gebhart/patrepeval huggingface dataset:
Virulence factors are released from Pseudomonas aeruginosa in association with membrane vesicles during normal growth and exposure to gentamicin: a novel mechanism of enzyme secretion (1995)

Pseudomonas aeruginosa blebs-off membrane vesicles (MVs) into culture medium during normal growth. Release of these vesicles increased approximately threefold after exposure of the organism to four times the MIC of gentamicin. Natural and gentamicin-induced membrane vesicles (n-MVs and g-MVs and g-MVs, respectively) were isolated by filtration and differential centrifugation, and several of their biological activities were characterized. Electron microscopy of both n-MVs and g-MVs revealed that they were spherical bilayer MVs with a diameter of 50 to 150 nm. Immunoelectron microscopy and Western blot (immunoblot) analysis of the vesicles demonstrated the presence of B-band lipopolysaccharide (LPS), with a slightly higher proportion of B-band LPS in g-MVs than in n-MVs. A-band LPS was occasionally detected in g-MVs but not in n-MVs. In addition to LPS, several enzymes, such as phospholipase C, protease, hemolysin, and alkaline phosphatase, which are known to contribute to the pathogenicity of Pseudomonas infections were found to be present in both vesicle types. Both types of vesicles contained DNA, with a significantly higher content in g-MVs. These vesicles could thus play an important role in genetic transformation and disease by serving as a transport vehicle for DNA and virulence factors and are presumably involved in septic shock.
Experimental comparison of binary joint transform correlators used for fingerprint identification (1996)

We compare the experimental performance of 12 variations
of the binary joint transform correlator (BJTC) when used for fingerprint
identification. Three hardware architectures were used: a single spatial
light modulator (SLM) BJTC, a BJTC using two input SLMs, and a chirpencoded
BJTC using two input SLMs. These correlators were implemented
on the same hardware setup with minor modifications. With each
hardware configuration, four binarization techniques were implemented:
global threshold, Fourier plane windowing, frame subtraction, and frame
subtraction followed by windowing. A set of 10 experiments was used to
characterize the output peak intensity, peak-to-noise ratio, and discrimination
ratio. The same set of experiments was run on each of the 12
correlator variants.
Blue Dextran: Influence on Chromatographic Profile and Immunoreactivity of Human Follicle-Stimulating Hormone (HFSH) (1975)

When FSH is chromatographed on G-100 Sephadex in the absence of Blue Dextran, it elutes as a single peak in the region of monomeric FSH. The addition of Blue Dextran causes a significant portion of FSH, iodinated or uniodinated, to elute in the region of the void volume. When standard curves for FSH are performed under identical conditions, with tracer 125I-FSH from the void volume, and from the FSH monomer region, maximal immunoreactivity was significantly greater for the Blue Dextran-associated tracer.
Pyruvate oxidase contributes to the aerobic growth efficiency of Escherichia coli (2001)

The metabolic importance of pyruvate oxidase (PoxB), which converts pyruvate directly to acetate and CO(2), was assessed using an isogenic set of genetically engineered strains of Escherichia coli. In a strain lacking the pyruvate dehydrogenase complex (PDHC), PoxB supported acetate-independent aerobic growth when the poxB gene was expressed constitutively or from the IPTG-inducible tac promoter. Using aerobic glucose-limited chemostat cultures of PDH-null strains, it was found that steady-states could be maintained at a low dilution rate (0.05 h(-1)) when PoxB is expressed from its natural promoter, but not at higher dilution rates (up to at least 0.25 h(-1)) unless expressed constitutively or from the tac promoter. The poor complementation of PDH-deficient strains by poxB plasmids was attributed to several factors including the stationary-phase-dependent regulation of the natural poxB promoter and deleterious effects of the multicopy plasmids. As a consequence of replacing the PDH complex by PoxB, the growth rate (mu(max)), growth yield (Y(max)) and the carbon conversion efficiency (flux to biomass) were lowered by 33%, 9-25% and 29-39% (respectively), indicating that more carbon has to be oxidized to CO(2) for energy generation. Extra energy is needed to convert PoxB-derived acetate to acetyl-CoA for further metabolism and enzyme analysis indicated that acetyl-CoA synthetase is induced for this purpose. In similar experiments with a PoxB-null strain it was shown that PoxB normally makes a significant contribution to the aerobic growth efficiency of E. coli. In glucose minimal medium, the respective growth rates (mu(max)), growth yields (Y(max)) and carbon conversion efficiencies were 16%, 14% and 24% lower than the parental values, and correspondingly more carbon was fluxed to CO(2) for energy generation. It was concluded that PoxB is used preferentially at low growth rates and that E. coli benefits from being able to convert pyruvate to acetyl-CoA by a seemingly wasteful route via acetate.
Inflammation markers and risk factors for recurrence in 35 patients with a posttraumatic chronic subdural hematoma: a prospective study (2004)

Brain trauma causes the onset of an inflammatory process within the dural border cell layer; high levels of inflammatory cytokines were significantly correlated with recurrence and layering CSDH. A prolonged postoperative antiinflammatory medicine given as prophylaxis may help prevent the recurrence of a CSDH.
Epithelial wound closure in the rabbit cornea. A biphasic process. (1986)

The rapid and complete repair of the corneal epithelium following ocular surgery or trauma is essential for the maintenance of normal visual acuity. In this study the authors examined epithelial wound healing in the rabbit after cells were mechanically removed leaving the basal lamina intact. The decrease in wound area (mm2/hr) was neither linear nor amenable to simple kinetic analysis. However, analysis of the data in terms of the decrease in wound radius (mm/hr) revealed a biphasic process consisting of an initial latent phase with no epithelial movement (5.5 +/- .3 hr), followed by a linear healing phase. The rate of epithelial movement in the linear healing phase was 64 +/- 2 microns/hr. Neither the latent phase nor the rate of epithelial migration during the healing phase was affected by variations in initial wound size. Ultrastructural studies demonstrated that during the latent phase there was an increased desquamation of surface cells as well as cellular and subcellular reorganization of the basal cells. At the end of the latent phase, the leading edge of the wound was composed of a single cell layer. The onset of epithelial migration coincided with the first ultrastructural observation of typical ruffled membranes and filopodia. This work demonstrates that the analysis of the decrease in wound radius provides a straightforward and accurate means to assess the kinetics and therapeutic modulation of epithelial wound healing.
Direct Observation of the p188 Mediated Membrane Sealing with Atomic Force Microscopy (2006)

Cite This Article Lee, R. C., Despa, F., Tang, X., Titushkin, I., Cho, M. (2006). Direct Observation of the p188 Mediated Membrane Sealing with Atomic Force Microscopy. Molecular & Cellular Biomechanics, 3(4), 185–186.
Microbial dysbiosis and colon carcinogenesis: could colon cancer be considered a bacteria-related disease? (2013)

Colorectal cancer (CRC) is posing an increasingly important burden on the health care system, with western countries seeing a growing incidence of the disease. Except for germline DNA mutations which have been attributed to less than 5% of patients, little is known about the main causes of CRC. However, environment factors such as food, lifestyle and medication are now suspected to have a major influence on inducing cancers. Today, exhaustive quantitative and qualitative evaluation of all environmental factors is not possible. Various environment-induced diseases have been characterized based on colon microflora, also called microbiota, analyses. Growing data have shown specific changes in microflora (i.e. dysbiosis) in the stools of patients with colon cancer or those adherent to the colonic mucosa. Thus, it appears that microbiota may be considered a platform offering host and environment interactions for studying CRCs. The hypothesis that colon cancer might be a bacteria-related disease is suggested and perspectives are discussed.
Forty Gb/s hybrid silicon Mach-Zehnder modulator with low chirp (2011)

We demonstrate a hybrid silicon modulator operating up to 40 Gb/s with 11.4 dB extinction ratio. The modulator has voltage-length product of 2.4 V-mm and chirp of -0.75 over the entire bias range. As a switch, it has a switching time less than 20 ps.
Evaluation of loss and change of specificity resulting from random mutagenesis of an antibody VH region (1995)

Most data available from in vivo sources regarding the impact of somatic hypermutation on Ab V region structure and function are heavily biased due to the influence of clonal selection. In an effort to address this issue directly, we "randomly" introduced point mutations throughout the length of the VH region of an anti-p-azophenylarsonate (Ars) Ab expressed as an Fab in the phage display format. This was accomplished by means of an error-prone PCR with two protocols, which resulted in two mutant libraries. The nature of the nucleotide substitutions obtained from each protocol differed from each other and resulted in different frequencies of phage clones that did not appear to contain Fab on their surfaces. However, the majority of mutants in both libraries lacked detectable Fab expression. Screening of the library containing the most expressed Fabs for those that had gained affinity for structurally related haptens yielded two independent mutants that lacked detectable affinity for Ars and had high affinity for p-azophenylsulfonate. These mutants both contained amino acid substitutions from Asn to Ser or Thr at VH CDR1 position 35, a putative Ars contact residue. In this paper, we discuss the significance of these data with regard to the frequencies of V region loss of function, gain of increased affinity, and gain of altered specificity that result from somatic hypermutation in vivo.
Affinity and Cross-Reactivity Engineering of CTLA4-Ig To Modulate T Cell Costimulation (2012)

CTLA4-Ig is an Fc fusion protein containing the extracellular domain of CTLA-4, a receptor known to deliver a negative signal to T cells. CTLA4-Ig modulates T cell costimulatory signals by blocking the CD80 and CD86 ligands from binding to CD28, which delivers a positive T cell costimulatory signal. To engineer CTLA4-Ig variants with altered binding affinity to CD80 and CD86, we employed a high-throughput protein engineering method to map the ligand binding surface of CTLA-4. The resulting mutagenesis map identified positions critical for the recognition of each ligand on the three CDR-like loops of CTLA-4, consistent with the published site-directed mutagenesis and x-ray crystal structures of the CTLA-4/CD80 and CTLA-4/CD86 complexes. A number of single amino acid substitutions were identified that equally affected the binding affinity of CTLA4-Ig for both ligands as well as those that differentially affected binding. All of the high-affinity variants showed improved off-rates, with the best one being a 17.5-fold improved off-rate over parental CTLA4-Ig binding to CD86. Allostimulation of human CD4(+) T cells showed that improvement of CD80 and CD86 binding activity augmented inhibition of naive and primed T cell activation. In general, increased affinity for CD86 resulted in more potent inhibition of T cell response than did increased affinity for CD80. Optimization of the affinity balance to CD80 and CD86 to particular disease settings may lead to development of a CTLA4-Ig molecule with improved efficacy and safety profiles.
Internet X.509 Certificate Request Message Format (1999)

This document describes the Certificate Request Message Format (CRMF). This syntax is used to convey a request for a certificate to a Certification Authority (CA) (possibly via a Registration Authority (RA)) for the purposes of X.509 certificate production. The request will typically include a public key and associated registration information.
Influence of polarity on carrier transport in semipolar (2021¯) and (202¯1) multiple-quantum-well light-emitting diodes (2012)

We investigate the influence of polarity on carrier transport in single-quantum-well and multiple-quantum-well (MQW) light-emitting diodes (LEDs) grown on the semipolar (202¯1) and (2021¯) orientations of free-standing GaN. For semipolar MQW LEDs with the opposite polarity to conventional Ga-polar c-plane LEDs, the polarization-related electric field in the QWs results in an additional energy barrier for carriers to escape the QWs. We show that semipolar (2021¯) MQW LEDs with the same polarity to Ga-polar c-plane LEDs have a more uniform carrier distribution and lower forward voltage than (202¯1) MQW LEDs.
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments (2010)

Single-click, self-updating web installation is available at http://proteome.gs.washington.edu/software/skyline. This web site also provides access to instructional videos, a support board, an issues list and a link to the source code project.
Long-Lasting and Permanent Fillers: Biomaterial Influence over Host Tissue Response (2007)

There is an obvious need for serious, precise, and objective studies on most of the available fillers, which have not been properly scientifically studied on human skin.
The two‐step lysis system of pneumococcal bacteriophage EJ‐1 is functional in Gram‐negative bacteria: triggering of the major pneumococcal autolysin in Escherichia coli (1996)

The holin function Ejh of the pneumococcal bacteriophage EJ‐1 has been characterized. It shows structural features similar to, and functionally complemented, the prototype member of the holin family. In Escherichia coli and Pseudomonas putida the Ejh product caused cellular death, and changes in cell morphology could be accounted for by lesions in the cytoplasmic membrane. Expression of ejh resulted in the inhibition of growth in a variety of phylogenetically distant bacterial genera, suggesting a broad spectrum of action. Concomitant expression of the ejh and ejl (encodes a lysin) genes led to lysis of E. coli and P. putida cells. Remarkably, the Ejl lysin was able to attack murein from bacteria lacking choline in their sacculi, which suggests that pneumococcal lysins have a broader substrate specificity than previously assumed. Furthermore, the Ejh holin was able to trigger activity of the major pneumococcal autolysin cloned and expressed in E. coli , and this raised new questions about the regulation of this model autolysin. A new function for holins in systems where the phage lysin is supposed to be associated with the membrane is proposed.
Simultaneous measurement of strain and temperature using Bragg gratings written in germanosilicate and boron-codoped germanosilicate fibers (1999)

A new fiber Bragg grating sensor configuration is presented for simultaneous measurement of strain and temperature. The sensor utilizes the effect of boron codoping on the temperature dependence of the refractive index in germanosilicate fibers. By writing gratings with dose wavelengths in undoped acid boron doped fibers, different temperature sensitivities are obtained while strain sensitivities remain the same. These gratings are then spliced to obtain a simple sensor head suitable for applications in smart structures and composite materials.
Lysosomal Glycosphingolipid Recognition by NKT Cells (2004)

NKT cells represent a distinct lineage of T cells that coexpress a conserved alphabeta T cell receptor (TCR) and natural killer (NK) receptors. Although the TCR of NKT cells is characteristically autoreactive to CD1d, a lipid-presenting molecule, endogenous ligands for these cells have not been identified. We show that a lysosomal glycosphingolipid of previously unknown function, isoglobotrihexosylceramide (iGb3), is recognized both by mouse and human NKT cells. Impaired generation of lysosomal iGb3 in mice lacking beta-hexosaminidase b results in severe NKT cell deficiency, suggesting that this lipid also mediates development of NKT cells in the mouse. We suggest that expression of iGb3 in peripheral tissues may be involved in controlling NKT cell responses to infections and malignancy and in autoimmunity.
Is dentistry worth investing in? An opinion on the views of the financial community (2011)

Shane Stack, a partner at Medical Money Management, independent financial advisors to the medical and dental professions, seeks to explore the question on the minds of most dental students and newly qualified dentists considering a career as a practitioner or owner: is it worth the investment?
The capsule polysaccharide synthesis locus of streptococcus pneumoniae serotype 14: Identification of the glycosyl transferase gene cps14E (1996)

To identify a chromosomal region of Streptococcus pneumoniae serotype 14 involved in capsule polysaccharide synthesis, two strategies were used: (i) Tn916 mutagenesis, followed by the characterization of four unencapsulated mutants, and (ii) cross-hybridization with a capsule polysaccharide synthesis gene (cps) probe from S. agalactiae, which has a structurally similar capsule. The two approaches detected the same chromosomal region consisting of two adjacent EcoRI fragments. One of these EcoRI fragments was cloned and hybridized with a cosmid library. This resulted in clone cMKO2. A similar cosmid clone was obtained from an unencapsulated Tn916 mutant, Spnl4.H. Sequence analysis of the two cosmid clones revealed that in the Tn916 mutant, a gene, cps14E, which is homologous to other bacterial genes encoding glycosyl transferases, had been inactivated. An open reading frame immediately downstream of cps14E, designated cps14F, shows no significant homology with any known genes or proteins. A functional assay showed that cps14E encodes a glycosyl transferase and that a gene-specific knockout mutant lacks this enzyme activity, whereas inactivation of cps14F does not have this effect.
RAG-2 expression is not essential for chicken immunoglobulin gene conversion. (1992)

Chicken B cells diversify their immunoglobulin genes by gene conversion in the bursa of Fabricius. The avian leukosis virus-induced B-cell line DT40 continues to diversify its immunoglobulin light chain locus by gene conversion during in vitro passage. Since a variable(diversity)joining recombination-activating gene, RAG-2, is specifically expressed in chicken B cells undergoing immunoglobulin gene conversion, it has been suggested that RAG-2 may be involved in the immunoglobulin gene conversion process. We previously reported high ratios of targeted to random integration after transfection of genomic DNA constructs into DT40. This allows us to easily investigate the function of a gene product by gene disruption. We show here that subclones of DT40 maintain the ability to diversify their immunoglobulin light chain locus by gene conversion even after both copies of the RAG-2 coding regions are deleted. These results demonstrate that the RAG-2 product is not required for gene conversion activity in the immunoglobulin light chain locus.
OXIDANT MECHANISMS IN TOXIC ACUTE RENAL FAILURE* (1999)

Over the last decade, there is accumulating evidence for a role of reactive oxygen metabolites in the pathogenesis of a variety of renal diseases, including gentamicin, glycerol, cisplatin, and cyclosporine A models of toxic acute renal failure. Gentamicin has been shown both in in vitro and in vivo studies to enhance the generation of reactive oxygen metabolites. Iron is important in models of tissue injury, presumably because it is capable of catalyzing free-radical formation. Gentamicin has been shown to cause release of iron from renal cortical mitochondria. Scavengers of reactive oxygen metabolites as well as iron chelators provide protection in gentamicin-induced nephrotoxicity. In glycerol-induced acute renal failure, an animal model of rhabdomyolysis, there is enhanced generation of hydrogen peroxide, and scavengers of reactive oxygen metabolites and iron chelators provide protection. Although the dogma is that the myoglobin is the source of iron, recent studies suggest that cytochrome P450 may be an important source of iron in this model. In addition, there are marked alterations in antioxidant defenses, such as glutathione, as well as changes in heme oxygenase. Several recent in vitro and in vivo studies indicate an important role of reactive oxygen metabolites in cisplatin-induced nephrotoxicity. Thus, catalytic iron is increased both in vitro and in vivo by cisplatin, and iron chelators as well as hydroxyl radical scavengers have been shown to be protective. Recent studies indicate that cytochrome P450 may also be an important source of the catalytic iron in cisplatin nephrotoxicity. Cyclosporine A has been shown to enhance generation of hydrogen peroxide in vitro and enhance lipid peroxidation in vitro and in vivo. Antioxidants have been shown to be protective in cyclosporine A nephrotoxicity. This collective body of evidence suggests an important role for reactive oxygen metabolites in toxic acute renal failure and may provide therapeutic opportunities of preventing or treating acute renal failure in humans.
A protective effect of sulindac against chemically‐induced primary colonic tumours in mice (1988)

Sulindac, a non-steroidal anti-inflammatory drug, has been reported to lead to tumour regression in cases of human polyposis coli. We have investigated the effects of this drug on the growth of 1,2-dimethylhydrazine (DMH)-induced mouse colonic tumours. In one experiment, DMH and oral sulindac were administered concurrently to a group of mice for a period of up to 24 weeks, while a control group of animals received DMH only for the same period. Sulindac caused a significant reduction in both the number of mice with colonic tumours and the number of tumours per mouse. In a second experiment, two groups of mice which had already been treated with DMH for 17 weeks received either sulindac or not for 78 days. In this experiment sulindac had no effect. These results demonstrate that sulindac has a protective effect against the chemical induction of colonic tumours in mice, but does not cause the regression of established tumours.