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Biomedical subjects

D Yan

Publications and source records attributed to D Yan.

At least 37 records · Page 2Linked to original sources

Estimating the dose variation in a volume of interest with explicit consideration of patient geometric variation.

A method to measure the effects of internal organ motion and deformation and patient setup error on cumulative dose variation in a volume of interest is proposed. The method uses multiple CT scans and electronic portal images of a single patient to numerically simulate dose-volume effects over the entire course of the patient's external beam treatment. The results are expressed in the form of a novel dose-volume histogram, called an expected dose-volume histogram (EDVH).

Humans↗

Monitor unit settings for intensity modulated beams delivered using a step-and-shoot approach.

Two linear accelerators have been commissioned for delivering IMRT treatments using a step-and-shoot approach. To assess beam startup stability for 6 and 18 MV x-ray beams, dose delivered per monitor unit (MU), beam flatness, and beam symmetry were measured as a function of the total number of MU delivered at a clinical dose rate of 400 MU per minute. Relative to a 100 MU exposure, the dose delivered per MU by both linear accelerators was found to be within +/-2% for exposures larger than 4 MU. Beam flatness and symmetry also met accepted quality assurance standards for a minimum exposure of 4 MU. We have found that the performance of the two machines under study is well suited to the delivery of step-and-shoot IMRT. A system of dose calculation has also been commissioned for applying head scatter corrections to fields as small as 1x1 cm2. The accuracy and precision of the relative output calculations in water was validated for small fields and fields offset from the axis of collimator rotation. For both 6 and 18 MV x-ray beams, the dose per MU calculated in a water phantom agrees with measured data to within 1% on average, with a maximum deviation of 2.5%. The largest output factor discrepancies were seen when the actual radiation field size deviated from the set field size. The measured output in water can vary by as much 16% for 1x1 cm2 fields, when the measured field size deviates from the set field size by 2 mm. For a 1 mm deviation, this discrepancy was reduced to 8%. Steps should be taken to ensure collimator precision is tightly controlled when using such small fields. If this is not possible, very small fields should not contribute to a significant portion of the treatment, or uncertainties in the collimator position may effect the accuracy of the dose delivered.

Particle Accelerators↗

Cloning and functional expression of human retinal kir2.4, a pH-sensitive inwardly rectifying K(+) channel.

To identify novel potassium channel genes expressed in the retina, we screened a human retina cDNA library with an EST sequence showing partial homology to inwardly rectifying potassium (Kir) channel genes. The isolated cDNA yielded a 2,961-base pair sequence with the predicted open reading frame showing strong homology to the rat Kir2. 4 (rKir2.4). Northern analysis of mRNA from human and bovine tissues showed preferential expression of Kir2.4 in the neural retina. In situ hybridization to sections of monkey retina detected Kir2.4 transcript in most retinal neurons. Somatic hybridization analysis and dual-color in situ hybridization to metaphase chromosomes mapped Kir2.4 to human chromosome 19 q13.1-q13.3. Expression of human Kir2. 4 cRNA in Xenopus oocytes generated strong, inwardly rectifying K(+) currents that were enhanced by extracellular alkalinization. We conclude that human Kir2.4 encodes an inwardly rectifying K(+) channel that is preferentially expressed in the neural retina and that is sensitive to physiological changes in extracellular pH.

Amino Acid Sequence↗

Beryllofluoride mimics phosphorylation of NtrC and other bacterial response regulators.

Two-component systems, sensor kinase-response regulator pairs, dominate bacterial signal transduction. Regulation is exerted by phosphorylation of an Asp in receiver domains of response regulators. Lability of the acyl phosphate linkage has limited structure determination for the active, phosphorylated forms of receiver domains. As assessed by both functional and structural criteria, beryllofluoride yields an excellent analogue of aspartyl phosphate in response regulator NtrC, a bacterial enhancer-binding protein. Beryllofluoride also appears to activate the chemotaxis, sporulation, osmosensing, and nitrate/nitrite response regulators CheY, Spo0F, OmpR, and NarL, respectively. NMR spectroscopic studies indicate that beryllofluoride will facilitate both biochemical and structural characterization of the active forms of receiver domains.

Aspartic Acid↗

Targeted protein footprinting: where different transcription factors bind to RNA polymerase.

Gene transcription is regulated through the interactions of RNA polymerase (RNAP) with transcription factors, such as the bacterial sigma proteins. We have devised a new strategy that relies on targeted protein footprinting to make an extensive survey of proximity to the protein surface. This involves attaching cutting reagents randomly to lysine residues on the surface of a protein such as sigma. The lysine-labeled sigma protein is then used to cleave the polypeptide backbones of the RNAP proteins at exposed residues adjacent to the sigma binding site. We used targeted protein footprinting to compare the areas near which sigma(70), sigma(54), sigma(38), sigma(E), NusA, GreA, and omega bind to the protein subunits of Escherichia coli RNAP. The sigma proteins and NusA cut sites in similar regions of the two large RNAP subunits, beta and beta', outlining a common surface. GreA cuts a larger set of sites, whereas omega shows no overlap with the others, cutting only the beta' subunit at a unique location.

Bacterial Proteins↗

"Switch I" mutant forms of the bacterial enhancer-binding protein NtrC that perturb the response to DNA.

NtrC (nitrogen regulatory protein C) is a bacterial enhancer-binding protein of 469 residues that activates transcription by sigma(54)-holoenzyme. A region of its transcriptional activation (central) domain that is highly conserved among homologous activators of sigma(54)-holoenzyme-residues 206-220-is essential for interaction with this RNA polymerase: it is required for contact with the polymerase and/or for coupling the energy from ATP hydrolysis to a change in the conformation of the polymerase that allows it to form transcriptionally productive open complexes. Several mutant NtrC proteins with amino acid substitutions in this region, including NtrC(A216V) and NtrC(G219K), have normal ATPase activity but fail in transcriptional activation. We now report that other mutant forms carrying amino acid substitutions at these same positions, NtrC(A216C) and NtrC(G219C), are capable of activating transcription when they are not bound to a DNA template (non-DNA-binding derivatives with an altered helix-turn-helix DNA-binding motif at the C terminus of the protein) but are unable to do so when they are bound to a DNA template, whether or not it carries a specific enhancer. Enhancer DNA remains a positive allosteric effector of ATP hydrolysis, as it is for wild-type NtrC but, surprisingly, appears to have become a negative allosteric effector for some aspect of interaction with sigma(54)-holoenzyme. The conserved region in which these amino acid substitutions occur (206-220) is equivalent to the Switch I region of a large group of purine nucleotide-binding proteins. Interesting analogies can be drawn between the Switch I region of NtrC and that of p21(ras).

Adenosine Triphosphatases↗

A model to accumulate fractionated dose in a deforming organ.

PURPOSE: Measurements of internal organ motion have demonstrated that daily organ deformation exists throughout the course of radiation treatment. However, a method of constructing the resultant dose delivered to the organ volume remains a difficult challenge. In this study, a model to quantify internal organ motion and a method to construct a cumulative dose in a deforming organ are introduced. METHODS AND MATERIALS: A biomechanical model of an elastic body is used to quantify patient organ motion in the process of radiation therapy. Intertreatment displacements of volume elements in an organ of interest is calculated by applying an finite element method with boundary conditions, obtained from multiple daily computed tomography (CT) measurements. Therefore, by incorporating also the measurements of daily setup error, daily dose delivered to a deforming organ can be accumulated by tracking the position of volume elements in the organ. Furthermore, distribution of patient-specific organ motion is also predicted during the early phase of treatment delivery using the daily measurements, and the cumulative dose distribution in the organ can then be estimated. This dose distribution will be updated whenever a new measurement becomes available, and used to reoptimize the ongoing treatment. RESULTS: An integrated process to accumulate dosage in a daily deforming organ was implemented. In this process, intertreatment organ motion and setup error were systematically quantified, and incorporated in the calculation of the cumulative dose. An example of the rectal wall motion in a prostate treatment was applied to test the model. The displacements of volume elements in the rectal wall, as well as the resultant doses, were calculated. CONCLUSION: This study is intended to provide a systematic framework to incorporate daily patient-specific organ motion and setup error in the reconstruction of the cumulative dose distribution in an organ of interest. The realistic dose distribution in an organ of interest gives the true dose-volume relationship, and may play an important role in the evaluation of the dose response of human organs. Dose reconstruction during the course of treatment delivery can also be used as an important feedback for the online optimization of individual treatment plans.

Biomechanical Phenomena↗

Amplified proinflammatory cytokine expression and toxicity in mice coexposed to lipopolysaccharide and the trichothecene vomitoxin (deoxynivalenol).

A single oral exposure to the trichothecene vomitoxin (VT) has been previously shown in the mouse to increase splenic mRNA levels for several cytokines in as little as 2 h. Since one underlying mechanism for these effects likely involves superinduction of transiently expressed cytokine genes, VT may also potentially amplify cytokine responses to inflammatory stimuli. To test this possibility, the effects of oral VT exposure on tumor necrosis factor-alpha (TNF-alpha), interleukin-6 (IL-6), and IL-1beta expression were measured in mice that were intraperitoneally injected with lipopolysaccharide (LPS), a prototypic inflammatory agent. As anticipated, VT alone at 1, 5, and 25 mg/kg body weight increased splenic mRNA expression of all three cytokines after 3 h in a dose-response fashion. LPS injection at 1 and 5 mg/kg body weight also induced proinflammatory cytokine mRNA expression. There was a synergistic increase in TNF-alpha splenic mRNA levels in mice treated with both VT and LPS as compared to mice treated with either toxin alone, whereas the effects were additive for IL-6 and IL-1beta mRNA expression. When relative mRNA levels were examined over a 12-h period in mice given LPS (1 mg/kg) and/or VT (5 mg/kg), significant enhancement was observed up to 6, 12, and 3 h for TNF-alpha, IL-6, and IL-1beta, respectively. When plasma cytokine concentrations were measured, TNF-alpha was found to peak at 1 h and was significantly increased at 1, 3, and 6 h if mice were given LPS and VT, whereas LPS or VT alone caused much smaller increases in plasma TNF-alpha Plasma IL-6 peaked at 3 h in LPS, VT, and LPS/VT groups, with the combined toxin group exhibiting additive effects. Plasma IL-1beta was not detectable. The potential for VT and LPS to enhance toxicity was examined in a subsequent study. Mortality was not observed up to 72 h in mice exposed to a single oral dose of VT at 25 mg/kg body weight or to an intraperitoneal dose of LPS at 1 or 5 mg/kg body weight; however, all mice receiving VT and either LPS dose became moribund in less than 40 h. The principal histologic lesions in the moribund mice treated with VT and LPS were marked cell death and loss in thymus, Peyer's patches, spleen, and bone marrow. In all of these lymphoid tissues, treatment-induced cell death had characteristic histologic features of apoptosis causing lymphoid atrophy. These results suggest that LPS exposure may markedly increase the toxicity of trichothecenes and that the immune system was a primary target of these interactive effects.

Animals↗

Structural features of the ligand-binding domain of the serotonin 5HT3 receptor.

The nicotinic acetylcholine receptor (AChR) and the serotonin type 3 receptor (5HT3R) are members of the ligand-gated ion channel gene family. Both receptors are inhibited by nanomolar concentrations of d-tubocurarine (curare) in a competitive fashion. Chemical labeling studies on the AChR have identified tryptophan residues on the gamma (gammaTrp-55) and delta (deltaTrp-57) subunits that interact with curare. Comparison of the sequences of these two subunits with the 5HT3R shows that a tryptophan residue is found in the homologous position in the 5HT3R (Trp-89), suggesting that this residue may be involved in curare-5HT3R interactions. Site-directed mutagenesis at position Trp-89 markedly reduces the affinity of the 5HT3R for the antagonists curare and granisetron but has little effect on the affinity for the agonist serotonin. To further examine the role of this region of the receptor in ligand-receptor interactions, alanine-scanning mutagenesis analysis of the region centered on Trp-89 (Thr-85 to Trp-94) was carried out, and the ligand binding properties of the mutant receptors were determined. Within this region of the receptor, curare affinity is reduced by substitution only at Trp-89, whereas serotonin affinity is reduced only by substitution at Arg-91. On the other hand, granisetron affinity is reduced by substitutions at Trp-89, Arg-91, and Tyr-93. This differential effect of substitutions on ligand affinity suggests that different ligands may have different points of interaction within the ligand-binding pocket. In addition, the every-other-residue periodicity of the effects on granisetron affinity strongly suggests that this region of the ligand-binding site of the 5HT3R (and by inference, other members of the ligand-gated ion channel family) is in a beta-strand conformation.

Amino Acid Sequence↗

Managing geometric uncertainty in conformal intensity-modulated radiation therapy.

The geometric precision of radiotherapy treatments must increase if the objectives of dose escalation and increased disease control are to be achieved. There are multiple strategies for increasing the geometric precision of a radiotherapy treatment system, including immobilization and setup aids for reducing random and systematic components of setup errors and organ motion alike. Alternatively, more complex strategies can be implemented based on additional information acquired over the course of treatment. Generally, these strategies can be divided into two categories: off-line and on-line. The strategies that are implemented in the clinic must consider the required geometric precision for a given treatment. From this specification, it is possible to select the appropriate strategies and approaches. The cost associated with each approach must also be considered. Once a system for delivery has been designed, the residual uncertainties must still be considered in the planning process. Parallel to the development of strategies for reducing uncertainty, progress is being made in better relating these residual uncertainties to margins for use in treatment planning. This article reviews advances in reducing uncertainty.

Cost-Benefit Analysis↗

Mutations affecting motifs of unknown function in the central domain of nitrogen regulatory protein C.

The positive control function of the bacterial enhancer-binding protein NtrC resides in its central domain, which is highly conserved among activators of sigma54 holoenzyme. Previous studies of a small set of mutant forms specifically defective in transcriptional activation, called NtrC repressor [NtrC(Rep)] proteins, had enabled us to locate various functional determinants in the central domain. In this more comprehensive survey, the DNA encoding a major portion of the central domain was randomly mutagenized and mutated ntrC genes were introduced into the cell via multicopy expression plasmids. DNA sequencing of 95 isolates identified by a preliminary phenotypic screen revealed that the lesions in them caused 55 distinct single amino acid substitutions at 44 different positions. Assays of glnA transcription in vivo and in vitro yielded two conclusions. First, of the 41 mutant proteins that could be purified, 17 (1 known, 16 new) showed no detectable activity in either assay, thus qualifying them as true NtrC(Rep) proteins. These contained residue changes in six of the seven highly conserved regions in the central domain, including two never studied before. Second, some mutant proteins were inactive in vivo but were either marginally or fully active in vitro. Their surprising lack of activity in vivo may be accounted for by high levels of expression, which apparently decreased activation by these mutant proteins but not by wild-type NtrC (NtrCWT). Of particular interest were a subset of these proteins that exhibited greater transcriptional activation than NtrCWT at low concentrations. Their elevated activation capacities remain to be explained.

Amino Acid Sequence↗

Surgical treatment of patent ductus arteriosus (PDA) through mini subaxillary extrapleural approach.

In this study, a new surgical technique for the surgical treatment of patent ductus arteriosus (PDA) is evaluated. The subaxillary extrapleural approach was performed on 836 patients with patent ductus arteriosus. And 20 of these patients were evaluated for postoperative outcomes compared with the routine technique. The results indicated that the new method is safe, less traumatic and has better cosmetic effects. It is concluded in this article that the subaxillary extrapleural approach for PDA is a good modification to the routine surgical technique, that is surgery through the posterolateral approach.

Cardiac Surgical Procedures↗

[Study on the relationship between perinatal hypoxia and concentration of endothelin-1 in amniotic fluid].

OBJECTIVE: To investigate the relationship between endothelin-1 (ET-1) concentration in amniotic fluid (AF) and perinatal hypoxia. METHODS: 161 cases were measured for amniotic fluid(AF) ET-1 levels by radioimmunoassay. 110 cases of normal pregnancy were included in control group among which 30 term pregnancies were simultaneously measured for maternal and umbilical plasma ET-1. 51 cases of intrauterine hypoxia were the study group. RESULTS: (1) The AF ET-1 levels showed increasing trend after 14 weeks (P < 0.01). (2) Fetal plasma ET-1 levels were significantly higher than that of maternal plasma ET-1 levels, but lower than those of AF ET-1 (P < 0.01). The ET-1 levels of umbilical plasma had positive correlation with those of AF ET-1 (r = 0.952, P < 0.01), but there is no correlation with levels of maternal plasma ET-1 (r = 0.338, P < 0.05). (3) In study group, the level of AF ET-1 was elevated with severity of hypoxia, the average level of AF ET-1 in cases of intrauterine hypoxia was (30.654 +/- 5.832) ng/L. In cases of severe neonatal asphyxia it was (960.650 +/- 236.698) ng/L. CONCLUSIONS: The ET-1 exists in AF and gradually increases while pregnancy advanced. AF ET-1 levels can be served as a marker to predict perinatal hypoxia.

Adult↗

[The changes in arteriography in extremities sustaining high tension electric injuries].

OBJECTIVE: Because it is difficult to estimate the extent and degree of damage to the blood vessels of extremities sustaining high tension electrical injuries, arteriography was carried out to evaluate the vascular changes. METHODS: Selective arteriography was carried out 29 times for 26 extremities in 17 patients suffering from > 380 V electrical injuries. RESULTS: The arteriography showed that the injured arteries were narrowed and occluded, and vascular branches decreased or disappeared. Recanalization of the partially occluded arteries or collateral circulation formation was found after decompression. CONCLUSION: Arteriography is valuable to evaluate the vascular changes in high tension electrical injuries of extremities.

Adolescent↗

Biochemical characterization and subcellular localization of the mouse retinitis pigmentosa GTPase regulator (mRpgr).

The retinitis pigmentosa GTPase regulator (RPGR) gene encodes a protein homologous to the RCC1 guanine nucleotide exchange factor and is mutated in 20% of patients with X-linked retinitis pigmentosa. We have characterized the full-length and variant cDNAs corresponding to the mouse homolog of the RPGR gene (mRpgr). Comparison with the human cDNA revealed sequence identity primarily in the region of RCC1 homology repeats. As in humans, the mRpgr gene maps within 50 kilobases from the 5'-end of the Otc gene. The mRpgr transcripts are detected as early as E7 during embryonic development and are expressed widely in the adult mice. Variant mRpgr isoforms are generated by alternative splicing and by utilizing two in-frame initiation codons. The products of mRpgr cDNAs migrate aberrantly in SDS-polyacrylamide gels because of a charged domain. In transfected COS cells, the mRpgr protein is isoprenylated and is localized in the Golgi complex. This subcellular distribution is not observed after treatments with brefeldin A or mevastatin and when the conserved isoprenylation sequence (CTIL) at the carboxyl terminus is deleted or mutagenized. These studies suggest a role for the mRpgr protein in Golgi transport and form the basis for investigating the mechanism of photoreceptor degeneration in X-linked retinitis pigmentosa.

Alternative Splicing↗

Mutation of a gene encoding a protein with extracellular matrix motifs in Usher syndrome type IIa.

Usher syndrome type IIa (OMIM 276901), an autosomal recessive disorder characterized by moderate to severe sensorineural hearing loss and progressive retinitis pigmentosa, maps to the long arm of human chromosome 1q41 between markers AFM268ZD1 and AFM144XF2. Three biologically important mutations in Usher syndrome type IIa patients were identified in a gene (USH2A) isolated from this critical region. The USH2A gene encodes a protein with a predicted size of 171.5 kilodaltons that has laminin epidermal growth factor and fibronectin type III motifs; these motifs are most commonly observed in proteins comprising components of the basal lamina and extracellular matrixes and in cell adhesion molecules.

Amino Acid Sequence↗

Ammonia acquisition in enteric bacteria: physiological role of the ammonium/methylammonium transport B (AmtB) protein.

Homologues of the amtB gene of enteric bacteria exist in all three domains of life. Although their products are required for transport of the ammonium analogue methylammonium in washed cells, only in Saccharomyces cerevisiae have they been shown to be necessary for growth at low NH4+ concentrations. We now demonstrate that an amtB strain of Escherichia coli also grows slowly at low NH4+ concentrations in batch culture, but only at pH values below 7. In addition, we find that the growth defect of an S. cerevisiae triple-mutant strain lacking the function of three homologues of the ammonium/methylammonium transport B (AmtB) protein [called methylammonium/ammonium permeases (MEP)] that was observed at pH 6.1 is relieved at pH 7.1. These results provide direct evidence that AmtB participates in acquisition of NH4+/NH3 in bacteria as well as eucarya. Because NH3 is the species limiting at low pH for a given total concentration of NH4+ + NH3, results with both organisms indicate that AmtB/MEP proteins function in acquisition of the uncharged form. We confirmed that accumulation of [14C]methylammonium depends on its conversion to gamma-N-methylglutamine, an energy-requiring reaction catalyzed by glutamine synthetase, and found that at pH 7, constitutive expression of AmtB did not relieve the growth defects of a mutant strain of Salmonella typhimurium that appears to require a high internal concentration of NH4+/NH3. Hence, contrary to previous views, we propose that AmtB/MEP proteins increase the rate of equilibration of the uncharged species, NH3, across the cytoplasmic membrane rather than actively transporting-that is, concentrating-the charged species, NH4+.

Bacterial Proteins↗