Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “data resolution”

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 937 records · Page 52Linked to original sources

Crystallographic studies on a family B DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis strain KOD1.

A hyperthermostable family B DNA polymerase from the hyperthermophilic archaeon, Pyrococcus kodakaraensis strain KOD1, has been crystallized by the hanging-drop vapor diffusion method at 293 K with 2-methyl-2,4-pentanediol as the precipitant. The diffraction pattern of a crystal extends to 3.0 A resolution, and two full sets of 3.0 A resolution diffraction data for native crystals were successfully collected at 290 K and 100 K upon exposure to synchrotron radiation at KEK-PF, Japan. The crystals belong to the space group, P212121, with unit-cell dimensions of a = 112.8, b = 115.4, and c = 75.4 A at 290 K, and a = 111.9, b = 112.4, and c = 73.9 at 100 K. Structural analysis by means of the multiple isomorphous replacement method is now in progress.

Crystallography, X-Ray↗

Coupling between local cerebral blood flow and metabolism after hypertonic/hyperoncotic fluid resuscitation from hemorrhage in conscious rats.

The effects of small volume hypertonic/hyperoncotic fluid resuscitation from hemorrhage on brain metabolism and blood flow were evaluated by autoradiographic techniques with high spatial resolution. The data were compared to fluid resuscitation with a volume equal to shed blood of isotonic 6% hydroxyethyl starch solution (HES) and a control group without hemorrhage and fluid resuscitation (n = 6 in each group). In conscious rats, volume-controlled hemorrhage for 30 min (30 mL/kg body weight, resulting in a blood loss of approximately 50% of the circulating blood volume) was followed by intravenous infusion of a hypertonic/hyperoncotic saline hydroxyethyl starch solution (HTHO; 7.5% saline/10% hydroxyethyl starch, 4.0 mL/kg body weight). Local cerebral blood flow (LCBF) and local cerebral glucose utilization (LCGU) were measured in 34 brain structures 2 h after fluid resuscitation by means of the quantitative autoradiographic iodo [14C]antipyrine and 2-[14C]-deoxy-D-glucose methods. Compared to the untreated control group, LCBF increased significantly in all brain regions analyzed after fluid resuscitation with HTHO (mean, +63%) or HES (mean, +56%). The increases in LCBF after fluid resuscitation were sufficient to restore cerebral oxygen delivery to the level calculated for the untreated control group. LCGU was unchanged after fluid resuscitation. The close relationship between LCGU and LCBF observed in the control group (r = 0.95) was preserved after hemorrhage and fluid resuscitation with HTHO (r = 0.97) and HES (r = 0.96), although the LCBF-to-LCGU ratio was reset to a higher level (1.5 mL/mumol in the control group and 2.7 mL/mumol after fluid resuscitation with HTHO and HES, P < 0.05). We conclude that the increase in LCBF compensates for the reduction of arterial oxygen content to maintain cerebral oxygen delivery. Therefore, "small volume resuscitation" appears to be as effective as resuscitation with large volumes of isotonic HES in meeting the circulatory and metabolic demands of the brain tissue within the first 2 h after fluid resuscitation from hemorrhage.

Animals↗

The immunologic basis for hepatitis C infection.

PURPOSE OF REVIEW: The host immune system is arguably involved in nearly every step of hepatitis C virus (HCV) infection. In patients, the outcome, whether it is a natural infection or results from an interferon-alpha-based treatment, is determined by a series of complex host-virus interactions. In this review, we focus on the state of research addressing the immune mechanisms critical for viral clearance and disease resolution. Additional discussion is devoted to the evasion and blockade tactics of HCV as well as to current efforts aimed at disrupting the replication cycle of this well-evolved virus. Current theories of immune-mediated injury of hepatocytes are also discussed. RECENT FINDINGS: Strong and persistent CD8 and CD4 T-cell responses are critical in HCV clearance. Although each may play a unique role in the process, the intrahepatic interferon (IFN)-gamma produced by these cells is central to their antiviral action. IFN-alpha/beta alone, without triggering subsequent HCV-specific T-cell responses, may not lead to a sustained viral response in vivo. Synergism among several immune cells, including T, NK, and NKT cells is important for disease resolution. Additional data raise the possibility that viral clearance and liver injury are mediated through different effector mechanisms of T cells. HCV employs evasion and sabotage tactics to escape from the host's immune system. HCV NS3/4A serine protease can block viral activation of a key transcription factor in initiating cellular IFN response. A newly identified NS3 protease inhibitor can result in a reduction of viremia, illustrating the potential of the viral-enzyme-targeted drug in patients. SUMMARY: Current data provide a rationale to further explore immune augmentation as a therapeutic intervention in HCV infection.

Journal Article↗

Gadolinium-enhanced elliptically reordered three-dimensional MR angiography in the assessment of hand vascularization before radial artery harvest for coronary artery bypass grafting: first experience.

RATIONALE AND OBJECTIVES: To assess the suitability of contrast-enhanced magnetic resonance angiography (MRA) in the preoperative evaluation of hand vasculature in potential candidates for radial artery bypass grafting. METHODS: In 21 patients, gadobenate dimeglumine-enhanced, three-dimensional gradient-echo sequences of both hands were performed, as well as a Doppler ultrasound study with radial artery compression. Doppler findings were correlated with MRA, focusing on the assessment of anastomoses between the vascular bed of the ulnar and radial arteries. RESULTS: One individual had to be excluded because of accidentally disclosed metal foreign bodies. Sufficient depiction of the hand vasculature was achieved in the remainder. Seventeen patients had evidence of adequate collateral flow between the ulnar and radial artery supply on Doppler ultrasound. Three patients exhibited inadequate collateral flow, with angiographic signs of vessel occlusion or missing collaterals between the palmar arches. Two patients presented with stenosis or occlusion of the radial artery. Magnetic resonance angiograms displayed great variations in hand vasculature and collateral formation, with no mismatch compared with Doppler ultrasound results. CONCLUSIONS: Contrast-enhanced MRA displays vascularization of the hand in detail and supplies ultrasound flow measurements for radial artery harvest, with high-resolution angiographic data about possible vessel variations and the presence of anastomoses between the radial or ulnar artery supply.

Adult↗

Functional anatomic imaging in radiation therapy planning.

Improvements in techniques for the delivery of curative radiation have paralleled the advances in three-dimensional imaging devices, specifically, computed tomography and magnetic resonance imaging. These modalities supply the high-resolution image data which, when transferred to radiotherapy computers, allows the construction of a "virtual patient" and calculation of radiation dose that can be delivered within a three-dimensional volume. Although anatomic methods have long been the main stay of cancer imaging, it now clear that functional imaging, provided by positron emission tomography and other nuclear medicine techniques, provides additional critical information regarding tumor biologic activity. The additional step of fusion of functional and anatomic images further refines radiation treatment planning.

Aged↗

Peatland hydrology and carbon release: why small-scale process matters.

Peatlands cover over 400 million hectares of the Earth's surface and store between one-third and one-half of the world's soil carbon pool. The long-term ability of peatlands to absorb carbon dioxide from the atmosphere means that they play a major role in moderating global climate. Peatlands can also either attenuate or accentuate flooding. Changing climate or management can alter peatland hydrological processes and pathways for water movement across and below the peat surface. It is the movement of water in peats that drives carbon storage and flux. These small-scale processes can have global impacts through exacerbated terrestrial carbon release. This paper will describe advances in understanding environmental processes operating in peatlands. Recent (and future) advances in high-resolution topographic data collection and hydrological modelling provide an insight into the spatial impacts of land management and climate change in peatlands. Nevertheless, there are still some major challenges for future research. These include the problem that impacts of disturbance in peat can be irreversible, at least on human time-scales. This has implications for the perceived success and understanding of peatland restoration strategies. In some circumstances, peatland restoration may lead to exacerbated carbon loss. This will also be important if we decide to start to create peatlands in order to counter the threat from enhanced atmospheric carbon.

Carbon↗

Organization of transmembrane helices in photosystem II: comparison of plants and cyanobacteria.

Electron microscopy and X-ray crystallography are revealing the structure of photosystem II. Electron crystallography has yielded a 3D structure at sufficient resolution to identify subunit positioning and transmembrane organization of the reaction-centre core complex of spinach. Single-particle analyses are providing 3D structures of photosystem II-light-harvesting complex II supercomplexes that can be used to incorporate high-resolution structural data emerging from electron and X-ray crystallography. The positions of the chlorins and metal centres within photosystem II are now available. It can be concluded that photosystem II is a dimeric complex with the transmembrane helices of CP47/D2 proteins related to those of the CP43/D1 proteins by a twofold axis within each monomer. Further, both electron microscopy and X-ray analyses show that P(680) is not a 'special pair' and that cytochrome b559 is located on the D2 side of the reaction centres some distance from P(680). However, although comparison of the electron microscopy and X-ray models for spinach and Synechococcus elongatus show considerable similarities, there seem to be differences in the number and positioning of some small subunits.

Crystallography, X-Ray↗

Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome.

As part of the effort to sequence the genome of Rattus norvegicus, we constructed a physical map comprised of fingerprinted bacterial artificial chromosome (BAC) clones from the CHORI-230 BAC library. These BAC clones provide approximately 13-fold redundant coverage of the genome and have been assembled into 376 fingerprint contigs. A yeast artificial chromosome (YAC) map was also constructed and aligned with the BAC map via fingerprinted BAC and P1 artificial chromosome clones (PACs) sharing interspersed repetitive sequence markers with the YAC-based physical map. We have annotated 95% of the fingerprint map clones in contigs with coordinates on the version 3.1 rat genome sequence assembly, using BAC-end sequences and in silico mapping methods. These coordinates have allowed anchoring 358 of the 376 fingerprint map contigs onto the sequence assembly. Of these, 324 contigs are anchored to rat genome sequences localized to chromosomes, and 34 contigs are anchored to unlocalized portions of the rat sequence assembly. The remaining 18 contigs, containing 54 clones, still require placement. The fingerprint map is a high-resolution integrative data resource that provides genome-ordered associations among BAC, YAC, and PAC clones and the assembled sequence of the rat genome.

Animals↗

Genome mapping by fluorescent fingerprinting.

The construction of sequence-ready maps of overlapping genomic clones is central to large-scale genome sequencing. We have implemented a method for fluorescent fingerprinting of bacterial clones to assemble contig maps. The method utilizes three spectrally distinct fluorescently tagged dideoxy ATPs to specifically label the HindIII termini in HindIII and Sau3AI restriction digests of clones that are multiplexed prior to electrophoresis and data collection. There is excellent reproducibility of raw data, improved resolution of large fragments, and concordance between the results obtained using this and the equivalent radioactive protocol. This method also allows detection of smaller overlaps between clones when compared to the analysis of restriction digests on nondenaturing agarose gels.

Chromosome Mapping↗

Visualizing interfacial structure at non-common-atom heterojunctions with cross-sectional scanning tunneling microscopy.

We describe how cross-sectional scanning tunneling microscopy (STM) may be used to image the interfacial bonding across the nearly lattice-matched, non-common-atom GaSb/InAs heterojunction with atomic-scale precision. The method, which takes advantage of the length difference between interfacial and bulk bonds, appears equally applicable to AlSb/InAs and suggests how one might recover the complete structure of either heterojunction from atomic-resolution STM data.

Journal Article↗

Phase fluctuations and the pseudogap in YBa(2)Cu(3)O (x).

The thermodynamics of the superconducting transition is studied as a function of doping using high-resolution expansivity data of YBa(2)Cu(3)O (x) single crystals and Monte Carlo simulations of the anisotropic 3D- XY model. We directly show that T(c) of underdoped YBa(2)Cu(3)O (x) is strongly suppressed from its mean-field value (T(MF)(c)) by phase fluctuations of the superconducting order parameter. For overdoped YBa(2)Cu(3)O (x) fluctuation effects are greatly reduced and T(c) approximately T(MF)(c). We find that T(MF)(c) exhibits a similar doping dependence as the pseudogap energy, naturally suggesting that the pseudogap arises from phase-incoherent Cooper pairing.

Journal Article↗

A complexity view of rainfall.

We show that rain events are analogous to a variety of nonequilibrium relaxation processes in Nature such as earthquakes and avalanches. Analysis of high-resolution rain data reveals that power laws describe the number of rain events versus size and number of droughts versus duration. In addition, the accumulated water column displays scale-less fluctuations. These statistical properties are the fingerprints of a self-organized critical process and may serve as a benchmark for models of precipitation and atmospheric processes.

Climate↗

Electronic quasiparticle renormalization on the spin wave energy scale.

High-resolution photoemission data of the (110) iron surface reveal the existence of well-defined metallic surface resonances in good correspondence to band calculations. Close to the Fermi level, their dispersion and momentum broadening display anomalies characteristic of quasiparticle renormalization due to coupling to bosonic excitations. Its energy scale exceeds that of phonons by far, and is in striking coincidence with that of the spin wave spectrum in iron. The self-energy behavior thus gives spectroscopic evidence of a quasiparticle mass enhancement due to electron-magnon coupling.

Journal Article↗

Geometry of intensive scalar dissipation events in turbulence.

The maxima of the scalar dissipation rate in turbulence appear in the form of sheets and correspond to the potentially most intensive scalar mixing events. Their cross section extension determines a locally varying diffusion scale of the mixing process and extends the classical Batchelor picture of one mean diffusion scale. The distribution of the local diffusion scales is analyzed for different Reynolds and Schmidt numbers with a fast multiscale technique applied to very high-resolution simulation data. The scales always take values across the whole Batchelor range and beyond. Furthermore, their distribution is traced back to the distribution of the contractive short-time Lyapunov exponent of the flow.

Journal Article↗

K-site splitting in KTiOPO4 at room temperature.

The room-temperature structure of potassium titanyl phosphate (KTiOPO4, KTP) with Pna2(1) symmetry has been studied by means of synchrotron radiation. Each of the two crystallographically unique K1 and K2 cations is split over two sites that are shifted along the c direction by 0.287 (13) and 0.255 (13) A for the K1a/b and K2a/b pairs, respectively. The refined populations of the minor K1b and K2b sites are 0.102 (12) and 0.132 (17), respectively. It is shown that accurate high-resolution synchrotron data (Rmerged = 0.015 for 25 010 reflections, 9456 unique, sintheta/lambda limit > 1.0) are required for the determination of a reliable structure model.

Journal Article↗

Solving non-centrosymmetric two-dimensional crystal structures by dynamic electron diffraction.

Despite the fast increase in expertise developed in the field of electron crystallography, dynamic scattering effects still remain a severe obstacle in this field, a hurdle that is being circumvented rather than fully tackled. In this paper, a new way of straightforward interpretation of conventional many-beam zone-axis dynamical electron diffraction patterns is presented that helps to solve the phase problem for non-centrosymmetric two-dimensional crystal structures, in particular if these contain only a few heavier atoms. While the implementation of this method is easiest for fairly weak multiple scattering, its extension to arbitrarily strong dynamical effects is mentioned. A method to obtain high-resolution diffraction data in the presence of specimen bending is proposed.

Journal Article↗

The NADP(H)-binding component (dIII) of human heart transhydrogenase: crystallization and preliminary crystallographic analysis.

Transhydrogenase is a membrane protein which uses the energy of the proton motive force to drive the reduction of NADP(+) by NADH. The enzyme has three domains: dII spans the membrane, while dI and dIII protrude from the membrane and contain the binding sites for NAD(H) and NADP(H), respectively. DIII from human heart transhydrogenase has been expressed in Escherichia coli. The purified protein has been crystallized with bound NADP(+) using the hanging-drop vapour-diffusion method with ammonium sulfate as a precipitant. The crystals belong to the tetragonal space group P4(1)22 or P4(3)22, with unit-cell parameters a = b = 58.1, c = 251.0 A. A 2.1 A resolution native data set has been collected with an R(merge) of 6. 8%.

Binding Sites↗