Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “deep transfer model”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 289 records · Page 16Linked to original sources
PubMed1993

Stress and strain distribution in the bone surrounding a new design of dental implant: a comparison with a threaded Branemark type implant.

The stress and strain distributions in the bone surrounding a new dental implant, designed specifically for use with a bioactive porous coating and thus having a fully bonded interface to the bone, have been analysed. The new implant geometry was slightly tapered, with deep concentric grooves to allow bone ingrowth and load transfer, and had a parallel cylindrical section at the neck. The results have been compared with stress and strain predictions in the bone surrounding a 'Branemark type' threaded implant with a fully bonded interface. Under axial loading both implant types produced similar stress and strain distributions with a higher level of stress in the cortical bone surrounding the neck of the implant. Under lateral loading a high stress concentration was found in the neck region of both implants, but this was lower around the neck of the new design compared with the threaded implant. When the new implant was surrounded by cancellous bone, the reduction in the stress concentration was up to 50 per cent. This reduction should help to reduce fatigue failure and bone resorption in this area under lateral loading.

Bone Density↗
PubMed2002

Using deeply trapped intermediates to map the cytochrome c folding landscape.

Replacement of iron with cobalt(III) selectively introduces a deep trap in the folding-energy landscape of the heme protein cytochrome c. Remarkably, neither the protein structure nor the folding thermodynamics is perturbed by this metal-ion substitution, as shown by data from spectroscopic and x-ray diffraction experiments. Through kinetics measurements, we have found parallel folding pathways involving several different misligated Co(III) species, and, as these folding intermediates persist for several hours under certain conditions, we have been able to elucidate fully their spectroscopic properties. The results, along with an analysis of the fluorescence energy-transfer kinetics during refolding, show that rapidly equilibrating populations of compact and extended polypeptide conformations are present until all molecules have reached the native structure. These measurements provide direct evidence that collapsed denatured structures are not substantially more stable than extended conformations of cytochrome c.

Animals↗
PubMed2006

Experimental fragmentation studies with 12C therapy beams.

High-energy beams of (12)C ions in the range of 80-430 MeV u(-1) delivered by the heavy-ion synchrotron SIS-18 are used for radiotherapy of deep-seated localized tumors at the treatment unit at GSI Darmstadt. In order to improve the physical database, the fragmentation characteristics along the penetration path in tissue were investigated experimentally by using a water phantom as tissue-equivalent absorber. Measurements were performed at specific energies of 200 and 400 MeV u(-1) of the incident (12)C ions and at six different depths before and behind the Bragg peak. Secondary fragments with nuclear charges Z(f) = 1-5 were identified by scintillation detectors using DeltaE-E and time-of-flight techniques. The preliminary results include energy- and angular distributions, fragment yields, build-up curves and attenuation of the primary carbon projectiles.

Animals↗
PubMed2001

Structure of the UDP-glucosyltransferase GtfB that modifies the heptapeptide aglycone in the biosynthesis of vancomycin group antibiotics.

BACKGROUND: Members of the vancomycin group of glycopeptide antibiotics have an oxidatively crosslinked heptapeptide scaffold decorated at the hydroxyl groups of 4-OH-Phegly4 or beta-OH-Tyr6 with mono- (residue 6) or disaccharides (residue 4). The disaccharide in vancomycin itself is L-vancosamine-1,2-glucose, and in chloroeremomycin it is L-4-epi-vancosamine-1,2-glucose. The sugars and their substituents play an important role in efficacy, particularly against vancomycin-resistant pathogenic enterococci. RESULTS: The glucosyltransferase, GtfB, that transfers the glucose residue from UDP-glucose to the 4-OH-Phegly4 residue of the vancomycin aglycone, initiating the glycosylation pathway in chloroeremomycin maturation, has been crystallized, and its structure has been determined by X-ray analysis at 1.8 A resolution. The enzyme has a two-domain structure, with a deep interdomain cleft identified as the likely site of UDP-glucose binding. A hydrophobic patch on the surface of the N-terminal domain is proposed to be the binding site of the aglycone substrate. Mutagenesis has revealed Asp332 as the best candidate for the general base in the glucosyltransfer reaction. CONCLUSIONS: The structure of GtfB places it in a growing group of glycosyltransferases, including Escherichia coli MurG and a beta-glucosyltransferase from T4 phage, which together form a subclass of the glycosyltransferase superfamily and give insights into the recognition of the NDP-sugar and aglycone cosubstrates. A single major interdomain linker between the N- and C- terminal domains suggests that reprogramming of sugar transfer or aglycone recognition in the antibiotic glycosyltransferases, including the glycopeptide and also the macrolide antibiotics, will be facilitated by this structural information.

Amino Acid Sequence↗
PubMed1996

Mechanism of unassisted ion transport across membrane bilayers.

To establish how charged species move from water to the nonpolar membrane interior and to determine the energetic and structural effects accompanying this process, we performed molecular dynamics simulations of the transport of Na+ and Cl- across a lipid bilayer located between two water lamellae. The total length of molecular dynamics trajectories generated for each ion was 10 ns. Our simulations demonstrate that permeation of ions into the membrane is accompanied by the formation of deep, asymmetric thinning defects in the bilayer, whereby polar lipid head groups and water penetrate the nonpolar membrane interior. Once the ion crosses the midplane of the bilayer the deformation "switches sides"; the initial defect slowly relaxes, and a defect forms in the outgoing side of the bilayer. As a result, the ion remains well solvated during the process; the total number of oxygen atoms from water and lipid head groups in the first solvation shell remains constant. A similar membrane deformation is formed when the ion is instantaneously inserted into the interior of the bilayer. The formation of defects considerably lowers the free energy barrier to transfer of the ion across the bilayer and, consequently, increases the permeabilities of the membrane to ions, compared to the rigid, planar structure, by approximately 14 orders of magnitude. Our results have implications for drug delivery using liposomes and peptide insertion into membranes.

Cell Membrane Permeability↗
PubMed1994

Radiation factors in space and a system for their monitoring.

The radiation environment is of special concern when the spaceship flies in deep space. The annual fluence of the galactic cosmic rays is approximately 10(8) cm-2 and the absorbed dose of the solar cosmic rays can reach 10 Gy per event behind the shielding thickness of 3-5 g cm-2 Al. For the radiation environment monitoring it is planned to place a measuring complex on the space probes "Mars" and "Spectr" flying outside the magnetosphere. This complex is to measure: cosmic rays composition, particle flux, dose equivalent, energy and LET spectra, solar X-rays spectrum. On line data transmission by the space probes permits to obtain the radiation environment data in space.

Cosmic Radiation↗
PubMed2002

F+ tunable laser activity and interaction of atomic halogens (F, Cl and Br) at the low coordinated surface sites of SrOAb initio and DFT calculations.

The twofold potential of F+ color centers at the low coordinated surfaces of SrO for providing tunable laser activity and adsorption properties for atomic halogens (F, Cl and Br) has been investigated using ab initio electronic structure calculations. SrO clusters of variable sizes were embedded in simulated Coulomb fields that closely approximate the Madelung fields of the host surfaces and the nearest neighbor ions to F+ were allowed to relax to equilibrium. Based on Stokes shifted optical transition bands and horizontal shifts along the configuration coordinate diagrams, the F+ laser activity was found to decrease as the coordination number of the surface ions decreases from 5 (flat) to 4 (edge) to 3 (corner). An attempt has been made to explain this result in terms of Madelung potentials and optical-optical conversion efficiencies. All relaxed excited states are deep below the conduction bands of the perfect ground states, implying that F+ is a laser-suitable defect. The most laser active flat surface is the least probable for relaxed excited state orientational destruction of F+. The excited state at the edge has the highest energy, implying exciton (energy) transfer to the flat and edge sites. F+ relaxation and defect-formation energies increase with increasing surface coordination number. The Glasner-Tompkins relation between the fundamental optical absorption of F+ in solids and the fundamental absorption of the host crystals can be generalized to include the low coordinated surfaces of SrO. The F+ color center changes the nature of halogen-surface interaction (adsorption energies) from physical adsorption to chemical adsorption. The halogen-surface interactions increase with increasing electronegativity of the halogen. The calculated adsorption energies can be explained in terms of surface electrostatic potentials, and the covalent spin pairing mechanism plays a dominant role in determining adsorbate-substrate interactions.

Computer Simulation↗
PubMedDate not supplied

Issues in deep space radiation protection.

The exposures in deep space are largely from the Galactic Cosmic Rays (GCR) for which there is as yet little biological experience. Mounting evidence indicates that conventional linear energy transfer (LET) defined protection quantities (quality factors) may not be appropriate for GCR ions. The available biological data indicates that aluminum alloy structures may generate inherently unhealthy internal spacecraft environments in the thickness range for space applications. Methods for optimization of spacecraft shielding and the associated role of materials selection are discussed. One material which may prove to be an important radiation protection material is hydrogenated carbon nanofibers.

Aluminum↗
PubMed2005

Leucyl-tRNA synthetase from the ancestral bacterium Aquifex aeolicus contains relics of synthetase evolution.

The editing reactions catalyzed by aminoacyl-tRNA synthetases are critical for the faithful protein synthesis by correcting misactivated amino acids and misaminoacylated tRNAs. We report that the isolated editing domain of leucyl-tRNA synthetase from the deep-rooted bacterium Aquifex aeolicus (alphabeta-LeuRS) catalyzes the hydrolytic editing of both mischarged tRNA(Leu) and minihelix(Leu). Within the domain, we have identified a crucial 20-amino-acid peptide that confers editing capacity when transplanted into the inactive Escherichia coli LeuRS editing domain. Likewise, fusion of the beta-subunit of alphabeta-LeuRS to the E. coli editing domain activates its editing function. These results suggest that alphabeta-LeuRS still carries the basic features from a primitive synthetase molecule. It has a remarkable capacity to transfer autonomous active modules, which is consistent with the idea that modern synthetases arose after exchange of small idiosyncratic domains. It also has a unique alphabeta-heterodimeric structure with separated catalytic and tRNA-binding sites. Such an organization supports the tRNA/synthetase coevolution theory that predicts sequential addition of tRNA and synthetase domains.

Amino Acid Sequence↗
PubMed2002

Limiting metabolic rate (thermal work limit) as an index of thermal stress.

The development of a rational heat stress index called thermal work limit (TWL) is presented. TWL is defined as the limiting (or maximum) sustainable metabolic rate that euhydrated, acclimatized individuals can maintain in a specific thermal environment, within a safe deep body core temperature (< 38.20 degrees C) and sweat rate (< 1.2 kg/hr(-1)). The index has been developed using published experimental studies of human heat transfer, and established heat and moisture transfer equations through clothing. Clothing parameters can be varied and the protocol can be extended to unacclimatized workers. The index is designed specifically for self-paced workers and does not rely on estimation of actual metabolic rates, a process that is difficult and subject to considerable error. The index has been introduced into several large industrial operations located well inside the tropics, resulting in a substantial and sustained fall in the incidence of heat illness. Guidelines for TWL are proposed along with recommended interventions. TWL has application to professionals from both the human and engineering sciences, as it allows not only thermal strain to be evaluated,. but also the productivity decrement due to heat (seen as a reduced sustainable metabolic rate) and the impact of various strategies such as improved local ventilation or refrigeration to be quantitatively assessed.

Acclimatization↗
PubMed2005

Effect of chaotropic anions on the sodium transport by the Na,K-ATPase.

The effect of choline iodide, bromide and chloride on the kinetics of the electrogenic sodium transport by the Na,K-ATPase was investigated in a model system of ATPase-containing membrane fragments adsorbed on the lipid bilayer membrane. The kinetic parameters of Na(+) transport were determined from short circuit currents after fast release of ATP from its caged precursor. The falling phase of the current transients could be fitted by a single exponential with the time constant, tau (2). Its temperature dependence allowed an estimation of the activation energy of the rate-limiting reaction step, the conformation transition E(1)/E(2). Choline iodide and bromide caused a decrease of the activation energy as well as the overall rate of the process expressed as the pre-exponential factor A of the Arrhenius equation. If choline iodide or bromide were present on the cytoplasmic and extracellular sides of the protein, the temperature dependent changes were more pronounced than when present on the cytoplasmic side only. These results can be explained by an effect of the anions on water structure on the extracellular surface of the protein, where a deep access channel connects the ion-binding sites with the solution. Chloride ions also caused a deceleration of the electrogenic transport, however, in contrast to iodide or bromide, they did not affect the activation energy, and were more effective when added on the cytoplasmic side. This effect can be explained by asymmetric screening of the negative surface charges which leads to a transmembrane electric potential that modifies the ion transfer.

Adenosine Triphosphate↗
PubMed1989

Three-dimensional reconstruction of the ribosome from Escherichia coli.

Three-dimensional image reconstruction has been applied to electron micrographs of noncrystalline, negatively stained ribosomes obtained from Escherichia coli. Several independent reconstructions all show an overall appearance resembling models that had been derived earlier by direct visual interpretation of electron micrographs. The reconstructed ribosomes show numerous structural details not recognized previously, some of which may be functionally significant. A large elongate cavity (approximately 8-nm long x 5-nm wide x 6-nm [maximal] deep) is present on the surface of the ribosome near the base of its stalk and is identifiable as a portion of a feature termed the interface canyon, which was detected in prior reconstructions of the large ribosomal subunit (Radermacher, M., T. Wagenknecht, A. Verschoor, and J. Frank. 1987. EMBO (Eur. Mol. Biol. Organ.) J. 6:1107-1114). On the back of the ribosome, near the base of the central protuberance, is a hole leading to the interface canyon, which likely represents an exit site for the elongating polypeptide produced during protein biosynthesis. The exposed portion of the interface canyon appears well suited to bind two tRNA molecules in a configuration that is consistent with biochemical and structural data on the mechanism of peptide bond biosynthesis.

Escherichia coli↗
PubMed2003

Single eubacterial origin of eukaryotic sulfide:quinone oxidoreductase, a mitochondrial enzyme conserved from the early evolution of eukaryotes during anoxic and sulfidic times.

Mitochondria occur as aerobic, facultatively anaerobic, and, in the case of hydrogenosomes, strictly anaerobic forms. This physiological diversity of mitochondrial oxygen requirement is paralleled by that of free-living alpha-proteobacteria, the group of eubacteria from which mitochondria arose, many of which are facultative anaerobes. Although ATP synthesis in mitochondria usually involves the oxidation of reduced carbon compounds, many alpha-proteobacteria and some mitochondria are known to use sulfide (H2S) as an electron donor for the respiratory chain and its associated ATP synthesis. In many eubacteria, the oxidation of sulfide involves the enzyme sulfide:quinone oxidoreductase (SQR). Nuclear-encoded homologs of SQR are found in several eukaryotic genomes. Here we show that eukaryotic SQR genes characterized to date can be traced to a single acquisition from a eubacterial donor in the common ancestor of animals and fungi. Yet, SQR is not a well-conserved protein, and our analyses suggest that the SQR gene has furthermore undergone some lateral transfer among prokaryotes during evolution, leaving the precise eubacterial lineage from which eukaryotes obtained their SQR difficult to discern with phylogenetic methods. Newer geochemical data and microfossil evidence indicate that major phases of early eukaryotic diversification occurred during a period of the Earth's history from 1 to 2 billion years before present in which the subsurface ocean waters contained almost no oxygen but contained high concentrations of sulfide, suggesting that the ability to deal with sulfide was essential for prokaryotes and eukaryotes during that time. Notwithstanding poor resolution in deep SQR phylogeny and lack of a specifically alpha-protebacterial branch for the eukaryotic enzyme on the basis of current lineage sampling, a single eubacterial origin of eukaryotic SQR and the evident need of ancient eukaryotes to deal with sulfide, a process today germane to mitochondrial quinone reduction, are compatible with the view that eukaryotic SQR was an acquisition from the mitochondrial endosymbiont.

Amino Acid Sequence↗
PubMed1983

Magnetic induction heating of tissue: numerical evaluation of tumor temperature distributions.

A one dimensional (radial) numerical model based on the bioheat transfer equation has been developed and applied to the abdomen and pelvis heated by a concentric magnetic induction electrode. This model consists of four normal tissue regions: viscera, muscle, fat and skin. Each region is assigned thermal properties characteristic of that region and power deposition values consistent with those for this mode of heating. Tumors of 2, 4 and 7 cm thicknesses are positioned in five different radial locations ranging from the central axis to the skin surface. Two blood perfusion models of the tumor are considered: the uniformly perfused model and an annular model. Tumor temperature distributions are considered acceptable if the average tumor temperature plus and minus two standard deviations lie between 42 degrees C and 60 degrees C. To stimulate practical clinical restrictions, muscle and fat temperatures are not allowed to exceed 44 degrees C, significant portions of the viscera (except for a 1 cm thick band) are not allowed to exceed 42 degrees C, and the total absorbed power required to maintain steady state cannot exceed one kilowatt. Over 100 possible cases are presented in a compact form. A conclusion drawn from this study is that with few exceptions, only small tumors in the muscle annulus are heated adequately with this modality. Large tumors will have significant unheated portions if the specified limitations are not exceeded. While this heating modality can raise the necrotic core of a tumor to high temperatures, it cannot adequately heat well perfused regions of a deep seated tumor. These conclusions are borne out clinically and are discussed in a companion paper.

Diathermy↗
PubMed2007

Evolution of the diverse biological roles of inositols.

Several of the nine hexahydroxycylohexanes (inositols) have functions in Biology, with myo-inositol (Ins) in most of the starring roles; and Ins polyphosphates are amongst the most abundant organic phosphate constituents on Earth. Many Archaea make Ins and use it as a component of diphytanyl membrane phospholipids and the thermoprotective solute di-L-Ins-1,1'-phosphate. Few bacteria make Ins or use it, other than as a carbon source. Those that do include hyperthermophilic Thermotogales (which also employ di-L-Ins-1,1'-phosphate) and actinomycetes such as Mycobacterium spp. (which use mycothiol, an inositol-containing thiol, as an intracellular redox reagent and have characteristic phosphatidylinositol-linked surface oligosaccharides). Bacteria acquired their Ins3P synthases by lateral gene transfer from Archaea. Many eukaryotes, including stressed plants, insects, deep-sea animals and kidney tubule cells, adapt to environmental variation by making or accumulating diverse inositol derivatives as 'compatible' solutes. Eukaryotes use phosphatidylinositol derivatives for numerous roles in cell signalling and regulation and in protein anchoring at the cell surface. Remarkably, the diradylglycerol cores of archaeal and eukaryote/bacterial glycerophospholipids have mirror image configurations: sn-2,3 and sn-1,2 respectively. Multicellular animals and amoebozoans exhibit the greatest variety of functions for PtdIns derivatives, including the use of PtdIns(3,4,5)P3 as a signal. Evolutionarily, it seems likely that (i) early archaeons first made myo-inositol approx. 3500 Ma (million years) ago; (ii) archeons brought inositol derivatives into early eukaryotes (approx. 2000 Ma?); (iii) soon thereafter, eukaryotes established ubiquitous functions for phosphoinositides in membrane trafficking and Ins polyphosphate synthesis; and (iv) since approx. 1000 Ma, further waves of functional diversification in amoebozoans and metazoans have introduced Ins(1,4,5)P3 receptor Ca2+ channels and the messenger role of PtdIns(3,4,5)P3.

Biological Evolution↗
PubMed2001

A mobile system for the treatment of accidental hypothermia with extracorporeal circulation.

When deep accidental hypothermia causes circulatory failure, the best chance of survival is treatment with extracorporeal circulation (ECC) and warming of the blood. This may be difficult to achieve if the patient is first admitted to a hospital without a department of thoracic surgery. Our aim was to test a lightweight mobile system for ECC. The equipment could be transported almost anywhere, making it possible to start ECC on the spot and during transfer. The system was tested on six hypothermic pigs, two of the pigs at the institute laboratory, two of the pigs in a normal ambulance, and two of the pigs in an air force rescue helicopter. All of the pigs were transported back to the institute for warming to normal temperature. After warming, and the ECC stopped, all the pigs were in sinus rhythm and had an obviously satisfactory circulation. It is possible to bring a lightweight ECC system to the unstable patient. Treatment is possible in any hospital, ambulance or helicopter.

Accidents↗
PubMed2026

Investigating cross-organism prediction of prokaryotic essential proteins using unsupervised language model and ensemble strategy.

Cross-organism prediction of essential proteins is a critical task for drug discovery and microbial engineering, yet the generalizability of existing machine learning models across diverse species remains a significant challenge. In this study, we propose DeepPEP, a large language model-based framework designed to reliably transfer essential protein annotations between distantly related organisms. Utilizing 66 curated prokaryotic datasets, we systematically evaluated DeepPEP's cross-organism performance under various conditions. Initial pairwise predictions revealed a correlation between performance and evolutionary distance; however, further investigation demonstrated that integrating training data from multiple organisms yields superior predictive power. In a benchmark scenario designed to simulate real-world applications, DeepPEP outperformed the state-of-the-art tool Geptop 2.0, showcasing a robust ability to identify species-specific essential proteins. Finally, a case study on novel genomes confirmed the model's practical effectiveness. Our results suggest that DeepPEP is a powerful strategy for prokaryotic essential protein prediction, and the rigorous evaluation framework established in this study provides a new benchmark for the field.

Large Language Models↗
PubMed2002

Quantitative assessment of the long term behaviour of 90Sr in Lake Uruskul, Southern Urals, Russia.

The present paper is aimed at assessing the long term behaviour of 90Sr migration from water to bottom sediments of Lake Uruskul, Southern Urals, Russia. The lake was contaminated following the nuclear accident at the Mayak nuclear complex in 1957 (the Kyshtym accident). Some transfer parameters relevant to the behaviour of 90Sr in the water-sediment system were evaluated: a) the radionuclide migration velocity from the water column to the bottom sediment, b) the radionuclide migration rate from bottom sediment to water, and c) the radionuclide migration rate from bottom sediment to deep sediment. The estimated values of the above parameters were 6.4 x 10(-1) m s(-1), 5.7 x 10(-10) s(-1) and 5.2 x 10(-10) s(-1), respectively. These values were compared with data obtained for some Italian lakes contaminated by 90Sr after the nuclear weapons tests fallout. The relatively low radionuclide migration from water to sediment of these lakes is reflected by the values of the ratio migration velocity/migration rate from sediment to water (4 m and 12 m) that are significantly lower than the corresponding value in the Russian lake (112 m). The peculiar hydrochemical conditions of Lake Uruskul (high pH, high mineralisation, etc.) are considered to be responsible for the high radionuclide migration from water to sediment.

Environmental Monitoring↗