Biomedical subjects

X Di

Publications and source records attributed to X Di.

At least 19 recordsLinked to original sources

PubMed2006

LdCompare: rapid computation of single- and multiple-marker r2 and genetic coverage.

UNLABELLED: The scale of genetic-variation datasets has increased enormously and the linkage equilibrium (LD) structure of these polymorphisms, particularly in whole-genome association studies, is of great interest. The significant computational complexity of calculating single- and multiple-marker correlations at a genome-wide scale remains challenging. We have developed a program that efficiently characterizes whole-genome LD structure on large number of SNPs in terms of single- and multiple-marker correlations. AVAILABILITY: LdCompare is licensed under the GNU General Public License (GPL). Source code, documentation, testing datasets and precompiled executables are available for download at: http://www.affymetrix.com/support/developer/tools/devnettools.affx

Algorithms↗

PubMed2002

Analysis of high density expression microarrays with signed-rank call algorithms.

MOTIVATION: We consider the detection of expressed genes and the comparison of them in different experiments with the high-density oligonucleotide microarrays. The results are summarized as the detection calls and comparison calls, and they should be robust against data outliers over a wide target concentration range. It is also helpful to provide parameters that can be adjusted by the user to balance specificity and sensitivity under various experimental conditions. RESULTS: We present rank-based algorithms for making detection and comparison calls on expression microarrays. The detection call algorithm utilizes the discrimination scores. The comparison call algorithm utilizes intensity differences. Both algorithms are based on Wilcoxon's signed-rank test. Several parameters in the algorithms can be adjusted by the user to alter levels of specificity and sensitivity. The algorithms were developed and analyzed using spiked-in genes arrayed in a Latin square format. In the call process, p-values are calculated to give a confidence level for the pertinent hypotheses. For comparison calls made between two arrays, two primary normalization factors are defined. To overcome the difficulty that constant normalization factors do not fit all probe sets, we perturb these primary normalization factors and make increasing or decreasing calls only if all resulting p-values fall within a defined critical region. Our algorithms also automatically handle scanner saturation.

Algorithms↗

PubMed2001

[A further study on potential of microsatellite analysis of urine in diagnosis of bladder cancer].

OBJECTIVES: To investigate the application value of microsatellite analysis of voided urine in diagnosis of bladder cancer and compare the advantages and disadvantages of this method and urine cytology. METHODS: Thirteen microsatellite markers, including the nine markers used in the authors' previous study and another four new markers, were tested on urine DNA from 143 individuals with or without bladder lesions in a blinded fashion. Urine cytology was applied at the same time. RESULTS: The urine DNA from 89% (97/109) of the patients with bladder cancer, 86% (6/7) of the patients with inverted papilloma of the bladder, 3 out of 7 patients with cystitis and one patient with hematuria of unknown cause showed alterations, at least, in one of the 13 microsatellite markers, while the 19 individuals without bladder lesion had no change at any of these loci. Nucleic atypia or suspicious cancer cells were detected by routine cytology in the urine of the 3 patients with cystitis and one patient with hematuria of unknown cause who showed alterations of microsatellite in their urine sediments. Among the 81 cases of bladder cancer whose urine was examined by both microsatellite analysis and routine cytology, 73 cases (90%), of various stage or grade, were identified by microsatellite analysis, while only 41 cases (51%), mainly at advanced stage, were detected by cytology. Cancer cells were detected in the urine sediments of 4 of the 12 cases that were not identified by microsatellite analysis. CONCLUSION: Microsatellite analysis of urine is useful for detection of bladder cancer. Microsatellite analysis and urine cytology could be complementary to each other.

Female↗

PubMed2001

A comparison between microsatellite analysis and cytology of urine for the detection of bladder cancer.

We have studied, in a blinded fashion, cytology and microsatellite analysis on urine sediments of 143 Chinese with or without bladder lesions. Microsatellite analysis succeeded in all 143 individuals, while cytology could not be performed on 42 subjects due to insufficient urine samples. Both microsatellite analysis and routine urine cytology succeeded in 81 bladder cancer patients. Seventy-three patients (90%) were identified by microsatellite analysis, while only 41 patients (51%) were identified by cytology. However, four patients were identified by routine cytology but not by microsatellite analysis. Our results proved that microsatellite analysis is more sensitive than routine cytology but the two methods are complementary to each other.

Adult↗

PubMed2001

Presence of DNA fragmentation and lack of neuroprotective effect in DFF45 knockout mice subjected to traumatic brain injury.

BACKGROUND: Apoptosis plays an important pathophysiologic role in neuronal cell loss and associated neurologic deficits following traumatic brain injury (TBI). DNA fragmentation represents one of the characteristic biochemical features of neuronal apoptosis and is observed after experimental TBI. DFF45 and DFF40 are essential for DNA fragmentation in various models of apoptosis. MATERIALS AND METHODS: We used mice deficient in DFF45 and wild-type controls. Oligonucleosomal DNA fragmentation induced by TBI was analyzed using in vivo and in vitro assays. Expression and integrity of DFF45 and DFF40 proteins was assessed by Western analysis. Other outcome measurements included neurologic scoring, learning/memory tests, lesion volume measurements (MRI), and assessment of cell viability in vitro among others. RESULTS: We compared the effects of controlled cortical impact (CCI) trauma in DFF45 knockout mice and wild-type controls. Analysis of TBI-induced DNA fragmentation in brain cortex from wild-type and DFF45 knockout mice indicates that, although somewhat delayed, oligonucleosomal cleavage of DNA occurs after TBI in DFF45 knockout mice. DFF45 knockouts showed no significant differences in behavioral outcomes or lesion volumes after TBI as compared to wild-type controls. Using an in vitro reconstitution system, we also demonstrated that cleavage of DFF45 by caspase-3 is not sufficient for DNA fragmentation induced by protein extracts from rat brain cortex. We found that endonuclease activity induced in rat brain cortex following TBI depends on the presence of Mg2+ and Ca2+, but is not inhibited by Zn2+. Primary neuronal cultures from DFF45 knockouts failed to show DNA laddering in response to staurosporine, but did show prominent, albeit delayed, DNA fragmentation following treatment with etoposide. In contrast, primary neurons from wild-type animals demonstrated marked DNA fragmentation following treatment with staurosporine or etoposide. CONCLUSIONS: The results of this study suggest that, in addition to DFF45/40, other endonucleases may be essential for chromatin degradation during neuronal apoptosis in adult brain after TBI.

Animals↗

PubMed2001

[The role of dexamethasone on airway wall remodeling].

OBJECTIVE: To investigate the role of inhaled dexamethasone on airway wall remodeling. METHODS: Asthmatic guinea pig models were established, after guinea pigs inhaled ovalbumin and dexamethasone, the thickness of airway wall was determined by contour tracing, using a digitizing pad and microcomputer. To culture airway smooth muscle cells, observe the effect of histamine, thromboxane A(2) and dexamethasone on cultured cells. RESULTS: The mean thickness of airway smooth muscle in asthma group was (90 +/- 14) micrometer, greater than that of control (54 +/- 7) micrometer (P < 0.01); the airway smooth muscle layer in dexamethasone group (61 +/- 11) micrometer was thinner than that of asthma group (P < 0.01). [(3)H]-TdR incorporation in histamine group (2 950 +/- 205) counts/min was higher, comparing to that of the control (613 +/- 52) counts/min (P < 0.01); [(3)H]-TdR incorporation in dexamethasone group was (1 067 +/- 96) counts/min, lower than those of histamine group (P < 0.01). CONCLUSIONS: Dexamethasone could prevent airway remodeling, and had no harmful effect on airway wall.

Administration, Inhalation↗

PubMed2001

[Construction and expression of a new humanized salmon calcitonin variant].

OBJECTIVE: To study the reduction of immunogenicity of salmon calcitonin (sCT). METHODS: A new (11-17) humanized salmon calcitonin variant gene (11-17) hsCT was designed and synthesized to construct recombinant expression vector and express in E.coli G1724 with tryptophan. The fusion protein of humanized salmon calcitonin and thioredoxin (Trx-hsCT) obtained from the bacterial by means of osmotic pressure; The bioactivity of Trx-hsCT was estimated by serum calcium reduction method in rat; The quantitative Western blot analysis was used for detecting the immunogenicity of hsCT. RESULTS: Recombinant expressing vector pTrxFus-hsCT was expressed in high level and soluble in E.coli G1724, reaching 46% of total bacterial protein and obtaining the fusion protein of 90% purity; Special bioactivity of hsCT was preserved that of half pre-sCT and its immunogenicity reduced over 50% that of pre-sCT. CONCLUSION: Obtain a new humanized salmon calcitonin variant(11-17) hsCT which maintains a rather high bioactivity over pre-sCT and decreases distinctly its immunogenicity.

Animals↗

PubMed2000

Brain lactate uptake increases at the site of impact after traumatic brain injury.

Although glucose is the main carbohydrate energy substrate for the normal brain, several studies published over the last 10 years now challenge this assumption. The activated brain increases its metabolism to meet increased energy demands by glycolysis after injury. In vitro studies now show that lactate alone can serve as an energy source to maintain synaptic function. In this study, we used 14C-lactate to test the hypothesis that blood lactate is acutely taken up by the injured brain, after fluid percussion injury (FPI) in the rat. 50 microCi radioactive lactate was injected i.v. immediately after FPI, in injured and sham rats. After 30 min, the brain was removed, frozen, and cut into 20 microm sections for autoradiography. Uptake of 14C-label was mainly concentrated at the injury site (2.5 times greater) although uninjured brain also took up the 14C-label. This increased concentration of radioactive lactate at the injury site suggests that the injured brain may use the lactate as an energy source.

Animals↗

PubMed2000

Dicyclomine, an M1 muscarinic antagonist, reduces infarct volume in a rat subdural hematoma model.

The rat subdural hematoma (SDH) model produces a zone of ischemic brain damage within the hemisphere beneath the SDH. Previous studies have measured large increases in extracellular acetylcholine during cerebral ischemia in the rat. We examined infarct volume after selectively blocking muscarinic M1 receptors with dicyclomine during SDH. Rats were anesthetized with isoflurane (2%), intubated, and femoral artery and vein cannulated. Autologous blood (0.375 ml) was injected (0.05 ml/min) under the dura of the right parietal cortex. Dicyclomine (5 mg/kg, i.v.) was injected at 5 min after and again at 2 h after completion of the subdural blood infusion. Blood pressure and intracranial pressure (ICP) were continuously measured. At 4 h after SDH rats were euthanized, brains sectioned, and immunoreacted with glia fibrillary acidic protein. Cortical infarct volume was quantified in coronal brain sections at 0.7-mm intervals from +1.0 mm to -3.9 mm relative to bregma. Infarct volume in drug-treated rats (n = 10) 22.1 +/- 6.99 mm3 was significantly smaller (p < 0.02) than vehicle treated rats (n = 10) 56.7 +/- 9.59 mm3. ICP, blood pressure and cerebral perfusion pressure were not significantly different between groups. These data suggest that activation of M1 muscarinic receptors during an ischemic event may contribute to the development of subsequent pathology.

Animals↗

PubMed2000

Evidence for lactate uptake after rat fluid percussion brain injury.

UNLABELLED: Traumatic brain injury (TBI) places enormous early energy demand on brain tissue to reinstate normal ionic balance. Glucose declines and lactate increases after TBI as demonstrated in clinical and lab studies, suggesting increased glycolysis. This led us to hypothesize that high extracellular fluid (ECF) lactate may be beneficial after TBI. We measured cerebral dialysate lactate and glucose, and arterial lactate and glucose, before & after rat Fluid Percussion Injury (FPI) (2.06 +/- 0.13 atm) with and without i.v. lactate infusion (100 mM x 4.5 hours) to test the hypotheses that arterial lactate determines ECF lactate. 14C-lactate autoradiography was also performed, to demonstrate whether lactate is taken up by traumatized brain. RESULTS: Dialysate lactate was always significantly higher than arterial. After lactate infusion, both the dialysate and the arterial lactate were significantly increased (P < 0.0001). Dialysate lactate increased within 10 min. following FPI, with significantly higher values in the lactate infusion group (82% higher with lactate infusion after FPI). Dialysate glucose fell following FPI, with a more severe decline in the saline group (129% lower), suggesting lactate infusion preserves or "spares" glucose in ECF. In our autoradiographic study, i.v. 14C-lactate accumulated at the injury site, with levels 2-4 times higher than in contralateral cortex. In conclusion, arterial lactate augmentation thus increases brain dialysate lactate and results in less reduction in ECF glucose, after FPI. Infused lactate accumulates at the injury site, where metabolism is probably the greatest.

Animals↗

PubMed2000

Mechanical injury alters volume activated ion channels in cortical astrocytes.

UNLABELLED: Although astrocytic swelling is likely to mediate brain edema and high ICP after traumatic brain injury, the mechanism is not understood. We employed whole cell patch clamp electrophysiology and a stretch injury model to understand whether volume regulating ion currents are altered following cell injury. Mixed rat astrocytes and neurons were co-cultured on deformable silastic membranes. Mild-moderate cell injury was produced using a timed pulse of pressurized air to deform the silastic substrates by 6.5 mm. Then, ion currents were recorded with patch clamp methods. Cells were held at -65 mV and were stepped to +10 mV to monitor current changes. RESULTS: In unstretched astrocytes, small amplitude currents were obtained under isotonic conditions. Hypotonic solution activated an outwardly-rectifying current which reversed near -40 mV. This current resembled a previously reported anion current whose activation may restore cell volume by mediating a net solute efflux. In contrast, stretch injured cells exhibited a large amplitude, nonrectifying current. This current was not due to non-specific ionic leakage, since it was fully suppressed by the cation channel blocker gadolinium. Activation of novel stretch-activated cation currents may exacerbate cell swelling in injured astrocytes. Stretch injured astrocytes thus express a dysfunctional cation current as opposed to an osmoregulatory anion current. This mechanism, if present in vivo, may contribute to the cytotoxic swelling seen after traumatic brain injury.

Animals↗

PubMed2000

Lactate/glucose dynamics after rat fluid percussion brain injury.

Traumatic brain injury (TBI) places enormous early energy demand on brain tissue to reinstate normal ionic balance. Clinical studies have demonstrated a decline in extracellular fluid (ECF) glucose and an increase in lactate after TBI. In vitro studies suggest that this increase in lactate is mediated by increased glutamate and may provide a metabolic substrate for neurons, to aid in ionic restoration. This led us to hypothesize that high ECF lactate may be beneficial in recovery following TBI, where major ionic flux has been shown to occur. In this study, we measured cerebral dialysate lactate and glucose, and arterial lactate and glucose, before and after rat lateral fluid percussion brain injury (FPI; 2.06 +/- 0.13 atm) with and without IV lactate infusion (100 mM X 0.65 mL/h X 5 h) to test the hypothesis that arterial lactate can influence ECF lactate. Dialysate lactate increased within 10 min following FPI, with higher values in the lactate infusion group. Following FPI, the dialysate lactate increase was 238% with lactate infusion versus 171% increase with saline infusion. Dialysate glucose fell immediately following FPI, with a more severe decline in the saline group. The glucose decrease was 231% greater in the IV saline group. Furthermore, in the lactate infusion group, the dialysate glucose levels recovered to baseline levels by 4 h after injury, whereas they remained depressed through out the experiment, in the saline infusion group. We conclude that arterial lactate augmentation can increase brain dialysate lactate, and result in more rapid recovery of dialysate glucose after FPI. This may indicate a beneficial role for lactate, that may be potentially useful in the clinical situation, after TBI.

Animals↗

PubMed2000

[Determination of three principal components in chuanjing tablets by using high performance liquid chromatography].

Uniform design method was employed to optimize the mobile phase of HPLC in order to determine simultaneously three principal components, theophylline, amobarbital and methylephedrine hydrochloride, in Chuanjing tablet, a compound preparation for asthma and cough. The stationary phase was ODS and the optimal mobile phase composition was V (0.015 mol/L phosphate buffer containing 0.3% triethylamine, pH 4.9): V (methanol) = 35:65. The detection was performed at 215 nm and the sensitivity was time programmed for simultaneous determination of minor and major components. Caffeine was selected as the internal standard. A baseline separation was achieved within 10 min. The linear ranges for theophylline, amobarbital and methylephedrine hydrochloride were 0.03 g/L-0.20 g/L, 7.5 mg/L-50.0 mg/L and 7.5 mg/L-50.0 mg/L, recoveries 99.7%-102.6%, 98.5%-100.2% and 98.0%-102.7%, inter-day RSDs 0.23%-1.2%, 0.35%-2.5%, 0.33%-1.6% respectively. This HPLC method is rapid and accurate, and suitable for the quality control of the preparation.

Amobarbital↗

PubMed1999

Effects of levonorgestrel-releasing subdermal contraceptive implants on bone density and bone metabolism.

A prospective, randomized clinical trial observed the effects of Norplant long-term contraceptive implants and domestic implants similar to Norplant on bone mineral density and bone metabolism in female acceptors for 1 year. Bone mineral density (BMD) and bone mineral content (BMC) of lumbar 2-4 and proximal femur of 61 normal women of child-bearing age were measured by dual energy x-ray absorptiometry (DEXA) before and 12 months after implants insertion in both groups. BMD and BMC of lumbar 2-4 in both groups 12 months after implant insertion significantly increased (p < 0.01); with an average increase of 2.40% and 3.34%, respectively in the Norplant implant group, and 2.75% and 4.47%, respectively in the domestic implant group. Urine hydroxyproline and creatinine ratio (Hop/Cr) in the domestic implant group significantly decreased (p < 0.01). There was no significant differences in the effects on BMD and BMC of lumbar spine and femur and on bone metabolism between the two groups of contraceptive implants (p > 0.05). Levonorgestrel releasing contraceptive subdermal implants were not deleterious to the skeleton in women of child-bearing age. There was no significant effect on achieving maximum bone mass in young women.

Absorptiometry, Photon↗

PubMed1999

Reducing hemoglobin oxygen affinity does not increase hydroxyl radicals after acute subdural hematoma in the rat.

Extensive evidence is available to show the importance of ischemia after severe human head injury. We have previously shown that pharmacologically increasing the release of oxygen in brain tissue where the local oxygen pressure is low reduces infarct size in animal models. To study the possible negative effects of this strategy, we tested the effect of an allosteric modifier of hemoglobin (RSR13) on free radical production in the rat acute subdural hematoma (ASDH) model, both under normoxic as well as under hyperoxic, normobaric conditions. When compared to baseline, induction of ASDH resulted in a significant increase (p < 0.05) in 2,3-DHBA (2,3 dihydroxybenzoic acid, produced from salicylate after attack by hydroxyl radicals) at 30 and 60 min postinduction, both for the control group (39% and 91%) as well as the RSR13-treated group (41% and 62%). The 2,5-DHBA also increased significantly (p < 0.05) in the drug-treated animals at the 30- and 60-min time points when compared to baseline (49% and 77%). At all time points, except the 30-min, the increase in 2,3-DHBA was less marked in the RSR13 animals than in the control group. Similarly, the 2,5-DHBA increase after ASDH was lower at all time points except for the 30-min time point in the RSR13-treated group. These results indicate that enhanced tissue oxygen release by the allosteric modifier of hemoglobin RSR13 does not increase hydroxyl radical production after ASDH. Clinical trials are needed to test this compound in humans after severe head injury.

Aniline Compounds↗

PubMed1999

Fluid percussion brain injury exacerbates glutamate-induced focal damage in the rat.

The role of glutamate-mediated neuronal damage in neurotrauma remains controversial. The cerebral levels measured in patients by microdialysis are sufficient to kill neurons in culture, but not in the intact brain of the normal rat. A synergistic effect between excitatory amino acid-mediated damage and other posttrauma mechanisms must therefore be proposed, if glutamate is indeed a significant cause of posttraumatic brain damage. The presence of such a synergistic mechanism was therefore investigated by combining in vivo glutamate perfusion and fluid percussion injury (FPI). Twenty-four adult male Sprague Dawley rats were randomly assigned to three groups: (1) vehicle (n = 9): mock cerebrospinal fluid (CSF) perfusion plus FPI; (2) glutamate + FPI (n = 9): 0.1 M glutamate intracortical perfusion plus FPI; and (3) glutamate without FPI (n = 6). After preparation for central FPI, at a moderate level of injury (2 +/- 0.5 atm), glutamate or mock CSF perfusion was performed via a CMA/12 microdialysis probe (3 mm). Animals were then perfusion fixed, under deep anesthesia, after 3-h survival, for volumetric histopathology. The glutamate perfusion + FPI group (2.42 +/- 1.63 mm3) produced a significantly bigger lesion than mock CSF perfusion + FPI (0.063 +/- 0.41 mm3) and glutamate perfusion alone (1.00 +/- 0.47 mm3). Traumatic brain injury thus seems to enhance glutamate-mediated brain damage, and this may be due to qualitative changes induced in ion channels and receptors, such as the N-methyl-D-aspartate channel, after shear injury.

Animals↗

PubMed1998

Increased free radical production due to subdural hematoma in the rat: effect of increased inspired oxygen fraction.

Acute subdural hematoma (ASDH) complicates about 15%-20% of severe head injury patients and is one of the major causes for bad outcome, yet the pathomechanisms involved are not well understood. This study has employed a recently developed technique to determine whether ASDH induces free radicals in the underlying brain. We also studied the effect of increased inspired oxygen fraction (FiO2) on free radical production, both in the normal rat brain and after ASDH induction. Twelve male Sprague Dawley rats were studied over 5 h (2 h of FiO2 = 30%, 3 h of FiO2 = 100%). Hydroxyl radical production was measured with microdialysis using the salicylate trapping technique by quantitating the 2,3 dihydroxy benzoic acid (2,3 DHBA) and 2,5 dihydroxy benzoic acid (2,5 DHBA), degradation products, in either noninjured brain (n = 6) or after ASDH (n = 6). Both 2,3 DHBA and 2,5 DHBA increased significantly by 39% and 108%, respectively, after the induction of the SDH (p < 0.05). By increasing the FiO2 to 100%, 2 h after ASDH induction, the 2,3 DHBA and 2,5 DHBA further increased only slightly (ns). After increasing the FiO2 to 100% in the noninjured group, the mean level of 2,3 DHBA increased by 56% (p = 0.06, ns). The level of 2,5 DHBA in the dialysate increased significantly by 56% (p < 0.05), when the FiO2 was increased to 100% ASDH results in a significant increase in free radical production. At the same time, prolonged increase in FiO2 does not lead to further increase in free radical production in the injured brain.

Acute Disease↗

PubMed1998

[The expression study of human stem cell factor (hSCF) in E. coli].

OBJECTIVE: To improve the expression level of recombinant human stem cell factor (rhSCF). METHODS: With PCR techniques and synthesized oligonucleotide as primers, the number of nucleotides between the SD sequence and the starting codon ATG of human stem cell factor cDNA was altered, and the preferable codons of E. coli in the N-terminal amino acid sequence were selected. RESULTS: SDS-PAGE electrophoresis indicated that the ratio of expressed rhSCF to total E. coli proteins increased from 12% to 40% by thermal inducing. With DNA sequencing, the reading frame of the gene was proved to be correct. The sequence of 17 N-terminal amino acids of purified recombinant hSCF has been proved to be identical to the natural hSCF, except the first amino acid-Met. CONCLUSIONS: These studies suggest that the 5'-flanking region of hSCF cDNA plays an important role in its gene expression.

Amino Acid Sequence↗