gebhart/patrepeval huggingface dataset:
Mechanisms and functions of p38 MAPK signalling (2010)

The p38 MAPK (mitogen-activated protein kinase) signalling pathway allows cells to interpret a wide range of external signals and respond appropriately by generating a plethora of different biological effects. The diversity and specificity in cellular outcomes is achieved with an apparently simple linear architecture of the pathway, consisting of a core of three protein kinases acting sequentially. In the present review, we dissect the molecular mechanisms underlying p38 MAPK functions, with special emphasis on the activation and regulation of the core kinases, the interplay with other signalling pathways and the nature of p38 MAPK substrates as a source of functional diversity. Finally, we discuss how genetic mouse models are facilitating the identification of physiological functions for p38 MAPKs, which may impinge on their eventual use as therapeutic targets.
Molecular Evolution of Lysin Motif-Type Receptor-Like Kinases in Plants (2007)

The lysin motif (LysM) domain is an ancient and ubiquitous protein module that binds peptidoglycan and structurally related molecules. A genomic survey in a large number of species spanning all kingdoms reveals that the combination of LysM and receptor kinase domains is present exclusively in plants. However, the particular biological functions and molecular evolution of this gene family remain largely unknown. We show that LysM domains in plant LysM proteins are highly diversified and that a minimum of six distinct types of LysM motifs exist in plant LysM kinase proteins and five additional types of LysM motifs exist in nonkinase plant LysM proteins. Further, motif similarities suggest that plant LysM motifs are ancient. Although phylogenetic signals are not sufficient to resolve the earliest relationships, plant LysM motifs may have arisen through common ancestry with LysM motifs in other kingdoms. Within plants, the gene family has evolved through local and segmental duplications. The family has undergone further duplication and diversification in legumes, where some LysM kinase genes function as receptors for bacterial nodulation factor. Two pairs of homeologous regions were identified in soybean (Glycine max) based on microsynteny and fluorescence in situ hybridization. Expression data show that most plant LysM kinase genes are expressed predominantly in the root and that orthologous LysM kinase genes share similar tissue expression patterns. We also examined synteny around plant LysM kinase genes to help reconstruct scenarios for the evolution of this important gene family.
Plasma-Polymerized Allylamine Film Used as a New Solid Phase in Immunoradiometric Assay(IRMA): Effect of Antibody(F(ab')2Fragment) Concentration on Dose Response in Two-Site IRMA. (1992)

Allylamine (ALAM) film was plasma-polymerized on a flat glass (referred to as ALAM(GLA): GLA refers to a flat glass plate) for use as a solid phase in two-site immunoradiometric assay (two-site IRMA). Adsorption of F(ab')2 anti-human immunoglobulin G [formula: see text] to ALAM(GLA) was larger than adsorption on a polyvinyl chloride plate (referred to as PVC). Contrary to the expectation that the dose response for human IgG (hIgG) on ALAM (GLA) was better than that on PVC, the dose responses on both solid phases were the same. This phenomenon was independent of molecular size of the antigen (Ag) (hIgG or Fc fragment of hIg G (hIgG-Fc)) and also the reaction with protein A (pA). Because direct measurements of binding with 125I-labeled hIgG (hIgG*) or hIgG-Fc (hIgG-Fc*) showed no difference between ALAM(GLA) and PVC, the phenomenon was not due to the second step in the system of two-site IRMA (an Ag--Ab reaction (Ab refers to antibody)). These results indicated that the phenomenon was due to the first step (the adsorption of [formula: see text] to a solid phase). When the concentration of [formula: see text] immobilized on the solid phases was lowered, a significant increase in the dose response was observed for ALAM(GLA).
Gentamicin antibacterial activity in the presence of human polymorphonuclear leukocytes (1979)

Complete protection of Staphylococcus aureus Wood 46 from gentamicin bactericidal activity was documented for microorganisms located within polymorphonuclear leukocytes. The highest, still ineffective gentamicin concentration tested in the phagocytic assay was 80 times higher than the minimal concentration required to kill uningested organisms. Extracellular gentamicin activity was unaffected by the phagocytic process as demonstrated by microbiological and enzymatic assays, and liberation of intracellular S. aureus by lysis of neutrophils showed the bacteria to be fully susceptible to the antibiotic. These results were corroborated by studies performed with [14C]gentamicin; binding of the labeled antibiotic by resting neutrophils, or by neutrophils ingesting live, killed S. aureus or endotoxin-coated paraffin particles, showed no statistical differences and never exceeded 20% of the extracellular concentration. These results show that intraleukocytic S. aureus are protected from the bactericidal action of gentamicin and suggest that this protection can be explained by poor intracellular penetration of the antibiotic.
Plasma and Cerebrospinal Fluid Concentrations of 4-Aminopyridine following Intravenous Injection and Metered Intrathecal Delivery in Canines (1995)

Potassium channel blockade by 4-aminopyridine (4-AP) has been shown to initiate modest levels of functional recovery in spinal-injured dogs and people following intravenous administration; however, the relevant central nervous system (CNS) concentration mediating these effects is not known. We have determined the concentrations of 4-aminopyridine in plasma and cerebrospinal fluid following intravenous administration (0.5 mg/kg) in large (> 22 kg) dogs, using liquid column chromatography. Plasma levels are initially high (> 1 microgram/mL) and fall rapidly to levels less than 100 ng/mL by about 2 h postinjection. A characteristic secondary peak in plasma 4-AP is observed at about 1 h postinjection. Corresponding concentrations of 4-AP in CSF were relatively stable for nearly 2 h, never exceeding (as a mean) 50 ng/mL within the first 2 h postinjection. We suggest behavioral recovery in clinical cases of spinal cord injury in both dogs and humans is mediated by such low (< 50 ng/mL) concentrations of 4-AP bathing the lesion. Since the adverse side effects that accompany IV administration of the drug limit its potential clinical usefulness, we have evaluated the feasibility of an alternate route of administration, continuous metered delivery of 4-AP into the spinal cord's subarachnoid space. This is accomplished by using a surgically implantable pump and delivery catheter. The pump itself can be interrogated, and is fully programmable, by noninvasive telemetry. Intrathecal delivery rates of between 1 and 60 micrograms of 4-AP per hour never produced detectable levels of the drug in plasma or cervically sampled CSF in dogs independent of the amount or duration of infusion (hours to days). The levels of 4-AP in lumbar samples of CSF near the lumbar delivery site suggest a very steep gradient of the drug, with local concentrations easily reaching 1 microgram/mL or higher (10- to 20-fold higher than can be safely produced by IV administration). The most frequent adverse reaction to intrathecal 4-AP delivery was a mild hindlimb tremor, fully reversible following reduction in the rate of drug delivery or termination of delivery. This route of drug administration relative to clinical spinal cord injury is discussed.
Identification of Glycosylphosphatidylinositol-Anchored Proteins in Arabidopsis. A Proteomic and Genomic Analysis (2003)

In a recent bioinformatic analysis, we predicted the presence of multiple families of cell surface glycosylphosphatidylinositol (GPI)-anchored proteins (GAPs) in Arabidopsis (G.H.H. Borner, D.J. Sherrier, T.J. Stevens, I.T. Arkin, P. Dupree [2002] Plant Physiol 129: 486-499). A number of publications have since demonstrated the importance of predicted GAPs in diverse physiological processes including root development, cell wall integrity, and adhesion. However, direct experimental evidence for their GPI anchoring is mostly lacking. Here, we present the first, to our knowledge, large-scale proteomic identification of plant GAPs. Triton X-114 phase partitioning and sensitivity to phosphatidylinositol-specific phospholipase C were used to prepare GAP-rich fractions from Arabidopsis callus cells. Two-dimensional fluorescence difference gel electrophoresis and one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis demonstrated the existence of a large number of phospholipase C-sensitive Arabidopsis proteins. Using liquid chromatography-tandem mass spectrometry, 30 GAPs were identified, including six beta-1,3 glucanases, five phytocyanins, four fasciclin-like arabinogalactan proteins, four receptor-like proteins, two Hedgehog-interacting-like proteins, two putative glycerophosphodiesterases, a lipid transfer-like protein, a COBRA-like protein, SKU5, and SKS1. These results validate our previous bioinformatic analysis of the Arabidopsis protein database. Using the confirmed GAPs from the proteomic analysis to train the search algorithm, as well as improved genomic annotation, an updated in silico screen yielded 64 new candidates, raising the total to 248 predicted GAPs in Arabidopsis.
The synthesis and DNA footprinting of acridine-linked netropsin and distamycin bifunctional mixed ligands (1988)

The new synthetic acridine-linked netropsins (9a–c) and distamycin (10a–c) are bifunctional mixed ligands which bind to DNA by both intercalation and minor-groove association and show enhanced preference for A–T rich sites.
Effects of plate preparation on results in microbial mutation assays (1992)

Glucose autoclaved in an alkaline phosphate solution (heated glucose+salts, HGS) results in the production of a moiety that is nonmutagenic but can interact with a series of 4-[2-(aryl)ethenyl]-2,6-dimethylphenols to result in an increase in bacterial revertants that is dependent on the amount of HGS in the minimal agar plates. The reaction between the HGS and the chemical to form a mutagen is independent of the presence of bacteria, does not result in a nutritive analog to enhance growth of the auxotrophic bacteria, and is effective only in Salmonella typhimurium and Escherichia coli strains that contain the plasmid pKM101. A sufficient amount of this glucose product may be formed in normal plate preparation to produce apparent mutagenic activity of these chemicals.
Evaluation of treatment response of cilengitide in an experimental model of breast cancer bone metastasis using dynamic PET with 18F-FDG. (2007)

The purpose of this study was the assessment of the feasibility of dynamic positron emission tomography (PET) studies with fluorine-18 fluorodeoxyglucose ((18)F-FDG) to quantify effects of the cyclic Arg-Gly-Asp peptide cilengitide, which targets the ανβ 3 and ανβ 5 integrin receptors in rats with breast cancer bone metastases. Rats were inoculated with MDA-MB-231 breast cancer cells, followed by the development of lytic lesions in the hind leg. Rats with lytic lesions were treated with cilengitide five times weekly on a continuous basis from days 30 to 55 after tumor cell inoculation. Dynamic PET studies with (18)F-FDG were performed in untreated (n=9), controlled (n=4) and treated rats (n=6). The data were assessed using learning-machine two-tissue compartmental analysis. The (18)F-FDG kinetic parameters obtained by two-tissue compartmental model learning-machine showed significant differences when individual parameters were compared between the control group and treated animals. Quantitative assessment of the tracer kinetics and the application of classification analysis to the data provided us with evidence to identify those tumors that demonstrated effect of cilengitide treatment. The transport rate K1 and the phosphorylation rate k3 were significantly different (P=0.033 and 0.038, respectively). Classification analysis based on support vector machines ranking feature elimination of the combination of PET parameters revealed an overall accuracy of 80.0% between treated animals and the control group. We were able to identify 83.3% treated animals compared with the control group based on k2 and VB. In conclusion, the results revealed that cilengitide treatment of experimental breast cancer bone metastases had a significant therapeutic impact on (18)F-FDG kinetics.
Clonal expansion of ovarian germline stem cells during niche formation inDrosophila (2003)

Stem cell niches are specific regulatory microenvironments formed by neighboring stromal cells. Owing to difficulties in identifying stem cells and their niches in many systems, mechanisms that control niche formation and stem cell recruitment remain elusive. In the Drosophila ovary, two or three germline stem cells (GSCs) have recently been shown to reside in a niche, in which terminal filaments (TFs) and cap cells are two major components. We report that signals from newly formed niches promote clonal expansion of GSCs during niche formation in the Drosophila ovary. After the formation of TFs and cap cells, anterior primordial germ cells (PGCs) adjacent to TFs/cap cells can develop into GSCs at the early pupal stage while the rest directly differentiate. The anterior PGCs are very mitotically active and exhibit two division patterns with respect to cap cells. One of these patterns generates two daughters that both contact cap cells and potentially become GSCs. Our lineage tracing study confirms that one PGC can generate two or three GSCs to occupy a whole niche ('clonal expansion'). decapentaplegic (dpp), the Drosophila homolog of human bone morphogenetic protein 2/4, is expressed in anterior somatic cells of the gonad, including TFs/cap cells. dpp overexpression promotes PGC proliferation and causes the accumulation of more PGCs in the gonad. A single PGC mutant for thick veins, encoding an essential dpp receptor, loses the ability to clonally populate a niche. Therefore, dpp is probably one of the mitotic signals that promote the clonal expansion of GSCs in a niche. This study also suggests that signals from newly formed niche cells are important for expanding stem cells and populating niches.
Androgen receptor gene mutations in hormone-refractory prostate cancer (1999)

Prostate cancer is considered to be one of the most hormone-dependent human malignancies. As a key mediator of hormonal response, the androgen receptor (AR) is believed to have an important role in the progression of prostate cancer. Mutations in the coding region of the AR gene have been found in both untreated and hormone-refractory prostate cancer, but the frequency of such mutations at different stages of the disease is poorly documented and even contradictory results have been published. In the present study, the frequency of AR gene mutations was determined in 30 locally recurrent and two metastatic hormone-refractory prostate tumours using the polymerase chain reaction (PCR), non-radioactive single strand conformation polymorphism (SSCP), and sequencing. The length of the polymorphic CAG repeat, which is inversely correlated with the ability of the AR to activate transcription, was also analysed as well as the GGC repeat. Twelve samples were known to contain an AR gene amplification. Altogether, one point mutation (Gly(674)-->Ala) and one microsatellite mutation (CAG(20)-->CAG(18)) were found, both in cancers containing the AR gene amplification. The mean lengths of the polymorphic CAG and GGC repeats were similar to those observed in the normal population. These results favour the view that mutations in the AR gene are rare in hormone-refractory prostate cancer and do not play an important role, at least, in local relapse. Instead, the amplification and consequent overexpression of the wild-type AR gene seem to be the most common alteration involving the AR in hormone-refractory prostate cancer.
Generating Electrospray from Microchip Devices Using Electroosmotic Pumping (1997)

A method of generating electrospray from solutions emerging from small channels etched on planar substrates is described. The fluids are delivered using electroosmotically induced pressures and are sprayed electrostatically from the terminus of a channel by applying an electrical potential of sufficient amplitude to generate the electrospray between the microchip and a conductor spaced from the channel terminus. No major modification of the microchip is required other than to expose a channel opening. The principles that regulate the fluid delivery are described and demonstrated. A spectrum for a test compound, tetrabutylammonium iodide, that was continuously electrophoresed was obtained by coupling the microchip to an ion trap mass spectrometer.
Detection of Near-Atmospheric Concentrations of CO 2 by an Olfactory Subsystem in the Mouse (2007)

Carbon dioxide (CO2) is an important environmental cue for many organisms but is odorless to humans. It remains unclear whether the mammalian olfactory system can detect CO2 at concentrations around the average atmospheric level (0.038%). We demonstrated the expression of carbonic anhydrase type II (CAII), an enzyme that catabolizes CO2, in a subset of mouse olfactory neurons that express guanylyl cyclase D (GC-D+ neurons) and project axons to necklace glomeruli in the olfactory bulb. Exposure to CO2 activated these GC-D+ neurons, and exposure of a mouse to CO2 activated bulbar neurons associated with necklace glomeruli. Behavioral tests revealed CO2 detection thresholds of approximately 0.066%, and this sensitive CO2 detection required CAII activity. We conclude that mice detect CO2 at near-atmospheric concentrations through the olfactory subsystem of GC-D+ neurons.
Rate Coefficients for the Reactions of Hydroxyl Radicals with Methane and Deuterated Methanes (1997)

The rate coefficients for the reaction of OH with CH3D (k1), CH2D2 (k2), CHD3 (k3), CD4 (k4), and CH4 (k5) as well as that of OD with CH4 (k6) have been measured using the pulsed photolytic production of OH followed by its detection via pulsed laser induced fluorescence. k1−k4 and k6 were measured between ∼220 and ∼415 K, while k5 was measured down to 195 K. The measured rate coefficients do not strictly obey the Arrhenius expression. However, below 298 K, they can be represented by the expressions (in cm3 molecule-1 s-1): k1 = (3.11 ± 0.44) × 10-12 exp[−(1910 ± 70)/T]; k2 = (2.3 ± 1.2) × 10-12 exp[−(1930 ± 250)/T]; k3 = (1.46 ± 0.22) × 10-12 exp[−(1970 ± 70)/T]; k4 = (1.00 ± 0.22) × 10-12 exp[−(2100 ± 120)/T]; k5 = (1.88 ± 0.11) × 10-12 exp[−(1695 ± 30)/T]; k6 = (1.68 ± 0.12) × 10-12 exp[−(1640 ± 40)/T]. The obtained values of the rate coefficients and kinetic isotope effects are compared with values previously measured or calculated by other groups. The atmospheric implications of this data are briefly discussed.
The promoting molecular mechanism of alpha-fetoprotein on the growth of human hepatoma Bel7402 cell line (2002)

These results demonstrate that AFP is a potential growth factor to promote the proliferation of human hepatoma Bel 7402 cells. Its growth-regulatory effects are mediated by its specific plasma membrane receptors coupled with its transmembrane signaling transduction through the pathway of cAMP-PKA and intracellular calcium to regulate the expression of oncogenes.
Motionless volumetric photoacoustic microscopy with spatially invariant resolution (2017)

Abstract Photoacoustic microscopy (PAM) is uniquely positioned for biomedical applications because of its ability to visualize optical absorption contrast in vivo in three dimensions. Here we propose motionless volumetric spatially invariant resolution photoacoustic microscopy (SIR-PAM). To realize motionless volumetric imaging, SIR-PAM combines two-dimensional Fourier-spectrum optical excitation with single-element depth-resolved photoacoustic detection. To achieve spatially invariant lateral resolution, propagation-invariant sinusoidal fringes are generated by a digital micromirror device. Further, SIR-PAM achieves 1.5 times finer lateral resolution than conventional PAM. The superior performance was demonstrated in imaging both inanimate objects and animals in vivo with a resolution-invariant axial range of 1.8 mm, 33 times the depth of field of the conventional PAM counterpart. Our work opens new perspectives for PAM in biomedical sciences.
Recent advancements in cloning by somatic cell nuclear transfer (2012)

Somatic cell nuclear transfer (SCNT) cloning is the sole reproductive engineering technology that endows the somatic cell genome with totipotency. Since the first report on the birth of a cloned sheep from adult somatic cells in 1997, many technical improvements in SCNT have been made by using different epigenetic approaches, including enhancement of the levels of histone acetylation in the chromatin of the reconstructed embryos. Although it will take a considerable time before we fully understand the nature of genomic programming and totipotency, we may expect that somatic cell cloning technology will soon become broadly applicable to practical purposes, including medicine, pharmaceutical manufacturing and agriculture. Here we review recent progress in somatic cell cloning, with a special emphasis on epigenetic studies using the laboratory mouse as a model.
Increased susceptibility to maternal aneuploidy demonstrated by comparative genomic hybridization analysis of human MII oocytes and first polar bodies (2006)

Single cell comparative genomic hybridization (CGH) was employed to extensively investigate 24 unfertilized or in vitromatured meiosis II oocytes and their corresponding first polar bodies (PBs), to determine how and whether all 23 chromosomes participate in female meiosis I errors and to accurately estimate the aneuploidy rate in the examined cells. Results were obtained for 15 oocytes and 16 PBs, representing 23 eggs (MII oocyte-PB complexes) donated from 15 patients (average age 32.2 years). Abnormalities were detected in ten eggs, giving an overall aneuploidy rate of 43.5%. In all, fourteen anomalies were scored, with the fertilized oocyte being at risk of monosomy in eight cases and at risk of trisomy in six; chromosomes of various sizes participated. CGH was able to give a comprehensive aneuploidy rate, as both absence of chromosomal material and the presence of extra copies were accurately scored. The aneuploidy mechanisms determined were: classical whole univalent non-disjunction; chromatid predivision prior to anaphase I, leading to metaphase II imbalance. There was also evidence of germinal mosaicism for a trisomic cell line. Three patients appeared to be predisposed to meiosis I errors, based on the presence of either multiple abnormalities in one or more of their examined cells, or of the same type of abnormality in all of their cells. Exclusion of these susceptible patients reduces the aneuploidy rate to 20%. Various hypotheses are put forward to explain these observations in order to stimulate research into the complex nature of female meiotic regulation.