Biomedical subjects

P Zhang

Publications and source records attributed to P Zhang.

At least 37 records · Page 2Linked to original sources

PubMed2005

Quantum heat engine with multilevel quantum systems.

By reformulating the first law of thermodynamics in the fashion of quantum-mechanical operators on the parameter manifold, we propose a universal class of quantum heat engines (QHE) using the multilevel quantum system as the working substance. We obtain a general expression of work for the thermodynamic cycle with two thermodynamic adiabatic processes, which are implied in quantum adiabatic processes. We also classify the conditions for a 3-level QHE to extract positive work, which is proved to be looser than that for a 2-level system under certain conditions. As a realistic illustration, a 3-level atom system with dark state configuration manipulated by a classical radiation field is used to demonstrate our central idea.

Journal Article↗

PubMed2005

Cooling mechanism for a nanomechanical [corrected] resonator by periodic coupling to a Cooper pair box.

We propose and study an active cooling mechanism for the nanomechanical resonator (NAMR) based on periodical coupling to a Cooper pair box (CPB), which is implemented by a designed series of magnetic flux pluses threading through the CPB. When the initial phonon number of the NAMR is not too large, this cooling protocol is efficient in decreasing the phonon number by 2 to 3 orders of magnitude. Our proposal is theoretically universal in cooling various boson systems of a single mode. It can be specifically generalized to prepare the nonclassical state of the NAMR.

Journal Article↗

PubMed2005

Wheat genetic diversity trends during domestication and breeding.

It has been claimed that plant breeding reduces genetic diversity in elite germplasm which could seriously jeopardize the continued ability to improve crops. The main objective of this study was to examine the loss of genetic diversity in spring bread wheat during (1) its domestication, (2) the change from traditional landrace cultivars (LCs) to modern breeding varieties, and (3) 50 years of international breeding. We studied 253 CIMMYT or CIMMYT-related modern wheat cultivars, LCs, and Triticum tauschii accessions, the D-genome donor of wheat, with 90 simple sequence repeat (SSR) markers dispersed across the wheat genome. A loss of genetic diversity was observed from T. tauschii to the LCs, and from the LCs to the elite breeding germplasm. Wheat's genetic diversity was narrowed from 1950 to 1989, but was enhanced from 1990 to 1997. Our results indicate that breeders averted the narrowing of the wheat germplasm base and subsequently increased the genetic diversity through the introgression of novel materials. The LCs and T. tauschii contain numerous unique alleles that were absent in modern spring bread wheat cultivars. Consequently, both the LCs and T. tauschii represent useful sources for broadening the genetic base of elite wheat breeding germplasm.

Breeding↗

PubMed2005

Comparison of intravenous ibutilide vs. propafenone for rapid termination of recent onset atrial fibrillation.

This study was to evaluate the efficacy and safety of ibutilide and propafenone given intravenously in converting recent onset atrial fibrillation (AF). Eighty-two consecutive patients with AF (onset in 2 h to 90 days) were randomly assigned to receive two 10-min infusions, 10 min apart, of either ibutilide (1 mg) or propafenone (70 mg). The treatment was considered successful if sinus rhythm occurred within 90 min after the beginning of infusion. Ibutilide had a significantly higher rate of cardioversion than propafenone (70.73 vs. 48.78%, p = 0.043). The patients with shorter AF duration or smaller left atrium diameter had a higher success rate. Nonsustained monomorphic ventricular tachycardia was the most serious adverse effect of ibutilide in 9.76% of patients, and hypotension and heart pause were the major serious adverse events in 17.07% of patients treated with propafenone. Ibutilide is more effective than intravenous propafenone for the cardioversion of recent onset AF, and the adverse effects are rare and transient.

Adult↗

PubMed2005

Robertsonian translocations in wheat arise by centric misdivision of univalents at anaphase I and rejoining of broken centromeres during interkinesis of meiosis II.

The mechanism of origin of Robertsonian translocations was investigated in plants monosomic for chromosome 1A of wheat and 1H(t) of Elymus trachycaulus by GISH. Chromosomes 1A and 1H(t) stayed univalent in all metaphase I cells analyzed, suggesting that Robertsonian translocations do not originate from meiotic recombination in centromeric regions with shared DNA sequence homology. At ana-/telophase I, the 1H(t) and 1A univalents underwent either chromosome or chromatid segregation and misdivided in 6-7% of the pollen mother cells. None of the ana-/telophases I analyzed had Robertsonian translocations, which were only observed in 2% of the "half tetrads" at ana-/telophase II. The frequency of Robertsonian translocations observed at ana-/telophase II corresponds well with the number of Robertsonian translocations (1-4%) detected in progenies derived from plants monosomic for group-1 chromosomes of wheat (1A, 1B, and 1D) and 1H(t) of E. trachycaulus. Our data suggest that Robertsonian translocations arise from centric misdivision of univalents at ana-/telophase I, followed by segregation of the derived telocentric chromosomes to the same nucleus, and fusion of the broken ends during the ensuing interkinesis.

Anaphase↗

PubMed2004

Selection and validation of differentially expressed genes in head and neck cancer.

We applied a robust combinatorial (multi-test) approach to microarray data to identify genes consistently up- or down-regulated in head and neck squamous cell carcinoma (HNSCC). RNA was extracted from 22 paired samples of HNSCC and normal tissue from the same donors and hybridized to the Affymetrix U95A chip. Forty-two differentially expressed probe sets (representing 38 genes and one expressed sequence tag) satisfied all statistical tests of significance and were selected for further validation. Selected probe sets were validated by hierarchical clustering, multiple probe set concordance, and target-subunit agreement. In addition, real-time PCR analysis of 8 representative (randomly selected from 38) genes performed on both microarray-tested and independently obtained samples correlated well with the microarray data. The genes identified and validated by this method were in comparatively good agreement with other rigorous HNSCC microarray studies. From this study, we conclude that combinatorial analysis of microarray data is a promising technique for identifying differentially expressed genes with few false positives.

Algorithms↗

PubMed2004

Effectiveness of sodium hypochlorite in preventing inoculation of periapical tissues with contaminated patency files.

The aim of this study was to analyze the effectiveness of 5.25% sodium hypochlorite (NaOCI) in preventing inoculation of periapical tissues with contaminated patency files. Twenty-eight extracted human permanent teeth with single canals were used in the study. Group I teeth were filled with NaOCl, and #15 stainless steel files contaminated with Streptococcus sanguis (ATCC #10556) were allowed to pass through the NaOCI into the culture medium. The teeth in group II were also filled with NaOCl, but the contaminated files used in group II canals were immersed in NaOCl for 10 s prior to being placed into the canals and cultured. The negative control group used sterile files (0% growth), the first positive control group used contaminated patency files in teeth with empty canals (100% growth), and the second positive control group placed contaminated files into broth next to teeth filled with NaOCl (to evaluate potential chlorine leakage; 100% growth). The experimental results showed no positive growth of S. sanguis for groups I and II, indicating that the NaOCl present in the canal after irrigation was sufficient to kill the test organism.

Dental Alloys↗

PubMed2004

Acute alcohol intoxication during hemorrhagic shock: impact on host defense from infection.

BACKGROUND: Acute alcohol intoxication is a frequent underlying condition associated with traumatic injury. Our studies have demonstrated that acute alcohol intoxication significantly impairs the immediate hemodynamic, metabolic, and inflammatory responses to hemorrhagic shock. This study investigated whether acute alcohol intoxication during hemorrhagic shock would alter the outcome from an infectious challenge during the initial 24 hr recovery period. METHODS: Chronically catheterized male Sprague Dawley rats were randomized to acute alcohol intoxication (EtOH; 1.75 g/kg bolus followed by a constant 15 hr infusion at 250-300 mg/kg/hr) or isocaloric isovolemic dextrose infusion (dex; 3 ml + 0.375 ml/hr). EtOH and dex were assigned to either fixed-volume (50%) hemorrhagic shock followed by fluid resuscitation with Ringer's lactate (EtOH/hem, dex/hem) or sham hemorrhagic shock (EtOH/sham, dex/sham). Indexes of circulating neutrophil function (apoptosis, phagocytosis, oxidative burst) were obtained at baseline, at completion of hemorrhagic shock, and at the end of fluid resuscitation. Bacterial clearance, lung cytokine expression, and myeloperoxidase activity were determined at 6 and 18 hr after an intratracheal challenge with Klebsiella pneumoniae (10 colony-forming units). RESULTS: Mean arterial blood pressure was significantly lower in acute alcohol intoxication-hemorrhagic shock animals throughout the hemorrhagic shock. In sham animals, acute alcohol intoxication alone did not produce significant changes in neutrophil apoptosis or phagocytic activity but significantly suppressed phorbol myristic acid (PMA)-stimulated oxidative burst. Hemorrhagic shock produced a modest increase in neutrophil apoptosis and suppression of neutrophil phagocytic capacity but significantly suppressed PMA-stimulated oxidative burst. Acute alcohol intoxication exacerbated the hemorrhagic shock-induced neutrophil apoptosis and the hemorrhagic shock-induced suppression of phagocytosis without further affecting PMA-stimulated oxidative burst. Fluid resuscitation did not restore neutrophil phagocytosis or oxidative burst. Acute alcohol intoxication decreased (-40%) 3-day survival from K. pneumoniae in hemorrhagic shock animals, impaired bacterial clearance during the first 18 hr postinfection, and prolonged lung proinflammatory cytokine expression. CONCLUSIONS: These results demonstrate that the early alterations in metabolic and inflammatory responses to hemorrhagic shock produced by acute alcohol intoxication are associated with neutrophil dysfunction and impaired host response to a secondary infectious challenge leading to increased morbidity and mortality.

Alcoholic Intoxication↗

PubMed2004

Direct visualization of receptor arrays in frozen-hydrated sections and plunge-frozen specimens of E. coli engineered to overproduce the chemotaxis receptor Tsr.

We have recently reported electron tomographic studies of sections obtained from chemically fixed E. coli cells overproducing the 60-kDa chemotaxis receptor Tsr. Membrane extracts from these cells prepared in the presence of Tween-80 display hexagonally close-packed microcrystalline assemblies of Tsr, with a repeating unit large enough to accommodate six Tsr molecules arranged as trimers of receptor dimers. Here, we report the direct visualization of the Tsr receptor clusters in (i) vitrified cell suspensions of cells overproducing Tsr, prepared by rapid plunge-freezing, and (ii) frozen-hydrated sections obtained from cells frozen under high pressure. The frozen-hydrated sections were generated by sectioning at -150 degrees C using a diamond knife with a 25 degrees knife angle, with nominal thicknesses ranging from 20 to 60 nm. There is excellent correspondence between the spatial arrangement of receptors in thin frozen-hydrated sections and the arrangements found in negatively stained membrane extracts and plunge-frozen cells, highlighting the potential of using frozen-hydrated sections for the study of macromolecular assemblies within cells under near-native conditions.

Bacterial Proteins↗

PubMed2004

An evidence ontology for use in pathway/genome databases.

An important emerging need in Model Organism Databases (MODs) and other bioinformatics databases (DBs) is that of capturing the scientific evidence that supports the information within a DB. This need has become particularly acute as more DB content consists of computationally predicted information, such as predicted gene functions, operons, metabolic pathways, and protein properties. This paper presents an ontology for encoding the type of support and the degree of support for DB assertions, and for encoding the literature source in which that support is reported. The ontology includes a hierarchy of 35 evidence codes for modeling different types of wet-lab and computational evidence for the existence of operons and metabolic pathways, and for gene functions. We also describe an implementation of the ontology within the Pathway Tools software environment, which is used to query and update Pathway/Genome DBs such as EcoCyc, MetaCyc, and HumanCyc.

Computational Biology↗

PubMed2004

Molecular epidemiology of two fowl cholera outbreaks on a free-range chicken layer farm.

Two outbreaks of fowl cholera on a multiage free-range egg farm were investigated. The outbreaks occurred in 1994 and 2002. A total of 22 strains of Pasteurella multocida were available for study, 11 from the 1994 outbreak and 11 from the 2002 outbreak. Lesions typical of acute fowl cholera were seen in the 1994 outbreak, whereas both acute and chronic fowl cholera occurred in the 2002 outbreak. The isolates were examined in an extended phenotypic typing methodology, by a P. multocida-specific polymerase chain reaction (PCR), by the Heddleston somatic serotyping scheme, and by restriction endonuclease analysis (REA) typing using the enzyme HpaII. All 22 strains had the same phenotypic properties, all were confirmed as P. multocida by PCR, all were Heddleston serovar 4, and all had the same REA pattern. The results indicate that these 2 outbreaks were caused by the same clone of P. multocida--despite the 8-year time period between the outbreaks.

Animal Husbandry↗

PubMed2003

Laser-energy transfer and enhancement of plasma waves and electron beams by interfering high-intensity laser pulses.

The effects of interference due to crossed laser beams were studied experimentally in the high-intensity regime. Two ultrashort (400 fs), high-intensity (4 x 10(17) and 1.6 x 10(18) W/cm(2)) and 1 microm wavelength laser pulses were crossed in a plasma of density 4 x 10(19) cm(3). Energy was observed to be transferred from the higher-power to the lower-power pulse, increasing the amplitude of the plasma wave propagating in the direction of the latter. This results in increased electron self-trapping and plasma-wave acceleration gradient, which led to an increased number of hot electrons (by 300%) and hot-electron temperature (by 70%) and a decreased electron-beam divergence angle (by 45%), as compared with single-pulse illumination. Simulations reveal that increased stochastic heating of electrons may have also contributed to the electron-beam enhancement.

Journal Article↗

PubMed2003

Gene content and organization of an 85-kb DNA segment from the genome of the phytopathogenic mollicute Spiroplasma kunkelii.

Spiroplasma kunkelii, the causative agent of corn stunt disease in maize (Zea maysL.), is a helical, cell wall-less prokaryote assigned to the class Mollicutes. As part of a project to sequence the entire S. kunkelii genome, we analyzed an 85-kb DNA segment from the pathogenic strain CR2-3x. This genome segment contains 101 ORFs and two tRNA genes. The majority of the ORFs code for predicted proteins that can be assigned to respective clusters of orthologous groups (COGs). These COGs cover diverse functional categories including genetic information storage and processing, cellular processes, and metabolism. The most notable gene cluster in this genome segment is a super-operon capable of encoding 24 ribosomal proteins. The organization of genes in this operon reflects the unique evolutionary position of the spiroplasma. Gene duplications, domain rearrangements, and frameshift mutations in the segment are interpreted as indicators of phase variation in the spiroplasma. To our knowledge, this is the first analysis of a large genome segment from a plant pathogenic spiroplasma.

Base Sequence↗

PubMed2003

Heterogeneity of endocytic proteins: distribution of clathrin adaptor proteins in neurons and glia.

Clathrin adaptor protein (AP)180 is a synaptic protein that regulates the assembly of clathrin-coated vesicles. Several endocytic proteins including AP2, CALM, and epsin 1 have functions or molecular structures similar to AP180. We determined if AP180 associates with functional synapses in cultured hippocampal neurons. We also compared the expression pattern of AP180 with the other endocytic proteins. The distribution of AP180 corresponded with the synaptic vesicle-associated protein synapsin I, and with functional presynaptic terminals labeled with the styryl dye FM1-43. Synaptic AP2 colocalized with AP180, but the distribution of AP2 was not limited to synapses of neurons and it was also expressed in glia. CLAM and epsin 1 immunoreactivities were also detected in both neurons and glia. Unlike AP180, the neuronal immunoreactivity of CALM was not intense in the synaptic puncta. Epsin 1 immunoreactivity was found in both synaptic and extrasynaptic sites, and its synaptic distribution only partially overlapped with that of AP180. These results support roles for AP180 in synaptic function in neurons. The findings also provide information on the distribution of AP2, CALM, and epsin 1 in cells of the nervous system that suggest different roles for these endocytic proteins in the biology of these cells.

Adaptor Proteins, Vesicular Transport↗

PubMed2003

The new RENT family of repetitive elements in Nicotiana species harbors gene regulatory elements related to the tCUP cryptic promoter.

The tCUP cryptic constitutive promoter was discovered in the tobacco genome by T-DNA (transfer DNA) tagging with a promoterless GUS-nos gene. Here, we show that the portion of the tCUP sequence containing a variety of cryptic gene regulatory elements is related to a new family of moderately repetitive sequences (10(2) copies), the RENT (repetitive element from Nicotiana tabacum) family. The RENT family is found only in certain Nicotiana species. Five RENT elements were cloned and sequenced. The RENT elements are a minimum of 5 kb in length and share 80-90% sequence similarity throughout their length. The 5' termini are the same in the isolated RENT family members and are characterized by a conserved border sequence (TGTTGA(T or C)ACCCAATTTT(T or C)). The 3' ends of RENT sequence similarity vary in location and sequence. The tCUP cryptic promoter originated from a unique truncated RENT element that interrupts a phytochelatin synthase-like gene that may have undergone rearrangements prior to or resulting from T-DNA insertion. No evidence was found for expressed coding regions within the RENT elements; however, like the cryptic gene regulatory elements within the tCUP sequence, the isolated RENT elements possess promoter activity and translational enhancer activity.

Base Sequence↗

PubMed2003

Developmental and hormonal signals dramatically alter the localization and abundance of insulin receptor substrate proteins in the mammary gland.

Insulin receptor substrates (IRS) are central integrators of hormone, cytokine, and growth factor signaling. IRS proteins can be phosphorylated by a number of signaling pathways critical to normal mammary gland development. Studies in transgenic mice that overexpress IGF-I in the mammary gland suggested that IRS expression is important in the regulation of normal postlactational mammary involution. The goal of these studies was to examine IRS expression in the mouse mammary gland and determine the importance of IRS-1 to mammary development in the virgin mouse. IRS-1 and -2 show distinct patterns of protein expression in the virgin mouse mammary gland, and protein abundance is dramatically increased during pregnancy and lactation, but rapidly lost during involution. Consistent with hormone regulation, IRS-1 protein levels are reduced by ovariectomy, induced by combined treatment with estrogen and progesterone, and vary considerably throughout the estrous cycle. These changes occur without similar changes in mRNA levels, suggesting posttranscriptional control. Mammary glands from IRS-1 null mice have smaller fat pads than wild-type controls, but this reduction is proportional to the overall reduction in body size. Development of the mammary duct (terminal endbuds and branch points) is not altered by the loss of IRS-1, and pregnancy-induced proliferation is not changed. These data indicate that IRS undergo complex developmental and hormonal regulation in the mammary gland, and that IRS-1 is more likely to regulate mammary function in lactating mice than in virgin or pregnant mice.

Adipose Tissue↗

PubMed2002

Nestin-containing cells express glial fibrillary acidic protein in the proliferative regions of central nervous system of postnatal developing and adult mice.

We are interested in the expression patterns of nestin, an embryonic intermediate filament that represent a neural precursor marker, in the mammalian central nervous system. With an immunohistochemical approach, distribution of nestin-containing cells and their colocalization with glial fibrillary acidic protein (GFAP) or neuronal nuclear specific protein (NeuN) were studied in adult and postnatal days 2-30 (P2-30) mice. Nestin-immunoreactivity was predominately distributed in certain proliferative regions, such as cerebral cortex, hippocampus, hypothalamus, subfornical organ, cerebellar cortex, area postrema, midline raphe glial structures, as well as ependymal and subependymal zones of the brain and spinal cord. The majority of nestin-immunoreactive cells, characterized by astroglial profiles of multiple and radial processes, showed a partial overlapping distribution with that of GFAP-immunoreactive astroglial cells. Double immunofluorescence confirmed that about 77% of these nestin-immunoreactive cells exhibited GFAP-immunoreactivity, indicating that a large percentage of nestin-expressing cells may have committed to astroglial cells. In developing mice, down-regulation of nestin expression was observed between P7 and P14. Although co-expression of nestin and NeuN occurred in cortical neurons of P2-7 mice, nestin-containing cells showing NeuN-immunoreactivity disappeared in CNS in older animals. Our results reveal the distribution pattern of nestin-containing neural precursors in the postnatal CNS and provide evidence on their differentiation fate to neurons and astrocytes, suggesting that nestin-containing glial cells may play an important role in remodeling and repairing in the postnatal and adult central nervous system.

Aging↗

PubMed2002

A direct mixed-body boundary element method for packed silencers.

Bulk-reacting sound absorbing materials are often used in packed silencers to reduce broadband noise. A bulk-reacting material is characterized by a complex mean density and a complex speed of sound. These two material properties can be measured by the two-cavity method or calculated by empirical formulas. Modeling the entire silencer domain with a bulk-reacting lining will involve two different acoustic media, air and the bulk-reacting material. Traditionally, the interior silencer domain is divided into different zones and a multi-domain boundary element method (BEM) may be applied to solve the problem. However, defining different zones and matching the elements along each interface is tedious, especially when the zones are intricately connected. In this paper, a direct mixed-body boundary element method is used to model a packed silencer without subdividing it into different zones. This is achieved by summing up all the integral equations in different zones and then adding the hypersingular integral equations at interfaces. Several test cases, including a packed expansion chamber with and without an absorbing center bullet, and a parallel baffle silencer, are studied. Numerical results for the prediction of transmission loss (TL) are compared to experimental data.

Journal Article↗