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Results for “Partially Identified Models”

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At least 307 records · Page 17Linked to original sources

PubMed1996

[Prognostic factors of Pneumocystis carinii pneumonia in AIDS].

OBJECTIVES: Identify prognosis factors in Pneumocystis carinii pneumonia at diagnosis and construct a model to predict mortality according to these prognosis factors. METHODS: Seventy-seven consecutive cases of proven AIDS-related Pneumocystis carinii pneumonia (67 men, 10 women, mean age 37.2 years) were reviewed to determine the most accurate initial prognostic factors and estimate an individual prediction of death. A stepwise logistic regression analysis was performed. Three kinds of data were entered into the logistic model: historical data, clinical and laboratory data obtained within the first 24 hours of diagnosis, and specific data related to chest X-ray and bronchoalveolar lavage results. RESULTS: The sum of arterial partial pressure of oxygen and carbon dioxide (PaO2 + PaCO2) and serum albumin level best predicted a fatal outcome in multivariate analysis. CONCLUSION: The logistic equation provided by the model might be used to accurately and quickly identify the patients with severe Pneumocystis carinii pneumonia who might benefit from supportive intensive care.

AIDS-Related Opportunistic Infections↗

PubMed2005

Identification of reaction networks for bioprocesses: determination of a partially unknown pseudo-stoichiometric matrix.

In this paper we propose a methodology to determine the structure of the pseudo-stoichiometric coefficient matrix K in a mass balance-based model and to identify its coefficients from a set of available data. The first stage consists in estimating the number of reactions that must be taken into account to represent the main mass transfer within the bioreactor. This provides the dimension of K. Then we propose a method to directly determine the structure of the matrix (i.e. mainly its zeros and the signs of its coefficients). These methods are illustrated with simulations of a process of lipase production from olive oil by Candida rugosa.

Algorithms↗

PubMed2002

Clinical study to identify specific characteristics of cancer newly developed in the remnant stomach.

BACKGROUND: Cancer newly developed in the remnant stomach (CRS) after partial gastrectomy is worthy of attention not only because it is a typical model of carcinogenesis but also from the aspect of cancer diagnosis. METHODS: We treated 47 patients with CRS in the 20 years from 1979 to 1998. Clinicopathological variables, as well as long-term survival results after the second surgery, were reviewed to clarify whether there were any differences in the characteristics of this disease entity compared with the usual primary gastric cancer. RESULTS: The mean time interval between the initial surgery and surgery for CRS was 25.8 years for patients with CRS with previous benign gastric lesions, and 10.6 years for those with previous gastric cancer. CRS was frequently detected at an early stage in the patients with previous cancer, and in the patients who had undergone reconstruction by the Billroth I method (regardless of the primary nature of the disease). Cancers with a differentiated histology developed more frequently in the patients who had undergone the initial surgery for cancer disease. Long-term survival results after the second surgery clearly demonstrated that surgical treatment for CRS was as effective as that for primary cancer in the upper stomach (PUC). In addition, it was confirmed that new lymphatic drainage into the lower mediastinum or the jejunal mesentery had developed after the initial gastric surgery. CONCLUSION: The findings suggested that patients with CRS and those with PUC should be treated similarly, although the findings of a high incidence of lymph node metastasis to the lower mediastinum and/or to the jejunal mesentery in the CRS patients should be taken into consideration.

Aged↗

PubMed2003

Identification of regions of the tomato gamma-glutamyl kinase that are involved in allosteric regulation by proline.

The first step of proline biosynthesis is catalyzed by gamma-glutamyl kinase (GK). To better understand the feedback inhibition properties of GK, we randomly mutagenized a plasmid carrying tomato tomPRO1 cDNA, which encodes proline-sensitive GK. A pool of mutagenized plasmids was transformed into an Escherichia coli GK mutant, and proline-overproducing derivatives were selected on minimal medium containing the toxic proline analog 3,4-dehydro-dl-proline. Thirty-two mutations that conferred 3,4-dehydro-dl-proline resistance were obtained. Thirteen different single amino acid substitutions were identified at nine different residues. The residues were distributed throughout the N-terminal two-thirds of the polypeptide, but 9 mutations affecting 6 residues were in a cluster of 16 residues. GK assays revealed that these amino acid substitutions caused varying degrees of diminished sensitivity to proline feedback inhibition and also resulted in a range of increased proline accumulation in vivo. GK belongs to a family of amino acid kinases, and a predicted three-dimensional model of this enzyme was constructed on the basis of the crystal structures of three related kinases. In the model, residues that were identified as important for allosteric control were located close to each other, suggesting that they may contribute to the structure of a proline binding site. The putative allosteric binding site partially overlaps the dimerization and substrate binding domains, suggesting that the allosteric regulation of GK may involve a direct structural interaction between the proline binding site and the dimerization and catalytic domains.

Alleles↗

PubMed1985

Refinement of a molecular model for lamprey hemoglobin from Petromyzon marinus.

A molecular model for the protein and ambient solvent of the complex of cyanide with methemoglobin V from the sea lamprey Petromyzon marinus yields an R-factor of 0.142 against X-ray diffraction data to 2.0 A resolution. The root-mean-square discrepancies from ideal bond length and angle are, respectively, 0.014 A and 1.5 degrees. Atoms that belong to planar groups deviate by 0.012 A from planes determined by a least-squares procedure. The average standard deviation for chiral volumes, peptide torsion angle and torsion angles of side-chains are 0.150 A3, 2.0 degrees and 19.4 degrees, respectively. The root-mean-square variation in the thermal parameters of bonded atoms of the polypeptide backbone is 1.21 A2; the variation in thermal parameters for side-chain atoms is 2.13 A2. The model includes multiple conformations for 11 side-chains of the 149 amino acid residues of the protein. We identify 231 locations as sites of water molecules in full or partial occupancy. The sum of occupancy factors for these sites is approximately 154, representing 28% of the 550 molecules of water within the crystallographic asymmetric unit. The environment of the heme in the cyanide complex of lamprey methemoglobin resembles the deoxy state of the mammalian tetramer. In particular, the bond between atom NE2 of the proximal histidine and the Fe lies 5.1 degrees from the normal of the heme plane. In deoxy- and carbonmonoxyhemoglobins, the deviations from the normal to the heme plane are 7 to 8 degrees and 1 degree, respectively. Furthermore, the inequality in the distance of atom CD2 of the proximal histidine from the pyrrole nitrogen of ring-C of the heme (distance = 3.29 A) and CE1 from the pyrrole nitrogen of ring-A (distance = 3.06 A) is characteristic of deoxyhemoglobin, not carbonmonoxyhemoglobin, where these distances are equal. Finally, a hydrogen bond exists between carbonyl 111 and the hydroxyl of tyrosine 149. The corresponding hydrogen link in the mammalian tetramer is central to the T to R state transition and is present in deoxyhemoglobin but absent in carbonmonoxyhemoglobin. We suggest that the low affinity of oxygen for lamprey hemoglobin may be a consequence of these T-state geometries.

Amino Acid Sequence↗

PubMed2026

Understanding tumor adaptations and resistance to MET inhibitors in MET-altered non-small cell lung cancer.

AIM: Type Ib MET inhibitors are clinically active in selected MET-altered non-small cell lung cancer, particularly tumors with MET exon 14 skipping or MET amplification, but acquired resistance remains incompletely understood. Here, we investigated resistance across biologically distinct MET-altered contexts, including MET exon 14 skipping, MET amplification, and MET overexpression. METHODS: Paired baseline and progression samples from seven patients treated with tepotinib or capmatinib were analyzed using spatial transcriptomics, whole-exome sequencing, RNA sequencing, CRISPR screening, and drug-combination assays. Patient-derived cultures and resistant cell-line models were used to explore resistance-associated changes. RESULTS: MET inhibitor resistance was heterogeneous, with persistence of the initial MET alteration in most evaluable cases and emergence of patient-specific genomic events. Three main resistance-associated, often overlapping, routes were identified: on-target MET evolution through kinase-domain alterations; extracellular matrix and tumor-microenvironment remodeling, including collagen and fibronectin upregulation, complement-related signaling, and partial EMT-associated programs; and bypass signaling involving EGFR/HER, MAPK, and PI3K/Akt pathways. In vitro models reproduced several tumor-cell-intrinsic features but only partially captured microenvironment-associated changes. CONCLUSIONS: MET inhibitor resistance in this cohort involved overlapping, context-dependent genomic, phenotypic, and signaling adaptations, supporting combination strategies for MET-altered lung cancer.

CRISPR screen↗

PubMed2005

Model-based detection of partially obstructed endotracheal tube.

OBJECTIVES: A five-element lumped pulmonary model was developed to estimate respiratory mechanics automatically and noninvasively. The model was applied to diagnose obstructed endotracheal tube. Events like bronchospasm and stiff chest wall were also tested to determine the specificity of the diagnosis. Cases with positive end-expiratory pressure were also included in the analysis to see the effects of positive end-expiratory pressure on the model. DESIGN: Randomized controlled animal study. SETTING: University department of anesthesiology. SUBJECTS: Ten anesthetized, paralyzed, and mechanically ventilated mongrel dogs (19-45 kg) of either gender. INTERVENTIONS: Two levels of upper airway obstruction were induced in ten dogs by partially constricting the endotracheal tube. Acute bronchial constriction was produced in five dogs by injecting methacholine through a central venous catheter. In the same five dogs, the chest wall was stiffened by wrapping a pressure cuff around the chest. Positive end-expiratory pressure was also applied as a separate event in these five animals. MEASUREMENTS AND MAIN RESULTS: Airway pressure and flow were continuously recorded at the mouth. Model parameters were iteratively identified until the root mean square error between respiratory impedance (obtained from airway pressure and flow) and model-predicted impedance (calculated using Ohm's law) was minimum. The peak inspiratory pressure increased and the peak expiratory flow rate decreased with increasing levels of partial obstruction. The value of the model parameters R(1) and C(2) increased and C(1) decreased with partial obstructed endotracheal tube, whereas R(1) increased and L and C(2) decreased with bronchospasm. With stiff chest wall, R(2) increased and C(2) decreased. With positive end-expiratory pressure, the L parameter decreased and no significant change in other model parameters was observed. Obstructed endotracheal tube is indicated if R(1) increased > or =30%, C(1) decreased > or =10%, and C(2) increased > or =10% from baseline. The test results using 45 events, including control, three complications, and positive end-expiratory pressure, show that when the model is used to diagnose obstructed endotracheal tube, the method has a sensitivity of 90% and specificity of 97%. CONCLUSIONS: During an obstructed endotracheal tube, model parameters change such that the event can be diagnosed noninvasively, automatically, and accurately. The model differentiates between upper airway obstruction and complications like bronchospasm and stiff chest wall.

Airway Resistance↗

PubMed1997

Inheritance of hypoxic exercise tolerance in mice.

All mammals tested, when exposed acutely to a degree of hypoxia above some threshold, exhibit a reduced capacity to perform work. Chronic hypoxic exposure is usually associated with some degree of acclimation resulting in partial recovery of the preexposure work capacity. The present study reports that, among mice, interindividual variability in recovery of ability to tolerate a standardized hypoxic exercise [t(et); time elapsed in treadmill exercise in hypoxia until 4-s failure to avoid a grid configured to deliver a mild aversive current (0.15 mA)], after 8 weeks' exposure to half-atmospheric pressure, is influenced predominantly by two unlinked genes of major effect. Two approaches were taken toward genetic characterization. In one, a maximum-likelihood procedure was applied to 11 models of genetic determinacy in the t(et) distributions of BALB/cBy (C) and C57BL/6By (B6) parental inbred strains, their F1 hybrid, and the backcross (BC) generations. Breeding tests of the resulting candidate "best-fit" major locus inheritance models involved repeated cycles of selecting, as the progenitor of a new BC generation, the male with the highest value of the test variable in the previous BC generation, and breeding him to C females. Mice from each of four distinct phenotypes appearing in BC3 were bred to C mice, producing distributions expected from two-locus segregation. The second approach was based upon CXB/By RI strain distribution pattern and derivative breeding tests to reveal phenotypic distributions consistent with two-locus inheritance of tet. Melding these results with a positional cloning strategy may permit relating a behavioral difference to specific heritable elements and identifying their products as the (partial) physiological substrata of the behavior.

Animals↗

PubMed2002

Aflatoxin, hepatitis and worldwide liver cancer risks.

Aflatoxins are among the most potent mutagenic and carcinogenic substances known. Differential potency of aflatoxin among species can be partially attributed to differences in metabolism; however, current information on competing aspects of metabolic activation and detoxification of aflatoxin in various species does not identify an adequate animal model for humans. Risk of liver cancer is influenced by a number of factors, most notably carriage of hepatitis B virus as determined by the presence in serum of the hepatitis B surface antigen (HBsAg+ or HBsAg-). About 50 to 100% of liver cancer cases are estimated to be associated with persistent infection of hepatitis B (or C) virus. The potency of aflatoxin in HBsAg+ individuals is substantially higher (about a factor of 30) than the potency in HBsAg- individuals. Thus, reduction of the intake of aflatoxins in populations with a high prevalence of HBsAg+ individuals will have greater impact on reducing liver cancer rates than reductions in populations with a low prevalence of HbsAg+ individuals. The present analysis suggests that vaccination against hepatitis B (or protection against hepatits C), which reduces prevalence of carriers, would reduce the potency of the aflatoxins in vaccinated populations and reduce liver cancer risk.

Aflatoxins↗

PubMed2025

Demonstrating the potential of untargeted hair proteomics for personalized biomarkers in stress-associated disorders.

Biomarker research in psychopathology increasingly employs high-dimensional Omics approaches. Yet, proteomics based on human hair remain largely unexplored, despite its potential to efficiently capture stable biological signals accumulated over weeks to months. This study leveraged machine learning to investigate the potential of the hair proteome-all detectable peptides and proteins-as a biomarker source for stress-associated psychopathology. We analyzed protein profiles from hair segments of women with non-suicidal self-injury disorder and healthy controls (N = 68). Of 1114 identified proteins, 611 were sufficiently abundant for analyses. Partial Least Squares Discriminant Analysis achieved stable 84.4 % cross-validated accuracy for classification of clinical groups (p < .001), outperforming models based on data-derived clusters (60 %), stress-related proteins (73 %), and simulated hair cortisol from meta-analytic effect sizes (53-59 %). Predicted class probabilities strongly correlated with clinical symptoms and well-being (r > .60). Key predictive proteins were linked to pain perception, oxidative stress, and cholesterol homeostasis. Approximately 15 % of proteins differed significantly between groups, with the strongest candidates related to ribosomal function-an emerging target in depression. These findings establish hair proteomics as a promising, non-invasive biomarker source for psychiatric research with potential clinical applications in risk assessment and personalized interventions.

Humans↗

PubMed2001

New World monkey efficacy trials for malaria vaccine development: critical path or detour?

Neither GMP malaria antigens nor GMP vaccines have been compared for efficacy in monkeys and humans. It is too risky to base categorical (go/no go) development decisions on results obtained using partially characterized (non-GMP) antigens, adjuvants that are too toxic for human use or unvalidated primate models. Such practices will lead to serious errors (e.g. failure to identify and stop flawed efforts, rejection of effective vaccine strategies) and unjustifiable delays. Successful malaria vaccine development will emphasize definitive field trials in populations at risk of malaria to define and improve vaccine efficacy.

Animals↗

PubMed2002

Detecting and quantifying sunflower oil adulteration in extra virgin olive oils from the eastern mediterranean by visible and near-infrared spectroscopy.

One hundred and thirty-eight oil samples have been analyzed by visible and near-infrared transflectance spectroscopy. These comprised 46 pure extra virgin olive oils and the same oils adulterated with 1% (w/w) and 5% (w/w) sunflower oil. A number of multivariate mathematical approaches were investigated to detect and quantify the sunflower oil adulterant. These included hierarchical cluster analysis, soft independent modeling of class analogy (SIMCA method), and partial least squares regression (PLS). A number of wavelength ranges and data pretreatments were explored. The accuracy of these mathematical models was compared, and the most successful models were identified. Complete classification accuracy was achieved using 1st derivative spectral data in the 400-2498 nm range. Prediction of adulterant content was possible with a standard error equal to 0.8% using 1st derivative data between 1100 and 2498 nm. Spectral features and chemical literature were studied to isolate the structural basis for these models.

Food Contamination↗

PubMed2006

Application of Fourier transform midinfrared spectroscopy to the discrimination between Irish artisanal honey and such honey adulterated with various sugar syrups.

A collection of authentic artisanal Irish honeys (n = 580) and certain of these honeys adulterated by fully inverted beet syrup (n = 280), high-fructose corn syrup (n = 160), partial invert cane syrup (n = 120), dextrose syrup (n = 160), and beet sucrose (n = 120) was assembled. All samples were adjusted to 70 degrees Bx and scanned in the midinfrared region (800-4000 cm(-1)) by attenuated total reflectance sample accessory. By use of soft independent modeling of class analogy (SIMCA) and partial least-squares (PLS) classification, authentic honey and honey adulterated by beet sucrose, dextrose syrups, and partial invert corn syrup could be identified with correct classification rates of 96.2%, 97.5%, 95.8%, and 91.7%, respectively. This combination of spectroscopic technique and chemometric methods was not able to unambiguously detect adulteration by high-fructose corn syrup or fully inverted beet syrup.

Beta vulgaris↗

PubMed2003

A computational study to elucidate the extraordinary reactivity of three-membered heterocycles in nucleophilic substitution reactions.

The accelerated rates of small-membered heterocycles relative to acyclic analogues are typically rationalized solely in terms of relief of ring strain. The relative rates of attack of ammonia on oxirane, oxetane, thiirane, and thietane were determined computationally in the gas phase at the MP2(Full)/6-31+G(d) level with respect to the model acyclic compounds methoxyethane and thiomethylethane. Because the cyclic ether and thioether pairs have very similar strain energies, they should react at similar rates by the S(N)2 mechanism if the degree of strain energy release in the transition state is approximately equal. The reactivity of the four-membered rings could be explained almost entirely by relief of strain. The three-membered rings reacted at rates at least 10(6) times faster than calculated from ring strain considerations alone. The electronic distribution of the transition states was determined using AIM methodology and found to indicate that bond cleavage was virtually complete, while bond formation was incomplete. Calculation of atomic charges by the Mulliken, AIM, CHELPG, and NBO methods indicated that positive charge at the reaction center was significantly lower for the three-membered rings than other members of the series. A simple electrostatic model identified differences in energy sufficient to account for the observed rate acceleration. The unique topological features of a three-membered ring make it possible for the partially negatively charged oxygen or sulfur to reduce the positive charge on the reaction center.

Journal Article↗

PubMed2004

Solution structure of a ubiquitin-like domain from tubulin-binding cofactor B.

Proper folding and assembly of tubulin alphabeta-heterodimers involves a stepwise progression mediated by a group of protein cofactors A through E. Upon release of the tubulin monomers from the chaperonin CCT, they are acted upon by each cofactor in the folding pathway through a unique combination of protein interaction domains. Three-dimensional structures have previously been reported for cofactor A and the C-terminal CAP-Gly domain of cofactor B (CoB). Here we report the NMR structure of the N-terminal domain of Caenorhabditis elegans CoB and show that it closely resembles ubiquitin as was recently postulated on the basis of bioinformatic analysis (Grynberg, M., Jaroszewski, L., and Godzik, A. (2003) BMC Bioinformatics 4, 46). CoB binds partially folded alpha-tubulin monomers, and a putative tubulin-binding motif within the N-terminal domain is identified from sequence and structure comparisons. Based on modeling of the homologous cofactor E ubiquitin-like domain, we hypothesize that cofactors B and E may associate via their beta-grasp domains in a manner analogous to the PB1 and caspase-activated deoxyribonuclease superfamily of protein interaction domains.

Amino Acid Sequence↗

PubMed2003

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies.

The spliced alignment of expressed sequence data to genomic sequence has proven a key tool in the comprehensive annotation of genes in eukaryotic genomes. A novel algorithm was developed to assemble clusters of overlapping transcript alignments (ESTs and full-length cDNAs) into maximal alignment assemblies, thereby comprehensively incorporating all available transcript data and capturing subtle splicing variations. Complete and partial gene structures identified by this method were used to improve The Institute for Genomic Research Arabidopsis genome annotation (TIGR release v.4.0). The alignment assemblies permitted the automated modeling of several novel genes and >1000 alternative splicing variations as well as updates (including UTR annotations) to nearly half of the approximately 27 000 annotated protein coding genes. The algorithm of the Program to Assemble Spliced Alignments (PASA) tool is described, as well as the results of automated updates to Arabidopsis gene annotations.

Algorithms↗

PubMed2006

Cell-derived anaphylatoxins as key mediators of antibody-dependent type II autoimmunity in mice.

Complement C5a, a potent anaphylatoxin, is a candidate target molecule for the treatment of inflammatory diseases, such as myocardial ischemia/reperfusion injury, RA, and the antiphospholipid syndrome. In contrast, up until now, no specific contribution of C5a and its receptor, C5aR, was recognized in diseases of antibody-dependent type II autoimmunity. Here we identify C5a as a novel key mediator of autoimmune hemolytic anemia (AIHA) and show that mice lacking C5aR are partially resistant to this IgG autoantibody-induced disease model. Upon administration of anti-erythrocyte antibodies, upregulation of activating Fcgamma receptors (FcgammaRs) on Kupffer cells, as observed in WT mice, was absent in C5aR-deficient mice, and FcgammaR-mediated in vivo erythrophagocytosis was impaired. Surprisingly, in mice deficient in FcgammaRI and FcgammaRIII, anti-erythrocyte antibody-induced C5 and C5a production was abolished, demonstrating the existence of a previously unidentified FcgammaR-mediated C5a-generating pathway. These results show that the development of a full-blown antibody-dependent autoimmune disease requires C5a--produced by and acting on FcgammaR--and may suggest therapeutic benefits of C5 and/or C5a/C5aR blockade in AIHA and other diseases closely related to type II autoimmune injury.

Anemia, Hemolytic, Autoimmune↗

PubMed1992

Characterization and regulation of the 58,000-dalton cellular inhibitor of the interferon-induced, dsRNA-activated protein kinase.

The P68 protein kinase is a serine/threonine kinase induced by interferon treatment and activated by double-stranded RNAs (dsRNAs). Once activated, the kinase phosphorylates its natural substrate, the alpha subunit of eukaryotic initiation factor 2 (eIF-2) leading to potential limitations in functional eIF-2 and decreases in protein synthesis initiation. We have recently purified from influenza virus-infected cells a P68 kinase inhibitor, found to be a 58-kDa cellular protein. We have now investigated the mechanisms by which the 58-kDa inhibitor regulates P68 kinase activity and how the inhibitor itself is controlled. The 58-kDa inhibitor did not function by degrading or sequestering the dsRNA activator of P68 but could repress phosphorylation of eIF-2 alpha by an already activated protein kinase. Utilizing antibody prepared against a 58-kDa-specific peptide, we showed that the 58-kDa proteins from infected and uninfected cells were present in equivalent amounts. Although kinase inhibitory activity could not be detected in crude uninfected cell extracts, ammonium sulfate treatment unmasked this activity and allowed purification of the cellular inhibitor with identical chromatographic properties as that from influenza virus-infected cells. Finally, we have identified and partially purified a specific inhibitor of the 58-kDa protein which we refer to as an "anti-inhibitor." Based on these data, we present a model depicting the complex regulation of the interferon-induced protein kinase in eukaryotic cells.

Amino Acid Sequence↗