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PubMed1997

Ischemic tissue oxygen capacitance after hyperbaric oxygen therapy: a new physiologic concept.

In an effort to better understand the effects of hyperbaric oxygen therapy on ischemic tissue, we monitored the real-time changes in subcutaneous tissue oxygen tension before, during, and after exposure to hyperbaric oxygen treatments. We identified an elevation of the tissue oxygen partial pressure to over 300 mmHg during the treatment period (up from a baseline mean of 24 mmHg) in a sustained ischemia rabbit ear model (n = 22 rabbits). There was no sustained change in tissue oxygen tension beyond the period of treatment. This manner of response is consistent with several current theories used to explain the mechanism of action of hyperbaric oxygen therapy. It is also consonant with our opinion that molecular oxygen, when delivered at high pressure, can function both as a respiratory metabolite and as a signal transducer. We also studied the impact of nontherapeutic 100% oxygen at 1 atm on tissue. The sustained peak tissue oxygen tension during such challenges increased in direct proportion to the number of hyperbaric oxygen treatments given. The clinical relevance and extension of these findings are discussed.

Animals↗

PubMed1995

Identification of rat pancreatic duct cells by their expression of cytokeratins 7, 19, and 20 in vivo and after isolation and culture.

Cells from the excretory ducts of the pancreas are thought to be capable of differentiating into exocrine and endocrine cells. To study this in rat models, markers must be found to identify the cells under different experimental conditions. We tested antibodies to different cytokeratins (CKs) by immunocytochemical staining on pancreatic tissue sections from normal rats, after partial pancreatectomy, and after isolation and culture of duct fragments. Monoclonal antibodies to human CK7, CK19, and CK20 were found to react specifically on rat pancreas tissue, as shown by Western blotting. CK20 and CK19 were immunocytochemically detected only in cells of the ductal system, from centroacinar cells to main ducts. CK7 was expressed by islets of Langerhans and by duct cells from main, inter-, and intralobular ducts, but not by centroacinar and terminal duct cells. CKs 7, 19, and 20 were also expressed in proliferating duct cells during tissue regeneration and after isolation and different periods of culture. We conclude that CKs 7, 19, and 20 are very useful markers to study the differentiation of rat duct cells under experimental conditions in vivo and in vitro.

Animals↗

PubMed2003

A Bayesian neural network approach for modelling censored data with an application to prognosis after surgery for breast cancer.

A Bayesian framework is introduced to carry out Automatic Relevance Determination (ARD) in feedforward neural networks to model censored data. A procedure to identify and interpret the prognostic group allocation is also described. These methodologies are applied to 1616 records routinely collected at Christie Hospital, in a monthly cohort study with 5-year follow-up. Two cohort studies are presented, for low- and high-risk patients allocated by standard clinical staging. The results of contrasting the Partial Logistic Artificial Neural Network (PLANN)-ARD model with the proportional hazards model are that the two are consistent, but the neural network may be more specific in the allocation of patients into prognostic groups. With automatic model selection, the regularised neural network is more conservative than the default stepwise forward selection procedure implemented by SPSS with the Akaike Information Criterion.

Bayes Theorem↗

PubMed2026

CRISPR screening identifies DTX4 governing alveolar macrophage cholesterol efflux in pulmonary alveolar proteinosis.

Pulmonary alveolar proteinosis (PAP) is a rare pulmonary syndrome characterized by impaired surfactant clearance, driven by dysfunctional cholesterol efflux in alveolar macrophages (AMs). However, the molecular determinants governing AM cholesterol homeostasis remain incompletely defined. Here, through a genome-wide CRISPR screen in foamy macrophages and bulk RNA sequencing of AMs from PAP patients, we identify DTX4 as a pivotal regulator of cholesterol efflux in AMs. In mice, AAV-mediated silencing of DTX4 led to excessive AM lipid accumulation, exacerbated proteinosis, increased lung opacities, and deteriorated pulmonary function. Similarly, DTX4 depletion in primary AMs impaired cholesterol efflux and promoted intracellular lipid deposition. Conversely, AM-specific overexpression of DTX4 in the Csf2ra-/- PAP model markedly alleviated lipid accumulation, mitigated alveolar proteinosis, restored lung densities, and rescued pulmonary function. Mechanistically, DTX4 stabilizes the GM-CSF receptor via an E3-independent interaction to sustain JAK2/STAT5 signaling, which reciprocally maintains DTX4 transcription. This positive-feedback loop drives PPARγ expression, and its disruption in PAP impairs cholesterol efflux, a defect partially reversible by ectopic PPARγ expression. Collectively, our findings identify DTX4 as a central orchestrator of AM cholesterol efflux and surfactant homeostasis, positioning it as a promising therapeutic target for PAP.

Animals↗

PubMed1991

Drugs, sex and HIV: a mathematical model for New York City.

A data-based mathematical model was formulated to assess the epidemiological consequences of heterosexual, intravenous drug use (IVDU) and perinatal transmission in New York City (NYC). The model was analysed to clarify the relationship between heterosexual and IVDU transmission and to provide qualitative and quantitative insights into the HIV epidemic in NYC. The results demonstrated the significance of the dynamic interaction of heterosexual and IVDU transmission. Scenario analysis of the model was used to suggest a new explanation for the stabilization of the seroprevalence level that has been observed in the NYC IVDU community; the proposed explanation does not rely upon any IVDU or sexual behavioural changes. Gender-specific risks of heterosexual transmission in IVDUs were also explored by scenario analysis. The results showed that the effect of the heterosexual transmission risk factor on increasing the risk of HIV infection depends upon the level of IVDU. The model was used to predict future numbers of adult and pediatric AIDS cases; a sensitivity analysis of the model showed that the confidence intervals on these prediction estimates were extremely wide. This prediction variability was due to the uncertainty in estimating the values of the models' thirty variables (twenty biological-behavioural transmission parameters and the initial sizes of ten subgroups). However, the sensitivity analysis revealed that only a few key variables were significant in contributing to the AIDS case prediction variability; partial rank correlation coefficients were calculated and used to identify and to rank the importance of these key variables. The results suggest that long-term precise estimates of the future number of AIDS cases will only be possible once the values of these key variables have been evaluated accurately.

Female↗

PubMed2003

Lipid bilayer simulations of CXCR4 with inverse agonists and weak partial agonists.

CXCR4 is a G protein-coupled receptor (GPCR) that has multiple critical functions in normal and pathologic physiology that include regulation of the metastatic behavior of mammary carcinoma, and utilization as a coreceptor for infection by T-tropic strains of human immunodeficiency virus-1. Molecular dynamic simulations of the rhodopsin-based homology model of CXCR4 were performed in a solvated lipid bilayer to reproduce the microenvironment of this integral membrane protein. The amino acids in CXCR4 necessary for interaction with an inverse agonist, T140, and a weak partial agonist, AMD3100, identified by alanine scanning mutants, were spatially consistent when computationally docked. Whereas T140 binds residues in extracellular domains and regions of the hydrophobic core proximal to the cell surface, amino acids in the central hydrophobic core are critical to binding of AMD3100. The physical localization of T140 binding to CXCR4 by biochemical analyses corroborated the molecular and computational approaches. The structural basis for the interaction of T140 and AMD3100 with CXCR4 confirms that the mechanisms used by these agents are different. This complementary utilization of molecular, physical, and computation analysis provides a powerful approach to elucidate GPCR conformation.

Amino Acid Substitution↗

PubMed1998

Multivariable prediction of seizure outcome one year after resective epilepsy surgery: development of a model with independent validation.

PURPOSE: To identify predictors of seizure-outcome after epilepsy surgery and validate the findings in an independent series of patients. To use the results to develop a predictive model. METHODS: Sequential patients undergoing resective surgery for medically intractable epilepsy were identified at Yale New Haven Hospital (1987-1990, group 1) and Columbia Presbyterian Hospital (1991-1994, group 2). Information about seizure outcome and predictors of outcome was obtained from medical chart review. Good seizure-outcome was defined as having been seizure-free for one year beginning with discharge from the hospital. Multiple logistic regression was used to develop a model of predictors in group 1. It was then validated in group 2. RESULTS: There were 133 patients in group 1 and 81 in group 2. In a multivariable analysis, independent predictors of outcome in group 1 were presence of mesial temporal sclerosis based on postsurgical pathological analysis (MTS) (relative risk (RR) = 1.47), having a known underlying etiology (RR = 1.32), and partial seizures only (RR = 1.17). In group 2, the findings for each factor were similar to those in group 1: MTS, RR = 1.49; etiology, RR = 1.32; and partial seizures, RR = 1.24. Used in combination, these three factors can identify patients with nearly a 100% chance of being seizure-free (all three factors present) versus less than a 50% chance (none of the three factors present). CONCLUSIONS: With independent validation of the findings, we can be reasonably certain that the three factors identified in this analysis are meaningful and generalizable predictors of seizure outcome following epilepsy surgery. Use of predictive models should be considered in future studies to convert study results into clinically relevant statements about a particular patient's likelihood of surgical success.

Adolescent↗

PubMed1995

Simultaneous measurement of glucose and glutamine in aqueous solutions by near infrared spectroscopy.

A method is described for measuring the concentrations of both glucose and glutamine in binary mixtures from near infrared (NIR) absorption spectra. Spectra are collected over the range from 5000-4000/cm (2.0-2.5 microns) with a 1-mm optical path length. Glucose absorbance features at 4710, 4400, and 4300/cm and glutamine features at 4700, 4580, and 4390/cm provide the analytical information required for the measurement. Multivariate calibration models are generated by using partial least squares (PLS) regression alone and PLS regression combined with a preprocessing digital Fourier filtering step. The ideal number of PLS factors and spectral range are identified separately for each analyte. In addition, the optimum Fourier filter parameters are established for both compounds. The best overall analytical performance is obtained by combining Fourier filtering and PLS regression. Glucose measurements are established over the concentration range from 1.66-59.91 mM, with a standard error of prediction (SEP) of 0.32 mM and a mean percent error of 1.84%. Glutamine can be measured over the concentration range from 1.10-30.65 mM with a SEP of 0.75 mM and a mean percent error of 6.67%. These results demonstrate the analytical utility of NIR spectroscopy for monitoring glucose and glutamine levels in mammalian and insect cell cultures.

Buffers↗

PubMed1991

Cell surface proteins of Entamoeba histolytica.

To ask what is new in Entamoeba histolytica research, one need look no further than the surface of this protozoan parasite. In the past year the cloning and partial characterization of five different surface antigens have been reported, a remarkable result of international research efforts against amebiosis. One of these proteins is the first protective immunogen identified in the animal model of amebic liver abscess. Barbara Mann and William Petri review these recent results, propose a nomenclature for the gene family of E. histolytica galactose lectins and discuss the roles of the different surface proteins in adhesion.

Journal Article↗

PubMed1998

MtENOD16 and 20 are members of a family of phytocyanin-related early nodulins.

We have identified two single-copy genes from the model legume. Medicago truncatula (MtENOD16 and 20) whose expression can be correlated with early stages of root nodulation and whose predicted coding sequences are partially homologous to both pea/vetch ENOD5 and soybean N315/ENOD55. Database searching and sequence alignment have defined the encoded early nodulins as a distinct sub-family of phytocyanin-related proteins, although the absence of key ligands implies that they are unlikely to bind copper. Molecular modelling based on known phytocyanin structure has been used to predict the 3-dimensional conformation of the principle globular domain of MtENOD16/20. Additional structural features common to both early nodulin and phytocyanin precursors include an N-terminal transit peptide, a highly variable (hydroxy)proline-rich sequence which probably undergoes extensive post-translational modification, and a hydrophobic C-terminal tail.

Amino Acid Sequence↗

PubMed2001

Nitration of succinyl-CoA:3-oxoacid CoA-transferase in rats after endotoxin administration.

The tyrosine nitration of proteins has been observed in diverse inflammatory conditions and has been linked to the presence of reactive nitrogen species. From many in vitro experiments, it is apparent that tyrosine nitration may alter the function of proteins. A limited number of experiments under in vivo conditions also demonstrate that protein nitration is associated with altered cellular processes. To understand the association of protein nitration with the pathogenic mechanism of the disease, it is essential to identify specific protein targets of nitration with in vivo or intact tissue models. Using anti-nitrotyrosine antibodies, we demonstrated the accumulation of nitrotyrosine in a 52-kDa protein in rat kidney after lipopolysaccharide treatment. The 52-kDa protein was purified and identified with partial sequence as succinyl-CoA:3-oxoacid CoA-transferase (SCOT; EC ). Western blot analysis revealed that the nitration of this mitochondrial enzyme increased in the kidneys and hearts of lipopolysaccharide-treated rats, whereas its catalytic activity decreased. These data suggest that tyrosine nitration may be a mechanism for the inhibition of SCOT activity in inflammatory conditions. SCOT is a key enzyme for ketone body utilization. Thus, tyrosine nitration of the enzyme with sepsis or inflammation may explain the altered metabolism of ketone bodies present in these disorders.

Amino Acid Sequence↗

PubMed2004

pH-dependent Interactions of the carboxyl-terminal helix of steroidogenic acute regulatory protein with synthetic membranes.

Steroidogenic acute regulatory (StAR) protein facilitates import of cholesterol into adrenal and gonadal mitochondria where cholesterol is converted to pregnenolone, initiating steroidogenesis. StAR acts exclusively on the outer mitochondrial membrane (OMM) by unknown mechanisms. To identify StAR domains involved in membrane association, we reacted N-62 StAR with small unilamellar vesicles (SUVs) composed of lipids resembling the OMM. Solvent-exposed domains were digested with trypsin, Asp-N, or pepsin at different pH levels, and StAR peptides protected from proteolysis were identified by mass spectrometry. At pH 4 SUVs completely protected residues 259-282; at pH 6.5 this region was partially digested into 254-272, 254-273, and 254-274. Computer-graphic modeling of N-62 StAR indicated these peptides correspond to the C-terminal alpha4 helix and that residues Leu(275), Thr(263), and Arg(272) in alpha4 form stabilizing interactions with Gln(128), Asp(150), and Asp(106) in adjacent loops. CD spectroscopy of a 37-mer model of alpha4 (residues 247-287) indicated a random coil in aqueous buffer, but in 40% methanol the peptide was alpha-helical and achieved maximal alpha-helicity at pH 5.0 in the presence of SUVs. Reacting the 37-mer with diethyl pyrocarbamate incorporated into SUVs increased the number of modified residues. Thus the C-terminal alpha4 helix is critically involved in the membrane association of StAR with OMM lipids. The membrane association and the alpha-helical structure of the C terminus in the presence of OMM lipids are also pH-dependent. These results further support StAR undergoing a pH-dependent change in its conformation when interacting with the acidic phospholipid head groups of a membrane.

Amino Acid Sequence↗

PubMed2006

MotifScorer: using a compendium of microarrays to identify regulatory motifs.

UNLABELLED: We describe MotifScorer, a program for systematic genome-wide identification of transcription sites. The program uses a compendium of gene expression microarrays and implements state-of-art partial least squares (PLSs) based regression and stepwise regression procedures. Candidate motifs from the upstream sequences of groups of co-regulated genes are identified and assigned a score using genomic background models and available motif finding tools. The use of a large library of expression data allows statistical comparative analysis of the specificity of motifs identified in different conditions. AVAILABILITY: MotifScorer, which is written in Java and Matlab, manual and example files are available from the authors.

Algorithms↗

PubMed2006

c-Jun/AP-1 controls liver regeneration by repressing p53/p21 and p38 MAPK activity.

The AP-1 transcription factor c-Jun is a key regulator of hepatocyte proliferation. Mice lacking c-Jun in the liver (c-jun (Deltali*)) display impaired liver regeneration after partial hepatectomy (PH). This phenotype correlates with increased protein levels of the cdk-inhibitor p21 in the liver. We performed PH experiments in several double-knockout mouse models to genetically identify the signaling events regulated by c-Jun. Inactivation of p53 in c-jun (Deltali*) mice abrogated both hepatocyte cell cycle block and increased p21 protein expression. Consistently, liver regeneration was rescued in c-jun (Deltali*) p21 (-/-) double-mutant mice. This indicated that c-Jun controls hepatocyte proliferation by a p53/p21-dependent mechanism. Analyses of p21 mRNA and protein expression in livers of c-jun (Deltali*) mice after PH revealed that the accumulation of p21 protein is due to a post-transcriptional/post-translational mechanism. We have investigated several candidate pathways implicated in the regulation of p21 expression, and observed increased activity of the stress kinase p38 in regenerating livers of c-jun (Deltali*) mice. Importantly, conditional deletion of p38alpha in livers of c-jun (Deltali*) mice fully restored hepatocyte proliferation and attenuated increased p21 protein levels after PH. These data demonstrate that c-Jun/AP-1 regulates liver regeneration through a novel molecular pathway that involves p53, p21, and the stress kinase p38alpha.

Animals↗

PubMed1992

Cellular processing of growth hormone in IM-9 cells: evidence for exocytosis of internalized hormone.

IM-9 cells extensively internalize [125I]human (h) GH at physiological temperatures, yet little is known regarding the final destination of internalized hormone and its receptor. We studied this by first binding [125I]hGH to the cell surface at 4 C, and then following its fate during a subsequent incubation at 30 C in isotope-free medium. Cell-associated radioactivity decreased with time at 30 C, with a biphasic pattern suggestive of a rapid (but minor) and a slow component. The kinetics of the latter were critically influenced by NH4Cl and were abolished at 20 C. Intracellular (acid-resistant) [125I]hGH first increased with time at 30 C until it reached a maximum after 1 h, then declined continuously upon prolonged incubation. The radioactivity released by the cells was recovered in the medium as both trichloroacetic acid-precipitable material and trichloroacetic acid-soluble fragments. After sodium dodecyl sulfate-polyacrylamide gel electrophoresis under reducing conditions, one major band migrating with an estimated mol wt of 22,000 was identified, presumably corresponding to intact [125I]hGH. These data suggest exocytosis of intact hormone via recycling endosomes and degradation in the lysosomes, respectively. Computer modelling was consistent with two intracellular compartments acting partially in series and probably corresponding to these two organelles. When analyzed by computer curve fitting, this model accurately described the kinetics of [125I]hGH internalization. So, receptor-mediated endocytosis and subsequent exocytosis are part of the GH pathway in IM-9 cells. In as much as they reflect pathways of GH receptors, these processes contribute to receptor down-regulation and could provide an explanation for release into the medium of the high affinity GH-binding protein.

Cell Line↗

PubMed1999

Estrogen receptor immunoreactivity in the adult primate brain: neuronal distribution and association with p75, trkA, and choline acetyltransferase.

The neuroactive steroid hormone, estrogen, has been implicated in both the prevention and treatment of Alzheimer's disease. Interactions between estrogen and neurotrophic systems may partially explain the beneficial effects of estrogen therapy. Previous studies have identified estrogen binding sites colocalized with neurotrophin-related proteins and mRNA within the rodent brain. Extending these studies to a model more relevant to human systems, we have mapped the distribution of estrogen receptor alpha (ER-alpha)-immunoreactive neurons in adult nonhuman primate brains. In addition, we used double-label immunohistochemistry to examine colocalization of ER-alpha with the low- and high-affinity neurotrophin receptors, p75 and trkA, and with the cholinergic marker choline acetyltransferase. Large numbers of ER-alpha-immunoreactive cells were detected in several amygdaloid and hypothalamic nuclei. ER-alpha-labeled cells were also found in the lateral septum, nucleus of the stria terminals, subfornical organ, and periaqueductal gray. Only rare, scattered ER-alpha-immunoreactive cells were noted in the cholinergic basal forebrain. In contrast to rodents, no cells exhibited ER-alpha and p75 or ER-alpha and trkA double-labeling. However, ER-labeled neurons in the amygdala, a region containing putative nerve growth factor-producing cells and exhibiting a role in memory, were densely and specifically invested with cholinergic terminals projecting from the basal forebrain. Estrogen-labeled neurons were also present in the lateral septal nucleus, a system that receives hippocampal inputs and projects to the neurotrophin-sensitive medial septum. Thus, interactions between neurotrophin-sensitive neurons and ER-bearing neurons exist in the primate brain, providing a potential paracrine basis for estrogen-state modulation of vulnerability to Alzheimer's disease.

Animals↗

PubMed1999

[Psychosocial determinants of lithium compliance in patients with bipolar disorder].

Physical, cognitive, and social factors play a central role in the lithium compliance of people with bipolar disorder. However, studies provide only a partial understanding of this phenomenon and there is currently no nursing model that takes into consideration a combination of factors. This study, based on Pender's preventive health beliefs model, was intended to identify the psychosocial determinants of lithium compliance. A random sample (n = 149) of outpatients at a large Montreal psychiatric hospital was used to measure lithium compliance on the basis of 5 criteria: compliance according to the nurse and according to the patient, appointment compliance, and compliance according to two criteria related to hyperuricemia. Polytomous logistic regression analyses were computed by regressing a composite of these criteria on sociodemographic variables and on the variables of the Pender model: susceptibility, seriousness, control over health, motivation to be healthy, perceived benefits and obstacles, and triggering factors. It appears that being female, being elderly, living with a partner, and perceived treatment benefits and obstacles are determining factors in lithium compliance. These results are all the more important in light of Quebec's newly implemented drug insurance plan, which could increase the obstacles to medication. Nurses will have to be increasingly vigilant with respect to these new obstacles and will have to adjust their interventions accordingly.

Adult↗

PubMed1997

Prediction of complete gene structures in human genomic DNA.

We introduce a general probabilistic model of the gene structure of human genomic sequences which incorporates descriptions of the basic transcriptional, translational and splicing signals, as well as length distributions and compositional features of exons, introns and intergenic regions. Distinct sets of model parameters are derived to account for the many substantial differences in gene density and structure observed in distinct C + G compositional regions of the human genome. In addition, new models of the donor and acceptor splice signals are described which capture potentially important dependencies between signal positions. The model is applied to the problem of gene identification in a computer program, GENSCAN, which identifies complete exon/intron structures of genes in genomic DNA. Novel features of the program include the capacity to predict multiple genes in a sequence, to deal with partial as well as complete genes, and to predict consistent sets of genes occurring on either or both DNA strands. GENSCAN is shown to have substantially higher accuracy than existing methods when tested on standardized sets of human and vertebrate genes, with 75 to 80% of exons identified exactly. The program is also capable of indicating fairly accurately the reliability of each predicted exon. Consistently high levels of accuracy are observed for sequences of differing C + G content and for distinct groups of vertebrates.

Animals↗