gebhart/patrepeval huggingface dataset:
Fibroblast Growth Factor 9 Secretion Is Mediated by a Non-cleaved Amino-terminal Signal Sequence (2000)

Fibroblast growth factors are a family of intercellular signaling molecules with multiple and varied roles in animal development. Most are exported from cells by means of a classical amino-terminal signal sequence that is cleaved from the mature protein during its passage through the secretory pathway. Fibroblast growth factor-9 (Fgf-9) does not contain a recognizable signal sequence, although it is efficiently secreted. In this study, we show that Fgf-9 enters the endoplasmic reticulum and traverses the Golgi complex in a similar manner to other constitutively secreted proteins. Deletion and point mutation analysis has revealed an atypical non-cleaved signal sequence within the amino-terminal region of Fgf-9. Moreover, the first 28 amino acids of Fgf-9 can function as an efficient non-cleaved signal peptide when appended to the amino terminus of green fluorescent protein.
Writing, supporting, and evaluating tripwire: a publically available security tool (1994)

Tripwire is an integrity checking program written for the Unix environment that gives system administrators the ability to monitor file systems for added, deleted, and modified files. First released in November of 1992, Tripwire has undergone several updates and is in current use at thousands of machines worldwide. This paper begins with a brief overview of what Tripwire does and how it works. We discuss how certain implementation decisions affected the course of Tripwire development. We also present other applications that have been found for Tripwire. These unanticipated uses guided the demands of some users, and we describe how we addressed some of these demands without compromising the ability of Tripwire to serve as a useful security tool. We also discuss the process of releasing, and then supporting, a widely available and widely used tool across the Internet, and how meeting users&amp;apos; high expectations affects this process. How these issues affected Tripwire, done as as an independent study by an undergraduate, is also discussed. Software tools that were used in developing and maintaining Tripwire are presented. Finally, we discuss problems that remain unresolved and some possible solutions.
Sensitivity of 3T3 cells to low serum concentration and the associated problems of serum withdrawal. (1994)

The sensitivity of cells to serum deprivation depends upon whether they are transformed. Most supplies of 3T3 cells are of this type and are considerably less sensitive than untransformed cells. In addition, the apparently simple manoeuvre of reducing serum levels has considerable effects on cell fragility, viability, growth rate and metabolism, which were found to be due to small changes in pH, substrate availability, cell density and other parameters, many of which cannot be attributed to the absence of growth factors from the medium. Supplementation of medium with bovine serum albumin (BSA) to compensate for low normal serum protein did not aid growth nor offset the disturbances caused by low serum levels themselves. Problems associated with the altered precursor availability for DNA, RNA and protein synthesis are also discussed.
Monoclonal antibodies : preparation and use of monoclonal antibodies and engineered antibody derivatives (2000)

ANTIBODIES AS LABORATORY AND THERAPEUTIC REAGENS. Introduction: antibody specifity and diversity. Antibody specificity: protein structure. The immunoglobulin constant region: form and functions. The cells that make antibody. The basis of antibody specificity and diversity: unique genetic mechanisms. Polyclonal antisera. Monoclonal antibodies. The major differences between monoclonal and polyclonal antibodies. Applications of antibodies in the laboratory. Therapeutic applications of antibodies. Improving on nature - antibody engineering. Replacing nature- antibodies from gene libraries. Conclusions. HYBRIDOMA TECHNOLOGY: MAKING MONOCLONAL ANTIBODIES. Introduction. Theoretical basis. Cell culture. Screening assay. Immunization. Myeloma cells. Fusion protocol. Post-fusion care. Cloning. Cryopreservation. Specificity and isotyping. Myoplasma. Large scale antibody production. Antibody purification. Storage and quality control. ANTIBODY ENGINEERING. Introduction. Choice of antibody designs to suit specific applications. Chimeric and humanized whole antibodies. Single domain antigen binding fragments. Engineering antibody fragments. Expression of antibody fragments. Purification of scFv antibody fragments. Phage display. APPLICATIONS OF MONOCLONAL ANTIBODIES TO THE STUDY OF MOLECULES IN SOLUTION. Introduction. ELISA (enzyme linked immuno-adsorbent assay). Protein epitope delineation. Assays of antibody-bound antigen. Immunoaffinity chromatography. Western blotting. Immunoprecipitation and radiolabel synthesis/processing. Immuno-organelle binding assays. APPLICATIONS OF MONOCLONAL ANTIBODIES IN MICROBIOLOGY. Introduction. Diagnosing infection. Viruses. Mycoplasma and chlamydia. Applications in bacteriology. Parasitic and fungal infections. APPLICATIONS OF MONOCLONAL ANTIBODIES TO THE STUDY OF CELLS AND TISSUES. Introduction. The complexity of cells: the human CD antigens illustrate the heterogeneity of cellular composition. Cell markers: identification and enumeration of specific cell types. Antibody-based cell separation. Antibody-based cell destruction or agglutination. Analysis of function. Tissue analysis.
Nitric oxide mediates glutamate-linked enhancement of cGMP levels in the cerebellum. (1989)

Nitric oxide, which mediates influences of numerous neurotransmitters and modulators on vascular smooth muscle and leukocytes, can be formed in the brain from arginine by an enzymatic activity that stoichiometrically generates citrulline. We show that glutamate and related amino acids, such as N-methyl-D-aspartate, markedly stimulate arginine--citrulline transformation in cerebellar slices stoichiometrically with enhancement of cGMP levels. N omega-monomethyl-L-arginine blocks the augmentation both of citrulline and cGMP with identical potencies. Arginine competitively reverses both effects of N omega-monomethyl-L-arginine with the same potencies. Hemoglobin, which complexes nitric oxide, prevents the stimulation by N-methyl-D-aspartate of cGMP levels, and superoxide dismutase, which elevates nitric oxide levels, increases cGMP formation. These data establish that nitric oxide mediates the stimulation by glutamate of cGMP formation.
Exact mass measurement on an electrospray ionization time‐of‐flight mass spectrometer: error distribution and selective averaging (2003)

An automated, accurate and reliable way of acquiring and processing flow injection data for exact mass measurement using a bench-top electrospray ionization time-of-flight (ESI-TOF) mass spectrometer is described. Using Visual Basic programs, individual scans were selected objectively with restrictions on ion counts per second for both the compound of interest and the mass reference peaks. The selected "good scans" were then subjected to two different data-processing schemes ("combine-then-center" and "center-then-average"), and the results were compared at various ion count limit settings. It was found that, in general, the average of mass values from individual scans is more accurate than the centroid mass value of the combined (same) scans. In order to acquire a large number of good scans in one injection (to increase the sampling size for statistically valid averaging), an on-line dilution chamber was added to slow down the typically rapid mass chromatographic peak decay in flow-injection analysis. This simple addition worked well in automation without the need for manual sample dilution. In addition, by dissolving the reference compound directly into the mobile phase, manual syringe filling can be eliminated. Twenty-seven samples were analyzed with the new acquisition and process routines in positive electrospray ionization mode. For the best method found, the percentage of samples with RMS error less than 5 ppm was 100% with repetitive injection data (6 injections per sample), and 95% with single injection data. Afterwards, 31 other test samples were run (with MW ranging from 310 to 3493 Da, 21 samples in ESI+ and 10 in ESI- mode) and processed with similar parameters and 100% of them were mass-calculated to RMS error less than 5 ppm also.
Tetrazolium-based assays for cellular viability: a critical examination of selected parameters affecting formazan production. (1991)

The hydrogen acceptor 3-(4,5-dimethylthiazol-2-yl)-2,5 diphenyltetrazolium bromide (MTT) is commonly utilized to estimate cellular viability in drug screening protocols. The present investigation was prompted, in part, by observations that reduction of MTT to its colored reaction product, MTT formazan, varied between cell lines and with culture age. A correlation was established between the D-glucose concentration of the culture medium at the time of assay and the production of MTT formazan for cell lines representing seven tumor histologies. A decrease in the concentration of D-glucose from culture medium was accompanied by a decrease in MTT specific activity (MTT formazan/microgram cell protein) for a number of cell lines. Cells which extensively metabolized D-glucose exhibited the greatest reduction in MTT specific activity. Further evidence that the D-glucose concentration of the culture medium played an important role in MTT reduction was provided by experiments which demonstrated that transfer of cells to a glucose-free medium (L-15) was accompanied by an immediate decrease in MTT reduction which was pH independent. These studies suggested that cellular transport and constant metabolism of glucose were required for maximum MTT reduction. Decreases in the cellular concentration of the reduced pyridine nucleotides NADH and NADPH were accompanied by concomitant decreases in MTT formazan production. MTT formazan varied significantly among cell lines in both the kinetics of its formation and the degree of saturability exhibited. Apparent IC50 values for Adriamycin varied, in a cell line-specific manner, with MTT exposure time. These results indicate that MTT specific activity is significantly influenced by a number of parameters and suggest that assay conditions should be established which minimize their effects.
Malondialdehyde and Antioxidant Enzyme Levels in the Aqueous Humor of Rabbits in Endotoxin-Induced Uveitis (2003)

Oxygen free radicals may be implicated as a mediator of inflammation in endotoxin-induced uveitis. The increase in free radicals in the aqueous humor may play a role in the pathogenesis of endotoxin-induced uveitis.
Presence of Variations in Ribosomal Protein L16 Corresponding to Susceptibility of Enterococci to Oligosaccharides (Avilamycin and Evernimicin) (2000)

Fragments (414 bp) of the gene-encoding ribosomal protein L16 from Enterococcus faecium and Enterococcus faecalis that were resistant and susceptible to the oligosaccharide antibiotics avilamycin and evernimicin (SCH 27899) were sequenced and compared. The susceptible E. faecalis and E. faecium isolates had sequences that were similar to those of the type strains. All resistant E. faecalis isolates contained the same base pair variation [CGT (Arg-56) --> CAT (His-56)]. The same variation and two additional variations [ATC (Ile-52) --> ACC (Thr-52) and ATC (Ile-52) --> AGC (Ser-52)] were found in the resistant E. faecium isolates. This study indicated that resistance to the oligosaccharides in enterococci is associated with variations in the ribosomal protein L16.
Oligodeoxynucleotides with Conjugated Dihydropyrroloindole Oligopeptides: Preparation and Hybridization Properties (1995)

Synthesis of a new class of conjugates between oligodeoxyribonucleotides (ODNs) and minor groove binders (MGBs) is described. The MGBs are analogs of the potent antibiotic CC-1065 and consist of repeating 1,2-dihydro-3H-pyrrolo[3,2-e]indole-7-carboxylate (DPI) subunits with N-3 carbamoyl or tert-butyloxycarbonyl groups (CDPI or BocDPI subunits, respectively). The ODN-MGB conjugates were obtained by postsynthetic modification of 5'- or 3'-amino-tailed ODNs with the 2,3,5,6-tetrafluorophenyl (TFP) esters of CDPI1-3 or BocDPI1-2 or by ODN synthesis using a CDPI3-modified controlled pore glass (CPG) support. The hybridization properties of MGB-tailed octathymidylates were determined; they varied with respect to the site of conjugation (3' or 5'), the nature of the linker, the length of the DPI oligopeptide, and the type of N-3 substitution. Optical melting studies showed that the linkage of CDPI1-3 residues to (dTp)8 significantly increased the stability of hybrids formed by the latter with poly(dA). The extent of stabilization increased with the length of the peptide. When CDPI3 was conjugated to either end of (dTp)8, the melting temperature (Tm) of the hybrid formed with poly(dA) was increased by 43-44 degrees C. Free CDPI3 stabilized the (dTp)8-poly(dA) hybrid by only 2 degrees C, thus demonstrating the importance of conjugation. (dTp)8-CDPI1-3 conjugates also formed stabilized duplexes with poly(rA). The extent of stabilization was half that observed with poly(dA).
Treatment of Autoimmune Disease by Intense Immunosuppressive Conditioning and Autologous Hematopoietic Stem Cell Transplantation (1998)

Multiple sclerosis, systemic lupus erythematosus, and rheumatoid arthritis are immune-mediated diseases that are responsive to suppression or modulation of the immune system. For patients with severe disease, immunosuppression may be intensified to the point of myelosuppression or hematopoietic ablation. Hematopoiesis and immunity may then be rapidly reconstituted by reinfusion of CD34(+) progenitor cells. In 10 patients with these autoimmune diseases, autologous hematopoietic stem cells were collected from bone marrow or mobilized from peripheral blood with either granulocyte colony-stimulating factor (G-CSF) or cyclophosphamide and G-CSF. Stem cells were enriched ex vivo using CD34(+) selection and reinfused after either myelosuppressive conditioning with cyclophosphamide (200 mg/kg), methylprednisolone (4 g) and antithymocyte globulin (ATG; 90 mg/kg) or myeloablative conditioning with total body irradiation (1,200 cGy), methylprednisolone (4 g), and cyclophosphamide (120 mg/kg). Six patients with multiple sclerosis, 2 with systemic lupus erythematosus, and 2 with rheumatoid arthritis have undergone hematopoietic stem cell transplantation. Mean time to engraftment of an absolute neutrophil count greater than 500/microL (0.5 x 10(9)/L) and a nontransfused platelet count greater than 20,000/microL (20 x 10(9)/L) occurred on day 10 and 14, respectively. Regimen-related nonhematopoietic toxicity was minimal. All patients improved and/or had stabilization of disease with a follow-up of 5 to 17 months (median, 11 months). We conclude that intense immunosuppressive conditioning and autologous T-cell-depleted hematopoietic transplantation was safely used to treat these 10 patients with severe autoimmune disease. Although durability of response is as yet unknown, all patients have demonstrated stabilization or improvement.
Drug-Induced Hypoglycemic Coma in 102 Diabetic Patients (1999)

Hypoglycemic coma is a serious and not an uncommon problem among elderly patients with diabetes mellitus and treated with insulin and/or oral hypoglycemic drugs. Risk factors contribute substantially to the morbidity and mortality of patients with drug-induced hypoglycemic coma. Enhanced therapeutic monitoring may be warranted when hypoglycemic drugs are administered to an elderly patient with the above predisposing factors and potentiating drugs for hypoglycemia.
The sound of touch (2013)

Recent work has shown that the body provides an interesting interaction platform. We propose a novel sensing technique based on transdermal low-frequency ultrasound propagation. This technique enables pressure-aware continuous touch sensing as well as arm-grasping hand gestures on the human body. We describe the phenomena we leverage as well as the system that produces ultrasound signals on one part of the body and measures this signal on another. The measured signal varies according to the measurement location, forming distinctive propagation profiles which are useful to infer on-body touch locations and on-body gestures. We also report on a series of experimental studies with 20 participants that characterize the signal, and show robust touch and gesture classification along the forearm.
Detection and characterization of ceramide-1-phosphate phosphatase activity in rat liver plasma membrane. (1993)

A calcium-dependent ceramide (Cer) kinase was recently detected in human leukemia (HL-60) cells (Kolesnick, R.N., and Hemer, M.R. (1990) J. Biol. Chem. 265, 18803-18808) where it may function in terminating the regulatory effects of Cer, and in synaptic vesicles (Bajjalieh, S. M., Martin, T. F. J., and Floor, E. (1989) J. Biol. Chem. 264, 14354-14360). We now demonstrate that the addition of both Cer-1-phosphate (Cer-1-P) and a short-acyl chain analog of Cer-1-P,N-hexanoylsphingosine-1-phosphate (C6-Cer-1-P) to cultured cells and a variety of subcellular fractions results in rapid degradation to Cer and C6-Cer, respectively. The Cer-1-P phosphatase activity is enriched in a rat liver plasma membrane fraction and appears to be distinct from the phosphatase that hydrolyzes phosphatidic acid (PA), PA phosphohydrolase, as shown by the difference in sensitivity of Cer-1-P and PA hydrolysis to propranolol, detergent, and heat treatment. Moreover, the Km of Cer-1-P hydrolysis is 10-fold lower than the Km of PA hydrolysis in plasma membrane. PA is a noncompetitive inhibitor of Cer-1-P hydrolysis, with an inhibition constant 1-1.5-fold higher than the Km of Cer-1-P hydrolysis. In contrast, Cer-1-P does not inhibit PA hydrolysis. Finally, we describe the synthesis of a novel analog of Cer-1-P which is not hydrolyzed in vitro and in vivo and is internalized in cultured cells by endocytosis. These results are discussed in relation to the possible roles of Cer-1-P in regulating intracellular levels of Cer.
Botulinum toxin A treatment for contouring of the lower leg (2006)

Botulinum toxin treatment for enlarged gastrocnemius muscles is a non-invasive alternative method for the improvement of calf contours.
Experimental investigation and finite element simulation of streaming in blood in cylindrical models (2002)

Conventional ultrasound imaging sometimes experiences difficulties of distinguishing between stagnant blood from tissue, and clotted from unclotted blood. This distinction may have high value in managing trauma patients with internal hemorrhage. Acoustic streaming is a physical phenomenon resulting from the momentum transfer from an ultrasound beam to the fluid medium due to attenuation. The presence of streaming in a sonographically indeterminate region can help detect a pool of unclotted blood from clots or other soft tissue. We report here a quantitative study of streaming in blood in a tubular model and a large open space. The streaming was detected with real-time color Doppler imaging. The experimental results were compared with the analytical solution and finite element simulation. This study suggests that streaming velocity will approach an asymptotic value in large hematomas.
Oxidative interactions of synthetic lung epithelial lining fluid with metal-containing particulate matter (2001)

Epidemiology studies show association of morbidity and mortality with exposure to ambient air particulate matter (PM). Metals present in PM may catalyze oxidation of important lipids and proteins present in the lining of the respiratory tract. The present study investigated the PM-induced oxidation of human bronchoalveolar lavage (BAL) fluid (BALF) and synthetic lung epithelial lining fluid (sELF) through the measurement of oxygen incorporation and antioxidant depletion assays. Residual oil fly ash (ROFA), an emission source PM that contains approximately 10% by weight of soluble transition metals, was added (0-200 microg/ml) to BALF or sELF and exposed to 20% (18)O(2) (24 degrees C, 4 h). Oxygen incorporation was quantified as excess (18)O in the dried samples after incubation. BALF and diluted sELF yielded similar results. Oxygen incorporation was increased by ROFA addition and was enhanced by ascorbic acid (AA) and mixtures of AA and glutathione (GSH). AA depletion, but not depletion of GSH or uric acid, occurred in parallel with oxygen incorporation. AA became inhibitory to oxygen incorporation when it was present in high enough concentrations that it was not depleted by ROFA. Physiological and higher concentrations of catalase, superoxide dismutase, and glutathione peroxidase had no effect on oxygen incorporation. Both protein and lipid were found to be targets for oxygen incorporation; however, lipid appeared to be necessary for protein oxygen incorporation to occur. Based on these findings, we predict that ROFA would initiate significant oxidation of lung lining fluids after in vivo exposure and that AA, GSH, and lipid concentrations of these fluids are important determinants of this oxidation.
A new genus and species of stenolophina (Coleoptera: Carabidae: Harpalini) from New Zealand (1996)

'Haplanister crypticus' gen. et sp. nov. is described from various localities in New Zealand, where it is now widespread. Notwithstanding its relatively recent discovery and its current abundance in certain pastoral districts, it is known also from natural habitats. It remains unclear whether the species is a native that is now proliferating in artificial environments or an introduced alien that has not yet been recognised in its country of origin.
Further results on spectrum blind sampling of 2D signals (2002)

We address the problem of sampling of 2D signals with sparse multi-band spectral structure. We show that the signal can be sampled at a fraction of the its Nyquist density determined by the occupancy of the signal in its frequency domain, but without explicit knowledge of its spectral structure. We find that such a signal can almost surely be reconstructed from its multi-coset samples provided that a universal pattern is used. Also, the scheme can attain the Landau-Nyquist minimum density asymptotically. The spectrum blind feature of our reconstruction scheme has potential applications in Fourier imaging. We apply the sampling scheme on a test image to demonstrate its performance.
Wnt5aandWnt5bexhibit distinct activities in coordinating chondrocyte proliferation and differentiation (2003)

Proper longitudinal growth of long bones relies on the regulation of specific spatial patterns of chondrocyte proliferation and differentiation. We have studied the roles of two members of the Wnt family, Wnt5a and Wnt5b in long bone development. We show that Wnt5a is required for longitudinal skeletal outgrowth and that both Wnt5a and Wnt5b regulate the transition between different chondrocyte zones independently of the Indian hedgehog (Ihh)/parathyroid hormone-related peptide (PTHrP) negative feedback loop. We find that important cell cycle regulators such as cyclin D1 and p130, a member of the retinoblastoma family, exhibit complimentary expression patterns that correlate with the distinct proliferation and differentiation states of chondrocyte zones. Furthermore, we show that Wnt5a and Wnt5b appear to coordinate chondrocyte proliferation and differentiation by differentially regulating cyclin D1 and p130 expression, as well as chondrocyte-specific Col2a1 expression. Our data indicate that Wnt5a and Wnt5b control the pace of transitions between different chondrocyte zones.