medium through the second instar; third instar larvae were kept in 12-well plates (3 ml of medium per well) and transferred to 25-cm2 flasks (10 ml per flask) when they reached the fourth instar. First and second instar A. stephensi larvae were fed cultured cells once, and third or fourth instar larvae twice a day. Toxorhynchites amboinensis larvae were fed vesicles once during the first 4 days after hatching, and every 1 or 2 days thereafter. Each A. stephensi larva consumed approximately 2 X 10(6) cells, and T. amboinensis larvae 10 times more cells before pupating. Anopheles stephensi pupated after 7 to 8 days and adults emerged during days 9 to 11. Pupation in T. amboinensis began on day 21 after hatching and adults emerged 5 days later. Cell lines isolated from A. stephensi larvae or embryos of the ticks Rhipicephalus sanguineus and Anocentor (Dermacentor) nitens supported only limited growth of A. stephensi larvae. Defibrinated hamster (Mesocricetus auratus) blood, though readily ingested, did not support the growth of A. stephensi whereas larvae reared on blood cells plus T. amboinensis cells showed limited growth.
Interleukin‐8 secreted by endothelial cells induces Chemotaxis of melanoma cells through the chemokine receptor CXCR1 (2003)

There is increasing evidence that both cell adhesion molecules and soluble factors are involved in tumor metastasis. We have found that endothelial cells secrete chemoattractants that can induce melanoma cell chemotaxis. Protein separation on an ion-exchange column shows the association of IL-8 with fractions that contain the chemoattractant activity. This activity is completely lost from the conditioned medium after immunoprecipitation with anti-IL-8 antibodies, indicating that IL-8 is the major melanoma chemoattractant secreted by endothelial cells. IL-877, the predominant endothelial IL-8 isoform that contains 77 amino acids, is found to be twice as potent as the more common 72-amino acid isoform IL-872. Antibody inhibition studies indicate that the chemotactic response of melanoma cells is mediated by the CXC-chemokine receptor CXCR1 and not by the more promiscuous CXCR2. When stimulated by tumor necrosis factor alpha, the nonresponsive WM35 melanoma cells synthesize a higher level of CXCR1 and become chemotactic toward interleukin (IL)-8. Pretreatment of cells with pertussis toxin nullifies their chemotactic response, suggesting the involvement of G proteins. Antibodies against either IL-8 or CXCR1 inhibit melanoma transendothelial migration in a coculture assay by 30%. These results are consistent with a role for IL-8-induced chemotaxis in the transendothelial migration of melanoma cells.
The Effect of Boundary Selection on the Stability and Folding of the Third Fibronectin Type III Domain from Human Tenascin (1998)

Correct selection of domain boundaries is critical for structural analysis of single domains from multimodular proteins. Folding and stability studies of the third fibronectin type III domain from human tenascin (TNfn31-90) have shown that it is moderately stable (Delta G(D-N)(H2O) approximately 5 kcal mol-1) and folds with two-state kinetics. In an attempt to stabilize the protein, five domains were constructed with different combinations of extensions to the N- and C-termini. Thermal denaturation studies show that a specific two amino acid (Gly-Leu) extension at the C-terminus is primarily responsible for a significant increase in stability. The Delta Delta G(D-N)(H2O) of the Gly-Leu extension (TNfn3(1-92)) is 2.7 +/- 0.3 kcal mol-1. Refolding kinetics do not differ significantly, but unfolding is slowed 40-fold. Mutation of leucine 92 to alanine does not affect stability, indicating that the stability of the extension does not come from the packing of the leucine side chain. Hydrogen exchange data suggest that the extension adds new hydrogen bonds and strengthens existing hydrogen bonds in the C-terminal interaction with the A-B and E-F loops. Removal of a very small number of hydrogen bonds substantially increases the unfolding rate, a phenomenon which may be important in stress-relaxation of FNIII-containing muscle proteins such as titin. These experiments demonstrate the importance of a small number of additional long-range interactions in the overall formation of a compact independently folding beta-sheet module.
A Correlative Study of the Geometry and Anatomy of the Distal Femur (1990)

Sixteen knees were examined roentgenographically in the lateral plane. Ten knees were examined from autopsy subjects. The distal articular femur may be represented by three circular surfaces: (1) the floor of the patellar groove (articulating with the patella from 10 degrees to 100 degrees), (2) the posterior femoral condyles (articulating with the tibia from 10 degrees to 150 degrees), and (3) the distal condyles (articulating with the tibia from 0 degrees to 10 degrees). The radii of these surfaces, their angular arcs, and the distances between their centers varied with the size of the femur but fell within a narrow range. The radii of the patellar groove and the posterior femoral condyles averaged 24 mm and 21 mm, and the average angle subtended by these arcs was 90 degrees and 140 degrees, respectively. The average distance between the centers of these two circles was 20 mm. The femoral attachment of the synovial and patellar retinacular reflections was found in the area of the center of the patellar groove circle. The femoral attachments of the medial collateral and posterior cruciate ligaments and of the lateral collateral and anterior cruciate ligaments were found to be in the area of the center of the circle of the medial and lateral posterior femoral condylar circles, respectively.
Measurement of phase fluctuations on millimetric radiowave propagation (1971)

A method is described for measuring fluctuations in the phase of arrival of an 8 mm e.m. wave after propagation along a 4 km path using a 1-way radio link. Results and practical limitations of the method are given, together with the statistical assumptions made.
Involvement of Fis protein in replication of the Escherichia coli chromosome (1992)

We report evidence indicating that Fis protein plays a role in initiation of replication at oriC in vivo. At high temperatures, fis null mutants form filamentous cells, show aberrant nucleoid segregation, and are unable to form single colonies. DNA synthesis is inhibited in these fis mutant strains following upshift to 44 degrees C. The pattern of DNA synthesis inhibition upon temperature upshift and the requirement for RNA synthesis, but not protein synthesis, for resumed DNA synthesis upon downshift to 32 degrees C indicate that synthesis is affected in the initiation phase. fis mutations act synergistically with gyrB alleles known to affect initiation. oriC-dependent plasmids are poorly established and maintained in fis mutant strains. Finally, purified Fis protein interacts in vitro with sites in oriC. These interactions could be involved in mediating the effect of Fis on DNA synthesis in vivo.
Proteomics reveals multiple routes to the osteogenic phenotype in mesenchymal stem cells (2007)

The differences between the proteomic profiles of OS-stimulated hMSC and ECM-hMSC characterize different transitional phenotypes en route to becoming osteoblasts. This conclusion is arrived at via a three-mode tensor analysis validated using hMSC plated on laminin-5.
The Development of Gene Therapy for the Treatment of Cancer (1993)

Attempts at gene therapy for cancer are underway and have opened new possibilities for the development of cancer treatments.
Holey silicon as an efficient thermoelectric material (2010)

This work investigated the thermoelectric properties of thin silicon membranes that have been decorated with high density of nanoscopic holes. These "holey silicon" (HS) structures were fabricated by either nanosphere or block-copolymer lithography, both of which are scalable for practical device application. By reducing the pitch of the hexagonal holey pattern down to 55 nm with 35% porosity, the thermal conductivity of HS is consistently reduced by 2 orders of magnitude and approaches the amorphous limit. With a ZT value of ∼0.4 at room temperature, the thermoelectric performance of HS is comparable with the best value recorded in silicon nanowire system. © 2010 American Chemical Society.
Osmoprotectants in Halomonas elongata: high-affinity betaine transport system and choline-betaine pathway (1996)

The osmoregulatory pathways of the moderately halophilic bacterium Halomonas elongata DSM 3043 have been investigated. This strain grew optimally at 1.5 to 2 M NaCl in M63 glucose-defined medium. It required at least 0.5 M NaCl for growth, which is a higher concentration than that exhibited by the H. elongata type strain ATCC 33173. Externally provided betaine, choline, or choline-O-sulfate (but not proline, ectoine, or proline betaine) enhanced the growth of H. elongata on 3 M NaCl-glucose-M63 plates, demonstrating the utilization of these compounds as osmoprotectants. Moreover, betaine and choline stimulated the growth of H. elongata DSM 3043 over the entire range of salinity, although betaine was more effective than choline at salinities below and above the optimum. We found that H. elongata DSM 3043 has at least one high-affinity transport system for betaine (K(m) = 3.06 microM and Vmax = 9.96 nmol of betaine min(-1) mg of protein(-1)). Competition assays demonstrated that proline betaine and ectoine, but not proline, choline, or choline-O-sulfate, are also transported by the betaine permease. Finally, thin-layer chromatography and 13C-nuclear magnetic resonance analysis showed that exogenous choline was taken up and transformed to betaine by H. elongata, demonstrating the existence of a choline-glycine betaine pathway in this moderately halophilic bacterium.
In vivo spectrophotometric evaluation of skin barrier recovery after topical application of soybean phytosterols. (2008)

The skin's uppermost thin layer, stratum corneum, plays a crucial role in protecting the body against unwanted influences from the environment. Disruption of the stratum corneum, by tape stripping or chemical injury, results in epidermal recovery of the skin barrier. Soy phytosterols are widely used in the cosmetic field as active ingredients in creams and lipsticks. Furthermore, they deserve an important place among nutracosmeceuticals; in fact, after their absorption from the diet they are transferred from the plasma to the skin, playing an important role in the constitution of skin surface lipids. The aim of the present work was to study the effect of the topical application of soybean phytosterols on skin barrier recovery in human volunteers using the extent of methyl nicotinate (MN)-induced erythema in damaged skin as a parameter to evaluate the rate of stratum corneum recovery. MN was chosen as an erythematogenous substance for its capability to cause an erythema whose intensity and duration are proportional to the quantity of the substance that has entered the living epidermis over time. MN-induced erythema was monitored using reflectance spectrophotometry as a noninvasive instrumental technique. The results show clearly that soy phytosterols exert positive results on skin repair; in fact, three days after tape stripping, the sites treated with a formulation containing phytosterols showed an appreciable recovery of barrier function compared to those treated with a vehicle control without soy phytosterols.
Cathepsin B localizes to plasma membrane caveolae of differentiating myoblasts and is secreted in an active form at physiological pH (2006)

Our in vitro studies support a functional link between the induction of cathepsin B gene expression and the catabolic restructuring associated with myotube formation during myogenesis in vivo. We have tested two predictions that are basic to this hypothesis: (1) that active cathepsin B is localized to plasma membrane caveolae of fusing myoblasts; and (2) that active cathepsin B is secreted from fusing myoblasts at physiological pH. During differentiation, L6 rat myoblasts demonstrated a fusion-related increase in activity associated with the 25/26-kDa, fully processed, active form of cathepsin B. Immunocytochemical studies demonstrated a redistribution of lysosomal cathepsin B protein toward the membrane of fusing myoblasts, and a colocalization of cathepsin B with caveolin-3, the muscle-specific structural protein of membrane caveolae. Sucrose density fractionation and Western blot analysis demonstrated that an active form of cathepsin B localizes to caveolar fractions along with caveolin-3, annexin-VII, beta-dystroglycan and dystrophin. Finally, 'real-time' activity assays and Western blot analysis demonstrated that active cathepsin B is secreted from fusing myoblasts at physiological pH. Collectively, these studies support an association of active cathepsin B with plasma membrane caveolae and the secretion of active cathepsin B from differentiating myoblasts during myoblast fusion.
Enhanced hydroxyl radical generation by 2′‐methyl analog of MPTP: Suppression by clorgyline and deprenyl (1992)

Sodium salicylate was infused through a microdialysis probe placed in the striatum of anesthetized rats in order to assay the formation of hydroxyl radical (.OH) in the extracellular fluid in vivo. In addition to causing sustained dopamine release, intrastriatal infusion of the 2'-methyl analog of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (2'CH3-MPTP) increased the formation of 2,3-dihydroxybenzoic acid (2,3-DHBA), the nonenzymatic .OH adduct of salicylate in the brain dialysate. Inhibition of monoamine oxidase (MAO) by clorgyline and deprenyl completely blocked the formation of 2,3-DHBA and the sustained dopamine overflow induced by 2'-CH3-MPTP. The results indicate that the enhanced formation of cytotoxic .OH by 2'-CH3-MPTP is suppressed by MAO inhibitors. These data support the hypothesis that the protective effect of MAO inhibitors on the neurotoxicity induced by MPTP analogues may be due not only to the inhibition of MPTP metabolism by MAO but also the blockade of the formation of .OH free radicals. An enhanced generation of cytotoxic .OH free radicals in the striatum which in turn leads to oxidant damage may be relevant to the development of parkinsonism-like changes in animals produced by MPTP analogues.
Direct Ink Write 3D Printed Cellulose Nanofiber Aerogel Structures with Highly Deformable, Shape Recoverable, and Functionalizable Properties (2017)

Recent advancements in cellulosic aerogels have been extensive, but the lack of reproducible customization over the aerogel’s overall 3D structure has limited their ability to adapt to different application requirements. In this paper, high pressure homogenization and 2,2,6,6-tetramethyl-1-piperidinyloxy (TEMPO) modified cellulose nanofiber (T-CNF) was printed using direct-ink-write (DIW) into customizable 3D structures. After freeze-drying and cross-linking, highly deformable and shape recoverable T-CNF aerogel 3D structures were obtained. The 3D printed parts have a porosity of 98% and density of 26 mg/cm3. Due to their sustainability, biocompatibility, ultralight weight with high porosity, and deformability, the resultant aerogels have great potential for applications in thermal insulation, shock/vibration damping, and tissue engineering. In addition, the 3D printed T-CNF aerogels were templated to impart hydrophobicity and electromechanical properties. The resultant aerogels demonstrated potential for oil/water separation, and electronic related applications.
Activation of factor XII by dextran sulfate: the basis for an assay of factor XII (1983)

A system was developed for studying the activation of factor XII (Hageman factor) in the presence of dextran sulfate (DS). Salient features of the system included low ionic strength (0.08), low concentration of factor XII (approximately 1/10,000 that in normal plasma), and an excess of exogenous prekallikrein (PK). In this system, factor XII was rapidly converted to the 80,000 molecular weight (mol wt) form of factor XIIa (alpha-factor-XIIa). Once formed, the factor XIIa converted PK to kallikrein at a rate that was proportional to the amount of factor XII originally present in the incubation mixture. This system was used to construct a simple sensitive assay for factor XII in plasma and other biologic samples. The kallikrein produced was measured spectrophotometrically with the chromogenic substrate (H-D-Pro-Phe-Arg- p-nitroanilide (S-2302). This assay was shown to be independent of the high molecular weight kininogen and the PK content of the sample being analyzed. The measurements obtained were consistent with fundamental enzymologic principles and, if desired, could be processed with a simple calculator program to achieve linear standard curves. When applied to the quantitation of factor XII in plasma, the assay yielded values in close agreement with those determined by coagulant assay or by radial immunodiffusion.
Comparison of Protein Separations in Capillary Zone Electrophoresis and Capillary Isoelectric Focusing Interfacing with Electrospray Mass Spectrometry (1996)

On-line capillary zone electrophoresis/electrospray ionization mass spectrometry (CZE-ESMS) and capillary isoelectric focusing/electrospray ionization mass spectrometry (CIEF/ESMS) were employed for protein analysis. The separation mechanisms and the detection limits of CZE/ESMS and CIEF/ESMS were compared by using model proteins including cytochrome c (horse heart), ribonuclease A (bovine pancreas), myoglobin (horse heart), carbonic anhydrase I (human erythrocytes) and β-lactoglobulin A (bovine milk). The effect of a moving ionic boundary inside the electrophoresis capillary on the separation resolution of model proteins by CZE/ESMS and CIEF/ESMS is described. In CZE/ESMS, the formation of a moving ionic boundary due to the replacement of background electrolyte counterions with sheath liquid counterions can be eliminated by using a common counterion in both the background electrolyte and the sheath liquid. Additionally, the moving ionic boundary in CIEF/ESMS is minimized by combining cathodic mobilization with a gravity-induced hydrodynamic flow. The concentration detection limits of model proteins in a full-scan CIEF/ESMS analysis are in the region of 10-7 M, ∽20–50 times lower than that achievable using CZE/ESMS. Sample preconcentration taking place during the focusing step in CIEF is responsible for the improved detection limits.
Easy method to predict solvent accessibility from multiple protein sequence alignments (1998)

An easy and uncomplicated method to predict the solvent accessibility state of a site in a multiple protein sequence alignment is described. The approach is based on amino acid exchange and compositional preference matrices for each of three accessibility states: buried, exposed, and intermediate. Calculations utilized a modified version of the 3D―ali databank, a collection of multiple sequence alignments anchored through protein tertiary structural superpositions. The technique achieves the same accuracy as much more complex methods and thus provides such advantages as computational affordability, facile updating, and easily understood residue substitution patterns useful to biochemists involved in protein engineering, design, and structural prediction. The program is available from the authors; and, due to its simplicity, the algorithm can be readily implemented on any system. For a given alignment site, a hand calculation can yield a comparative prediction. Proteins 32:190–199, 1998. © 1998 Wiley-Liss, Inc.
Serological survey for antibodies reactive with Ehrlichia canis and E. chaffeensis in dogs from the Bloemfontein area, South Africa (1998)

Sera from 161 dogs in the Bloemfontein area in South Africa were tested for the presence of antibodies reactive with Ehrlichia canis and E. chaffeensis by indirect fluorescent antibody testing. Overall, 68 (42%) of the dogs had significant antibody titres (> or = 1/64) against E. canis and 61 (38%) had significant titres (> or = 1/64) against E. chaffeensis. Seven (11%) dogs had higher titres to E. chaffeensis than E. canis (1/2048 and 1/1024 (2 dogs); 1/1024 and 1/512 (2 dogs); 1/2048 and 1/512; 1/512 and 1/256 and 1/512 and < 1/64, respectively). The remaining seropositive dogs had equal (n = 26; 42%) or 2-(n = 17; 25%), 3-(n = 13; 2%) or 4-fold (n = 5; 7%) higher titres against E. canis. Dogs from economically depressed, high-density suburbs (60/112; 48%) had significantly higher prevalences of antibodies against E. canis than those from more affluent, low-density suburbs (8/49; 14%) (chi 2 = 19.38, p < 0.001). Higher titres to E. chaffeensis than E. canis were found in dogs from affluent, low-density suburbs (3/49) and in dogs from economically depressed, high-density suburbs (4/112).
Ultrafast Viscous Permeation of Organic Solvents Through Diamond-Like Carbon Nanosheets (2012)

Chemical, petrochemical, energy, and environment-related industries strongly require high-performance nanofiltration membranes applicable to organic solvents. To achieve high solvent permeability, filtration membranes must be as thin as possible, while retaining mechanical strength and solvent resistance. Here, we report on the preparation of ultrathin free-standing amorphous carbon membranes with Young's moduli of 90 to 170 gigapascals. The membranes can separate organic dyes at a rate three orders of magnitude greater than that of commercially available membranes. Permeation experiments revealed that the hard carbon layer has hydrophobic pores of ~1 nanometer, which allow the ultrafast viscous permeation of organic solvents through the membrane.
Toxicity of two carbamide peroxide products used in nightguard vital bleaching. (1993)

This study evaluated the effects of two generic classes of 10% carbamide-peroxide (CP) oxygenating agents (currently under clinical assessment for nightguard vital tooth bleaching) for lethality and genetic mutation after oral administration to mice, and for cellular cytotoxicity to mouse fibroblasts in vitro. The single dose LD50 values for a non-carbopol-containing CP (Gly-Oxide) and a carbopol-containing CP (Proxigel) in mice were found to be 143.8 mg/kg and 87.2 mg/kg, respectively. Genotoxicity, as measured by the Mouse Micronucleus test for mutagenicity, was negative for both 10% CP agents in comparison with positive and negative controls. Cytotoxicity as measured in the L929 fibroblast lysis assay resulted in 50% killing of L929 fibroblasts at 0.62 for the non-carbopol-containing CP and 1.88 mmol/L for the carbopol-containing CP. Both 10% CP agents were compared with seven widely-used dental products in the L929 fibroblast lysis assay and found to be no more toxic than these products.