gebhart/patrepeval huggingface dataset:
Bacterial genome size reduction by experimental evolution (2005)

Bacterial evolution toward endosymbiosis with eukaryotic cells is associated with extensive bacterial genome reduction and loss of metabolic and regulatory capabilities. Here we examined the rate and process of genome reduction in the bacterium Salmonella enterica by a serial passage experimental evolution procedure. The initial rate of DNA loss was estimated to be 0.05 bp per chromosome per generation for a WT bacterium and approximately 50-fold higher for a mutS mutant defective in methyl-directed DNA mismatch repair. The endpoints were identified for seven chromosomal deletions isolated during serial passage and in two separate genetic selections. Deletions ranged in size from 1 to 202 kb, and most of them were not associated with DNA repeats, indicating that they were formed via RecA-independent recombination events. These results suggest that extensive genome reduction can occur on a short evolutionary time scale and that RecA-dependent homologous recombination only plays a limited role in this process of jettisoning superfluous DNA.
The P2Y-like receptor GPR17 as a sensor of damage and a new potential target in spinal cord injury (2009)

Upon central nervous system injury, the extracellular concentrations of nucleotides and cysteinyl-leukotrienes, two unrelated families of endogenous signalling molecules, are markedly increased at the site of damage, suggesting that they may act as 'danger signals' to alert responses to tissue damage and start repair. Here we show that, in non-injured spinal cord parenchyma, GPR17, a P2Y-like receptor responding to both uracil nucleotides (e.g. UDP-glucose) and cysteinyl-leukotrienes (e.g. LTD4 and LTC4), is present on a subset of neurons and of oligodendrocytes at different stages of maturation, whereas it is not expressed by astrocytes. GPR17 immunoreactivity was also found on ependymal cells lining the central canal that still retain some of the characteristics of stem/progenitor cells during adulthood. Induction of spinal cord injury (SCI) by acute compression resulted in marked cell death of GPR17+ neurons and oligodendrocytes inside the lesion followed by the appearance of proliferating GPR17+ microglia/macrophages migrating to and infiltrating into the lesioned area. Moreover, 72 h after SCI, GPR17+ ependymal cells started to proliferate and to express GFAP, suggesting their activation and 'de-differentiation' to pluripotent progenitor cells. The in vivo knock down of GPR17 by an antisense oligonucleotide strategy during SCI induction markedly reduced tissue damage and related histological and motor deficits, thus confirming the crucial role played by this receptor in the early phases of tissue damage development. Taken together, our findings suggest a dual and spatiotemporal-dependent role for GPR17 in SCI. At very early times after injury, GPR17 mediates neuronal and oligodendrocyte death inside the lesioned area. At later times, GPR17+ microglia/macrophages are recruited from distal parenchymal areas and move toward the lesioned zone, to suggest a role in orchestrating local remodelling responses. At the same time, the induction of the stem cell marker GFAP in GPR17+ ependymal cells suggests initiation of repair mechanisms. Thus, GPR17 may act as a 'sensor' of damage that is activated by nucleotides and cysteinyl-leukotrienes released in the lesioned area, and could also participate in post-injury responses. Moreover, its presence on spinal cord pre-oligodendrocytes and precursor-like cells suggests GPR17 as a novel target for therapeutic manipulation to foster remyelination and functional repair in SCI.
Surface Energy of Microcrystalline Cellulose Determined by Capillary Intrusion and Inverse Gas Chromatography (2008)

Surface energy data for samples of microcrystalline cellulose have been obtained using two techniques: capillary intrusion and inverse gas chromatography. Ten microcrystalline cellulose materials, studied using capillary intrusion, showed significant differences in the measured surface energetics (in terms of total surface energy and the acid-base characteristics of the cellulose surface), with variations noted between the seven different manufacturers who produced the microcrystalline cellulose samples. The surface energy data from capillary intrusion was similar to data obtained using inverse gas chromatography with the column maintained at 44% relative humidity for the three samples of microcrystalline cellulose studied. This suggests that capillary intrusion may be a suitable method to study the surface energy of pharmaceutical samples.
Functional Properties of Improved Glycinin and β-nglycinin Fractions (2004)

ABSTRACT: Glycinin and β-conglycinin have unique functionality characteristics that contribute important properties in soy foods and soy ingredients. Limited functionality data have been published for glycinin and β-conglycinin fractions produced in pilot-scale quantities. Protein extraction conditions were previously optimized for our pilotscale fractionation process to maximize protein solubilization and subsequent product recovery. Glycinin, β-conglycinin, and intermediate (mixture of glycinin and β-conglycinin) fractions were prepared using optimized-process (OP) extraction conditions (10:1 water-to-flake ratio, 45°C) and previous conditions termed Wu process (WP) (15:1, 20°C). Viscosity, solubility, gelling, foaming, emulsification capacity, and emulsification activity and stability of the fractionated proteins, and soy protein isolate (SPI) produced from the same defatted soy white flakes were compared to evaluate functional properties of these different protein fractions. Differential scanning calorimetry, sodium dodecylsulfate-polyacrylamide gel electrophoresis, and surface hydrophobicity data were used to interpret functionality differences. OP β-conglycinin had more glycinin contamination than did the WP β-conglycinin. OP and WP solubility profiles were each similar for respective glycinin and β-conglycinin fractions. Emulsification activities and stabilities were higher for OP β-conglycinin and OP intermediate fractions compared with respective WP fractions. β-Conglycinin and SPI emulsification capacities (ECs) mirrored solubility profile, whereas glycinin ECs did not. OP glycinin had a higher foaming capacity than WP glycinin. OP and WP intermediate fraction apparent viscosities trended higher than those of other protein fractions. β-Conglycinin dispersions at pH 3 and 7 produced firm gels at 80°C, whereas glycinin dispersions formed weaker gels at 99°C and did not gel at 80°C.
J-aggregate formation of a carbocyanine as a quantitative fluorescent indicator of membrane potential (1991)

The spectral properties of a novel membrane potential sensitive probe (JC-1) were characterized in aqueous buffers and in isolated cardiac mitochondria. JC-1 is a carbocyanine with a delocalized positive charge. It formed under favorable conditions a concentration-dependent fluorescent nematic phase consisting of J-aggregates. When excited at 490 nm, the monomers exhibited an emission maximum at 527 nm and J-aggregates at 590 nm. Increasing concentrations of JC-1 above a certain concentration caused a linear rise in the J-aggregate fluorescence, while the monomer fluorescence remained constant. The membrane potential of energized mitochondria (negative inside) promoted a directional uptake of JC-1 into the matrix, also with subsequent formation of J-aggregates. The J-aggregate fluorescence was sensitive to transient membrane potential changes induced by ADP and to metabolic inhibitors of oxidative phosphorylation. The J-aggregate fluorescence was found to be pH independent within the physiological pH range of 7.15-8.0 and could be linearly calibrated with valinomycin-induced K+ diffusion potentials. The advantage of JC-1 over rhodamines and other carbocyanines is that its color altered reversibly from green to red with increasing membrane potentials. This can be exploited for imaging live mitochondria on the stage of a microscope.
Polarization-sensitive dual-wavelength spectroscopic optical coherence tomography (2003)

We analyse polarisation effects in spectroscopic optical coherence tomography. Birefringence induced changes in polarisation are wavelength dependent and the spectrum of the interference signal will therefore depend on the polarisation properties of the sample. We have avoided this problem by realising a combination of dual wavelength spectroscopic OCT system and polarisation sensitive detection.
Gaucher Disease (1999)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Internal Medicine HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Internal Medicine journal
Combining Rules and Cases to Learn Case Adaptation (1995)

Computer models of case-based reasoning (CBR) generally guide case adaptation using a fixed set of adaptation rules. A difficult practical problem is how to identify the knowledge required to guide adaptation for particular tasks. Likewise, an open issue for CBR as a cognitive model is how case adaptation knowledge is learned. We describe a new approach to acquiring case adaptation knowledge. In this approach, adaptation problems are initially solved by reasoning from scratch, using abstract rules about structural transformations and general memory search heuristics. Traces of the processing used for successful rule-based adaptation are stored as cases to enable future adaptation to be done by case-based reasoning. When similar adaptation problems are encountered in the future, these adaptation cases provide task- and domain-specific guidance for the case adaptation process. We present the tenets of the approach concerning the relationship between memory search and case adaptation, the...
Pharmacokinetics of Tissue Penetration of Antibiotics (1981)

Past efforts to characterize the ability of antibiotics to penetrate into tissues is reviewed, particularly the results of models that reflect the concentration of antibiotics in interstitial fluid (i.e., skin blisters, tissue chambers, skin chambers, wound exudates, implanted fibrin clots, and peripheral lymph). The preferable sources of such fluid appear to be skin chambers, suction-induced skin blisters, and peripheral lymph. Extent of penetration of antibiotics into tissue fluid is related to the amount of antibiotic not bound to protein. Protein binding is particularly inhibitory to penetration when greater than 80% of the antibiotic is bound. It is preferable to follow the extravascular concentrations of antibiotic for longer periods than is usually done. The ability of antibiotics to penetrate is best evaluated by use of the ratio of the area under the concentration curve (AUC) for antibiotic in the peripheral locus to the AUC for serum. Pharmacokinetic analysis should be done with data from each individual, not with data derived from curves using mean values. Penetration into fibrin, lymph, and chambers implanted in tissues follows Fick's law of diffusion. Lag times indicate the interval before penetration of antibiotic in serum to the peripheral locus may be observed. First-order, one-compartment, open models are applicable to the characterization of extravascular concentrations of antibiotics. The AUC for antibiotic in serum during a time interval is the factor determining the amount of agent that passes into an extravascular focus. Concentrations of drug in tissues are lower than those in serum; the peaks occur simultaneously or shortly after the maximal levels are reached in serum, and for most antibiotics the elimination of antibiotics from extravascular parts of the body is slower than from serum, particularly for agents with a half-life in serum of less than 4-5 hr.
Association of PSD‐95 with ErbB4 facilitates neuregulin signaling in cerebellar granule neurons in culture (2006)

The growth factor neuregulin 1 (NRG) selectively induces an increase in the gamma-aminobutyric acid (GABA)(A) receptor beta2 subunit protein in rat cerebellar granule neurons in culture. We previously demonstrated that NRG acts by triggering ErbB4 receptor phosphorylation and subsequent signaling through the mitogen-activated kinase (MAPK), phosphatidyl inositol-3 kinase (PI-3K) and cyclin-dependent kinase 5 (cdk5) pathways. In this report we show that the scaffolding protein, PSD-95, plays a key role in mediating the effects of NRG and that reducing its level attenuates the NRG-induced increase in beta2 subunit expression. PSD-95 appears to facilitate the effects of NRG through its association with ErbB4, an interaction that is augmented by NRG-activated cdk signaling. Inhibition of cdk activity with roscovitine attenuates the association of PSD-95 with ErbB4. The effects of cdk5 are not blocked by U0126, an inhibitor of MAPK signaling, indicating that cdk5 functions independently of cross-talk with this pathway. These findings raise the possibility that NRG-induced activation of cdk5 works in part by recruiting PSD-95, a protein involved in regulating synaptic plasticity, to associate with ErbB4. This interaction may be a positive feedback loop that augments NRG signaling and its downstream effects on GABA(A) receptor beta2 subunit expression.
A low-profile three-dimensional neural stimulating array with on-chip current generation (2005)

This paper describes a low-profile silicon microelectrode array for selectively stimulating in the central nervous system. The array consists of a number of 64-site 8-channel planar CMOS probes, a platform to support the probes on the cortical surface, spacers to hold the probes orthogonal to the platform, and a hybrid chip for platform address decoding. It features integrated circuitry with on-chip current generation to deliver biphasic currents from -127 microA to +127 microA to selected sites with 1 microA resolution and fold-down structures to reduce the vertical rise above the cortex for chronic implants. The output stimulating current has a differential nonlinearity of less than 0.8LSBs and a biphasic mismatch of less than 0.23LSBs. The average power dissipation to generate full-range biphasic pulses with pulse widths of 100 micros at a repetition rate of 500 Hz is about 97 microW per channel. The probes and the hybrid chip are fabricated in a 3 microm, p-sub/n-epi/p-well 2P/1M micromachined CMOS technology; the other structures use a simplified passive process.
Benign Breast Disease and the Risk of Breast Cancer (2005)

Risk factors for breast cancer after the diagnosis of benign breast disease include the histologic classification of a benign breast lesion and a family history of breast cancer.
O-DESULFATED HEPARIN IMPROVES OUTCOME AFTER RAT CEREBRAL ISCHEMIA/REPERFUSION INJURY (2007)

Our findings indicate that ODSH can be administered at a dose that provides postischemic anti-inflammatory neuroprotection without an increased risk of intracerebral hemorrhage.
Mechanisms of light scattering from biological cells relevant to noninvasive optical-tissue diagnostics (1998)

We have studied the optical properties of mammalian cell suspensions to provide a mechanistic basis for interpreting the optical properties of tissues in vivo. Measurements of the wavelength dependence of the reduced scattering coefficient and measurements of the phase function demonstrated that there is a distribution of scatterer sizes. The volumes of the scatterers are equivalent to those of spheres with diameters in the range between ~0.4 and 2.0 mum. Measurements of isolated organelles indicate that mitochondria and other similarly sized organelles are responsible for scattering at large angles, whereas nuclei are responsible for small-angle scattering. Therefore optical diagnostics are expected to be sensitive to organelle morphology but not directly to the size and shape of the cells.
Advancing the time of ovulation in the mare with a short‐term implant releasing the GnRH analogue deslorelin (1993)

A small, biocompatible and short-term implant releasing 1.5 mg or 2.25 mg of the GnRH analogue deslorelin was evaluated in 140 Hanoverian (warm blooded) mares during the 1990 breeding season (Study I). Mares in oestrus and with a follicle 40 +/- 2 mm in diameter were assigned alternately to treatment (70) or remained as untreated controls. Implants were administered subcutaneously, and intervals to ovulation determined by rectal examination and ultrasound at 12-h intervals. Since results with both doses of deslorelin were similar, data were pooled. Deslorelin implantation resulted in ovulations in 65 of 70 mares within 48 h (93%), while only 5 of 70 control mares ovulated within the same time period (7%) (P < 0.01). Most induced ovulations (63%) occurred 36-48 h after implantation. In Study II, 4 groups of 12 Hanoverian mares each were treated with 3,000 or 5,000 iu hCG, or a 2.25 mg deslorelin implant, or received placebo. All treatments resulted in 100% ovulations within 48 h, versus 25% ovulations in controls (P < 0.01), and 63%, 75% and 86% of these ovulations occurred 36-48 h after treatment with 3,000 and 5,000 iu hCG and deslorelin respectively. Hormonal response to deslorelin in treated mares, sampled every 12 h, consisted of elevations of FSH and LH concentrations of > 200% and > 300% baseline values at 12 h (P < 0.001), of 67% and 79% at 24 h (P < 0.01) and of 35% and 49% at 48 h (P < 0.05), respectively. No local reactions at the implantation site were observed.
Studies on Hanganutziu-Deicher Antigens-Antibodies (1986)

Sera of patients with various liver diseases were examined for the presence of Hanganutziu-Deicher (H-D) antibodies by enzyme immunoassay with high-molecular weight glycoprotein (HMWGP) isolated from bovine red blood cell stromata. IgG class H-D antibodies were demonstrated in sera of 5.9% of acute hepatitis, 28.1% of chronic hepatitis and 21.9% of liver cirrhosis patients. H-D specificity of the antibodies under investigation was determined by absorption experiments. Evidence was also presented that the H-D antibodies in the liver disease sera are directed to N-glycolyl neuraminic acid (NGNA) and/or NGNA-dependent determinants of HMWGP.
Phenotypic Effect of IsogenicuspA1anduspA2Mutations onMoraxella catarrhalis035E (1998)

The UspA surface antigen of Moraxella catarrhalis was recently shown to be comprised of two different proteins (UspA1 and UspA2) which share an internal region containing 140 amino acids with 93% identity (C. Aebi, I. Maciver, J. L. Latimer, L. D. Cope, M. K. Stevens, S. E. Thomas, G. H. McCracken, Jr., and E. J. Hansen, Infect. Immun. 65:4367-4377, 1997). Isogenic uspA1, uspA2, and uspA1 uspA2 mutants were tested in a number of in vitro systems to determine what effect these mutations, either individually or together, might exert on the phenotype of M. catarrhalis 035E. Monoclonal antibodies specific for UspA1 or UspA2 were used in an indirect antibody accessibility assay to prove that both of these proteins were expressed on the surface of M. catarrhalis. All three mutants grew in vitro at the same rate and did not exhibit autoagglutination or hemagglutination properties that were detectably different from those of the wild-type parent strain. When tested for the ability to adhere to human epithelial cells, the wild-type parent strain and the uspA2 mutant readily attached to Chang conjunctival cells. In contrast, the uspA1 mutant and the uspA1 uspA2 double mutant both attached to these epithelial cells at a level nearly 2 orders of magnitude lower than that obtained with the wild-type parent strain, a result which suggested that expression of UspA1 by M. catarrhalis is essential for attachment to these epithelial cells. Both the wild-type parent strain and the uspA1 mutant were resistant to the bactericidal activity of normal human serum, whereas the uspA2 mutant and the uspA1 uspA2 double mutant were readily killed by this serum. This latter result indicated that the presence of UspA2 is essential for expression of serum resistance by M. catarrhalis.
CD20 Expression in Normal Canine B Cells and in Canine non-Hodgkin Lymphoma (2005)

We examined the expression of CD20 in normal canine peripheral blood mononuclear cells, normal canine spleen, and canine non-Hodgkin lymphoma (NHL) to determine the feasibility of using this antigen as a diagnostic aid and as a possible target for therapy. An antibody generated against a C-terminal (intracytoplasmic) epitope of human CD20 recognized proteins of 32-36 kd in normal and malignant canine lymphocytes. This antibody showed restricted membrane binding in a subset of lymphocytes in peripheral blood, in the B-cell regions from a normal canine spleen and lymph node, and in malignant cells from 19 dogs with B-cell NHL, but not from 15 dogs with T-cell NHL. The patterns of CD20 reactivity in these samples overlapped those seen using an antibody that recognizes canine CD79a. This anti-CD20 antibody is therefore suitable as an aid to phenotype canine NHL. In contrast, normal canine B cells were not recognized by any of 28 antibodies directed against the extracellular domains of human CD20 (including the chimeric mouse-human antibody Rituximab) or by any of 12 antibodies directed against the extracellular domains of mouse CD20. Thus, the use of CD20 as a therapeutic target will require the generation of specific antibodies against the extracellular domains of canine CD20.
Noninvasive method for assessing the human circadian clock using hair follicle cells (2010)

A thorough understanding of the circadian clock requires qualitative evaluation of circadian clock gene expression. Thus far, no simple and effective method for detecting human clock gene expression has become available. This limitation has greatly hampered our understanding of human circadian rhythm. Here we report a convenient, reliable, and less invasive method for detecting human clock gene expression using biopsy samples of hair follicle cells from the head or chin. We show that the circadian phase of clock gene expression in hair follicle cells accurately reflects that of individual behavioral rhythms, demonstrating that this strategy is appropriate for evaluating the human peripheral circadian clock. Furthermore, using this method, we indicate that rotating shift workers suffer from a serious time lag between circadian gene expression rhythms and lifestyle. Qualitative evaluation of clock gene expression in hair follicle cells, therefore, may be an effective approach for studying the human circadian clock in the clinical setting.
Bis(acétamido-3 propanesulfonate-1) de calcium (N-acétylhomotaurinate de calcium) (1988)

Ca 2+ •2C 5 H 10 NO 4 S − cristallise dans P2 1 /c avec affinement jusqu'a 0,025. Les anions forment des couches paralleles a la face (010). Chaque couche contient deux feuillets lies par des liaisons hydrogene N−H... O. Le cation Ca 2+ est insere entre deux couches d'anions avec une coordination octaedre legerement deforme